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Preprint REVIEW | doi:10.20944/preprints202104.0461.v1

Germplasm Conservation: Instrumental in Agricultural Biodiversity-A Review

Veerala Priyanka, Rahul Kumar, Inderpreet Dhaliwal, Prashant Kaushik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Germplasm; Genetic plant resources; Preservation; Propagation; in vitro

Online: 19 April 2021 (11:28:31 CEST)

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Preprint REVIEW | doi:10.20944/preprints201807.0089.v1

The Importance of a Multidisciplinary Approach in the Management of a Patient with Type I Gaucher Disease

Miguel-Ángel Torralba-Cabeza, Susana Olivera-González, José-Luis Sierra-Monzón

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: multidisciplinary; Gaucher; genotype/phenotype correlation; genetic counselling

Online: 5 July 2018 (08:51:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.1705.v1

MixDeR: A SNP Mixture Deconvolution Workflow for Forensic Genetic Genealogy

Rebecca Mitchell, Michelle Peck, Erin Gorden, Rebecca Just

Subject: Biology And Life Sciences, Other Keywords: mixtures; SNPs; forensic genetic genealogy (FGG); investigative genetic genealogy (IGG); Kintelligence; software

Online: 24 July 2024 (14:45:02 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202312.2074.v1

Reconsideration of codon-anticodon wobble pairings in translation: decoding tables

Miki Wada

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: decoding; tRNA; wobble pairing; genetic code; inosine; translation

Online: 27 December 2023 (09:50:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0332.v1

Getting the Full Picture of Plankton in the Western Channel

Stern Rowena, Kathryn Picard, Jessica Clarke, Charlotte Walker, Claudia Martins, Clare Marshall, Ana Amorim, Malcolm Woodward, Claire Widdicombe, Glen Tarran, Martin Edwards

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Plankton; Monitoring; Harmful algae; microscopic; genetic; Western Channel

Online: 22 July 2022 (03:33:40 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202403.0950.v2

SSR Markers-Based DNA Fingerprinting for Varietal Identification in Mango Cultivars

Muhammad Aleem Ashraf, Javed Iqbal, Imran Shahid, Muhammad Kashif, Yufeng Li, Yu Kong, Naitong Yu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Mango tree; SSR markers; mango varieties; genetic diversity; cultivar identification diagram, loci, polymorphism; genetic resources in Pakistan; breeding; cultivar development

Online: 17 June 2024 (08:04:46 CEST)

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Preprint REVIEW | doi:10.20944/preprints202408.0719.v1

Exploring the Rise in Precocious Puberty: Interplay of Genetic and Environmental Factors

Jhancy Malay, Biji Thomas George, Rajani Dube, Subhranshu Sekhar Kar, Imran Rashid Rangraze

Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: precocious puberty; genetic factors; endocrinal factors; environmental factors

Online: 12 August 2024 (03:55:05 CEST)

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Preprint REVIEW | doi:10.20944/preprints202405.1165.v1

Tropical Fruit Virus Resistance in the Era of Next Generation Plant Breeding

Marcella Silva Vieira, Rafael Lara Rezende Cabral, Luíza Favaratto, Laiane Silva Maciel, André da Silva Xavier, Francisco Murilo Zerbini, Patricia M. B. Fernandes

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: virus genetic diversity; gene editing; plant disease; biotechnology.

Online: 17 May 2024 (11:43:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.1137.v2

Monitoring Method of VOCs Based on PID in Soil-water-gas Environment

Dong Dong, Yongjun Ren, Mengmeng Zhang, Xiujuan Feng, Kaiwei Liu

Subject: Environmental And Earth Sciences, Environmental Science Keywords: Photoionization detector; VOCs; Principal Component Analysis; Genetic Algorithm

Online: 17 January 2024 (09:25:24 CET)

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Preprint REVIEW | doi:10.20944/preprints202112.0331.v1

Visualizing the Complexity of Proteins in Living Cells With Genetic Code Expansion

Kanokpol Aphicho, Narongyot Kittipanukul, Chayasith Uttamapinant

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genetic code expansion; unnatural amino acid; fluorescence imaging

Online: 21 December 2021 (12:42:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202407.2452.v1

Heterozygous Smad4 Knock out Effect on Pancreatic and Body Weight Variation in F1 Population Using Mutant and Wild Type Collaborative Cross Mice

Osayd Zohud, Iqbal M. Lone, Kareem Midlej, Aysar Nashef, Imad Abu-Elnaaj, Fuad A. Iraqi

Subject: Biology And Life Sciences, Other Keywords: Smad4; pancreatic weight; genetic background; sex differences; Collaborative Cross; F1 mice; genetic modifiers; tumor suppressor gene

Online: 30 July 2024 (10:53:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.1677.v1

Global Genetic Algorithm for Automating and Optimizing Petroleum Well Deployment in Complex Reservoirs

Sonny Irawan, Dennis Delali Kwesi Wayo, Alfrendo Satyanaga, Jong Kim

Subject: Engineering, Chemical Engineering Keywords: Well deployment; Genetic Algorithms; CMG; Global Optimization; Reservoir

Online: 29 February 2024 (11:41:15 CET)

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Preprint REVIEW | doi:10.20944/preprints202310.0243.v1

Lupinus mutabilis Breeding in the Andes of Ecuador, Peru, and Bolivia: A Review

Diego Rodriguez-Ortega, José Luis Zambrano, Santiago Pereira-Lorenzo, Andres Torres, Angel Murillo

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Lupinus mutabilis; genetic diversity; breeding; anthracnose resistance; alkaloids

Online: 5 October 2023 (02:38:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0099.v1

Genetic Parameters of Growth Traits and Quantitative Genetic Metrics for Selection and Conservation of Mecheri Sheep of Tamil Nadu

B. Balasundaram, A.K. Thiruvenkadan, N. Murali, J. Muralidharan, D. Cauveri, Sunday O. Peters

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Genetic parameters, (Co)variance components, Mecheri sheep, Animal models, Maternal genetic influence, Inbreeding

Online: 6 December 2022 (10:03:11 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0509.v1

Genetic Variation of Native Perilla Germplasms Collected from South Korea Using SSR Markers and Morphological Characteristics

Jun Seok Oh, Kyu Jin Sa, Hyeon Park, Do Yoon Hyun, Sookyeong Lee, Ju-Hee Rhee, Ju Kyong Lee

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Perilla crop; genetic resources; morphological traits; principal component analysis; SSR marker; genetic variation

Online: 22 July 2021 (08:04:28 CEST)

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Preprint REVIEW | doi:10.20944/preprints202103.0209.v1

Genomic Mapping in Detection of Vascular Disorders

Sameer Quazi, Arnaud Capuzzo, Javid Ahmad Malik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genetic Mapping; Vascular system; Embryogenesis; Vascular disorder; PIk3CA gene

Online: 8 March 2021 (10:43:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints202405.0329.v1

Strategies for Breeding Programs to Reduce Post-harvest Water Loss in Fresh Market Peppers

Rego ER, Finger FL, Pessoa AMS, Silva Anderson Rodrigo da, Azevedo AA, Meira RMSA, da Silva ALBR, Silva RS, Rêgo MM

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: shelf life; genetic effects; diallel; narrow sense heritability

Online: 7 May 2024 (08:17:38 CEST)

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Preprint REVIEW | doi:10.20944/preprints202211.0106.v1

Chloroplast Genetics Engineering: from Bench to Blast Application of Chloroplast Genetic-Engineering in Basic Research

Bo Wang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Keywords: chloroplast genetic engineering; Homologus recombination; ORF; photosynthesis

Online: 7 November 2022 (04:31:29 CET)

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Working Paper ARTICLE

Optimized Surge Arrester Allocation Based on Genetic Algorithm and ATP Simulation in Electric Distribution Systems

Gabriel Rocha, Raphael Barradas, João Rodrigo Muniz, Ubiratan Bezerra, Igor Araújo, Daniel Costa, Abner Silva, Marcus Nunes, Jucileno Silva

Subject: Engineering, Electrical And Electronic Engineering Keywords: transient analysis; surge arrester allocation; genetic algorithm; ATP

Online: 1 September 2019 (09:59:23 CEST)

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Preprint REVIEW | doi:10.20944/preprints202009.0279.v1

The Population Genetics of Ploidy Change in Fungi

Aleeza C. Gerstein, Nathaniel Sharp

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: selection; mutation; genetic drift; adaptation; ploidy drive; genome instability

Online: 13 September 2020 (11:48:30 CEST)

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Preprint REVIEW | doi:10.20944/preprints202305.0472.v1

Progress toward Health System Readiness for Genome-Based Testing in Canada

Don Husereau, Eva Villalba, Vivek Muthu, Michael Mengel, Craig Ivany, Lotte Steuten, Daryl S. Spinner, Brandon Sheffield, Stephen Yip, Philip Jacobs, Terrence Sullivan

Subject: Public Health And Healthcare, Health Policy And Services Keywords: diagnostic molecular pathology; genetic testing; diagnostic services; technology assess- ment; biomedical; genetic services; financial support; clinical governance; health technology; healthcare innovation

Online: 8 May 2023 (08:36:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202010.0303.v1

Fuzzy Genetic Algorithm Approach for Verification of Reachability and Detection of Deadlock in Graph Transformation Systems

Nahid Salimi, Vahid Rafe, Hamed Tabrizchi, Amir Mosavi

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: fuzzy genetic algorithm; reachability property; deadlock; model checking

Online: 14 October 2020 (10:58:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202410.2433.v1

Heritability and Correlation Estimates for Serum Insulin-Like Growth Factor I Concentration, Weight, Weight Gain, and Height in Angus Beef Cattle in a Long-Term Divergent Selection Study for Serum Insulin-Like Growth Factor I (1989 to 2017)

Michael E Davis, Rosalia C. M. Simmen

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: beef cattle; IGF-I; genetic parameters; growth traits

Online: 30 October 2024 (14:02:09 CET)

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This study investigated the genetic parameters for serum IGF-I concentrations and growth traits in beef cattle. A divergent selection experiment for serum IGF-I concentration was initiated in 1989. One hundred spring-calving (50 high line and 50 low line) and 100 fall-calving (50 high line and 50 low line) Angus cows with unknown IGF-I concentrations were randomly assigned to the two divergent selection lines. For the 2009 through 2017 breeding seasons, the selection criterion in the two lines was changed from serum IGF-I concentration to high vs. low maintenance energy expected progeny differences (ME EPD). The number of records available for analysis varied from 2,056 for IGF-I concentration on day 42 of the postweaning performance test to 2,988 for birth weight, with the exception that only 617 records were available for IGF-I concentration at weaning. (Co)variance components were estimated for direct and maternal additive genetic effects using an animal model and multiple-trait, derivative-free, restricted maximum likelihood (MTDFREML) computer programs. Direct heritability estimates for serum IGF-I concentrations ranged from 0.34 ± 0.07 to 0.46 ± 0.07, whereas direct heritability estimates for weight traits ranged from 0.32 ± 0.05 to 0.39 ± 0.07. Maternal genetic effects on IGF-I were minimal, with estimates ranging from 0.02 ± 0.11 to 0.17 ± 0.05, and were similarly low for weight traits. Maternal permanent environmental effects were negligible for IGF-I but were larger for weight traits, especially for weaning weight (0.22 ± 0.04). Direct-maternal correlations for postweaning IGF-I concentrations were approximately -0.90. Genetic correlations of IGF-I concentration at weaning with postweaning IGF-I measures ranged from 0.63 to 0.90. Genetic correlations among IGF-I measures at the postweaning time points were also large (≥ 0.89). The genetic correlations of IGF-I with weight traits were generally low, with negative correlations observed for birth weight and small positive correlations for the other weight traits. Environmental and phenotypic correlations between IGF-I concentrations and growth traits were generally low, indicating that shared environmental influences are minimal and that circulating IGF-I has a modest impact on growth traits in beef cattle.

Preprint REVIEW | doi:10.20944/preprints202010.0149.v1

Advances in Melon Breeding (Cucumis melo L.): An Update

Hari Kesh, Prashant Kaushik

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: breeding; diversity; genetic engineering; genomics; male sterility; melon; QTLs

Online: 7 October 2020 (09:22:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0026.v1

Molecular Prevalence, Genetic Diversity, and Tissue Tropism of Bartonella Species in Small Mammals from Yunnan Province, China

Pei-Yu Han, Fen-Hui Xu, Jia-Wei Tian, Jun-Ying Zhao, Ze Yang, Wei Kong, Bo Wang, Li-Jun Guo, Yun-Zhi Zhang

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Bartonella; small mammals; genetic diversity; evolution; tissue tropism

Online: 1 April 2024 (17:07:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0613.v1

Assessment of Genetic Diversity in Winged Bean [Psophocarpus Tetragonolobus (L.) DC.] Accessions Using Morphological Traits and Microsatellite Markers

Temitope Esther Olatunde, Adeolu Moses Adebayo, Ayomide Ajoke Bhadmus, Idris Ishola Adejumobi, Olaniyi Oyatomi, Benjamin Faloye, Michael Abberton

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Accessions; genetic diversity; morphological traits; SSRs; winged bean

Online: 8 June 2023 (09:25:39 CEST)

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Preprint REVIEW | doi:10.20944/preprints202305.1297.v1

Recent Advances in Elucidating the Mechanism Underlying Proteinuric Kidney Disease/Nephrotic Syndrome: Lessons From Knockout/Transgenic Mouse Models

Ryosuke Saiki, Kan Katayama, Kaoru Dohi

Subject: Medicine And Pharmacology, Other Keywords: genetic kidney disease; knockout; nephrotic syndrome; proteinuria; transgenic

Online: 18 May 2023 (08:10:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0427.v1

Composition and Patterns of Taxa Assemblages in the Western Channel Assessed by 18S Sequencing, Microscopy and Flow Cytometry

Stern Rowena, Kathryn Picard, Jessica Clarke, Charlotte Walker, Claudia Martins, Clare Marshall, Ana Amorim, Malcolm Woodward, Claire Widdicombe, Glen Tarran, Martin Edwards

Subject: Environmental And Earth Sciences, Environmental Science Keywords: Plankton; Monitoring; Harmful algae; microscopic; genetic; Western Channel

Online: 22 December 2022 (11:34:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202212.0210.v1

Impact of Drought on Maize Yield and Exploration of In-Situ Maize Crop Genetic Resources for Drought Tolerance.

G MAHENDRA SINGH, Gokul Gosavi, Srinathareddy S, Shiv Shankar Patel, Pawan Singh Solanki, Feng Zhang, Jianchu Xu, V K Mishra, Sandeep Sharma

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Maize; drought; landrace; climate-change; crop genetic resources

Online: 13 December 2022 (01:07:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0735.v1

Transcriptional Reprogramming of Candida tropicalis in Response to Isoespintanol Treatment

Orfa Inés Contreras Martínez, Alberto Angulo Ortíz, Gilmar Santafé Patiño, Katia Aviña-Padilla, María Camila Velasco, Maria F. Yasnot-Acosta

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Transcriptomics; Candida tropicalis; isoespintanol; genetic dysregulation; mitochondria; cell wall

Online: 13 November 2023 (14:21:10 CET)

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Candida tropicalis, an opportunistic pathogen, ranks among the primary culprits of invasive candidiasis, a condition notorious for its resistance to conventional antifungal drugs. The urgency to combat these drug-resistant infections has spurred the quest for novel therapeutic compounds, with a particular focus on those of natural origin. In this study, we set out to evaluate the impact of Isoespintanol (ISO), a monoterpene derived from Oxandra xylopioides, on the transcriptome of C. tropicalis. Leveraging transcriptomics, our research aimed to unravel the intricate transcriptional changes induced by ISO within this pathogen. Our differential gene expression analysis unveiled 186 differentially expressed genes (DEGs) in response to ISO, with a striking 85% of these genes experiencing upregulation. These findings shed light on the multifaceted nature of ISO's influence on C. tropicalis, spanning a spectrum of physiological, structural, and metabolic adaptations. The upregulated DEGs predominantly pertained to crucial processes, including ergosterol biosynthesis, protein folding, response to DNA damage, cell wall integrity, mitochondrial activity modulation, and cellular responses to organic compounds. Simultaneously, 27 genes were observed to be repressed, affecting functions such as cytoplasmic translation, DNA damage checkpoints, membrane proteins, as well as metabolic pathways like trans-methylation, trans-sulfuration, and trans-propylamine. These results underscore the complexity of ISO's antifungal mechanism, suggesting that it targets multiple vital pathways within C. tropicalis. Such complexity potentially reduces the likelihood of the pathogen developing rapid resistance to ISO, making it an attractive candidate for further exploration as a therapeutic agent. In conclusion, our study provides a comprehensive overview of the transcriptional responses of C. tropicalis to ISO exposure. The identified molecular targets and pathways offer promising avenues for future research and the development of innovative antifungal therapies to combat infections caused by this pathogenic yeast.

Preprint REVIEW | doi:10.20944/preprints202305.2022.v1

Neuroendocrine Effects on the Risk of Metabolic Syndrome in Children

Giovanna Scorrano, Saverio La Bella, Sara Matricardi, Francesco Chiarelli, Cosimo Giannini

Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: Metabolic syndrome; obesity; neuroendocrine systems; stress response; genetic polymorphisms

Online: 30 May 2023 (02:27:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints201911.0286.v1

Indigenous Pig Genetic Resources in Southern Africa: Progress and Prospects

Tinyiko Edward Halimani, Obvious Mapiye, Tawanda Marandure, Diedre Januarie, Venancio Edward Imbayarwo Chikosi, Kennedy Dzama

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: diversity; conservation; animal genetic resources; indigenous pigs; southern Africa

Online: 24 November 2019 (14:47:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.1471.v1

Diversity and Evolution of the MHC Class II DRB Gene in an Alpine Ungulate, the Siberian Ibex (Capra sibirica), Experienced a Demographic Fluctuation in China

Pei-Pei Dong, Rui-Rui Wang, Shamshidin Abduriyim

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Mountain ungulate; MHC DRB gene; genetic diversity; population fluctuation

Online: 21 July 2023 (09:13:12 CEST)

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The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 came after found in only seven individuals, 14 PFAs occurred once (7 PFAs twice), implying high frequency of rare PFAs. Interestingly, more than half of the (15) PFAs were specific to clade I, only one and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sextual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The way of allele sharing and FST values between three clades were to some extent in agreement with pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed cross-species polymorphisms. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.

Preprint ARTICLE | doi:10.20944/preprints202408.2221.v1

Human-Activity-Mediated Gene Flows Are Involved in the Establishment of Magnaporthe oryzae Population Structures: A Population Genomic Analysis

Guohua Duan, Yuchan Liu, Cheng Zheng, Kaihui Yu, Jiahui Xie, Baohua Wang, Huakun Zheng, Wei Tang, Jiandong Bao, Zonghua Wang, Meilian Chen

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Magnaporthe oryzae; population structure; genetic diversity; gene flow

Online: 30 August 2024 (08:36:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.0568.v1

Risk Factor Analysis and Genetic Parameter Estimation for Pre-weaning Mortality Traits in Boer, Spanish, and Crossbred Goat Kids

Liuhong Chen, William Foxworth, Scott Horner, Mustafa Hitit, Negusse Kidane, Erdogan Memili

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: pre-weaning mortality; risk factors; goat; genetic parameter

Online: 11 March 2024 (17:44:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints202102.0470.v1

Assessing a Smart Technology versus a Mathematical model to Estimate the Transverse Shear Stress Distribution in a Rectangular Channel

Babak Lashkar-Ara, Niloofar Kalantari, Zohreh Sheikh Khozani, Amir Mosavi

Subject: Engineering, Civil Engineering Keywords: Smooth rectangular channel; Tsallis entropy; Genetic Programming (GP)

Online: 22 February 2021 (13:09:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints201705.0109.v1

The Genetic Structure of Turnip mosaic Virus Population Reveals the Rapid Expansion of a New Emergent Lineage in China

Xiangdong Li, Tiansheng Zhu, Xiao Yin, Chengling Zhang, Jia Chen, Yanping Tian, Jinliang Liu

Subject: Biology And Life Sciences, Plant Sciences Keywords: Turnip mosaic virus; Potyvirus; Genetic structure; Population; China

Online: 15 May 2017 (11:38:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.1663.v1

Genetic Algorithm based optimization of Clustering Algorithms for the Healthy Aging Dataset

Kahkashan Kouser, Amrita Priyam, Mansi Gupta, Sanjay Kumar, VANDANA BHATTACHARJEE

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Genetic Algorithms; Clustering; KMeans++; optimization

Online: 27 May 2024 (10:05:29 CEST)

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Preprint REVIEW | doi:10.20944/preprints202308.0706.v2

Dr Jekyll and Mr Hyde: From Two Branches of Immune Response to Three Types of Interferon Response

Brent Brown, Chinua Imarogbe, Ingo Fricke, Pascal Mensah

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Interferon; Innate; Adaptive; Genetic; Molecular

Online: 26 September 2023 (11:35:53 CEST)

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Interferons were the original prototype cytokine system discovered in 20th-century research. As the name implies, they were originally thought to be synthesised and secreted between cells. Thanks to technological advances, the processes involved in protein secretion can be explained comparatively more clearly at both the genetic and biochemical levels. The discovery of interferon (IFN) occurred when genetic research was still in its infancy. Franklin and Wilkins discovered the structure and function of deoxyribonucleic acid (DNA) at the same time as Crick and Watson; however, Isaacs and Lindemann, two scientists, described the first IFN in 1957. Mutations can be caused by inherent genetic protein synthesis and during infection as well as within IFN regulation pathways affecting cell proliferation. This remains central to host cell IFN synthesis and effects through IFN protein receptor subunits defined by 6 protein domains. Type II IFN is key to immune cell function secreted by a variety of immune cells, mainly natural killer (NK) as well as T cells. Single–stranded and/or double–stranded RNA/DNA viruses, as well as bacterial infections (e.g., Escherichia coli) and fungal infections (e.g., Aspergillus), also affect IFN regulation. Pathogenic proteins utilise intra/extracellular proteins that sense foreign antigens like Toll–like Receptors (TLRs), affected by mutations within the human cellular IFN transduction pathways. Since the discovery of the third IFN type in 2003, when immune cell phenotypes were further characterised, questions remain about the immunological mechanisms contributing to the regulation of the innate and adaptive host immune system. Alterations in the synthesis of type I/II/III host IFNs can differentially and beneficially alter homeostatic cellular pathways in pathological disease, with type I IFN being synthesised in cancer as well as by homeostatic cells. Therefore, considered here are the overall IFN molecular, cell regulatory mechanisms in the context of immune cell research developments.

Preprint CASE REPORT | doi:10.20944/preprints202306.0239.v1

Optimal Evaluation of Left Ventricular Hypertrophic Phenotype Using Parametric CMR Mapping and Genetic Testing

Andrés Felipe Barragán-Amado, Jaime A Parra, María C Manzur, Julian A Gelves-Meza, Claudia P Jaimes, María F Tamayo, Héctor M Medina, María Juliana Rodríguez-González

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Cardiomyopathy; Genetic disorders; Cardiovascular Imagen

Online: 5 June 2023 (05:02:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202304.0114.v1

Genetic Determinants of Atherogenic Indexes

Tomas Texis, Susana Rivera-Mancia, Eloisa Colin-Ramirez, Raul Cartas-Rosado, David Koepsell, Kenneth Rubio-Carrasco, Mauricio Rodriguez-Dorantes, Vanessa Gonzalez-Covarrubias

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Dyslipidemia; atherogenic indexes; genetic associations

Online: 7 April 2023 (05:24:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints202206.0284.v1

Building Consensus around the Assessment and Interpretation of Symbiodiniaceae Diversity

Sarah Davies, Matthew H. Gamache, Lauren I. Howe-Kerr, Nicola G. Kriefall, Andrew C. Baker, Anastazia T. Banaszak, Line K. Bay, Anthony J. Bellantuono, Debashish Bhattacharya, Cheong Xin Chan, Danielle C. Claar, Mary Alice Coffroth, Ross Cunning, Simon K. Davy, Javier del Campo, Erika M. Diaz-Almeyda, Jorg C. Frommlet, Lauren E. Fuess, Raul A. Gonzalez-Pech, Tamar L. Goulet, Kenneth D. Hoadley, Emily J. Howells, Benjamin C. C. Hume, Dustin W. Kemp, Carly, D. Kenkel, Sheila A. Kitchen, Todd C. LaJeunesse, Senjie Lin, Shelby McIlroy, Ryan McMinds, Matthew R. Nitschke, Clinton A. Oakley, Raquel S. Peixoto, Carlos Prada, Hollie M. Putnam, Kate Quigley, Hannah G. Reich, James Davis Reimer, Mauricio Rodriguez-Lanetty, Stephanie Rosalas, Osama S. Saad, Eugenia M. Sampayo, Scott Santos, Eiichi Shoguchi, Edward G. Smith, Michael Stat, Timothy G. Stephens, Marie E. Strader, David J. Suggett, Timothy D. Swain, Cawa Tran, Nikki Traylor-Knowles, Christian R. Voolstra, Mark E. Warner, Virginia M. Weis, Rachel Wright, Tingting Xiang, Hiroshi Yamashita, Maren Ziegler, Adrienne M.S. Correa, John Everett Parkinson

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Symbiodinaceae; genetic diversity; coral symbiosis

Online: 21 June 2022 (04:49:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints202309.0496.v1

Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

Simone Papalini, Valerio Di Vittori, Alice Pieri, Marina Allegrezza, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Elisa Bellucci, Tania Gioia, Luis Guasch, Karolina Susek, Maud Irène Tenaillon, Kerstin Neumann, Roberto Papa

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: plant genetic resources; population genomics; crop evolution; food legumes

Online: 7 September 2023 (09:23:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0029.v1

Variability of Genetic Characters Associated with Probiotic Functions in Lacticaseibacillus Species

Franca Rossi, Carmela Amadoro, Maria Pallotta, Giampaolo Colavita

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Lacticaseibacillus species; probiotic potential; genetic traits; presence in genomes

Online: 6 April 2022 (04:54:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0300.v1

Exploring Fusarium Head Blight Resistance In a Winter Triticale Germplasm Collection

Sydney Wallace, Bhavit Chhabra, Yanhong Dong, Xuefeng Ma, Gary Coleman, Vijay Tiwari, Nidhi Rawat

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Fusarium head blight; deoxynivalenol; triticale; genetic resistance; disease evaluation

Online: 12 April 2021 (12:49:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0305.v1

Distance Only Brings You Closer: Application of ISSR Markers to Analyze Molecular Relationships in Roses (Rosa spp.) - The Symbol of Love

Tanay Joshi, Santosh Kumar, Lalit Arya, Amritbir Riar

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ISSR; Rosa spp.; DNA fingerprinting; genotypes; genetic diversity

Online: 13 May 2021 (14:01:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0404.v1

Integration of Epidemiological and Genomic Data to Investigate H5N1 HPAI Outbreaks in Northern Italy in 2021-2022

Diletta Fornasiero, Alice Fusaro, Bianca Zecchin, Matteo Mazzucato, Francesca Scolamacchia, Grazia Manca, Calogero Terregino, Tiziano Dorotea, Paolo Mulatti

Subject: Biology And Life Sciences, Virology Keywords: HPAI; H5N1; Italy; genetic network; epidemiological investigation; contact tracing; ERGM

Online: 22 December 2022 (01:14:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints202409.1938.v1

Reducing Genotype-Environment Interaction Effects in a Genetic Improvement for Liptopenaeus vannamei

Tran Thi Mai Huong, Nguyen Huu Hung, Dinh Cong Tru, Vu Dinh Ty, Nguyen Hong Nguyen

Subject: Biology And Life Sciences, Aquatic Science Keywords: Breeding program; genetic parameters; selection response; genotype and environment

Online: 25 September 2024 (02:59:53 CEST)

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Preprint REVIEW | doi:10.20944/preprints202203.0295.v1

Genetic Diversity of Schistosoma Haematobium in Sub-Saharan Africa: A Systematic Review

Rabecca Tembo, Panji Nkhoma, Mildred Zulu, Florence Mwaba, John Yabe, Hikabasa Halwiindi, Moses Kamwela, King S. Nalubamba, Chummy S. Sikasunge, Andrew M. Phiri

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Urinary schistosomiasis; Schistosoma haematobium; sub-Saharan Africa; Genetic Diversity

Online: 22 March 2022 (04:25:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.1721.v1

Characteristics of Seismogenic Dust Particles from Mountain and Its Significance for Paleoseismic Records in Tufa Section: A Case Study of Jiuzhaigou, China

Shengwen Jing, Fudong Wang, Enrico Capezzuoli, Guoqing Huang, Junhao Li, Hanchao Jiang, Zijian Zhou, Xueqin Zhao, Faqin Dong, Andrea Brogi

Subject: Environmental And Earth Sciences, Geochemistry And Petrology Keywords: Jiuzhaigou; Tufa particulate matter; Sedimentation; Genetic analysis; Paleoearthquake

Online: 25 June 2023 (07:11:39 CEST)

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The sedimentary characteristics of the special interlayer contained in the section of the Sparking Lake dam revealed by the 8.8 Jiuzhaigou earthquake in 2017 are obviously different from the tufa in the dam body, and they are considered to be prehistoric flood relics. Based on the study of the particulate matter from the 8.8 Jiuzhaigou earthquake, this paper combines comparative petrographic, mineralogical, geochemical and chronological studies of the special interbedded sediments of the Sparking Lake dam with other genetic samples to obtain homology information and genetic links, as well as to explore the tufa depositional dynamics and earthquake disaster subsidence. The palaeoseismic benefit in the discontinuity layer is explored, and the palaeoseismic information embedded in the profiles is extracted, providing a new idea to reconstruct the palaeoseismic events in the tufa deposition sequence. According to X-ray diffraction, laser particle size analysis and scanning electron microscope experiments, the particulate matter in the Jiuzhaigou mountains has its own specific mineralogical characteristics. The mineral composition of the particulate matter is basically calcite. The particle size is large, and the single particle is mostly angular and subangular. The fracture morphology observed under the single particle microscope is uneven, showing the characteristics of dust caused by earthquake disasters. Geochemical analysis data show that the provenance of various types of particles in the same area is stable, indicating the homology of terrestrial carbonate sedimentation in the karst system. Combined with mineralogy and grain size morphology, the interbedded particles in the tufa depositional profile have the potential application of palaeoseismic archives to record extreme seismic events. The palaeoseismic date was inferred from the chronological data of special interlayered sediments in the tufa dam body. Therefore, the tufa bedding can be related to the palaeoearthquake, and the special interlayer of the tufa section can be used to reconstruct palaeoearthquakes.

Preprint ARTICLE | doi:10.20944/preprints201805.0089.v1

Conservation of Crop Genetic Resources in Italy with a Focus on Vegetables and a Case Study of a Neglected Race of Brassica oleracea

Karl Hammer, Vincenzo Montesano, Paolo Direnzo, Gaetano Laghetti

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: agrobiodiversity; vegetables; plant genetic resources; Italy; safeguarding; landraces

Online: 4 May 2018 (09:34:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0079.v1

Engineering of Synthetic Transcriptional Switches in Yeast

Masahiro Tominaga, Akihiko Kondo, Jun Ishii

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genetic switch; yeast; synthetic transcription factor; synthetic promoter; directed evolution

Online: 5 October 2021 (11:19:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202302.0475.v2

Liver Fibrosis in Individuals with Hepatitis C Virus Genotype 1B from Brazilian Eastern Amazon

Tatiane Lobato Da Silva, Apio Ricardo Nazareth Dias, Juarez Antônio Simões Quaresma, Luiz Fábio Magno Falcão

Subject: Biology And Life Sciences, Virology Keywords: Hepatitis C virus; Genetic; Chronic Hepatitis C; Liver; Elastography

Online: 22 May 2023 (13:56:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0281.v1

Genetic Algorithm Design of MOF-Based Gas Sensor Arrays for CO₂-in-Air Sensing

Brian A. Day, Christopher E. Wilmer

Subject: Chemistry And Materials Science, Applied Chemistry Keywords: genetic algorithms; MOFs; metal-organic frameworks; molecular modelling; arrays

Online: 21 December 2019 (10:55:20 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202007.0403.v2

Complete Quantum Information in the DNA Genetic Code

Michel Planat, Raymond Aschheim, Marcelo Amaral, Fang Fang, Klee Irwin

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA genetic code; informationally complete characters; finite groups,; hyperelliptic curve

Online: 6 October 2020 (10:11:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0016.v1

The IFIH1/MDA5 rs1990760 Gene Variant (946Thr) Differentiates Early Versus Late-Onset Skin Disease and Increased the Risk of Arthritis in a Spanish Cohort of Psoriatic Disease

Pablo Coto-Segura, Daniel Vazquez-Coto, Lucinda Velazquez-Cuervo, Claudia García-Lago, Eliecer Coto, Rubén Queiro

Subject: Medicine And Pharmacology, Dermatology Keywords: psoriasis; psoriatic arthritis; IFIH1; MDA5; polymorphism; genetic association

Online: 1 June 2023 (03:40:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1515.v1

Optimal Design of Laminates Orientation in a Composite Material by Genetics Algorithm and Simulated Annealing

Mauricio Torres Arellano, Aaron Burgos Vergara, Saul Piedra-Gonzalez, Erik Herrera, Edgar Adrian Franco-Urquiza

Subject: Engineering, Mechanical Engineering Keywords: composite material; laminates orientation; optimization; simulated annealing; genetic algorithm

Online: 22 September 2023 (09:07:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0156.v1

Flowering Phenology of Olive Cultivars in Two Climates Zones with Contrasting Temperatures (Subtropical and Mediterranean)

María Guacimara Medina-Alonso, José María Cabezas, Domingo Ríos–Mesa, Ignacio J. Lorite, Lorenzo León, Raúl De la Rosa

Subject: Biology And Life Sciences, Horticulture Keywords: Olea europaea L.; genetic variability; climate warming; chilling requirements

Online: 2 June 2023 (08:26:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0145.v1

Leaky Severe Combined Immunodeficiency in Mice Lacking Non-homologous End Joining Factors XLF and MRI

Sergio Castaneda-Zegarra, Qindong Zhang, Amin Alirezaylavasani, Marion Fernandez-Berrocal, Rouan Yao, Valentyn Oksenych

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: NHEJ; Cernunnos; Cyren; pro-B cells; lymphocyte; genetic interaction

Online: 6 September 2020 (15:50:10 CEST)

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Preprint REVIEW | doi:10.20944/preprints201912.0021.v1

Protein 0^th-Order Structure: The Key for Creating Entirely New Gene/Protein

Kenji Ikehara

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: protein 0th-order structure; origin of gene; origin of protein; origin of genetic code; GNC primeval genetic code hypothesis; SNS primitive genetic code hypothesis

Online: 3 December 2019 (11:10:12 CET)

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Preprint ARTICLE | doi:10.20944/preprints202406.0447.v1

Optimization of Parametric Equalizer Filters in In-Vehicle Audio Systems with Genetic Algorithm

Volkan Başay, Oğuzhan Coşkun, Güneş Yılmaz

Subject: Engineering, Electrical And Electronic Engineering Keywords: vehicle multimedia system; equal loudness contours; parametric equalizer filter; genetic algorithm

Online: 7 June 2024 (08:24:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0826.v1

SSR Based Genetic Diversity Analysis and Population Structure of Proso millet (Panicum miliaceum L.) in Kazakhstan

Meisam Zargar, Elmira Dyussibayeva, Aidyn Orazov, Aiym Zeinullina, Irina Zhirnova, Gulzat Yessenbekova, Aiman Rysbekova

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: proso millet collection; genetic diversity; SSR markers; agronomic traits

Online: 13 September 2023 (10:37:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0169.v1

The Supersymmetry Genetic Code Table and Quadruplet Symmetries of DNA Molecule Are the Unchangeable and Synchronized with the Codon Free Energy Mapping during Evolution

Marija Rosandic, Vladimir Paar

Subject: Biology And Life Sciences, Other Keywords: genetic code symmetry, mitochondrial genetic code, energy code, DNA quadruplet symmetry, classification of trinucleotides/codons

Online: 4 October 2023 (07:43:22 CEST)

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The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: 1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)], and 2) of bases in form of codons 3) direct – complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns, 4) A+T rich and C+G rich alternate codons in the same row between both columns of the genetic code, 5) the same position between divided and undivided codon boxes in relation to horizontal mirror symmetry axes. The SSyGC table has a unique physicochemical purine – pyrimidine symmetry net which is as the core symmetry common for all, more than thirty different nuclear and mitochondrial genetic codes. This net is present in the SSyGC table of all RNA and DNA living species. None of these symmetries is present in the Standard Genetic Code (SGC) table which is constructed on the alphabetic horizontal and vertical U-C-A-G order of bases. Here we show that the free energy value of each codon incorporated as fundamentally mapping the “energy code” in the SSyGC table is compatible with mirror symmetry. On the other hand, in the SGC table the same free energy values of codons are dispersed and a mirror symmetry between them is not recognizable. At the same time the mirror symmetry of the SSyGC table and the DNA quadruplets together with our classification of codons/trinucleotides are perfectly imbedded in the mirror symmetry energy mapping of codons/trinucleotides and point out in favor of maintaining the integrity of the genetic code and DNA genome. We also argue that physicochemical symmetries of the SSyGC table in the manner of the purine – pyrimidine symmetry net, the quadruplet symmetry of DNA molecule and the free energy of codons have remined unchanged during all of evolution. The unchangeable and universal symmetry properties of the genetic code, DNA molecule and energy code are decreasing disorder between codons/trinucleotides and shed a new light on evolution. Diversity in all living species on Earth is broad, but the symmetries of the Supersymmetry Genetic Code as the code of life and the DNA quadruplets related to the” energy code” are unique, unchangeable and have the power of natural laws.

Preprint ARTICLE | doi:10.20944/preprints202307.1933.v1

Utility of the Serum Protein Electrophoresis in the Opportunistic Screening for the Deficiency of Alpha-1 Antitrypsin

Beatriz Fernández-Gomez, Sebastian Menao-Guillén, Ayala Fernandez Gonzalez, Maria Arruebo Muñio, Monica Ramos Alvarez, Mercedes Inda Landaluce, Maria Angeles Castillo Arce, Miguel-Angel Torralba-Cabeza

Subject: Medicine And Pharmacology, Internal Medicine Keywords: Alpha-1 Antitrypsin; Protein electrophoresis; SERPINA1; screening; genetic counseling

Online: 28 July 2023 (10:24:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.1548.v1

Unravelling the Genetic Architecture of Serum Biochemical Indicators in Sheep

Mehmet Kizilaslan, Yunus Arzik, Sedat Behrem, Esra Yavuz, Stephen N. White, Mehmet Ulas Cinar

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Serum biochemical indicators, Ovis aries, GWAS, QTL, genetic correlation, heritability

Online: 21 June 2024 (16:51:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.0814.v1

Biogeography and Conservation in the Arabian Peninsula: A Present Perspective

Shahina A. Ghazanfar

Subject: Biology And Life Sciences, Plant Sciences Keywords: Arabian Peninsula; biogeography; conservation; CWR; ecoregions; endemism; floristics; genetic resources

Online: 12 June 2024 (11:54:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202409.0712.v1

Prevalence and Genetic Analysis of Porcine Circovirus Type 2 That Circulated between 2014 and 2021 in Jiangsu, China

Qi Xiao, Meng Qu, Jianping Xie, Cigen Zhu, Yuping Shan, Aihua Mao, Wenxian Qian, Jiaping Zhu, Jiahui Guo, Dong Lang, Jiaqiang Niu, Libin Wen, Kongwang He

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: porcine circovirus type 2; Jiangsu Province; genetic analysis; genotype

Online: 9 September 2024 (23:42:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.0268.v1

Genetic Mechanism of Geothermal Water in Huichang Fault Depression Basin, Southern Jiangxi Province, China: Based on Hydrochemical Characteristics

Jihong Han, Changsheng Huang, Lianyuan Chang, Pingping Hou, Yafeng Wang, Jin Zou, Chonghe Ren

Subject: Environmental And Earth Sciences, Geophysics And Geology Keywords: Huichang fault depression basin; geothermal fluids; hydrogeochemistry; genetic mechanism

Online: 6 May 2024 (10:14:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202311.0942.v1

Population Genetic Structure of a Viviparous Sand Lizard, the Phrynocephalus forsythii in the Tarim Basin, Xinjiang of China

Jiabao Duan, Luoxue Jiang, Tianying Chen, Wen Zhong, Wei Zhao, Yue Qi, Penghui Guo, You Li

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Phrynocephalus forsythii; microsatellite; genetic diversity; population structure

Online: 14 November 2023 (15:25:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202402.0966.v1

Genetic Variability and Interrelationships of Grain Quality, Cooking Quality and Nutritional Quality Traits in Cowpea: Implication for Cowpea Improvement

Michael M. Chipeta, Esnart Yohane, Jessica Kampanje-Phiri, John Kafwambira

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Consumer-preferred traits; cowpea, genetic variability; interrelationships; quality traits

Online: 19 February 2024 (03:32:06 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202201.0462.v1

Clinical Tick Borne Encephalitis in a Roe Deer (Capreolus capreolus L.)

Graziana Da Rold, Federica Obber, Isabella Monne, Adelaide Milani, Silvia Ravagnan, Federica Toniolo, Sofia Sgubin, Gianpiero Zamperin, Greta Foiani, Marta Vascellari, Petra Drzewniokova, Martina Castellan, Paola De Benedictis, Carlo Vittorio Citterio

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: roe deer; Tick-Borne Encephalitis; neurologic disease; pathology; genetic characterization

Online: 31 January 2022 (13:21:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202403.1134.v1

Investigating Genetic Diversity and Population Structure in Rice Breeding from Association Mapping of 116 Accessions Using 64 Polymorphic SSR Markers

Alok kumar Singh, Devendra Kumar, Donato Gemmati, Ranjith Kumar Ellur, Ashutosh Singh, Veronica Tisato, D.K. Dwivedi, Sanjay Kumar Singh, Kishor Kumar Sadasivuni, Nawaz Ahmad Khan, Ajay Vikram Singh

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Rice; Population structure; Genetic diversity; PIC; Association mapping; Variability

Online: 20 March 2024 (04:45:59 CET)

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Preprint REVIEW | doi:10.20944/preprints202307.1210.v1

Unveiling the Genetic Footprint: Exploring Somatic Mutations in Peripheral Arterial Diseases Progression

Amankeldi A. Salybekov, Mehdi Hassanpour

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: Peripheral arterial diseases; Somatic mutation; Thrombosis; Atherosclerosis; Inflammation; Genetic disorders

Online: 18 July 2023 (10:13:12 CEST)

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Preprint REVIEW | doi:10.20944/preprints202209.0263.v1

Phenotypic Variations, Environmental Effects and Genetic Basis Analysis of Grain Elemental Concentrations in Rice (Oryza sativa L.) for Improving Human Nutrition

Yheni Dwiningsih, Jawaher Alkahtani

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: rice; nutrient elements; toxic elements; phenotypic variance; genetic basis

Online: 19 September 2022 (05:31:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.0211.v1

Tobacco Smoking as an EDC in Aging

Ho-Sun Lee, Hyun-Kyung Na, Seong-Sil Chang, Soo-Young Kim, Chang Seong Kim, Yoonjeong Song, Mihi Yang

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: tobacco smoking; biological monitoring; adolescent; genetic polymorphism; addiction; mtDNA alteration; aging

Online: 4 January 2024 (03:43:27 CET)

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Working Paper ARTICLE

Utilization of a Wheat50K SNP Microarray-Derived High-Density Genetic Map for QTL Mapping of Plant Height and Grain Traits in Wheat

Yun Dong Lv, Zhang Chuan Liang, Rui Yv, Juntao Jian, Hui Jian Wu, Peng Xiao Song, Xin Jian Yao, Bo Peng Song, Yuan Ze Zhang, Dejun Han, Jie Dao Sun

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: wheat; plant height; grain traits; Wheat50K; genetic map; QTL

Online: 22 April 2021 (10:20:48 CEST)

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Plant height is significantly correlated with grain traits, which is a component of wheat yield. The purpose of this study is to investigate the main QTLs that control plant height and grain-related traits in multiple environments. In this study, we constructed a high-density genetic linkage map using the Wheat50K SNP Array to map quantitative trait loci (QTLs) for these traits in 198 recombinant inbred lines (RILs). The two ends of the chromosome were identified as re-combination-rich areas in all chromosomes except chromosome 1B. The middle area of the chro-mosomes was identified as the recombination-barren area. Both the genetic map and the physical map showed a significant correlation when p=0.001, with a correlation coefficient between 0.63 and 0.99. However, there was almost no recombination between 1RS and 1BS. In terms of plant height, 1RS contributed to the reduction of plant height by 3.43cm. In terms of grain length, 1RS contributed to the elongation of grain by 0.11mm. A total of 43 QTLs were identified, including 8 QTLs for Plant height(PH), 11 QTLs thousand grain weight(TGW), 15 QTLs for grain length(GL),and 9 QTLs for grain width(GW), which explained 1.36%–33.08% of the phenotypic variation. Seven were environment-stable QTLs, including two loci Qph.nwafu-4B and Qph.nwafu-4D that determined plant height. The explanation rates of phenotypic variation were 7.39%-12.26% and 20.11%-27.08%, respectively. One QTL, Qtgw.nwafu-4B, which influenced TGW, showed an explanation rate of 3.43%-6.85% for phenotypic variation, two co-segregating KASP markers were developed, the physical locations corresponding to KASP_AX-109316968 and KASP_AX-109519968 were 25.888344 MB and 25.847691 MB. Another QTL, Qgw.nwafu-4D, which determined grain width, had an explanation rate of 3.43%-6.85%. Three loci that affected the grain length were Qgl.nwafu-5A, Qgl.nwafu-5D.2 and Qgl.nwafu-6B, illustrating the explana-tion rates of phenotypic variation as 6.72%-9.59%, 5.62%-7.75%, and 6.68%-10.73%, respectively. Two QTL clusters were identified on chromosomes 4B and 4D.

Preprint ARTICLE | doi:10.20944/preprints202404.1902.v1

Genetic Gain and Inbreeding Rate in Different Simulated Genomic Selection Schemes for Grain Yield and Oil Content in Safflower

Huanhuan Zhao, Majid Khansefid, Zibei Lin, Matthew Hayden

Subject: Biology And Life Sciences, Plant Sciences Keywords: genetic gain; inbreeding rate; safflower; simulation; grain yield; seed oil content

Online: 29 April 2024 (10:28:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202410.0335.v1

THOP1 Is Entailed in a Genetic Fingerprint Associated with Late-Onset Alzheimer’s Disease

Sharlee Climer

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: THOP1; Alzheimer’ s disease; genetic risk factor; haplotype; BlocBuster

Online: 4 October 2024 (13:00:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0870.v1

Selection of Improved Banana Diploid Resistant to Fusarium oxysporum f. sp. cubense Races 1 and Subtropical 4

Welly Sacramento Santana, Anelita de Jesus Rocha, Wesley Barreto da Silva, Vanusia B. Oliveira Amorim, Andresa Priscila de Souza Ramos, Fernando Haddad, Edson Perito Amorim

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Musa spp; genetic resistance; Fusarium wilt

Online: 15 April 2024 (04:25:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.0274.v1

Constructing the Bounds for Neural Network Training Using Grammatical Evolution

Ioannis G. Tsoulos, Alexandros Tzallas, Evangelos Karvounis

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Neural networks; Genetic algorithms; Grammatical Evolution

Online: 5 October 2023 (10:59:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1482.v1

Comparative Proteomic Analysis of Toxoplasma gondii RH Wild-Type and Four SRS29B (SAG1) Knock-Out Clones Reveals Significant Differences between Individual Strains

Kai Pascal Alexander Hänggeli, Andrew Hemphill, Norbert Müller, Manfred Heller, Uldry Anne-Christine, Sophie Braga-Lagache, Joachim Müller, Ghalia Boubaker

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic manipulation; pleiotropic effects; systems biology

Online: 22 May 2023 (09:03:52 CEST)

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In T. gondii, as well as in other model organisms, gene knock-out using CRISPR-Cas9 is a suitable tool to identify the role of specific genes. The general consensus implies that only the gene of interest is affected by the knock-out. Is this really the case? In a previous study, we have generated knock-out (KO) clones of TgRH88_077450 (SRS29B; SAG1) which differed in the numbers of integrated dihydrofolate-reductase-thymidylate-synthase (MDHFR-TS) drug-selectable marker. Clones 18 and 33 had a single insertion of MDHFR-TS within SRS29B. Clone 6 was disrupted by the insertion of a short unrelated DNA-sequence, but the marker was integrated elsewhere. In clone 30, the marker was inserted into SRS29B and several other MDHFR-TS copies were found in the genome. KO and wild-type (WT) tachyzoites had similar shape, dimensions and vitality. This prompted us to investigate the impact of the genetic engineering as such on the overall proteome patterns of the four clones as compared to the respective WT. Comparative shotgun proteomics of the five strains was performed. Overall, 3236 proteins were identified. Principal component analysis of the proteomes revealed five distinct clusters corresponding to the five strains by both iTop3 and iLFQ algorithms. Detailed analysis of the differentially expressed proteins revealed that the target of the KO, srs29B, was lacking in all KO clones. Besides this protein, twenty other proteins were differentially expressed between KO clones and WT or between different KO clones. The protein exhibiting the highest variation between the five strains was srs36D encoded by TgRH_016110. The deregulated expression of SRS36D was further validated by quantitative PCR. Moreover, the transcript levels of three other selected SRS genes, namely SRS36B, SRS46, and SRS57 exhibited significant differences between individual strains. These results indicate that knocking out a given gene may affect the expression of other genes. Therefore, care must be taken when specific phenotypes are regarded as a direct consequence of the KO of a given gene.

Preprint ARTICLE | doi:10.20944/preprints202301.0075.v1

Deep Network Optimization Using a Genetic Algorithm for Recognizing Hand Gestures via EMG Signals

Kasra Sehat, Seyed Mohammadreza Shokouhyan, Nada K. Abdallah, Kinda Khalaf

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: EMG; optimization; genetic algorithm; deep learning

Online: 4 January 2023 (09:21:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0533.v1

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Carla L. Saldaña, Pedro Rodriguez-Grados, Julio C. Chávez-Galarza, Shefferson Feijoo, Juan Carlos Guerrero Abad, Héctor V. Vásquez, Jorge L. Maicelo, Jorge H. Jhoncon, Carlos I. Arbizu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: chloroplast; genetic resources; genomics capirona; phylogenomics

Online: 29 November 2021 (12:32:24 CET)

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Working Paper ARTICLE

Evaluation of the Gene Flow From East to West among Various Populations of Rajasthan, India

R.K. Kumawat, Pankaj Shrivastava, Shivani Dixit, Divya Shrivastava, G.K. Mathur, Gyaneshwer Chaubey

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Genetic affinity; STR; Rajasthan; Heterozygosity; Polymorphic

Online: 21 June 2020 (14:12:03 CEST)

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Working Paper REVIEW

Physicochemical Foundations of Life that Direct Evolution. Why Chance and Natural Selection cannot Explain Evolution

Didier Auboeuf

Subject: Biology And Life Sciences, Biophysics Keywords: evolution; genetic code; RNA; protein; physicochemistry

Online: 28 November 2019 (09:38:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.1384.v1

Mapping Quantitative Trait Locus (QTLs) for Hundred Pod and Seed Weight under Seven Environments in a RIL Cultivated Peanut (Arachis hypogaea L.) Population

Penghui Miao, Xinhao Meng, Zeren Li, Sainan Sun, Charles Y Chen, Xinlei Yang

Subject: Biology And Life Sciences, Plant Sciences Keywords: Cultivated peanut; HPW; HSW; Integrated genetic map; QTL mapping

Online: 18 August 2023 (13:05:33 CEST)

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Preprint REVIEW | doi:10.20944/preprints202303.0140.v1

Autoimmune Inflammatory Reactions Triggered by the COVID-19 Genetic Vaccines in Terminally Differentiated Tissues

Panagis Polykretis, Alberto Donzelli, Janci C. Lindsay, David Wiseman, Anthony M. Kyriakopoulos, Michael Mörz, Paolo Bellavite, Masanori Fukushima, Stephanie Seneff, Peter A. McCullough

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; genetic vaccines; adverse reactions; autoimmunity; immunohistochemistry; spike protein

Online: 8 March 2023 (02:57:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202203.0192.v1

Population Genetic Structure of the Bean Leaf Beetle Ootheca mutabilis (Coleoptera: Chrysomelidae) in Uganda

Dalton Kanyesigye, Vincent Pius Alibu, Wee Tek Tay, Polycarp Nalela, Pamela Paparu, Samuel Olaboro, Stanley Tamusange Nkalubo, Ismail Siraj Kayondo, Gonçalo Silva, Susan Elizabeth Seal, Michael Hilary Otim

Subject: Biology And Life Sciences, Insect Science Keywords: genetic differentiation; leaf beetle; mitochondrial DNA; microsatellites; haplotype; gene flow

Online: 14 March 2022 (16:48:57 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.1687.v1

Virulence of Circulating Marek’s Disease Virus Strains in Vaccinated Chicken Flocks in Taiwan: Data on Genetic Analysis of the meq Oncogene

Ming-Chu Cheng, Guan-Hua Lai, Yi-Lun Tsai, Yi-Yang Lien

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Marek’s disease virus; vaccinated chicken flocks; meq oncogene; genetic characteristics; virulence

Online: 25 September 2023 (11:24:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0304.v1

Longitudinal Survey of Coronavirus Circulation and Diversity in Insectivorous Bat Colonies in Zimbabwe

Vimbiso Chidoti, Helene De Nys, Valerie Pinarello, Getrude Mashura, Dorothee Misse, Laure Guerrini, Davies Pfukenyi, Julien Cappelle, Ngoni Chiweshe, Ahidjo Ayouba, Gift Matope, Martine Peeters, Elizabeth Gori, Mathieu Bourgarel, Florian Liegeois

Subject: Biology And Life Sciences, Virology Keywords: Bat Coronavirus (Bt CoVs); human-bat interaction; genetic diversity; reproductive phenology; Zimbabwe

Online: 23 March 2022 (02:55:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.0588.v1

Phytoene Desaturase (Pds) Gene-Derived Markers Identify “A” and “B” Genomes in Banana (Musa spp.)

Fernanda dos Santos Nascimento, Marcelly Santana Mascarenhas, Samantha Costa Boaventura, Carla Catharina Hora Souza, Andresa Priscila de Souza Ramos, Anelita de Jesus Rocha, Julianna Matos da Silva Soares, Leandro Eugenio Cardamone Diniz, Tiago Antônio De Oliveira Mendes, Claudia Fortes Ferreira, Edson Perito Amorim

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Gene composition; phytoene desaturase; molecular marker; genetic improvement; Musa spp.

Online: 8 January 2024 (11:27:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202308.1295.v1

Enzymatic Testing for Mucopolysaccharidosis Type I in Kuwaiti Newborns: A Pilot Study Toward Newborn Screening

Hind Alsharhan, Mohammad Z Haider, Bann Qadoura, Mariam Ayed, Gursev S Dhaunsi, Hessa Alkandari

Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: Mucopolysaccharidosis; lysosomal storage disorder; newborn screening; enzymatic testing; genetic testing

Online: 18 August 2023 (09:45:16 CEST)

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Introduction: Mucopolysaccharidosis type I (MPSI) is an autosomal recessive lysosomal storage disorder characterized by deficient or absent α-L-iduronidase (IDUA) enzyme activity due to pathogenic variants in IDUA gene. Early treatment with hematopoietic stem cell transplantation and/or enzyme replacement therapy is associated with improved outcomes in this progressive multisystem disease. The diagnosis is usually delayed due to late presentation and nonspecific symptoms resulting in high morbidity and mortality. The incidence of MPSI in US is estimated to be 0.26:100,000, however, it is unknown in Kuwait. This pilot study was undertaken to screen MPSI in all Kuwaiti neonates born at Farwaniya Hospital over a period of 12-months. This study examined the incidence of MPSI in a major center in Kuwait for inclusion in the national newborn screening program to enable its early detection and adequate treatment. Methods: All Kuwaiti neonates born at Farwaniya Hospital, Kuwait from December 2021 to December 2022, were screened for MPSI. The screening consisted of determining IDUA enzyme activity in dried blood spots (DBS)-derived samples by Tandem Mass Spectrometry. A follow-up genetic analysis of IDUA gene is planned to screen the cases with diminished IDUA enzyme activity as second-tier testing. Results: A total of 618 newborns, including 331 (54%) males and 287 (46%) females, were screened. Twenty of them had deficient IDUA enzyme activity but showed negative genetic testing for IDUA. However, we have diagnosed one additional female baby with MPSI, who belonged to Farwaniya Hospital, but the parents chose to deliver in a private hospital. She presented at age three months with recurrent upper airway infections, snoring and extensive Mongolian spots. The molecular study revealed previously reported pathogenic nonsense variant in IDUA c.1882C>T; p.(Arg628Ter), associated with severe phenotype. That being included, MPSI is estimated to be about 0.3% among tested females and 0.2% of all screened cases in Kuwait. Conclusion: Our study is the first to evaluate the incidence of MPSI in Kuwait. Given the single center, small number of screened babies and the short study duration thus far, it is premature to calculate the incidence of MPSI. It is anticipated that as the study continues and more infants are examined, we would be able to estimate the incidence of this disease in our population correctly. Further studies including screening newborns in all maternity hospitals in Kuwait are needed to calculate the actual incidence of MPSI. Our data supports including MPSI in national newborn screening program to allow early initiation of treatment and thus improve disease outcome.

Preprint ARTICLE | doi:10.20944/preprints202305.0989.v1

Identifying Genetic Architecture of Carcass and Meat Quality Traits in a Ningxiang Indigenous Pig Population

Shishu Yin, Gang Song, Ning Gao, Qin Zhang, Hu Gao, Qinghua Zeng, Peng Lu, Kang Xu, Jun He

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: genome-wide association study; carcass length; meat color; genetic parameter

Online: 15 May 2023 (07:25:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0563.v1

Two Comprehensive and Practical Methods for Simulating Pan Evaporation Under Different Climatic Conditions in Iran

Mohammad Hassan Dehghanipour, Hojat Karami, Hamidreza Ghazvinian, Zahra Kalantari, Amir Hossein Dehghanipour

Subject: Engineering, Civil Engineering Keywords: Iran; Pan Evaporation; Genetic Algorithm; MLP Neural Network; Experimental Relationship

Online: 31 August 2021 (11:20:33 CEST)

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Evaporation from surface water plays a key role in water accounting of basins, water resources management, and irrigation systems management, so simulating evaporation with high accuracy is very important. In this study, two methods for simulating pan evaporation under different climatic conditions in Iran were developed. In the first method, six experimental relationships (linear, quadratic, and cubic, with two input combinations) were determined for Iran’s six climate types, inspired by a multilayer perceptron neural network (MLP-NN) neuron and optimized with the genetic algorithm. The best relationship of the six was selected for each climate type, and the results were presented in a three-dimensional graph. In the second method, the best overall relationship obtained in the first method was used as the basic relationship, and climatic correction coefficients were determined for other climate types using the genetic algorithm optimization model. Finally, the accuracy of the two methods was validated using data from 32 synoptic weather stations throughout Iran. For the first method, error tolerance diagrams and statistical coefficients showed that a quadratic experimental relationship performed best under all climatic conditions. To simplify the method, two graphs were created based on the quadratic relationship for the different climate types, with the axes of the graphs showing relative humidity and temperature, and with pan evaporation was drawn as contours. For the second method, the quadratic relationship for semi-dry conditions was selected as the basic relationship. The estimated climatic correction coefficients for other climate types lay between 0.8 and 1 for dry, semi-dry, semi-humid, Mediterranean climates, and between 0.4 and 0.6 for humid and very humid climates, indicating that one single relationship cannot be used to simulate pan evaporation for all climatic conditions in Iran. The validation results confirmed the accuracy of the two methods in simulating pan evaporation under different climatic conditions in Iran.

Preprint REVIEW | doi:10.20944/preprints202011.0351.v1

The Beneficial Potential of Genetically Modified Stem Cells in the Treatment of Stroke: A Review

Mohammad Saied Salehi, Anahid Safari, Sareh Pandamooz, Benjamin Jurek, Etrat Hooshmandi, Maryam Owjfard, Mahnaz Bayat, Seyedeh Shaghayegh Zafarmand, Jaleel Miyan, Afshin Borhani-Haghighi

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Cell therapy; MCAO; Stroke; Genetic engineering; Growth factors; Stem cells

Online: 12 November 2020 (14:25:43 CET)

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Preprint ARTICLE | doi:10.20944/preprints201906.0241.v1

Moisture Estimation in Cabinet Dryer with Thin-Layer Relationships Using Genetic Algorithm and Neural Network

Behzad Maleki, Mahyar Ghazvini, Mohammad Hossein Ahmadi, Heydar Maddah, Shahab Shamshirband

Subject: Computer Science And Mathematics, Applied Mathematics Keywords: cabinet dryer; genetic algorithm; neural network; temperature; air velocity; moisture

Online: 24 June 2019 (10:05:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0934.v1

Algorithm Optimizer in GA-LSTM for Stock Price Forecasting

Yohanes Leonardus Sukestiyarno, Dian Tri Wiyanti, Lathifatul Azizah

Subject: Computer Science And Mathematics, Applied Mathematics Keywords: Time Series; Forecasting, Deep Learning; Genetic Algorithm; Long Short-Term Memory

Online: 12 May 2023 (11:07:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202302.0033.v1

Long-term SMN- and Ncald-ASO Combinatorial Therapy in SMA Mice and NCALD-ASO Treatment in hiPSC-Derived Motor Neurons Show Protective Effects

Anixa Muiños-Bühl, Karen K Ling, Roman Rombo, Eleonora Zilio, Frank Rigo, C. Frank Bennett, Brunhilde Wirth

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Neuromuscular disorder; NCALD; SMA; SMN2; Antisense oligonucleotide; Genetic modifier; Therapy; hiPSCs

Online: 2 February 2023 (07:54:05 CET)

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Preprint REVIEW | doi:10.20944/preprints202312.0368.v1

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

Nguyen Hong Nguyen

Subject: Biology And Life Sciences, Aquatic Science Keywords: genetic basis; genomic architecture; disease tolerance; population resilience and climate change

Online: 6 December 2023 (08:34:59 CET)

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Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease- and species-specific and contingent upon a multitude of factors. The field of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favourable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate to high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems, AI algorithms, and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.

Preprint ARTICLE | doi:10.20944/preprints201711.0079.v1

Cryptic Species Diversity of Rice Hopper Parasitoids in Southeast Asia

Christina Sann, Franziska Wemheuer, Alexis Beaurepaire, Rolf Daniel, silvio Erler, Stefan Vidal

Subject: Biology And Life Sciences, Insect Science Keywords: DNA barcoding; genetic diversity; hymenopteran parasitoids; Nephotettix spp.; Nilaparvata lugens; rice

Online: 13 November 2017 (17:06:38 CET)

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