陆地棉纤维品质性状关联分析及优异等位基因挖掘

张素君,李兴河,唐丽媛,王海涛,刘存敬,蔡肖,张香云,张建宏

植物遗传资源学报. 2021, 22(1): 214-228

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植物遗传资源学报 ›› 2021, Vol. 22 ›› Issue (1) : 214-228. DOI: 10.13430/j.cnki.jpgr.20200409003
论文

陆地棉纤维品质性状关联分析及优异等位基因挖掘

  • 张素君, 李兴河, 唐丽媛, 王海涛, 刘存敬, 蔡肖, 张香云, 张建宏
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Exploration of Elite Alleles Related with Fibre Quality Traits in Gossypium hirsutum L. by Association Analysis

  • ZHANG Su-jun, LI Xing-he, TANG Li-yuan, WANG Hai-tao, LIU Cun-jing, CAI Xiao, ZHANG Xiang-yun, ZHANG Jian-hong
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摘要

本研究检测了 214 个陆地棉材料在多环境下的纤维品质指标(上半部平均长度、断裂比强度、马克隆值、伸长率 和整齐度),选用在棉花基因组上均匀分布多态性较好的 259 个 SSR 标记对供试群体进行基因型检测,利用 Tassel 软件中的 GLM( Q)方法挖掘与纤维品质指标相关的 QTLs,依据表型效应值鉴别优异等位变异位点及典型材料。结果显示:同一纤维 品质性状在 3 个地点 2~3 年内变化趋势相对稳定,纤维上半部平均长度、断裂比强度和整齐度三者之间呈正相关( P<0.01), 纤维上半部平均长度 / 断裂比强度均和马克隆值 / 伸长率负相关。 259 个 SSR 标记共检测到 309 个等位基因,涉及 774 个基 因型,多态性信息含量( PIC, polymorphic information content)平均为 0.2688,基因多样性指数平均为 0.2239。按照基因型数 据可将该群体划分为 2 个亚群。通过关联分析获得与纤维品质相关的等位变异位点 134 个( P<0.01),在 3 个及以上环境中 均可检测到的位点有 30 个,有 3 个位点( NAU6177、 DPL0886、 NAU3607)在 7 个环境中分别与断裂比强度、马克隆值、伸长 率显著关联( P<0.01),最高表型变异解释率分别为 11.14%、 5.74% 和 13.99%。 31 个位点同时与 2 个及以上纤维品质指标相 关,其中, NAU 6177 与 5 个纤维品质指标均显著关联( P<0.01)。与已发表结果比对, 17 个 QTL 已被报道与纤维品质性状相 关, 10 个 QTL 与前人关联指标相同。分析多环境纤维品质关联位点的表型效应,获得 72 个等位变异位点, 5 份携带优异等 位基因载体材料。本研究在多环境下挖掘与陆地棉纤维品质指标关联的分子标记,同时鉴别携带优异等位变异基因的典型载 体材料,为棉花纤维品质分子标记辅助选择及目标基因定位提供有益信息。

Abstract

In this study, five fiber quality indexes( Fiber upper half mean length FUHML, Fiber strength FS, Micronaire value MV, Fiber elongation FE, Fiber uniformity FU) of 214 upland cotton materials were tested under seven environments, and Boxplot were drew by SPSS19.0, and the heritability, correlation and phenotypic effect values of the traits were calculated by using the phenotypic data analyzed by BLUP. 259 SSRs with high polymorphism and uniform distribution on 26 chromosomes were used to scan polymorphism in 214 cotton materials, the polymorphism information of primers were calculated by PowerMarker 3.25, and molecular marker data and phenotypic traits were analyzed by the method of GLM( General Linear Model)( Q) in TASSEL software, phenotypic effect values were used to identify excellent allelic variants and typical materials carrying elite alleles. The result showed that the same one fiber quality trait had a relatively stable change trend in two to three years in three regions. There were positive correlations among FUHML, FS and FU( P<0.01), and FUHML/FS and MV/FE were negatively correlated. A total of 309 alleles and 774 genotypes were detected. The average polymorphic information content( PIC) per marker was 0.2688, and the average genetic diversity index was 0.2239. Two hundred and fourteen upland cotton materials were divided into two subgroups by analysis of population genetic structure. A total of 134 loci associated with fiber quality traits were detected( P<0.01), among them, thirty loci could be detected stably in three or more environments. Three loci( NAU6177, DPL0886, NAU3607) were found to be significantly associated with FUHML/FS, MV and FE respectively in seven environments( P<0.01), the maximum explanation rate up to 11.14%, 5.74% and 13.99% respectively. Thirty-one loci related to more than two fiber traits simultaneously, including the loci near NAU6177 related to aforementioned five fiber quality indexes( P<0.01) . Compared with reported results, seventeen QTLs in this study has been reported to be related to fiber quality,in which 10 QTLs associated with the same traits. Based on the results, seventy-two alleles related with fiber quality were identified by phenotypic effect analysis respectively. Specifically, the allelic variation loci with the maximum increasing effect of FUHML, FS, MV and FE were NAU5387b( +0.95 mm), NAU5387b( +1.25 cN/tex), NAU943a( +0.40), and COT002a( +0.62) respectively, and the allelic variation loci with the maximum decreasing effect of FUHML, FS, MV and FE were NAU6177e( -1.21 mm), NAU6177d( -1.43 cN/tex), CIR286b( -0.78), and NAU5387b( -0.40) separately. Furthermore, five typical materials carrying elite alleles were selected, which were Ji 228( FUHML), Xinluzao 25( FUHML, FS), Ji N71( FS), Xinluzhong 36( MV) and Xuzhou 142( FE) . In conclusion, stable molecular markers associated with fiber quality were revealed by association analysis, and elite alleles and typical materials carrying elite alleles were identified, which could provide a reference for molecular assisted selection of upland cotton about fiber quality.

关键词

陆地棉 / SSR / 纤维品质 / 关联分析 / 等位变异

Key words

upland cotton / fiber quality / population structure / association analysis / allelic variation

引用本文

导出引用
张素君,李兴河,唐丽媛,王海涛,刘存敬,蔡肖,张香云,张建宏. 陆地棉纤维品质性状关联分析及优异等位基因挖掘. 植物遗传资源学报. 2021, 22(1): 214-228 https://doi.org/10.13430/j.cnki.jpgr.20200409003
ZHANG Su-jun,LI Xing-he,TANG Li-yuan,WANG Hai-tao,LIU Cun-jing,CAI Xiao,ZHANG Xiang-yun and ZHANG Jian-hong. Exploration of Elite Alleles Related with Fibre Quality Traits in Gossypium hirsutum L. by Association Analysis. Journal of Plant Genetic Resources. 2021, 22(1): 214-228 https://doi.org/10.13430/j.cnki.jpgr.20200409003

参考文献

[1].Fang L , Wang Q , Hu Y, Jia Y , Chen J, Liu B, Zhang Z Y, Guan X Y, Chen S Q, Zhou B L, Mei G F, Sun J L, Pan Z, He S P, Xiao S H, Shi W J, Gong W F, Liu J G, Ma J, Cai C P, Zhu X F, Guo W Z, Du X M, Zhang T Z. Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nature Genetics, 2017, 49(7):1089-1098
[2].杨君, 马峙英, 王省芬. 棉花纤维品质改良相关基因研究进展. 中国农业科学, 2016, 49(22): 4310-4322Yang J, Ma Z Y, Wang S F. Progress in studies on genes related to fiber quality improvement of cotton. Scientia Agricultura Sinica, 2016, 49(22):4310-4322
[3].Gill B, Singh P, Sohu R. Genetic analysis of fibre traits in upland cotton (Gossypium hirsutum L.). Journal of Cotton Research and Development, 2016, 30 (1): 22-28
[4].Gapare W, Conaty W, Zhu Q H, Liu S, Stiller W, Llewellyn D, Wilson I. Genome-wide association study of yield components and fibre quality traits in a cotton germplasm diversity panel. Euphytica, 2017, 213(3): 66
[5].Zhang Y, Wang X F, Li Z K, Zhang G Y, Ma Z Y. Assessing genetic diversity of cotton cultivars using genomic and newly developed expressed sequence tag derived microsatellite markers. Genetics and molecular research, 2011, 10: 1462-1470
[6].Clement J D, Constable G A, Stiller W N, Liu S M. Negative associations still exist between yield and fibre quality in cotton breeding programs in Australia and USA. Field Crops Research, 2012, 128: 1-7
[7].Said J I, Lin Z X, Zhang X L, Song M Z, Zhang J F. A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton. BMC Genomics, 2013,14: 776
[8].Said J I, Knapka J A, Song M Z, Zhang J F. Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum x G. barbadense populations. Molecular Genetics and Genomics, 2015a, 290(4):1615-1625
[9].Said J I, Song M Z, Wang H T, Lin Z X, Zhang X L, Fang D D, Zhang J F. A comparative Meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum x G. barbadense populations. Molecular Genetics and Genomics, 2015b, 290(3):1003-1025
[10].Zeng L H, Meredith W R, Osman A G, Boykin D L. Identification of associations between SSR markers and fiber traits in an exotic germplasm derived from multiple crosses among tetraploid species. Tag.theoretical Applied Genetics.theoretische Und Angewandte Genetik, 2009, 119: 93-103
[11].钱能. 陆地棉遗传多样性与育种目标性状基因(QTL)的关联分析. 南京: 南京农业大学. 2009, 73-86Qian N. Genetic diversity and association analysis of gene (QTL) of breeding target traits of upland cotton. Nanjing: Nanjing Agricultural University. 2009, 73-86
[12].贺道华, 邢宏宜, 赵俊兴, 李婷婷, 汤益, 曾舟. 棉花资源群体结构的推测与纤维品质的关联分析. 西北农林科技大学学报:自然科学版, 2011, 39(1): 103-112He D H, Xing H Y, Zhao J X, Li T T, Tang Y, Zeng Z. Population structure inferring and association analysis of fiber quality in cultivated cotton. Journal of Northwest A F University: Natural Sciences Edition, 2011, 39(1): 103-112
[13].郭玉平. 陆地棉产量、纤维品质等性状与 SSR 标记的关联分析. 泰安:山东农业大学. 2013, 35-39Guo Y P. Association analysis of upland cotton yield and fiber quality with SSR markers. Tai'an: Shandong Agricultural University. 2013, 35-39
[14].聂新辉, 尤春源, 鲍健, 李晓方,惠慧,刘洪亮,秦江鸿,林忠旭. 基于关联分析的新陆早棉花品种农艺和纤维品质性状优异等位基因挖掘. 中国农业科学, 2015, 48(15):2891-2910Nie X H, You C Y, Bao J, Li X F, Hui H, Liu H L, Qin J H, Lin Z X. Exploration of elite alleles of agronomic and fiber quality traits in Xinluzao cotton varieties by association analysis. Scientia Agricultura Sinica, 2015, 48(15): 2891-2910
[15].马君, 李波, 胡文冉, 杨洋.引进陆地棉种质材料纤维品质及农艺性状关联分析. 分子植物育种,2017,15 (8):3218-3230Ma J, Li B, Hu W R, Yang Y. Associated analysis of fiber quality and agronomic traits in cotton(Gossypium hirsutum) Germplasms. Molecular Plant Breeding, 2017,15 (8):3218-3230
[16].Sariful I M, Thyssen G N , Jenkins J N, Linghe Z , Delhom C D, Mccarty J C, Deng D D, Hinchliffe D J, Jones D C, Fang D D. A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC genomics, 2016, 17 (1) :903
[17].Sun Z, Wang X, Liu Z, Gu Q, Ma Z. Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L. Plant Biotechnology Journal, 2017, 15(8):982-996
[18].Li Z, Wang P, You C, Yu J, Zhang X, Yan F, Ye Z, Shen C, Li B, Guo K, Liu N, Thyssen G N, Fang D D, Lindsey K, Zhang X, Wang M, Tu L. Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton [published online ahead of print, 2020 Feb 3]. New Phytologist, 2020
[19].谭兆云. 陆地棉纤维品质QTL定位与qFS15精细定位及候选基因鉴定. 重庆: 西南大学, 2018, 15-16Tan Z Y. QTL mapping for fiber quality traits and fine mapping and candidate gene identification of qFS15 in upland cotton. Chongqing: Southwest University, 2018, 15-16
[20].张素君, 唐丽媛, 李兴河, 王海涛, 刘存敬, 张香云, 张建宏. SSR标记与陆地棉田间黄萎病抗性的关联分析. 华北农学报, 2018, 33(6): 152-159Zhang S J, Tang L Y, Li X H, Wang H T, Liu C J, Zhang X Y, Zhang J H. Association analysis of Verticillium wilt-resistance in upland cotton germplasm population based on SSR markers. Acta Agriculturae Boreali-Sinica, 2018, 33(6): 152-159
[21].Liang Z, Lü Y D, Cai C P, Tong X C, Chen X D, Zhang W, Du H, Guo X H, Guo W Z. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information. BMC Genomics, 2012, 13 (1): 539
[22].李小胜,陈珍珍. 如何正确应用SPSS 软件做主成分分析.统计研究, 2010,27 (8) : 105-108. https://doi.org/10.3969/j.issn.1002-4565.2010.08.016Li X S, Chen Z Z. How to apply SPSS software correctly to principal component analysis. Statistical Research, 2010,27( 8) : 105-108
[23].Liu K J, Muse S V. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21 (9): 2128-2129
[24].Pritchard J K, Wen W. Documentation for STRUCTURE Software:Version 2.2. Chicago: The University of Chicago Press, 2007
[25].Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Yogesh R, Buckler E S. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 2007, 23 (19) :2633-2635
[26].Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 2005, 14 (8): 2611-2620
[27].Yang X H, Gao S B, Xu S T, Zhang Z X, Prasanna L L, Li J S, Yan J B. Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Molecular Breeding, 2011, 28: 511-526
[28].邓先萍. 陆地棉栽培品种与野生种系尖斑棉杂交群体产量及纤维品质QTL定位. 重庆:西南大学, 2019,40-45Deng X P.QTL maping for yield and fiber quality traits from (G. hirsutum cultivar × G. hirsutum race punctatum) population. Chongqing: Southwest University, 2019, 40-45
[29].王金霞. 陆地棉栽培品种与野生种系帕默尔棉杂交群体纤维品质和产量QTL定位.重庆:西南大学, 2019, 40-45Wang J X. Maping QTL for yield and fiber quality traits from G.hirsutum cultivar × G. hirsutum race palmeri population. Chongqing: Southwest University, 2019, 40-45
[30].梁冰. 陆地棉早熟、产量及纤维品质性状与SSR分子标记的关联分析. 西安: 西北农林科技大学, 2014, 36-48Liang B. Association analysis of early maturity, yield and fiber quality traits in upland cotton using SSR markers. Xi’an: Northwest A F University, 2014, 36-48
[31].胡文静,张晓阳,张天真,郭旺珍. 陆地棉优质纤维QTL的分子标记筛选及优质来源分析[J].作物学报, 2008, 34(04): 578-586Hu W J, Zhang X Y, Zhang T Z, Guo W Z. Molecular tagging and source analysis of QTL for elite fiber quality in upland cotton. Acta Agronomica Sincia, 2008, 34(04): 578-586
[32].李昆. 强优势杂交棉中棉所66后代分离群体产量及纤维品质性状的QTL初步定位. 安阳: 中国农业科学院, 2010, 33-49Li K. Primary QTL mapping of yield and fiber quality traits in progeny groups of high advantage hybrid cotton CRI66. An’yang: Chinese academy of agricultural sciences, 2010, 33-49
[33].王义青. 陆地棉优异纤维品质及产量性状的QTL挖掘. 安阳:中国农业科学院, 2010.40-51Wang Y Q. Identification of QTLs for yield and elite fiber quality traits in upland cotton (Gossypium hirsutum). An’yang: Chinese academy of agricultural sciences, 2010, 40-51
[34].Mulugeta Seyoum Ademe. 陆地棉SSR遗传多样性及纤维品质和产量性状关联作图. 安阳: 中国农业科学院, 2015, 35-36Mulugeta Seyoum Ademe. Genetic diversity and association mapping of fiber yield and quality traits in upland cotton (Gossypium hirsutum L.). An’yang: Chinese academy of agricultural sciences, 2010, 40-51
[35].黎波涛. 陆地棉染色体片段代换系产量及纤维品质性状的遗传分析与主效QTL定位. 安阳: 中国农业科学院, 2016, 83-86Li B T. Genetic analysis and mapping of major QTL on yield and fiber quality related traits in cotton chromosome segment substitution lines. An’yang: Chinese academy of agricultural sciences, 2016, 83-86
[36].徐珍珍. 陆地棉(Gossypium hirsutum L.)优异纤维遗传组分的分子标记定位. 济南:山东师范大学, 2010, 44Xu Z Z. Mapping the Genetic Components of Excellent Fiber Quality in Upland Cotton (Gossypium hirsutm L.) by Molecular Markers. Jinan: Shangdong Normal University, 2010, 44
[37].Cai C P, Ye W X, Zhang T Z, Guo W Z. Association analysis of fiber quality traits and exploration of elite alleles in upland cotton cultivars/accessions (Gossypium hirsutum L.). Journal of Integrative Plant Biology, 2014, 56: 51-62
[38].Wang X Q, Yu Y, Li W, Guo H L, Lin Z X, Zhang X L. Association analysis of yield and fiber quality traits in Gossypium barbadense with SSRs and SRAPs. Genetics and Molecular Research, 2013, 12(3): 3353-3362
[39].王娟, 董承光, 刘丽, 孔宪辉, 王旭文, 余渝. 陆地棉主要产量相关性状的SSR标记关联分析. 植物遗传资源学报. 2017, 18(4):720-727Wang J, Dong C G, Liu L, Kong X H, Wang X W, Yu Y. Association analysis of yield-related traits with SSR markers in upland cotton(Gossypium hirsutum). Journal of Plant Genetic Resources, 2017, 18(4):720-727
[40].Abdurakhmonov I Y, Saha S, Jenkins J N, Buriev Z T, Shermatov S E, Scheffler B E, Pepper A E, Yu J Z, Kohel R J, Abdukarimov A. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica, 2009, 136(3): 401-417
[41].Breseghello F, Sorrells M E. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars, Genetics, 2006, 172(2): 1165-1177
[42].Lacape J M , Nguyen T B , Thibivilliers S , Bojinov B, Courtois B, Cantrell R G, Burr B, Hau B. A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum x Gossypium barbadense backcross population. Genome, 2003, 46(4):612-626
[43].Pritchard J K, Stephens M, Rosenberg N A, Donnelly P. Association mapping in structured populations. American Journal of Human Genetics, 2000, 67(1): 0-181
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