JIA-2020-2420 基于全基因组重测序发掘长片段InDels精细定位大豆株高QTL

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (7): 1903-1912.DOI: 10.1016/S2095-3119(21)63675-4

所属专题：油料作物合辑Oil Crops

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JIA-2020-2420 基于全基因组重测序发掘长片段InDels精细定位大豆株高QTL

收稿日期:2020-11-25 接受日期:2021-03-03 出版日期:2022-07-01 发布日期:2021-03-03

Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean (Glycine max L. Merr.)

LIU Chen^{1, 2*}, TIAN Yu^2*, LIU Zhang-xiong², GU Yong-zhe², ZHANG Bo³, LI Ying-hui², NA Jie¹, QIU Li-juan²

¹School of Life Sciences, Liaoning Normal University, Dalian 116081, P.R.China
² National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture and Rural Affairs/Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, P.R.China
³ School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA

Received:2020-11-25 Accepted:2021-03-03 Online:2022-07-01 Published:2021-03-03
About author:LIU Chen, E-mail: 1518753786@qq.com; TIAN Yu, E-mail: 82101181082@caas.cn; Correspondence QIU Li-juan, E-mail: qiulijuan@caas.cn; NA Jie, Tel: +86-411-85827090, E-mail: jiena@lnnu.edu.cn; LI Ying-hui, Tel: +86-10-82105843, E-mail: liyinghui@caas.cn * These authors contributed equally to this study.
Supported by:
This research was supported by the National Key R&D Program of China (2016YFD0100201 and 2020YFE0202300) and the Agricultural Science and Technology Innovation Program (ASTIP) of the Chinese Academy of Agricultural Sciences.

摘要/Abstract

摘要：

本研究在前期已发掘短片段InDels和SNPs基础上，基于全基因组重测序分析在一个重组自交系群体的两个亲本中品03-5373（ZP）和中黄13（ZH）之间检测到不均匀分布在大豆20条染色体上的13573个长片段InDels，其中，Chr11上最少，有321个，Chr18上最多，有1246个。长片段InDels在染色体两臂的平均密度显著高于着丝粒区，与大豆基因组注释基因的分布模式一致。位于基因区的长片段InDels有2704个，占总数目的19.9%，其中319个为可导致蛋白质序列截短或延长的大效应InDels。重点对前期鉴定的株高相关QTL（qPH16）进行分析，共鉴定到35个长片段InDels，并将其开发成InDel标记，其中26个InDel标记（74.3%）在ZP和ZH之间表现出明显的多态性。利用开发的标记结合已有的4个SNPs标记对由ZP和ZH衍生的242个重组自交系进行基因型鉴定和QTL定位，将qPH16的定位区间从原来的960 kb缩小到477.55 kb，包含65个注释基因。在SNPs和短片段InDels开发基础上，进一步开发长片段InDels，可为大豆重要农艺性状的遗传分析和分子辅助选择育种提供更加全面的遗传变异信息。

Abstract: With the development of sequencing technology, insertions-deletions (InDels) have been increasingly reported to be involved in the genetic deter mination of agronomical traits. However, most studies have focused on the identification and application of short-InDels (1–15 bp) for genetic analysis. The objective of this study was to deeply deploy long-InDels (>15 bp) for the genetic analysis of important agronomic traits in soybean. A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373 (ZP) and Zhonghuang 13 (ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18. Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level. A total of 2 704 (19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences. A previously identified QTL (qPH16) underlying plant height was further analyzed, and it was found that 26 out of 35 (74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH. Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH. As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes. Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

Key words: soybean , plant height , whole genome re-sequencing , long-InDels , QTL

. JIA-2020-2420 基于全基因组重测序发掘长片段InDels精细定位大豆株高QTL[J]. Journal of Integrative Agriculture, 2022, 21(7): 1903-1912.

LIU Chen, TIAN Yu, LIU Zhang-xiong, GU Yong-zhe, ZHANG Bo, LI Ying-hui, NA Jie, QIU Li-juan. Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean (Glycine max L. Merr.)[J]. Journal of Integrative Agriculture, 2022, 21(7): 1903-1912.

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