| Cotton is a leading fiber crop,and an important protein and oilseed crop that is grown extensively worldwide.Cottonseed is a significant byproduct of cotton and a source of edible oil,biofuel,and protein for animal feed.Upland cotton is the most widely grown Gossypium species worldwide,with high yield,wide adaptability and excellent fibre quality,but because of long-term domestication and aritfical selection,the genetic base within intra-species has narrowed and diversity has decreased,making it difficult to further enhance its breeding potential.G.hirsutum race punctatum is one of seven races of upland cotton,and has a high rate of fruiting,high-quality fiber,resistance to drought,and other excellent qualities.G.hirsutum race punctatum is somewhat distantly related to upland cotton cultivars,but the hybid between upland cotton cultivar and G.hirsutum race punctatum are fertile.Hence,the crosses between between upland cotton cultivar and G.hirsutum race punctatum will assist to enhance the genetic variety of upland cotton cultivars,as well as to investigate the superior genes of both and apply them to breed cotton for high yield and quality.A recombinant inred line population was established from a cross between G.hirsutum cultivar CCRI 35 and G.hirsutum race punctatum accession TX-230.on the one hand,SNP markers were developed by SLAF-Seq and were applied to construct a genetic linkage map.In addition,the SNP loci obtained from sequencing were re-filtered and analyzed,and multiple adjacent and tightly linked SNPs were tagged to form a SNPLDB.Five nutritional quality traits of cotton kernels were determined by Fourier NIR light scanner in six environments.For the five nutritional quality traits,QTL analysis was conducted by traditional and RTM-GWAS method.The following are the main results:1.SNP and SNPLDB markerA total of 37,912 aa × bb genotypic SNPs were obtained through re-filtering and re-analyzing the sequencing data,including 26,385 SNPs in the At subgenome and 11,527 SNPs in the Dt subgenome.A total of 13,130 SNPLDBs were obtained by tagging multiple adjacent and tightly linked SNPs into linkage disequilibrium segments(SNPLDBs),of which 8848 were in the At subgenome and 4282 in the Dt subgenome.2.Phenotype analysis of the nutritional quality of cotton kernelsProtein content,oil content and the four fatty acids were approximately normally distributed in all environments.All nutritional quality traits showed significant superparental segregation and were significantly influenced by environment and genotype.The protein content of cotton kernels was negatively correlated with oil content,palmitic acid content,stearic acid and oleic acid in all five environments,and positively correlated with linoleic acid content in all five environments.Oleic acid content was negatively correlated with linoleic acid content in all environments.3.Tranditional analysis of QTL for nutritional quality traitsA total of 187 QTL were located for nutritional quality traits in five environments,including 46 QTL for protein content,44 QTL for oil content,32 QTL for palmitic acid content,23 QTL for stearic acid content,18 QTL for oleic acid content and 24 QTL for linoleic acid content.One hundred and twenty QTL were located in At subgenome and 67 QTL were located in Dt subgenome.The LOD values of these QTL ranged from 2.01-15.03,with individual QTL explaining 5.2%-34.1%of the phenotypic variation.Of these QTL,94 QTL favourable alleles were derived from G.hirsutum race punctatum and 93 QTL favourable alleles were derived from CCRI 35.Twenty-eight QTL were detected in three or more environments,including four QTL detected in all five environments,eight QTL detected in four environments,and 16 QTL detected in three environments.In addition,78 QTL were located in 31 QTL clusters that disributed on 18 chromosomes.1.RTM-GWAS analysis of QTL for nutritional quality traitsA total of 296 QTL for nutritional quality traits were detected by using the RTM-GWAS method,with 99 QTL for both main effects and environmental interactions,85 QTL for main effects only,and 112 QTL for environmental interactions only.Among these QTL,35 QTL for protein,78 QTL for oil content,41 QTL for palmitic acid,54 QTL for stearic acid,38 QTL for oleic acid and 50 QTL for linoleic acid were identified on two chromosomes,namely the protein QTL on chromosome D03(qR-PC-17-1)and oil content QTL(qR-OC-17-3)on chromosome D03,and palmitic acid QTL(qR-PA-7-4)on chromosome A07.The favourable allele for qPC-17-1 was derived from CCRI35,while the favourable alleles for qR-PA-7-4 and qR-OC-17-3 were derived from G.hirsutum race punctatum accession TX-230.5.Candidate gene predictionThe gene function analysis and expression pattern analysis of the genes in the physical region of the land cotton genome corresponding to the three large contributing QTLs led to the hypothesis that the GH_A07G0049 gene is a candidate gene for qR-PA-7-4;the three genes GH_D03G1217,GH_D03G1221 and GH_D03G1223 are candidates for qR-PC-17-1/qR-OC-17-3. |
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