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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.    [点击复制]
  • CHEN Zheng-jie,WAN Yong-lu,ZHONG Wen-juan,et al.Development and Application of Soybean InDel Markers Based on Whole-genome Resequencing Datasets[J].植物遗传资源学报,2021,22(3):815-833.   [点击复制]
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基于大豆基因组重测序的InDel标记开发及应用
陈正杰,宛永璐,钟文娟,陈四维,周永航,石盛佳,蒋理,戢沛城,杨泽湖,毛正轩,牟方生
0
(四川省农业科学院经济作物育种栽培研究所,成都610300)
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。
关键词:  大豆  基因组重测序  InDel标记  遗传多样性分析  F1代真实性鉴定
DOI:10.13430/j.cnki.jpgr.20201028003
投稿时间:2020-10-28修订日期:2020-12-10
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
CHEN Zheng-jie, WAN Yong-lu, ZHONG Wen-juan, CHEN Si-wei, ZHOU Yong-hang, SHI Sheng-jia, JANG Li, JI Pei-cheng, YANG Ze-hu, MAO Zheng-xuan, Mou Fang-sheng
(Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300)
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.
Key words:  soybean  genome resequencing  InDel marker  genetic diversity analysis  F1 identification

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