| Cotton genus comprises of 4 cultivation species including Asian cotton (G. arboreum L.), African cotton (G. herbaceum L.), Upland cotton (G. hirsutum L.) and Sea-island cotton (G. barbadense L.). Upland cotton as the most widely cultivated cotton cultivars accounts for 90% of the world's total cotton production. Cotton is not only important textile fiber raw materials, but also important oil and protein resources. Cotton seed accounts for 10% of world's edible oil and 6% of world's plant protein. Cotton is an important economy mainstay of the agricultural structural adjustment and livestock development. The current objective of cotton breeding is still the improvement of yield and fiber quality. Unfortunately, the researches of seed traits, especially nutrition, are ignored. Cotton seed oil and protein content is still same as its 50 years ago or even 100 years ago. The genetic improvement of yield and fiber quality can ensure the competition with chemical fiber, and the modifying cotton seed as food and feed will provide people with adequate nutrition and food resources. Therefore, with the improvement of cotton yield and fiber quality, the improvement of cotton seed oil, fatty acid composition and protein content could exert the economic value of cotton. Cotton oil, fatty acid composition and protein content are quantitative traits controlled by multiple genes, so conventional quantitative genetics methods can only analyze these traits at the population level, and cannot analyze the effect and expression mode, and chromosome distribution of quantitative trait genes. Herein, (Yumian 1×T586) F2:7 recombinant inbred line population was used to construct upland cotton high-density genetic linkage map with SSR, SRAP, IT-ISJ and morphological markers, and also the QTLs of seed physical and nutritional quality traits were mapped in the present study. The results lay the foundation for molecular marker-assisted selection of upland cotton. The mainly results were as following:1. Phenotypic analysis of seed physical and nutritional quality traits The significant differences of physical and nutritional quality traits exist between parent Yumian 1 and T586. Yumian 1 had 10.67g for seed weight,1.43g for fuzz weight,11.79% for fuzz percentage,6.33g for kernel weight,4.34g for hull weight,59.30% for kernel percentage; about 50.28% for coarse protein contents,24.80% for coarse oil contents; while T586 had 13.02g for seed weight, 0g for fuzz weight,0% for fuzz percentage,8.66g for kernel weight,4.33g for hull weight,66.49% for kernel percentage; about 36.45% for coarse protein contents,36.85% for coarse oil contents. Compared with T586, Yumian 1 had high protein content and low fatty acid content, whereas T586 had low protein content and high fatty acid content. The fatty acid composition was similar in two cultivars. Transgressive high parent segregation appeared in seed physical and nutritional quality traits, and all traits showed continuous distribution and quantitative traits genetics characteristics controlled by multi-gene.The significant or extremely significant environment variances of seed physical and nutritional quality traits showed that seed physical and nutritional quality traits are affected by both genotype and environment. Significantly positive correlation existed between seed weight, seed kernel and seed shell was, and significantly positive correlation also existed between short fiber weight and short fiber. Significantly negative correlation existed between crude protein content and crude oil content. Significantly positive correlation existed between short fiber weight, short fiber rate and crude protein content whereas significantly negative correlation existed between short fiber weight, short fiber rate and crude oil content.2. SRAP polymorphism between mapping parentsA total of 1563 SRAP primer combinations produced a total of 88 polymorphic primer combinations. The polymorphic primers were used to genotyp the recombinant inbred line population, and 105 SRAP loci were obtained, averaging 1.16 informative SRAP loci per polymorphic primer combinations.3. Construction of upland cotton linkage mapA total of 105 SRAP loci, together with 567 SSR,64 IT-ISJ and 8 morphological loci, were employed to perform genetic linkage analysis, and a genetic linkage map comprising of 730 loci and 62 linkage groups was constructed, whereas 15 loci could not be located on any chromosome. The sixty-two linkage groups were distributed into all 26 chromosomes. The genetic linkage map consisted of 102 SRAP,556 SSR,64 IT-ISJ, and eight morphological markers, and covered 3434.3 cM or approximately 77.22% of the total recombination length of cotton genome. The average distance was 4.70 cM between two markers. Up to date, this map is the upland cotton linkage map with largest marker number and the most extensive genome coverage.4. QTL effect and favorable allele origin Based on MQM mapping, eighty-eight QTLs were identified for seed physical traits. Twenty-two QTLs for seed weight explained 3.4%～9.7% of seed weight variance. Favorable allele of eleven QTLs for seed weight originated from T586, whereas favorable allele of eleven QTLs for seed weight originated from Yumian 1. Eleven QTLs for fuzz weight explained 3.6%～63.9% of fuzz weight variance. Favorable allele of five QTLs for fuzz weight originated from T586, whereas favorable allele of six QTLs for fuzz weight originated from Yumian l.Ten QTLs for fuzz percentage explained 3.6%～75.3% of fuzz percentage variance. Favorable allele of three QTLs for fuzz percentage originated from T586, whereas favorable allele of seven QTLs for fuzz percentage originated from Yumian 1. Eighteen QTLs for kernel weight explained 3.6%～8.8% of kernel weight variance. Favorable allele of nine QTLs for kernel weight originated from T586, whereas favorable allele of nine QTLs for kernel weight originated from Yumian 1. Thirteen QTLs for hull weight explained 3.8%～7.9% of hull weight variance. Favorable allele of six QTLs for hull weight originated from T586, whereas favorable allele of seven QTLs for hull weight originated from Yumian 1. Fourteen QTLs for kernel percentage explained 3.6%～11.7% of kernel percentage variance. Favorable allele of ten QTLs for kernel percentage originated from T586, whereas favorable allele of four QTLs for kernel percentage originated from Yumian 1. Among eighty-eight QTLs for seed physical traits, fifty-seven (64.77%) QTLs explained 5-20% of the total phenotypic variation whereas twenty-nine (32.95%) QTLs explained less than 5% of the phenotypic variation. Two main-effect QTLs for fuzz weight and fuzz percentage explained about 53.6%,64.9% of phenotypic variation, respectively.Forty-three QTLs were identified for seed nutritional quality traits. Twelve QTLs for coarse protein contents explained 3.8%～28.8% of coarse protein contents variance. Favorable allele of two QTLs for coarse protein contents originated from T586, whereas favorable allele of ten QTLs for coarse protein contents originated from Yumian 1. Twelve QTLs for coarse oil contents explained 4.0%～23.0% of coarse oil contents variance. Favorable allele of eight QTLs for coarse oil contents originated from T586, whereas favorable allele of four QTLs for coarse oil contents originated from Yumian 1. Four QTLs for linoleic acid contents explained 3.5%～5.5% of linoleic acid contents variance. Favorable allele of one QTL for linoleic acid contents originated from T586, whereas favorable allele of three QTLs for linoleic acid contents originated from Yumian 1. Three QTLs for oleic acid contents explained 3.7%～11.3% of oleic acid contents variance. Favorable allele of three QTLs for oleic acid contents originated from T586. Five QTLs for palmitate acid contents explained 5.3%～7.0% of palmitate acid contents variance. Favorable allele of one QTL for palmitate acid contents originated from T586, whereas favorable allele of four QTLs for palmitate contents originated from Yumian 1. Seven QTLs for stearic acid contents explained 3.7%～9.3% of stearic acid contents variance. Favorable allele of four QTLs for stearic contents originated from T586, whereas favorable allele of three QTLs for stearic contents originated from Yumian 1. Among forty-three QTLs for seed nutritional quality traits, twenty-seven (62.79%) QTLs had effects controlling 5-20% of total phenotypic variation, and fourteen (32.56%) QTLs explained less than 5% of the phenotypic variation. Two main-effect QTLs for crude protein content and crude oil content explained about 23% and 22.5% of phenotypic variation, respectively.5. The interaction of QTL and environmentAmong the QTLs for physical traits, twenty seven QTLs (30.68%) could be identified simultaneously in 2 or 3 different environments, including six QTLs (27.27%) for seed weight, five QTLs (45.45%) for fuzz weight, three QTLs (30%) for fuzz percentage, six QTLs (33.33%) for kernel weight, six QTLs (46.15%) for hull weight, and two QTLs (14.28%) for kernel percentage, respectively.Among the QTL for seed nutritional quality traits, six QTL (25%) for coarse protein and coarse oil contents (each of three QTL) were identified in two environments. One QTL for oleic acid and palmitate acid was identified in two environments.6. QTL chromosome distributionAmong eighty-eight QTLs for physical traits, sixty-five are clustered. The QTLs for the seed weight, kernel weight and hull weight always clustered on the same chromosome region whereas QTLs for fuzz weigh and fuzz percentage always clustered on the same region. QTLs for fuzz weigh and fuzz percentage clustered on chr.3, chr.7, chr.13, chr.15, chr.20 and chr.21, and QTLs for seed weigh, kernel and hull weight clustered on chr.11, chr.12, chr.14, chr.15, chr.24 and chr.25. Five QTLs for kernel percentage clustered on chr.6, chr.8, chr.18, chr.20, chr.23 with QTLs for seed weight and kernel weight.Out of twenty-four QTLs for coarse protein and coarse oil contents,16 QTLs are clustered, including two main-effect QTLs, which accounted for 66.67% of all QTL for coarse protein and coarse oil contents.Main-effect QTLs for five physical traits, seed weight, kernel weight, hull weight, fuzz weigh, fuzz percentage, and two nutritional quality traits, coarse protein and coarse oil contents clustered on chromosome 12, suggesting these clustered QTLs maybe resulted from pleiotropy.
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