陆地棉棉籽相关性状的QTN挖掘及候选基因筛选OA北大核心CSTPCD

[Objective]Exploring the genetic loci and related genes that control cottonseed size traits to lay a foundation for subsequent study on the molecular mechanism cottonseed size formation.[Method]The upland cotton recombinant inbred line(RIL)population composed of 300 lines was used as the research material.Seven phenotypic traits including cottonseed index(SI),seed length-cutting acreage(SLA),seed length-cutting perimeter(SLP),seed length(SL),seed width(SW),length-width ratio(LWR)and seed roundness(SR)were evaluated in four environments.The RIL population was genotyped by liquid phase chip strategy.The high-quality single nucleotide polymorphism(SNP)markers and phenotypic data were subjected to perform genome-wide association study(GWAS),and quantitative trait nucleotides(QTNs)associated with cottonseed size-related traits were mined.The genetic effects of QTNs were analyzed to identify candidate genes.[Result]Seven cottonseed size-related traits showed a continuous normal distribution in four environments,which expressed a sizable phenotypic variation.The coefficient of variation ranged from 1.82%to 10.70%.The influencing effect on trait formation were basically as genotype＞environment＞genotype×environment,indicating suitability for GWAS analysis of these results.Correlation analysis showed that the seed index was significantly correlated with SLA,SLP,SL and SW,and LWR was significantly correlated with SR,indicating the possible existence of pleiotropic loci.GWAS was performed using the 3VmrMLM model,and a total of 47 QTNs were associated with these seven traits.A total of 11 QTNs were associated on chromosome A07,of which three physical loci in the region of 71.99-72.87 Mb,A07:71993462,A07:72067994 and A07:72198802 were very close and simultaneously associated with SI,SLA,SLP,SL and SW in four environments.The average value of R2 between markers was＞0.8(P＜0.001),showing a large linkage disequilibrium.Genetic effect analysis showed that there were two haplotypes in this region.Among these cottonseed size relating traits,haplotype and haplotype I were signifiⅡ cantly different,indicating that these loci directly affected cottonseed size traits and could be used for molecular marker-assisted selection.The expression patterns of the genes in the interval were analyzed using TM-1 transcriptome data.The results revealed that Gh_A07G1767 was preferentially expressed and Gh_A07G1766 specifically expressed at the stage of cottonseed development.These results speculated that these genes may play an important role in the growth and development of cottonseed.[Conclusion]47 QTNs were identified,and two candidate genes related to cottonseed development were screened.