长江中下游麦区小麦地方种质千粒重全基因组关联分析

doi:10.16036/j.issn.1000-2650.2019.04.002

摘要/Abstract

摘要： 【目的】高产是小麦育种的永恒主题,千粒重是产量构成的三因子之一。因此,发掘控制小麦千粒重QTL（quantitative trait loci）区段及其优异等位变异,对利用分子标记辅助选择进行小麦产量性状的遗传改良具有重要意义。【方法】以来自长江中下游麦区188份小麦地方种质为材料,在3个环境下对小麦千粒重进行表型鉴定;利用DArT芯片（diversity arrays technology）进行全基因组扫描,基于一般线性模型（Q+K）对小麦千粒重进行关联分析。【结果】千粒重表型鉴定发现来自江苏、浙江和湖北小麦地方种质具有较高千粒重;通过全基因关联分析,共获得8个DArT标记在2个及以上的环境中均与小麦千粒重显著关联,分布于小麦染色体1B、1D、3B、4B和5B上,其表型贡献率9.19%~12.65%。【结论】长江中下游麦区小麦地方种质千粒重表型变异丰富;在不同环境中均能关联到的标记为较为稳定的控制小麦千粒重位点。

关键词: 千粒重, 关联分析, 小麦地方种质, DArT芯片

Abstract: 【Objective】 High yield is the eternal theme of wheat breeding program and thousand kernel weight is one of the three factors of yield components. For exploring wheat grain weight QTLs and its allelic variations are great significance on genetic improvement of wheat yield traits using Marker-assisted selection. 【Method】 By investigated thousand kernel weight traits using 188 Chinese wheat lan-draces from the middle and lower reaches of the Yangtze River across three environments. Genome-wide association analysis was performed using wheat DArT-seq (diversity arrays technology) with general linear Q+K association models. 【Result】 The accessions, derived from Jiangsu, Zhejiang and Hubei Province,had good performance for thousand kernel weight traits. A total of 8 significant marker-trait associations (MTAs) were detected on chromosomes 1B, 1D, 3B, 4B, and 5B in more two environments. Single locus could explain 9.19% to 12.65% the observed phenotypic variation. 【Conclusion】 The thousand kernel weight traits performance are significant difference in Chinese wheat landraces from the middle and lower reaches of the Yangtze River; The stable loci associated with the thousand kernel weight are found in different environments.

Key words: thousand kernel weight, genome-wide association analysis, wheat landraces, DArT-seq

中图分类号:

S326

程宇坤, 李健, 姚方杰, 蒋云峰, 江千涛, 李伟, 蒲至恩, 邓梅, 魏育明, 陈国跃. 长江中下游麦区小麦地方种质千粒重全基因组关联分析[J]. 四川农业大学学报, 2019, 37(04): 434-441.

CHENG Yukun, LI Jian, YAO Fangjie, JIANG Yunfeng, JIANG Qiantao, LI Wei, PU Zhien, DENG Mei, WEI Yuming, CHEN Guoyue. Genome-Wide Association Study of Thousand Kernel Weight in Chinese Wheat Landraces in the Middle and Lower Reaches of the Yangtze River[J]. Journal of Sichuan Agricultural University, 2019, 37(04): 434-441.

参考文献

[1] 董玉琛, 郑殿升. 中国小麦遗传资源[M]. 北京: 中国农业出版社, 2000: 16-30.
[2] TANKSLEY S D, MCCOUCH S R.Seed bank and molecular maps: unlocking genetic potential from the wild[J]. Science, 1997, 277: 1063-1066.
[3] BOMER A, SCHUMANN E, FURSTE A, et al.Mapping of quan-titative trait loci determine agronomic important characters in he-xaploid wheat(Triticum aestivum L.)[J]. Theor Appl Genet, 2002, 105(5/6): 921-936.
[4] 郑有良, 颜济, 杨俊良. 小麦粒重基因定位研究[J]. 作物学报, 1993, 19(4): 304-308.
[5] RAMYA P, CHAUBAL A, KULKARNI K, et al.QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat[J]. Journal of Applied Genetics, 2010, 51(4): 421-429.
[6] GOLABADI M, ARZANI A, MIRMOHAMMADI-MAIBODY SAM, et al.Identification of microsatellite markers linked with yield co-mponents under drought stress at terminal growth stages in durum wheat[J]. Euphytica, 2010, 177(2): 207-221.
[7] GROOS C, ROBERT N, BERVAS E, et al.Genetic analysis of grain protein-content, rain yield and thousand kernel weight in bread wheat[J]. Theoretical and Applied Genetics, 2003, 106(6): 1032-1040.
[8] QUARRIE SA, STEED A, CALESTANI C, et a1. A high-density genetic map of hexaploid wheat(Triticum aestivum L.) from the cross Chinese Spring x SQl and its use to compare QTLs for grain yield across a range of environments[J].Theoretical and Applied Genetics, 2005, 110(5): 865-880.
[9] QUARRIE SA, QUARRIE SP, RADOSEVIC R, et al.Dissecting a wheat QTL for yield present in a range of environments: from the QTL to candidate genes[J]. Journal of Experimental Botany, 2006, 57(11): 2627-2637.
[10] TSILO T J, HARELAND G A, SIMSEK S, et al.Genome mapping of kernel characteristics in hard red spring wheat breeding lines[J]. Theoretical and Applied Genetics, 2010, 121(4): 717-730.
[11] WANG S, WU K, YUAN Q, et al.Control of grain size, shape and quality by OsSPLl6 in rice[J]. Nature Genetics, 2012, 44(8): 950-954.
[12] WANG L, GE H, HAO C, et a1. Identifying loci influencing 1 000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding[J]. PLoS One, 2012, 7(2): e29432.
[13] LI C L, BAI G H, CARVER B F, et al.Single nucleotide pol-ymorphism markers linked to QTL for wheat yield traits[J]. Eup-hytica, 2015, 206(1): 89-101.
[14] 孙宇慧, 刘天相, 石善党, 等. 小麦穗粒数及千粒重主效QTL共定位区QC-7AL的精细定位及遗传效应分析[J]. 麦类作物学报, 2018, 38(11): 1288-1292.
[15] MACKAY I, POWELL W.Methods for linkage disequilibrium mapping in crops[J]. Trends Plant Sciencs, 2007, 12(2): 57-63.
[16] 魏添梅, 昌小平, 闵东红, 等.小麦抗旱品种的遗传多样性分析及株高优异等位变异发掘[J]. 作物学报, 2010, 36(6): 895-904.
[17] 张学勇, 童依平, 游光霞, 等. 选择牵连效应分析: 发掘重要基因的新思路[J]. 中国农业科学, 2006, 39(8): 1526-1535.
[18] 李玮瑜, 张斌, 张嘉楠, 等. 利用关联分析发掘小麦自然群体旗叶叶绿素含量的优异等位变异[J]. 作物学报, 2012, 38(6): 962-970.
[19] MIR R R, KUMAR N, JAISWAL V, et al.Genetic dissection of grain weight in bread wheat through quantitative trait locus interval and association mapping[J]. Mol Breed, 2012, 29(4): 963-972.
[20] ZHANG D L, HAO C Y, WANG L F, et al.Identifying loci inf-luencing grain number by microsatellite screening in bread wheat (Triticum aestivum L.)[J]. Planta, 2012, 236: 1507-1517.
[21] 武玉国, 吴承来, 秦保平, 等. 黄淮冬麦区175个小麦品种的SSR多态性及其与株高、产量相关性状的关联分析[J]. 作物学报, 2012, 38(5): 1-11.
[22] 张国华, 高明刚, 张桂芝, 等. 黄淮麦区小麦品种(系)产量性状与分子标记的关联分析[J]. 作物学报, 2013, 39(7): 1187-1199.
[23] 李健. 长江中下游麦区小麦地方品种条锈病抗性全基因组关联分析[D]. 成都: 四川农业大学, 2018.
[24] MURRAY M G, THOMPSON W F.Rapid isolation of high mole-cular weight plant DNA[J]. Nucleic Acids Research, 1980, 8(19): 4323-4325.
[25] FIELLER E C, HARTLEY H O, PEARSON E S.Tests for rank correlation coefficients[J]. Biometrika, 1957, 44(3/4): 470.
[26] SMITH S E, KUEHL R O, RAY I M, et al.Evaluation of simple methods for estimating broad-sense heritability in stands of randomly planted genotypes[J]. Crop Science. 1998, 38(5): 1125-1129.
[27] PRITCHARD JK, STEPHENS M, DONNELLY P.Inference of population structure using multilocus genotype data[J]. Genetics, 2000, 155(2): 945-959.
[28] FALUSH D, STEPHENS M, PRITCHARD J K.Inference of po-pulation structure using multilocus genotype data: linked loci and correlated allele frequencies[J]. Genetics, 2003, 164(4): 1576-1587.
[29] HUBISZ MJ, FALUSH D, STEPHENS M, et al.Inferring weak population structure with the assistance of sample group informa-tion[J]. Molecular Ecology Resources, 2009, 9(5): 1322-1332.
[30] WANG Y S, BARRATT B J, CLAYTON D G, et al.Genome-wide association studies: theoretical and practical concerns[J]. Nature Reviews Genetics, 2005, 6(2): 109-118.
[31] ZHANG Z, ERSOZ E, LAI CQ, el a1. Mixed linear model approach adapted for genome-wide association studies[J]. Nature Genetics, 2010, 42(4): 355-360.
[32] CORE TEAM. R: A language and envi-ronment for statistical computing[M/OL]. Vienna, Austria: The R Foun-dation for Statistical Computing.2014[2017-05-23]. http: //www. R~project. org/.
[33] HUANG X Q, COSTER H, GANAL M W, et al.Advanced back-cross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat(Triticum aestivum L.)[J]. The-oretical and Applied Genetics, 2003, 106(8): 1379-1389.
[34] HUANG X Q, KEMPF H, GANAL M W, et al.Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat(Triticum aestivum L.)[J]. Theoretical and Applied Genetics, 2004, 109(5): 933-943.
[35] KUNERT A, NAZ A, DEDECK O, et al.AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat(T. turgidum ssp. dico-ccoides×T. tauschii)as a source of favourable alleles for milling and baking quality traits[J]. Theoretical and Applied Genetics, 2007, 115(5): 683-695.
[36] AMMIRAJU JSS, DHOLAKIA BB, SANTRA D K, et al.Identi-fication of inter simple sequence repeat (ISSR) markers associa-ted with seed size in wheat[J]. Theoretical and Applied Genetics, 2001, 102(5): 726-732.
[37] CAMPBELL BT, BAENZIGER P S, GILL K S, et al.Identifica-tion of QTLs and environmental interactions associated with ag-ronomic traits on chromosome 3A of wheat[J]. Crop Science, 2003, 43(4): 1493-1505.
[38] CAMPBELL K G, BERGMAN C J, GUALBERTO D G, et al.Quantitative trait loci associated with kernel traits in a soft×hard wheat cross[J]. Crop Science, 1999, 39(4): 1184-1195.
[39] GROOS C, ROBERT N, BERVAS E, et al.Genetic analysis of grain protein-content, grain yield and 1000-kernel weight in bread wheat[J]. Theoretical and Applied Genetics, 2003, 106(7): 1032-1040.
[40] KUMAR N, KULWAL P, BALYAN H, et al.QTL mapping for yield and yield contributing traits in two mapping populations of bread wheat[J]. Molecular Breeding, 2007, 19(2): 163-177.
[41] BORNER A, SCHUMANN E, FURSTE A, et al.Mapping of qu-antitative trait loci determining agronomic important characters in hexaploid wheat(Triticum aestivum L.)[J]. Theoretical and App-lied Genetics, 2002, 105(6/7): 921-936.
[42] QUARRIE SA, STEED A, CALESTANI C, et al.A high-density genetic map of hexaploid wheat(Triticum aestivum L.) from the cross Chinese Spring × SQ1 and its use to compare QTLs for grain yield across a range of environments[J]. Theoretical and Applied Genetics, 2005, 110: 865-880.
[43] VARSHNEY R K, PRASAD M, ROY J K, et al.Identification of eight chromosomes and a microsatellite marker on 1AS associated with QTL for grain weight in bread wheat[J]. Theoretical and Applied Genetics, 2000, 100: 1290-1294.
[44] 蒲艳艳. 小麦遗传图谱的构建及籽粒和产量性状的QTL定位[D]. 泰安: 山东农业大学, 2012.
[45] 廖祥政, 王瑾, 周荣华, 等. 发掘人工合成小麦中千粒重QTL的有利等位基因[J]. 作物学报, 2008, 34(11): 1877-1884
[46] 张桂芝. 小麦高密度遗传图谱构建和产量、穗部和籽粒大小性状QTL分析[D]. 泰安: 山东农业大学, 2014.
[47] 高明刚. 小麦高密度遗传图谱的构建和产量相关性状的QTL分析[D]. 山东农业大学, 2014.
[48] SOMERS D, ISAAC P, EDWARDS K.A high-density microsa-tellite consensus map for bread wheat(Triticum aestivum L.)[J]. Theoretical and Applied Genetics, 2004, 109: 1105-1114.
[49] REN Y, HE Z H, LI J, et al.QTL mapping of adult-plant resistance to stripe rust in a population derived from common wheat cultivars Naxos and Shanghai 3/Catbird[J]. Theoretical and Applied Genetics, 2012, 125(6): 1211-1221.
[50] VAZQUEZ M D, PETERSON C J, RIERA-LIZARAZU O, et al.Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat cultivar ‘Stephens’ in multi-environment trials[J]. Theoretical and Applied Genetics, 2012, 124(1): 1-11.
[51] ZWART R S, THOMPSON J P, MILGATE A W, et al.QTL map-ping of multiple foliar disease and root-lesion nematode resistan-ces in wheat[J]. Molecular Breeding, 2010, 26(1): 107-124.
[52] HOU L, CHEN X, WANG M, et al.Mapping a large number of QTL for durable resistance to stripe rust in winter wheat Druch-amp using SSR and SNP markers[J]. PLoS One, 2015, 10(5): e126794.
[53] BARIANA H S, BANSAL U K, SCHMIDT A, et al.Molecular mapping of adult plant stripe rust resistance in wheat and identifi-cation of pyramided QTL genotypes[J]. Euphytica, 2010, 176(2): 251-260.