title: Identification of stable quantitative trait loci (QTLs) for fiber quality traits across multiple environments in Gossypium hirsutum recombinant inbred line population.
abstract: BACKGROUND
  The identification of quantitative trait loci (QTLs) that are stable and consistent across multiple environments and populations plays an essential role in marker-assisted selection (MAS). In the present study, we used 28,861 simple sequence repeat (SSR) markers, which included 12,560 Gossypium raimondii (D genome) sequence-based SSR markers to identify polymorphism between two upland cotton strains 0-153 and sGK9708. A total of 851 polymorphic primers were finally selected and used to genotype 196 recombinant inbred lines (RIL) derived from a cross between 0 and 153 and sGK9708 and used to construct a linkage map. The RIL population was evaluated for fiber quality traits in six locations in China for five years. Stable QTLs identified in this intraspecific cross could be used in future cotton breeding program and with fewer obstacles.
  
  
  RESULTS
  The map covered a distance of 4,110 cM, which represents about 93.2 % of the upland cotton genome, and with an average distance of 5.2 cM between adjacent markers. We identified 165 QTLs for fiber quality traits, of which 47 QTLs were determined to be stable across multiple environments. Most of these QTLs aggregated into clusters with two or more traits. A total of 30 QTL clusters were identified which consisted of 103 QTLs. Sixteen clusters in the At sub-genome comprised 44 QTLs, whereas 14 clusters in the Dt sub-genome that included 59 QTLs for fiber quality were identified. Four chromosomes, including chromosome 4 (c4), c7, c14, and c25 were rich in clusters harboring 5, 4, 5, and 6 clusters respectively. A meta-analysis was performed using Biomercator V4.2 to integrate QTLs from 11 environmental datasets on the RIL populations of the above mentioned parents and previous QTL reports. Among the 165 identified QTLs, 90 were identified as common QTLs, whereas the remaining 75 QTLs were determined to be novel QTLs. The broad sense heritability estimates of fiber quality traits were high for fiber length (0.93), fiber strength (0.92), fiber micronaire (0.85), and fiber uniformity (0.80), but low for fiber elongation (0.27). Meta-clusters on c4, c7, c14 and c25 were identified as stable QTL clusters and were considered more valuable in MAS for the improvement of fiber quality of upland cotton.
  
  
  CONCLUSIONS
  Multiple environmental evaluations of an intraspecific RIL population were conducted to identify stable QTLs. Meta-QTL analyses identified a common chromosomal region that plays an important role in fiber development. Therefore, QTLs identified in the present study are an ideal candidate for MAS in cotton breeding programs to improve fiber quality.
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. jamshed_muhammad@yahoo.com.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Jamshed
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. youluyuan@hotmail.com.
authors.forename: Fei
authors.initials: F
authors.lastname: Jia
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. juwugong@126.com.|College of Agronomy, Xinjiang Agricultural University, Key Laboratory of Agro-Biotechnology, Urumqi, 830052, Xinjiang, China. juwugong@126.com.
authors.forename: Juwu
authors.initials: J
authors.lastname: Gong
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. palangaeddieh@yahoo.fr.
authors.forename: Koffi Kibalou
authors.initials: KK
authors.lastname: Palanga
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. syzmb@aliyun.com.
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. junwenlee@163.com.
authors.forename: Junwen
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. shh9119@163.com.
authors.forename: Haihong
authors.initials: H
authors.lastname: Shang
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. liuay@cricaas.com.cn.
authors.forename: Aiying
authors.initials: A
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. chentingting7039@126.com.
authors.forename: Tingting
authors.initials: T
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. 573500136@qq.com.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. 784182367@qq.com.
authors.forename: Juan
authors.initials: J
authors.lastname: Cai
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. gejiaoyu@163.com.
authors.forename: Qun
authors.initials: Q
authors.lastname: Ge
authors.affiliation: College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China. tigerliu@126.com.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Anyang College of Technology, Anyang, 455000, Henan, China. 25681755@qq.com.
authors.forename: Quanwei
authors.initials: Q
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. 740006344@qq.com.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. 1304717500@qq.com.
authors.forename: Yunna
authors.initials: Y
authors.lastname: Tan
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. harunbjri@yahoo.com.
authors.forename: Harun
authors.initials: H
authors.lastname: Or Rashid
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. zareensarfraz88@yahoo.com.
authors.forename: Zareen
authors.initials: Z
authors.lastname: Sarfraz
authors.affiliation: Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing, 100871, China. murtazapiracha@pku.edu.cn.
authors.forename: Murtaza
authors.initials: M
authors.lastname: Hassan
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. wkgong@aliyun.com.
authors.forename: Wankui
authors.initials: W
authors.lastname: Gong
authors.affiliation: State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China. yylcri@126.com.
authors.forename: Youlu
authors.initials: Y
authors.lastname: Yuan
mesh_terms: D002874:Chromosome Mapping; D032561:Cotton Fiber; D018744:DNA, Plant / Q000235:genetics; D004777:Environment; D008040:Genetic Linkage; D005819:Genetic Markers; D003368:Gossypium / Q000235:genetics*; D018895:Microsatellite Repeats; D010641:Phenotype; D000069600:Plant Breeding; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers