Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean
As a complement to single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs), biallelic insertions and deletions (InDels) represent powerful molecular markers with desirable features for filling the gap in current genetic linkage maps. In this study, 28,908 small InDel polymorphisms...
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2014-11-01
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Series: | The Plant Genome |
Online Access: | https://dl.sciencesocieties.org/publications/tpg/articles/7/3/plantgenome2014.04.0014 |
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doaj-0c9985f3f1674ea7bbc3b6bf45a1849b2020-11-25T03:10:47ZengWileyThe Plant Genome1940-33722014-11-017310.3835/plantgenome2014.04.0014plantgenome2014.04.0014Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in SoybeanYing-hui LiBo LiuJochen C. ReifYu-lin LiuHui-hui LiRu-zhen ChangLi-j uan QiuAs a complement to single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs), biallelic insertions and deletions (InDels) represent powerful molecular markers with desirable features for filling the gap in current genetic linkage maps. In this study, 28,908 small InDel polymorphisms (1–5 base pair, bp) distributed genome-wide were identified and annotated by comparison of a whole-genome resequencing data set from two soybean [ (L.) Merr.] genotypes, cultivar Zhonghunag13 (ZH) and line Zhongpin03-5373 (ZP). The physical distribution of InDel polymorphisms in soybean genome was uneven, and matched closely with the distribution of previously annotated genes. The average density of InDel in the arm region was significantly higher than that in the pericentromeric region. The genomic regions that were fixed between the two elites were elucidated. With this information, five InDel markers within a putative quantitative trait locus (QTL) for seed weight (SW), , were developed and used to genotype 254 recombinant inbred lines (RILs) derived from the cross of ZP × ZH. Adding these five InDel markers to previously used SNP and SSR markers facilitated the discovery of further recombination events allowing fine-mapping the QTL to a 0.5 Mbp region. Our study clearly underlines the high value of InDel markers for map-based cloning and marker-assisted selection in soybean.https://dl.sciencesocieties.org/publications/tpg/articles/7/3/plantgenome2014.04.0014 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ying-hui Li Bo Liu Jochen C. Reif Yu-lin Liu Hui-hui Li Ru-zhen Chang Li-j uan Qiu |
spellingShingle |
Ying-hui Li Bo Liu Jochen C. Reif Yu-lin Liu Hui-hui Li Ru-zhen Chang Li-j uan Qiu Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean The Plant Genome |
author_facet |
Ying-hui Li Bo Liu Jochen C. Reif Yu-lin Liu Hui-hui Li Ru-zhen Chang Li-j uan Qiu |
author_sort |
Ying-hui Li |
title |
Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean |
title_short |
Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean |
title_full |
Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean |
title_fullStr |
Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean |
title_full_unstemmed |
Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean |
title_sort |
development of insertion and deletion markers based on biparental resequencing for fine mapping seed weight in soybean |
publisher |
Wiley |
series |
The Plant Genome |
issn |
1940-3372 |
publishDate |
2014-11-01 |
description |
As a complement to single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs), biallelic insertions and deletions (InDels) represent powerful molecular markers with desirable features for filling the gap in current genetic linkage maps. In this study, 28,908 small InDel polymorphisms (1–5 base pair, bp) distributed genome-wide were identified and annotated by comparison of a whole-genome resequencing data set from two soybean [ (L.) Merr.] genotypes, cultivar Zhonghunag13 (ZH) and line Zhongpin03-5373 (ZP). The physical distribution of InDel polymorphisms in soybean genome was uneven, and matched closely with the distribution of previously annotated genes. The average density of InDel in the arm region was significantly higher than that in the pericentromeric region. The genomic regions that were fixed between the two elites were elucidated. With this information, five InDel markers within a putative quantitative trait locus (QTL) for seed weight (SW), , were developed and used to genotype 254 recombinant inbred lines (RILs) derived from the cross of ZP × ZH. Adding these five InDel markers to previously used SNP and SSR markers facilitated the discovery of further recombination events allowing fine-mapping the QTL to a 0.5 Mbp region. Our study clearly underlines the high value of InDel markers for map-based cloning and marker-assisted selection in soybean. |
url |
https://dl.sciencesocieties.org/publications/tpg/articles/7/3/plantgenome2014.04.0014 |
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