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首页 > 过刊浏览>2021年第22卷第3期 >815-833. DOI:10.13430/j.cnki.jpgr.20201028003
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基于大豆基因组重测序的InDel标记开发及应用
作者:
作者单位:

四川省农业科学院经济作物育种栽培研究所,成都610300

基金项目:

四川省财政创新提升工程“十三五”项目（2016ZYPZ-009）；四川省区域创新合作项目（2020YFQ0044）


Development and Application of Soybean InDel Markers Based on Whole-genome Resequencing Datasets
Author:
Affiliation:

Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300

Fund Project:

The 13th Five-Year Plan of Sichuan financial innovation and improvement project (2016ZYPZ-009)，Sichuan Regional Innovation Cooperation Project (2020YFQ0044)

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    摘要:

    大豆是我国重要的粮油作物，其中菜用大豆是营养丰富的蔬菜作物。然而，大豆中便于应用的分子标记较少。本研究选取18份大豆种质资源进行全基因组重测序分析，以此数据挖掘InDel位点，根据这些InDel位点开发分子标记，并验证这些InDel标记的有效性和应用价值。经过严格筛选，获得17,977个插入/缺失为13-50 bp适合琼脂糖凝胶电泳检测的高多态性InDel位点，每条染色体上分布505~1355个，平均分布密度为12.60~35.76个/Mb。随机挑选73个InDel标记在18份大豆中验证其有效性，结果43个具有多态性，多态性率为56.16%。利用25个多态性InDel标记对192份大豆种质资源（包含64份菜用大豆、65份春大豆、36份夏大豆、19份地方品种、8份野生大豆）进行遗传多样性分析，每个标记的信息多样性值PIC在0.17~0.46之间，平均为0.35。通过聚类分析，192份大豆被划分成24个亚群，成功将不同类型大豆划分到不同亚群。其中菜用大豆主要划分到第3#亚群，相似系数为0.66；少许划分到第1#亚群，相似系数为0.71。表明我国菜用大豆遗传背景较窄，今后菜用大豆杂交育种中应选择相似系数小的材料作为亲本以丰富遗传背景。另外，将这25个InDel标记用于13个杂交组合的F1代真实性鉴定，结果与F1代表型鉴定吻合，表明开发的InDel标记能有效鉴定不同杂交组合F1代真实性。本研究所开发的多态性InDel标记在大豆遗传多样性分析、杂交种纯度鉴定、遗传连锁图谱构建、基因定位和分子标记辅助选择育种等方面具有很好的应用前景。

    Abstract:

    Soybean (Glycine max (L.) Merr.) is one of the important grain and oil crops in China, and vegetable soybean is a nutrition-rich vegetable crop. However, few InDel markers are known for convenient use in soybean. In this study, 18 soybeans were tested for resequencing analysis, with InDel loci mined on the basis of the resequencing datasets, and the effectivity and application value of the InDel markers validated. After strict screening, 17,977 highly polymorphic InDel loci with Insert/Delete of 13-50 bp suitable for agarose gel electrophoresis detection were obtained. There were from 505 to 1355 InDel markers on each chromosome, and the average distribution density was 12.60-35.76 InDel/Mb across the chromosomes. Among the 73 InDel markers randomly selected for effectivity validation in 18 soybeans, 43 (56.16%) of the InDel markers showed polymorphism. Of those 73 InDel markers, 25 polymorphic InDel markers were used for genetic diversity analysis in 192 soybeans (including 64 vegetable soybeans, 65 spring soybeans, 36 summer soybeans, 19 landraces and 8 wild soybeans). The polymorphic information content (PIC) for each InDel marker was between 0.17 and 0.46 with an average of 0.35, and the 192 soybeans were classified into 24 groups with the different types in different groups. Among them, the vegetable soybeans were mainly classified into the 3# group with the genetic similarity coefficient of 0.66 and a few vegetable soybeans were classified into the 1# group with the genetic similarity coefficient of 0.71, which suggested that the genetic background of vegetable soybeans in China are relatively narrow, and we should select soybean lines with small genetic similarity coefficient as parents for breeding in future to enrich the genetic background. The 25 polymorphic InDel markers were also used to verify the F1 from 13 hybrid combinations, which agreed with the phenotypic identification, indicating the usefulness of the InDel markers developed for F1 identification. Taken together, the polymorphic InDel markers developed in this study will be widely used in genetic diversity analysis, hybrid identification, genetic linkage map construction, gene mapping and molecular marker assisted selection breeding in soybean.

    参考文献
    [1] 孙永刚. 栽培大豆起源与植物考古学研究. 农业考古,2013,000(006)：11-15Sun Y G. Study on the origin of cultivated soybean and plant Archaeology. Agricultural Archaeology,2013,000(006)：11-15
    [2] 盖钧镒,王明军. 中国毛豆生产的历史渊源与发展. 大豆科学,2002, 21(1)：7-13Gai J Y,Wang M J. Historical origin and development of maodou production in China. Soybean Science,2002, 21(1)：7-13
    [3] Konovsky J,Lumpkin T A,Mcclary D,O'Rourke A D. Edamame： the vegetable soybean. In： Understanding the Japanese Food Agrimarket： A Multifaceted Opportunity,1994
    [4] 赵璇,王玉岭,李占军,金素娟. 菜用大豆的发展现状及展望. 河北农业科学,2012,16(007)：39-41Zhao X,Wang Y L,Li Z J,Jin S J. Development status and prospect of vegetable soybean. Journal of Hebei Agicultural Science,2012,16(007)：39-41
    [5] 顾卫红,郑洪建,张燕,张国荣. 菜用大豆的国际需求及科研生产动态(综述). 上海农业学报,2002,018(002)：45-48Gu W H, Zheng H J,Zhang Y,Zhang G R. Trends in production, demand and research trends of vegetable soybean at home and abroad (Review). Acta Agriculturae Shanghai,2002,018(002)：45-48
    [6] 谢甫绨,谈伟,姜旭. 菜用大豆的价值与发展前景. 新农业,2010,000(010)：15-15Xie F D,Tan W,Jiang K. The value and development prospect of vegetable soybean. Xin nongye,2010,000(010)：15-15
    [7] 李清华. 34份菜用大豆品种主要农艺性状的主成分分析及遗传距离测定. 福建农业学报,2018,33(2)：136-143LI Q H．Principal component analysis on major agronomic traits and determination of genetic distance of thirty-four vegetable Soybean Cultivars. Fujian Journal of Agricultural Sciences,2018,33(2)：136-143
    [8] 汪桂凤,钟宣伯,查霆,周启政,何梦迪,唐桂香. 菜用大豆种质资源评价与筛选. 大豆科学,2019 038(002)：169-180Wang G F,Zhong X B,Zha T,Zhou Q Z,He M D,Tang G X. Evaluation and screening of fresh soybean germplasm. Soybean Science, 2019 038(002)：169-180
    [9] 邱丽娟,常汝镇,陈可明,谢华,李向华,关荣霞,孙建英. 中国大豆(Glycine max)品种资源保存与更新状况分析. 植物遗传资源学报,2002,3(002)：34-39Qiu L J,Chang R Z,Chen K M,Xie H,Li X H,Guan R X,Sun J Y. Analysis of conservation and regeneration statues for Chinese soybean germplasm. Journal of Plant Genetic Resources,2002,3(002)：34-39
    [10] 邱丽娟,常汝镇,袁翠平,关荣霞,刘章雄,李英惠. 国外大豆种质资源的基因挖掘利用现状与展望. 植物遗传资源学报,2006,7(1)：1-6Qiu L J,Chang R Z,Yuan C P,Guan R X,Liu Z X,Li Y H. Prospect and present statue of gene discovery and utilizationfor Introduced soybean germplasm. Journal of Plant Genetic Resources,2006,7(1)：1-6
    [11] 李之国,李喜焕,张彩英,马峙英. 基于农艺性状和AFLP位点的菜用大豆遗传多样性. 中国油料作物学报,2007,029(004)：391-396Li Z G,Li X H,Zhang C Y,Ma S Y. Genetic diversity assessment of vegetable soybean varieties based on agronomic characters and AFLPs. Chinese journal of oil crop sciences,2007,029(004)：391-396
    [12] 徐海风,杨加银,程保山. 26份菜用大豆品种(系)指纹图谱的构建及其遗传多样性分析. 江苏农业科学,2014,42(005)：145-148Xu H F,Yang J Y,Cheng B S. Construction and genetic diversity analysis of 26 vegetable soybean varieties. Jiangsu Agricultural Sciences,2014,42(005)：145-148
    [13] Fu-Ti X,Yoshihito T,Yasuo O. Phylogenetic Analysis of Vegetable-type(Edamame) and Grain-type Soybean[Glycine max(L.) Merr.]Cultivars Through ISSR Markers. Soybean science,2008,27(5)：732-739
    [14] Weber J L,David D,Heil J,Fan Y,Zhao C,Marth G. Human Diallelic Insertion/Deletion Polymorphisms. American Journal of Human Genetics,2002,71(4)：854-862
    [15] Barchi L,Lanteri S,Portis E,Acquadro A,Valè G,Toppino L,Rotino GL. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC genomics,2011,12(1)：304
    [16] Shen YJ,Jiang H,Jin JP,Zhang ZB,Xi B,He YY,Wang G, Wang C,Qian L,Li X. Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes. Plant physiology,2004,135(3)：1198-1205
    [17] 陆海燕,陈璐,王显生,赵涵,沈奇. 基于高通量测序的棉花InDel标记开发及其应用. 棉花学报,2019,31(004)：297-306Lu H Y,Chen L,Wang X S,Zhao H,Shen Q. Development and application of cotton InDel markers based on high throughput sequencing. Cotton Science,2019,31(004)：297-306
    [18] 赵庆英,张瑞娟,王瑞良,高建华,韩渊怀,杨致荣,王兴春. 基于名优谷子品种晋谷21全基因组重测序的分子标记开发. 作物学报,2018,044(005)：686-696
    [19] Sahu PK,Mondal S,Sharma D,Vishwakarma G,Das BK. InDel marker based genetic differentiation and genetic diversity in traditional rice (Oryza sativa L.) landraces of Chhattisgarh, India. PloS One,2017,12(11)：e0188864
    [20] 马小定,唐江红,张佳妮,崔迪,李慧,黎毛毛,韩龙植. 东乡野生稻与日本晴多态性标记的开发. 作物学报,2019,45(02)：160-165Ma X D,Tang J H,Zhang J N,Cui D,Li H,Li M M,Han L Z. Development of molecular markers polymorphic between Dongxiang wild rice and Geng rice cultivar ‘Nipponbare’. Acta Agronomica Sinica,2019,45(02)：160-165
    [21] Liu J,Qu J T,Yang C,Tang D G,Li J W,Lan H,Rong T Z. Development of genome-wide insertion and deletion markers for maize, based on next-generation sequencing data. BMC genomics,2015,16：601
    [22] 吴磊,王丹,苏文悦,郭长虹,束永俊. 利用比较基因组学开发山羊草属InDel分子标记. 作物学报,2012,38(007)：1334-1338Wu L,Wang D,Sun W Y,Guo C H,Su Y J. Developing InDel markers from aegilops genus based on comparative genomics. Acta Agronomica Sinica,2012,38(007)：1334-1338
    [23] 吴迷,汪念,沈超,黄聪,温天旺,林忠旭. 基于重测序的陆地棉InDel标记开发与评价. 作物学报,2019,045(002)：196-203Wu M,Wang N,Shen C,Huang C,Wen T W,Lin Z X. Development and evaluation of InDel markers in cotton based on whole-genome re-sequencing data. Acta Agronomica Sinica,2019,045(002)：196-203
    [24] Liu B,Wang Y,Zhai W,Deng J,Wang H,Cui Y,Cheng F,Wang X,Wu J. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theoretical and Applied Genetics,2013,126(1)：231-239
    [25] 张国儒,唐亚萍,杨涛,帕提古丽,王柏柯,李宁,王娟,李晓琴,余庆辉,杨生保. 基于重测序番茄InDel标记的开发. 分子植物育种,2019,(14)：4692-4697Zhang G R,Tang Y P,Yang T,Patiguli,Wang B K,Li N,Wang J,Li X Q,Yu Q H,Yang S B. Development of InDel markers for tomato based on re-sequencing data. Molecular Plant Breeding,2019,(14)：4692-4697
    [26] 李斯更,沈镝,刘博,邱杨,张晓辉,张忠华,王海平,李锡香. 基于黄瓜基因组重测序的InDel标记开发及其应用. 植物遗传资源学报,2013(02)：278-283Li S G,Shen D,Liu B,Qiu Y,Zhang X H,Zhang Z H,Wang H P,Li X X. Development and application of cucumber InDel markers based on genome re-sequencing. Journal of Plant Genetic Resources,2013(02)：278-283
    [27] 吉康娜,郅俊杰,林丹妮,颜爽爽,田时炳,曹必好,邱正坤. 基于茄子基因组重测序的InDel标记开发及应用. 植物遗传资源学报,2019,(5) ：1278-1288Ji K N,Zhi J J,Lin D N,Yan S S,Tian S B,Cao B H,Qiu Z K. Development and application of eggplant InDel markers based on whole genome re-sequencing datasets. Journal of Plant Genetic Resources,2019,(5) ：1278-1288
    [28] 郭广君,孙茜,刘金兵,潘宝贵,刁卫平,戈伟,高长洲,王述彬. 基于辣椒基因组重测序的InDel标记开发及应用. 江苏农业学报,2015,31(6)：1400-1406Guo G J,Sun Q,Liu J B,Pan B G,Diao W P,Ge W,Gao C Z,Wang S B. Development and application of pepper InDel markers based on genome re-sequencing. Jiangsu Journal of Agricultural sciences,2015,31(6)：1400-1406
    [29] Song X,Wei H,Cheng W,Yang S,Zhao Y,Li X,Luo D,Zhang H,Feng X. Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean. G3： Genes, Genomes, Genetics,2015,5(12)：2793-2799
    [30] 王嘉,曾召琼,梁建秋,于晓波,吴海英,张明荣. 基于全基因组重测序的大豆分子标记开发及籽粒蛋白质含量QTL定位. 中国农业科学,2019,52(16)：2743-2757Wang J,Zeng Z Q,Liang J Q,Yu X B,Wu H Y,Zhang M R. Development new molecular markers for quantitative trait locus (QTL) analysis of the seed protein content based on whole genome re-sequencing in soybean. Scientia Agricultura Sinica,2019,52(16)：2743-2757
    [31] 于莉莉,关荣霞,邱丽娟. 野生大豆(Glycine max L.)InDel标记的开发与利用. 第十届全国大豆学术讨论会,2017Yu L L,Guano R X,Qiu L J. Development and utilization of indel marker in wild soybean (Glycine max L.). The 10th National Soybean Symposium,2017
    [32] Stewart C N J,Via L E. A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques,1993,14(5)：748-750
    [33] Li H,Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics,2009
    [34] Li H,Handsaker B,Wysoker A,Fennell T,Ruan J,Homer N,Marth G,Abecasis G,Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics,2009,25(16)：2078-2079
    [35] Wang K,Li M,Hakonarson H. Wang K,Li M,Hakonarson HANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nuc Acids Res 38(16)： e164. Nuclc Acids Research,2010,38(16)：e164
    [36] Lalitha S. Primer Premier 5. Biotech Software Internet Report,2000,1(6)：270-272
    [37] Korbie D J,Mattick J S. Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nature Protocols,2008,3(9)：1452-1456
    [38] Nagy S,Poczai P,Cernák I,Gorji AM,Heged?s G,Taller J. PICcalc： An Online Program to Calculate Polymorphic Information Content for Molecular Genetic Studies. Biochemical Genetics,2012,50(9)：670-672
    [39] Rohlf FJ. NTSYS-PC, numerical taxonomy and multivariate analysis system version 2.11. 2000
    [40] 苏睿,林峻,陈鲤群,蔡伟文. 高通量自动化SNP检测技术研究进展. 中国细胞生物学学报,2019Sun R,Lin J,Chen L Q,Cai W W. Research progress of high throughput automated SNP detection technology. Chinese Journal of Cell Biology,2019
    [41] 张玉梅,王彪,张忠滨,武天龙. 优质、丰产菜用大豆新品种交大05-133的选育. 种子,2013,32(3)：102-104Zhang Y M,Wang B,Zhang Z B,Wu T L. Breeding for fine quality and high yield of vegetable soybean Jiaoda 133. Seed,2013,32(3)：102-104
    [42] 傅旭军,杨清华,袁凤杰,郁晓敏,金杭霞,朱申龙,朱丹华. 浙鲜9号的航天选育与特征特性分析. 核农学报,2019,033(005)：841-847Fu X J,Yang Q H,Yuan F J,Yu X M,Jin H X,Zhu S L,Zhu D H. Breeding of Zhexian No.9 by space mutation and variation analysis of its characters. Journal of Nuclear Agricultural Sciences,2019,033(005)：841-847
    [43] 甘柏君. 特异冬大豆贡选1号的生产用途. 四川农业科技,2008,000(005)：36-37Gan B J. Production use of special winter soybean gongxuan No.1. Science and technology of Sichuan agriculture,2008,000(005)：36-37
    [44] 王钰,马卉,许学,秦瑞英,杨剑波,汪秀峰. 水稻功能性插入缺失标记(InDel)的筛选与应用. 作物杂志,2019,000(004)：84-93Wang Y,Ma H,Xu X,Qin R Y,Yang J B,Wang X F. Screening and application of functional Insertion-Deletion markers (InDel) in Rice. Crops,2019,000(004)：84-93
    [45] 姚宗泽,李阳,郭宗娟,张思亲,胡晓,赵自仙. 杂交玉米品种家佳荣2号种子纯度的InDel分子标记鉴定. 江苏农业科学,2020,48(01)：85-90Yao Z Z,Li Y,Guo Z J,Zhang S Q,Hu X,Zhao Z X. Identification of seed purity of hybrid maize variety jiajiarong 2 by indel molecular markers. Jiangsu Agricultural Sciences,2020,48(01)：85-90
    [46] 张录霞,甘中祥,李倍金,魏强,闫德林,张勇,迟庆勇,彭刚. 利用InDel 标记鉴定加工番茄杂交种纯度. 分子植物育种,2016,14(6)：1533-1537Zhang L X,Gan Z X,Li B J,Wei Q,Yan D L,Zhang Y,Chi Q Y,Peng G. Hybrid purity identification of processed tomato by InDel markers. Molecular Plant Breeding,2016,14(6)：1533-1537
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陈正杰,宛永璐,钟文娟,等.基于大豆基因组重测序的InDel标记开发及应用[J].植物遗传资源学报,2021,22(3):815-833.

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