QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing
Leaf shape is an important trait that influences the utilization rate of light, and affects quality and yield of pea (Pisum sativum). In the present study, a joint method of high-density genetic mapping using specific locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA)...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00615/full |
| _version_ | 1811319780610670592 |
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| author | Yuanting Zheng Yuanting Zheng Fei Xu Qikai Li Gangjun Wang Na Liu Yaming Gong Lulu Li Zhong-Hua Chen Shengchun Xu |
| author_facet | Yuanting Zheng Yuanting Zheng Fei Xu Qikai Li Gangjun Wang Na Liu Yaming Gong Lulu Li Zhong-Hua Chen Shengchun Xu |
| author_sort | Yuanting Zheng |
| collection | DOAJ |
| description | Leaf shape is an important trait that influences the utilization rate of light, and affects quality and yield of pea (Pisum sativum). In the present study, a joint method of high-density genetic mapping using specific locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was applied to rapidly detect loci with leaf shape traits. A total of 7,146 polymorphic SLAFs containing 12,213 SNP markers were employed to construct a high-density genetic map for pea. We conducted quantitative trait locus (QTL) mapping on an F2 population to identify QTLs associated with leaf shape traits. Moreover, SLAF-BSA was conducted on the same F2 population to identify the single nucleotide polymorphism (SNP) markers linked to leaf shape in pea. Two QTLs (qLeaf_or-1, qLeaf_or-2) were mapped on linkage group 7 (LG7) for pea leaf shape. Through alignment of SLAF markers with Cicer arietinum, Medicago truncatula, and Glycine max, the pea LGs were assigned to their corresponding homologous chromosomal groups. The comparative genetic analysis showed that pea is more closely related to M. truncatula. Based on the sequencing results of two pools with different leaf shape, 179 associated markers were obtained after association analysis. The joint analysis of SLAF-seq and BSA showed that the QTLs obtained from mapping on a high-density genetic map are convincing due to the closely associated map region with the BSA results, which provided more potential markers related to leaf shape. Thus, the identified QTLs could be used in marker-assisted selection for pea breeding in the future. Our study revealed that joint analysis of QTL mapping on a high-density genetic map and BSA-seq is a cost-effective and accurate method to reveal genetic architecture of target traits in plant species without a reference genome. |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T12:48:31Z |
| publishDate | 2018-12-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-684585eb5d804eaf98d79487ebd5375c2022-12-22T02:46:18ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-12-01910.3389/fgene.2018.00615426389QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF SequencingYuanting Zheng0Yuanting Zheng1Fei Xu2Qikai Li3Gangjun Wang4Na Liu5Yaming Gong6Lulu Li7Zhong-Hua Chen8Shengchun Xu9Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaCollege of Agriculture & Biotechnology, Zhejiang University, Hangzhou, ChinaCentral Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaCollege of Agriculture & Biotechnology, Zhejiang University, Hangzhou, ChinaCentral Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaCentral Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaCentral Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaCollege of Agriculture & Biotechnology, Zhejiang University, Hangzhou, ChinaSchool of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaCentral Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, ChinaLeaf shape is an important trait that influences the utilization rate of light, and affects quality and yield of pea (Pisum sativum). In the present study, a joint method of high-density genetic mapping using specific locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was applied to rapidly detect loci with leaf shape traits. A total of 7,146 polymorphic SLAFs containing 12,213 SNP markers were employed to construct a high-density genetic map for pea. We conducted quantitative trait locus (QTL) mapping on an F2 population to identify QTLs associated with leaf shape traits. Moreover, SLAF-BSA was conducted on the same F2 population to identify the single nucleotide polymorphism (SNP) markers linked to leaf shape in pea. Two QTLs (qLeaf_or-1, qLeaf_or-2) were mapped on linkage group 7 (LG7) for pea leaf shape. Through alignment of SLAF markers with Cicer arietinum, Medicago truncatula, and Glycine max, the pea LGs were assigned to their corresponding homologous chromosomal groups. The comparative genetic analysis showed that pea is more closely related to M. truncatula. Based on the sequencing results of two pools with different leaf shape, 179 associated markers were obtained after association analysis. The joint analysis of SLAF-seq and BSA showed that the QTLs obtained from mapping on a high-density genetic map are convincing due to the closely associated map region with the BSA results, which provided more potential markers related to leaf shape. Thus, the identified QTLs could be used in marker-assisted selection for pea breeding in the future. Our study revealed that joint analysis of QTL mapping on a high-density genetic map and BSA-seq is a cost-effective and accurate method to reveal genetic architecture of target traits in plant species without a reference genome.https://www.frontiersin.org/article/10.3389/fgene.2018.00615/fullbulked segregant analysishigh-density genetic mapleaf shapePisum sativumspecific locus amplified fragment sequencing |
| spellingShingle | Yuanting Zheng Yuanting Zheng Fei Xu Qikai Li Gangjun Wang Na Liu Yaming Gong Lulu Li Zhong-Hua Chen Shengchun Xu QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing Frontiers in Genetics bulked segregant analysis high-density genetic map leaf shape Pisum sativum specific locus amplified fragment sequencing |
| title | QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing |
| title_full | QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing |
| title_fullStr | QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing |
| title_full_unstemmed | QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing |
| title_short | QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing |
| title_sort | qtl mapping combined with bulked segregant analysis identify snp markers linked to leaf shape traits in pisum sativum using slaf sequencing |
| topic | bulked segregant analysis high-density genetic map leaf shape Pisum sativum specific locus amplified fragment sequencing |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00615/full |
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