Jia, X.; Zhao, H.; Zhu, J.; Wang, S.; Li, M.; Wang, G. Quantitative Trait Loci Mapping and Candidate Gene Analysis for Fiber Quality Traits in Upland Cotton. Agronomy2024, 14, 1719.
Jia, X.; Zhao, H.; Zhu, J.; Wang, S.; Li, M.; Wang, G. Quantitative Trait Loci Mapping and Candidate Gene Analysis for Fiber Quality Traits in Upland Cotton. Agronomy 2024, 14, 1719.
Jia, X.; Zhao, H.; Zhu, J.; Wang, S.; Li, M.; Wang, G. Quantitative Trait Loci Mapping and Candidate Gene Analysis for Fiber Quality Traits in Upland Cotton. Agronomy2024, 14, 1719.
Jia, X.; Zhao, H.; Zhu, J.; Wang, S.; Li, M.; Wang, G. Quantitative Trait Loci Mapping and Candidate Gene Analysis for Fiber Quality Traits in Upland Cotton. Agronomy 2024, 14, 1719.
Abstract
Superior fiber quality is one of the most important objectives in cotton breeding. To detect the genetic basis underlying fiber quality, an F2 population containing 413 plants was constructed by crossing Jifeng 914 and Jifeng 173, both of which have superior fiber quality, with Jifeng 173 being better. Five fiber quality traits were investigated in the F2, F2:3, F2:4, and F2:5 populations. Quantitative trait loci (QTL) mapping was conducted based on a high-density genetic map containing 11,488 single nucleotide polymorphisms (SNPs) and spanning 4,202.12 cM in length. Transgressive segregation patterns and complex correlations in the five tested traits were observed. A total of 108 QTLs were found, including 27 for fiber length (FL), 16 for fiber strength (FS), 24 for micronaire (MC), 17 for fiber uniformity (FU), and 24 for fiber elongation rate (FE). Chromosome A7 contained 12 QTL, ranking the first. No QTL was found on chromosome D1 and D11. Each QTL contributed 1.98%–21.45% to the phenotypic variation (PV), including 13 major effect QTLs that contributed more than 10% toward PV. Two QTLs could be repeatedly detected in three populations, including qFL-D3-2 in F2, F2:4, and F2:5 with 9.18%–21.45% of PV, qFS-A11-1 in F2:3, F2:4 and F2:5 with 6.05%–10.41% of PV. Another seven stable QTLs could be detected in two populations, including four major effect QTLs: qFL-A12-3, qFS-D10-2, qMC-D6-2, and qMC-D8-1. Fourteen QTL-overlapping regions were found, which might explain the complex correlations among the five phenotypic traits. Four regions on chromosome A11, D3, D6, and D10 covered by both stable and major effect QTLs are promising for further fine mapping. The genomic regions of the two QTLs detected in three populations and the four major effect QTLs contain 810 genes. Gene functional analysis revealed that the annotated genes are mainly involved in protein binding and metabolic pathways. Fifteen candidate genes in the qFL-D3-2 region are highly expressed in fiber or ovules during fiber initiation, elongation, secondary cell wall thickening, or maturation stages. qRT-PCR revealed that Ghir_D03G005440.1 and Ghir_D03G011310.1 may play a role in promoting fiber initiation, Ghir_D03G006470.1 may be beneficial for promoting fiber elongation. This study provides more information for revealing the molecular genetic basis underlying cotton fiber quality.
Biology and Life Sciences, Agricultural Science and Agronomy
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