陆地棉(GossypiumhirsutumL.)是一种主要的纤维作物,在全世界范围内种植,具有重要的经济意义。印度拥有最大的棉花种植面积,但它的纤维产量仍然受到影响,在生产率方面排名第22位。棉花纤维产量性状的遗传改良是棉花育种的主要目标之一,但是对棉花纤维产量性状的遗传结构的理解仍然有限和不清楚。为了更好地破译与纤维产量性状相关的遗传变异,我们使用117份印度棉花种质对6个产量相关性状进行了全面的全基因组关联图谱研究。要做到这一点,我们使用基因分型测序(GBS)方法产生了2,41,086个高质量的单核苷酸多态性(SNP)标记。人口结构,PCA,亲属关系,系统发育分析将种质分为两个亚群,种质间相关性较弱。通过关联分析,205个SNPs和134个QTL被鉴定为与六个纤维产量性状显著相关。总的来说,在目前的研究中发现了39个新的QTL,而在比较分析中,95个QTL与现有的公共领域数据重叠。八个QTL,鉴定了qGhBN_SCY_D6-1、qGhBN_SCY_D6-2、qGhBN_SCY_D6-3、qGhSI_LI_A5、qGhLI_SI_A13、qGhLI_SI_D9、qGhBW_SCY_A10和qGhLP_BN_A8。这些纤维产量QTL的基因注释揭示了2,509个独特基因。这些基因主要针对不同的生物过程进行富集,如植物细胞壁合成,营养代谢,和营养生长发育中的基因本体论(GO)富集研究。此外,使用来自12个不同棉花组织的RNAseq数据进行基因表达分析,确定了40个候选基因(23个稳定基因和17个新基因)在纤维的不同阶段具有转录活性,胚珠,和种子发育。这些发现揭示了丰富的遗传元素挂毯,包括SNPs,QTL,和候选基因,并且在未来的印度棉花育种计划中可能具有提高纤维产量的巨大潜力。
Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of
cotton fiber yield traits is one of the major goals of
cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping
study using 117 Indian
cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current
study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment
study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.