QTL Mapping Of Cottonseed Nutritional Quality Traits In G.hirsutum Recombinant Inbred Lines With High Fiber Quality Cultivar/Lines As Parents

Cotton is not only an important natural fibre crop,but also a source crop of protein and oil.Proein,fatty acids and other nutrients of cottondseed can be used to make animal feed,edible blended oils and biofuels.For a long time,more research has been carried out on traits such as fibre and yield of cotton,but less attention has been paid to the improvement of cottonseed quality.Therefore,the research on the nutritional quality traits of cotton seeds can further increase the economic value of cotton.In order to explore the genetic characteristics of cottonseed nutritional quality traits of high-quality fiber varieties/strains,a recombinant inbred line(RIL)population was established from a cross between upland cotton high fiber quanlity line N274 and high fiber quality cultivar Yumian 1.Based on simplified genome sequencing technology(SLAF-seq),SNP markers were developed and used to construct the genetic map of RIL population.Fourier NIR light scanner were used to measure six nutritional quality traits,including protein content,oil content,linoleic acid content,oleic acid content,stearic acid content and palmitic acid content,in the RIL population under five environments.In addition,the SNP markers were integrated into SNPLDB markers and a restricted twophase multilocus genome-wide association analysis(RTM-GWAS)was used to detect nutritional quality QTL.The main findings were as follows.1.Phenotypic analysis of nutritional quality traits of cotton kernelsAll six nutritional quality traits in the five environments were continuously and approximately normally distributed,which were consistent with the inheritance of quantitative traits controlled by multiple genes.The ANOVA results showed that all traits were highly significantly influenced by genotype and environment.Correlation analysis showed that protein content was highly significantly negatively correlated with oil content,palmitic acid content,stearic acid content and oleic acid content,and highly significantly positively correlated with linoleic acid content.Oil content was highly significantly positively correlated with stearic acid content and oleic acid content,and highly significantly negatively correlated with linoleic acid content.Palmitic acid content and stearic acid content,oleic acid content and linoleic acid content all showed highly significant negative correlations.Oleic acid content and linoleic acid content showed highly significant negative correlations.2.SNP and SNPLDB marker analysisAfter filtering the SNP markers produced by SLAF-seq sequencing,a total of 11,439 SNP markers(aa × bb genotype)were obtained.Physical location annotation of these SNPs showed that most of them located in the gene spacer region(89.41%).In addition,a total of 3499 SNPLDBs were obtained by further combining multiple adjacent and tightly linked SNP markers into linkage disequilibrium segment markers(SNPLDBs),of which 2206 were located in the At subgenome and 1293 in the Dt subgenome.Chromosome A01 contained the most markers,whereas chromosome D03 contained the least markers.3.QTL analysis for nutritional quality of cotton kernelsBased a genetic linkage map containing 2127 SNP loci and 78 SSR loci constructed in our laboratory’s previous study,as well as nutritional quality phenotypic data of cotton kernel tested in five environments,a total of 127 QTL were detected,including 20 QTL for protein content,16 QTL for oil content,24 QTL for linoleic acid content,26 QTL for stearic acid oil content,17 QTL for oleic acid content,and 24 QTL for palmitic acid content.A total of 77 QTL were detected in At subgenome and 50 QTL were detected in Dt subgenome.Of these,six QTL(qLA＿A04.3,qLA＿D13.1,qOA＿D13.1,qPA＿A02.1,qPA＿A05.1,qPA＿D10.1)were detected in two environments,and one QTL(qLA＿A04.4)was detected in three environments.In addition,a total of 16 QTL clusters concentrated on 11 chromosomes and contained 67 QTL,accounting for 52.76% of all QTL.4.RTM-GWAS analysis of nutritional quality of cotton kernelsA total of 127 QTL for nutritional quality traits of cottonseed kernels were detected by Restricted Two-phase Multilocus Genome-wide Association Analysis(RTM-GWAS),including 17 QTL for protein,16 QTL for oil content,12 QTL for oleic acid,24 QTL for linoleic acid,33 QTL for stearic acid and 25 QTL for palmitic acid.Three protein content QTL,one oil content QTL,three oleic acid content QTL,seven linoleic acid content QTL,five stearic acid content QTL and three palmitic acid content QTL had both genotype master effects and QTL-environment interactions(QEI)effects.Linoleic acid content QTL qLA＿D13.1 was the QTL with the highest phenotypic contribution.5.qLA＿D13.1/qOA＿D13.1 candidate gene analysisThe environmentally stable linoleic acid content qLA＿D13.1 and oleic acid content QTL qLA＿D13.1 were the the highest contribution to the corresponding phenotypes.Therefore,the candidate genes in this QTL region were further analysed.The confidence interval size of these two QTLs was 0.23 Mb,and the interval contained 13 annotated genes,eight of which were expressed to varying degrees in the ovules.Functional analysis of these eight genes postulated GH＿D13G0188,involved in the flavonol metabolic pathway,and GH＿D13G0199,involved in the abscisic acid signalling pathway,as possible candidate genes.