title: Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China.
abstract: Since upland cotton was introduced into China during the 1920s-1950s, hundreds of inbreed cultivars have been developed. To explore the molecular diversity, population structure and elite alleles, 503 inbred cultivars developed in China and some foreign cultivars from the United States and the Soviet Union were collected and analyzed by 494 genome-wide SSRs (Simple Sequence Repeats).
  
  
  
  Four hundred and ninety-four pairs of SSRs with high polymorphism and uniform distribution on 26 chromosomes were used to scan polymorphisms in 503 nation-wide upland cottons. The programming language R was used to make boxplots for the phenotypic traits in different environments. Molecular marker data and 6 fiber quality traits were analyzed by the method of MLM (mixed linear model) (P + G + Q + K) in the TASSEL software package on the basis of the population structure and linkage disequilibrium analysis. The loci of elite allelic variation and typical materials carrying elite alleles were identified based on phenotypic effect values.
  
  
  
  A total of 179 markers were polymorphic and generated 426 allele loci; the population based on molecular diversity was classified into seven subpopulations corresponding to pedigree origin, ecological and geographical distribution. The attenuation distance of linkage disequilibrium dropped significantly up to 0-5 cM. Association mapping for fiber quality showed that 216 marker loci were associated with fiber quality traits (P < 0.05) explaining 0.58 % ~ 5.12 % of the phenotypic variation, with an average of 2.70 %. Thirteen marker loci were coincident with other studies, and three were detected for the same trait. Seven quantitative trait loci were related to known genes in fiber development. Based on phenotypic effects, 48 typical materials that contained the elite allele loci related to fiber quality traits were identified and are widely used in practical breeding.
  
  
  
  The molecular diversity and population structure of 503 nation-wide upland cottons in China were evaluated by 494 genome-wide SSRs, and association mapping for fiber quality revealed known and novel elite alleles. The molecular diversity provides a guide for parental mating in cotton breeding, and the association mapping results will aid in the fine-mapping genes related to fiber quality traits and facilitate further studies on candidate genes.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.|Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, 832011, Xinjiang, China.
authors.forename: Xinhui
authors.initials: X
authors.lastname: Nie
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Cong
authors.initials: C
authors.lastname: Huang
authors.affiliation: Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, 832011, Xinjiang, China.
authors.forename: Chunyuan
authors.initials: C
authors.lastname: You
authors.affiliation: Economic Crop Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
authors.forename: Wu
authors.initials: W
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Wenxia
authors.initials: W
authors.lastname: Zhao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Shen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Beibei
authors.initials: B
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Hantao
authors.initials: H
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Yan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Baoshen
authors.initials: B
authors.lastname: Dai
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Maojun
authors.initials: M
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
authors.forename: Xianlong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. linzhongxu@mail.hzau.edu.cn.
authors.forename: Zhongxu
authors.initials: Z
authors.lastname: Lin
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D032561:Cotton Fiber; D056726:Genetic Association Studies; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D007178:Inbreeding; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D010641:Phenotype; D011110:Polymorphism, Genetic; D019655:Quantitative Trait, Heritable
chemical_list: D005819:Genetic Markers
keywords: Association mapping; Elite allele; Fiber quality traits; Population structure; Upland cotton