基于反转录转座子及简单重复序列标记的裸大麦遗传多样性研究

doi:10.3969/j.issn.1004-1524.2018.03.01

浙江农业学报 ›› 2018, Vol. 30 ›› Issue (3): 357-365.DOI: 10.3969/j.issn.1004-1524.2018.03.01

基于反转录转座子及简单重复序列标记的裸大麦遗传多样性研究

王国荣¹, 华为², 陈功海³, 龙周锴¹, 李博¹, 张文英¹, 徐延浩^1,*

1.主要粮食作物产业化湖北省协同创新中心/长江大学农学院,湖北荆州 434025;
2.浙江省农业科学院作物与核技术利用研究所,国家大麦改良中心,浙江杭州 310021;
3.荆州市农业科学院,湖北荆州 434000

收稿日期:2017-11-09 出版日期:2018-03-20 发布日期:2018-03-21
通讯作者: *徐延浩,E-mail: xyh09@yangtzeu.edu.cn
作者简介:王国荣(1988—),男,云南玉溪人,硕士研究生,主要从事植物分子育种研究。E-mail: 294828485@qq.com
基金资助:
国家自然科学基金(31501309,31201212)

Genetic diversity in hulless barley by retrotransposons-based markers and simple sequence repeat (SSR) markers

WANG Guorong¹, HUA Wei², CHEN Gonghai³, LONG Zhoukai¹, LI Bo¹, ZHANG Wenying¹, XU Yanhao^1,*

1. Hubei Collaborative Innovation Center for Grain Industry / School of Agriculture, Yangtze University, Jingzhou 434025, China;
2. Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, National Barley Improvement Center, Hangzhou 310021, China;
3. Jingzhou Academy of Agricultural Sciences, Jingzhou 434000, China

Received:2017-11-09 Online:2018-03-20 Published:2018-03-21

摘要/Abstract

摘要： 为揭示裸大麦育成品种与种质资源材料的遗传结构,利用反转录转座子标记(反转录转座子-微卫星扩增多态性,REMAP;反向反转录转座子扩增多态性,IRAP)与简单重复序列(SSR)标记,分析63份裸大麦的遗传多样性。IRAP、REMAP、SSR标记分别检测到315、143、38个等位变化,变异范围分别为9~58、7~25、2~4个,平均每对引物检测24.23、14.30、2.38个等位变化。REMAP和IRAP单一标记多态性位点贡献率高于SSR标记。反转录转座子标记揭示材料间遗传相似性系数(GS)为0.452~0.937,平均为0.674,在GS值0.620水平上将63份材料分为2大类,分别包含20份和43份材料。SSR标记结果显示材料间GS为0.351~0.973,平均为0.716,在GS值0.620水平上将63份材料区分为2大类,分别包含2份和61份材料。反转录转座子标记聚类结果在GS值0.740水平上能区分西藏野生资源和栽培资源,但SSR标记不能有效区分这2类材料。反转录转座子标记的主坐标及群体结构分析结果与GS聚类分析结果一致性较高;SSR标记群体结构与主坐标分析、GS聚类分析结果存在明显差异。本研究表明,裸大麦材料遗传背景简单,亚类间缺少基因交流,反转录转座子标记在裸大麦品种亲缘关系鉴定中有一定的优势。反转录转座子标记与SSR标记的协同使用可为裸大麦遗传多样性分析、种质鉴定及亲本选配揭示更多有用信息。

关键词: 分子标记, 裸大麦, 遗传多样性, 群体结构分析

Abstract: To evaluate the genetic structure of hulless barley, retrotransposons-based markers (retrotransposon-microsatellite amplified polymorphism, REMAP; inter-retrotransposon amplified polymorphism, IRAP) and simple sequence repeat (SSR) markers were used to obtain the genetic data of 63 hulless barley materials. The IRAP, REMAP and SSR markers detected 315, 143 and 38 alleles, ranged from 9-58, 7-25, and 2-4, with an average of 24.23, 14.30, 2.38 alleles per marker, respectively. The contribution rate of single retrotransposons-based marker polymorphic site was higher than that of SSR marker. As revealed by retrotransposons-based markers, the genetic similarity (GS) among these 63 accessions was from 0.452 to 0.937, with the average of 0.674. The accessions were divided into two subgroups at the GS level of 0.620, which contained 20 and 43 materials, respectively. As revealed by SSR markers, GS among these 63 accessions was from 0.351 to 0.973, with the average of 0.716. The accessions were divided into two subgroups at the GS level of 0.620, which contained 2 and 61 materials, respectively. The wild hulless barley accessions was clustered into a small category by the retrotransposons-based markers at the GS level of 0.740. However, it was unable to distinguish the wild hulless barley from the cultured by SSR markers in the present study. The population structure revealed by retrotransposons-based markers was consistent with the principal coordinate analysis and genetic similarity analysis. However, the population structure revealed by SSR markers showed difference. It was shown that most of the accessions were with single genetic components. The retrotransposons-based markers had advantage in the identification of the relationship of hulless barleys. And more genetic information could be explored by combining the retrotransposons-based markers and SSR markers.

Key words: molecular markers, hulless barley, genetic diversity, population structure analysis

中图分类号:

S512.3

王国荣, 华为, 陈功海, 龙周锴, 李博, 张文英, 徐延浩. 基于反转录转座子及简单重复序列标记的裸大麦遗传多样性研究[J]. 浙江农业学报, 2018, 30(3): 357-365.

WANG Guorong, HUA Wei, CHEN Gonghai, LONG Zhoukai, LI Bo, ZHANG Wenying, XU Yanhao. Genetic diversity in hulless barley by retrotransposons-based markers and simple sequence repeat (SSR) markers[J]. , 2018, 30(3): 357-365.

参考文献

[1] 孟凡磊,强小林,佘奎军,等. 西藏主要农区青稞品种的遗传多样性分析[J]. 作物学报, 2007, 33(11): 1910-1914.
MENG F L, QIANG X L, SHE K J, et al.Genetic diversity analysis among hulless barley varieties from the major agricultural areas of Tibet[J]. Acta Agronomica Sinica,2007,33(11):1910-1914. (in Chinese with English abstract)
[2] 杨平,刘仙俊,刘新春,等. 利用SRAP标记研究四川高原青稞育成品种的遗传多样性[J]. 遗传, 2008, 30(1): 115-122.
YANG P, LIU X J, LIU X C, et al.Genetic diversity analysis of the developed qingke (hulless barley) varieties from the plateau regions of Sichuan in China revealed by SRAP markers[J]. Hereditas, 2008, 30(1): 115-122. (in Chinese with English abstract)
[3] 曾兴权,王玉林,徐齐君,等. 利用SSR引物分析西藏青稞种质资源的遗传多样性[J]. 麦类作物学报, 2013, 33(2): 260-267.
ZENG X Q, WANG Y L, XU Q J, et al.Asessment of geneic diversity in tibetan hulless barley germplasm (Hordeum vulgare L.var.nudum HK.f.) by SSR primers[J]. Journal of Triticeae Crops, 2013, 33(2): 260-267. (in Chinese with English abstract)
[4] FENG Z Y, ZHANG L L, ZHANG Y Z, et al.Genetic diversity and geographical differentiation of cultivated six-rowed naked barley landraces from the Qinghai-Tibet plateau of China detected by SSR analysis[J]. Genetics and Molecular Biology, 2006, 29(2): 330-338.
[5] 赖勇,王晋民,任龙,等. 大麦SSR标记遗传多样性及连锁不平衡分析[J]. 核农学报, 2016, 30(10): 1889-1897.
LAI Y, WANG J M, REN L, et al.Genetic diversity and linkage disequilibrium analysis of barley using SSR markers[J]. Journal of Nuclear Agrictultural Sciences, 2016, 30(10): 1889-1897. (in Chinese with English abstract)
[6] 巴桑玉珍,刘新春,付国勇,等. 青藏高原青稞耐寒种质资源基于SSR标记的遗传多样性及群体结构分析[J]. 麦类作物学报, 2017, 37(1): 40-47.
BASANG Y Z, LIU X C,FU G Y, et al.Genetic diversity and population structure analysis of hulless barley with cold tolerance from the Qinghai-Tibetan plateau revealed by SSR markers[J]. Journal of Triticeae Crops, 2017, 37(1): 40-47. (in Chinese with English abstract)
[7] KALENDAR R, FLAVELL A J, ELLIS T H N, et al.Analysis of plant diversity with retrotransposon-based molecular markers[J]. Heredity, 2011, 106(4): 520-530.
[8] TSIANTIS M.A transposon in tb1 drove maize domestication[J]. Nature Genetics, 2011, 43(11): 1048-1050.
[9] WICKER T, MAYER K F X, GUNDLACH H, et al. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives[J]. The Plant Cell, 2011, 23(5): 1706-1718.
[10] WICKER T, YU Y, HABERER G, et al.DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses[J]. Nature Communications, 2016, 7: 12790.
[11] 李书粉,李莎,邓传良,等. 转座子在植物 XY 性染色体起源与演化过程中的作用[J]. 遗传, 2015, 37(2): 157-164.
LI S F, LI S, DENG C L, et al.Role of transposons in origin and evolution of plant XY sex chromosomes[J]. Hereditas, 2015, 37(2): 157-164. (in Chinese with English abstract)
[12] CAMPBELL B C, LEMARE S, PIPERIDIS G, et al.IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley[J]. Molecular Breeding, 2011, 27(2): 193-206.
[13] SHANG Y, YANG F, SCHULMAN A H, et al.Gene Deletion in barley mediated by LTR-retrotransposon BARE[J]. Scientific Reports, 2017, 7:43766.
[14] MASCHER M, GUNDLACH H, HIMMELBACH A, et al.A chromosome conformation capture ordered sequence of the barley genome[J]. Nature, 2017, 544(7651): 427-433.
[15] CARVALHO A, GUEDES-PINTO H, MARTINS-LOPES P, et al.Genetic variability of old Portuguese bread wheat cultivars assayed by IRAP and REMAP markers[J]. Annals of Applied Biology, 2010, 156(3): 337-345.
[16] KALENDAR R, GROB T, REGINA M, et al.IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques[J]. Theoretical and Applied Genetics, 1999, 98(5): 704-711.
[17] SINGH S, NANDHA P S, SINGH J.Transposon-based genetic diversity assessment in wild and cultivated barley[J]. The Crop Journal, 2017, 5(4): 296-304.
[18] 张志仙,何道根,朱长志, 等.青花菜种质资源遗传多样性的SSR分析[J]. 浙江农业学报, 2017, 29(2): 228-235.
ZHANG Z X, HE D G, ZHU C Z, et al.Genetic diversity analysis of Brassica oleracea L. var. italica with SSR markers[J]. Acta Agriculturae Zhejiangensis, 2017, 29(2): 228-235. (in Chinese with English abstract)
[19] 张安世,张素敏,范定臣,等. 皂荚种质资源 SRAP 遗传多样性分析及指纹图谱的构建[J]. 浙江农业学报, 2017, 29(9): 1524-1530.
ZHANG A S, ZHANG S M, FAN D C, et al.Genetic diversity and fingerprints of Gleditsia sinensis germplasm based on SRAP[J]. Acta Agriculturae Zhejiangensis, 2017,29(9): 1524-1530. (in Chinese with English abstract)
[20] 黄孙平,陈黎,戴丽荷,等.鸡PRLR脚基因多态位点检测及其与产蛋性状的关联分析[J]. 浙江农业学报, 2015, 27(7): 1141-1147.
HUANG S P, CHEN L, DAI L H, et al.Polymorphism analysis of chicken PRLR genes and their association with layillg performances[J]. Acta Agriculturae Zhejiangensis, 2015, 27(7): 1141-1147. (in Chinese with English abstract)
[21] EVANNO G, REGNAUT S, GOUDET J.Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study[J]. Molecular Ecology, 2005, 14(8): 2611-2620.
[22] BISWAS M K, BAIG M, CHENG Y J, et al.Retro-transposon based genetic similarity within the genus Citrus and its relatives[J]. Genetic Resources and Crop Evolution, 2010, 57(7): 963-972.
[23] KIM H, TERAKAMI S, NISHITANI C, et al.Development of cultivar-specific DNA markers based on retrotransposon-based insertional polymorphism in Japanese pear[J]. Breeding Science, 2012, 62(1): 53-62.
[24] 杜晓云,罗正荣. 部分柿属植物IRAP反应体系的建立和指纹图谱构建[J]. 农业生物技术学报, 2016, 14(6): 931-936.
DU X Y, LUO Z R.Establishment of the inter-retrotransposon amplified polymorphism (IRAP) reaction system and construction of fingerprint in some Diospyros spp.[J]. Journal of Agricultural Biotechnology, 2016, 14(6): 931-936. (in Chinese with English abstract)
[25] 肖炳光,杨本超. 利用IRAP标记分析烤烟品种间遗传差异[J]. 西北植物学报, 2006, 26(6) : 1119-1124.
XIAO B G, YANG B C.Analysis of genetic differences among flue-cured tobacco varieties by IRAP markers[J]. Acta Botanica Boreali-Occidentalia Sinica, 2006, 26(6) : 1119-1124. (in Chinese with English abstract)
[26] 赖勇,贾建磊,王晋民,等. 外引大麦SSR标记遗传多样性及其与农艺性状的关联分析[J]. 麦类作物学报, 2017, 37(2): 197-204.
LAI Y, JIA J L, WANG J M, et al.Analysis of genetic diversity and association with agronomic traits in barley (Hordeum vulgare L.) introduced from abroad using SSR markers[J]. Journal of Triticeae Crops, 2017, 37(2): 197-204. (in Chinese with English abstract)
[27] 尚毅,华为,朱靖环,等. 浙江省裸大麦地方品种遗传多样性分析[J]. 麦类作物学报, 2014, 34(7): 922-928.
SHANG Y, HUA W, ZHU J H, et al.Genetic diversity of hulless barley landraces in Zhejiang[J]. Journal of Triticeae Crops, 2014, 34(7): 922-928. (in Chinese with English abstract)
[28] GUPTA P K, RUSTGI S, KULWAL P L.Linkage disequilibrium and association studies in higher plants: present status and future prospects[J]. Plant Molecular Biology, 2005, 57(4): 461-485.
[29] 王石平,张启发.高等植物基因组中的反转录转座子[J].植物学报,1998, 40(4): 291-297.
WANG S P,ZHANG Q F.Retrotranspoons in the genomes of higher plants[J]. Acta Botanica Sinica, 1998, 40(4): 291-297. (in Chinese with English abstract)
[30] SMYKAL P.Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification[J]. Journal of Applied Genetics, 2006,47(3): 221-230.

基于反转录转座子及简单重复序列标记的裸大麦遗传多样性研究

Genetic diversity in hulless barley by retrotransposons-based markers and simple sequence repeat (SSR) markers

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