Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height
Plant height is an important target for soybean breeding. It is a typical quantitative trait controlled by multiple genes and is susceptible to environmental influences. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from “Dongnong L13” and “Henong 60” in nine envir...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2020.00009/full |
| _version_ | 1811221262653980672 |
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| author | Yanlong Fang Shulin Liu Quanzhong Dong Kaixin Zhang Zhixi Tian Xiyu Li Wenbin Li Zhongying Qi Yue Wang Xiaocui Tian Jie Song Jiajing Wang Chang Yang Sitong Jiang Wen-Xia Li Hailong Ning |
| author_facet | Yanlong Fang Shulin Liu Quanzhong Dong Kaixin Zhang Zhixi Tian Xiyu Li Wenbin Li Zhongying Qi Yue Wang Xiaocui Tian Jie Song Jiajing Wang Chang Yang Sitong Jiang Wen-Xia Li Hailong Ning |
| author_sort | Yanlong Fang |
| collection | DOAJ |
| description | Plant height is an important target for soybean breeding. It is a typical quantitative trait controlled by multiple genes and is susceptible to environmental influences. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from “Dongnong L13” and “Henong 60” in nine environments at four locations over 6 years using interval mapping and inclusive composite interval mapping methods. We performed quantitative trait locus (QTL) analysis by applying pre-built simple-sequence repeat maps. We detected 48 QTLs, including nine significant QTLs detected by multiple methods and in multiple environments. Meanwhile, genotyping of all lines using the SoySNP660k BeadChip produced 54,836 non-redundant single-nucleotide polymorphism (SNP) genotypes. We used five multi-locus genome-wide association analysis methods to locate 10 quantitative trait nucleotides (QTNs), four of which overlap with previously located QTLs. Five candidate genes related to plant height are predicted to lie within 200 kb of these four QTNs. We identified 19 homologous genes in Arabidopsis, two of which may be associated with plant height. These findings further our understanding of the multi-gene regulatory network and genetic determinants of soybean plant height, which will be important for breeding high-yielding soybean. |
| first_indexed | 2024-04-12T07:56:18Z |
| format | Article |
| id | doaj.art-1c37c4e27c1341159c2439c41cc1df02 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T07:56:18Z |
| publishDate | 2020-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-1c37c4e27c1341159c2439c41cc1df022022-12-22T03:41:28ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-02-011110.3389/fpls.2020.00009473804Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant HeightYanlong Fang0Shulin Liu1Quanzhong Dong2Kaixin Zhang3Zhixi Tian4Xiyu Li5Wenbin Li6Zhongying Qi7Yue Wang8Xiaocui Tian9Jie Song10Jiajing Wang11Chang Yang12Sitong Jiang13Wen-Xia Li14Hailong Ning15Key Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaState Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaState Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaKey Laboratory of Soybean Biology, Ministry of Education/Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, ChinaPlant height is an important target for soybean breeding. It is a typical quantitative trait controlled by multiple genes and is susceptible to environmental influences. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from “Dongnong L13” and “Henong 60” in nine environments at four locations over 6 years using interval mapping and inclusive composite interval mapping methods. We performed quantitative trait locus (QTL) analysis by applying pre-built simple-sequence repeat maps. We detected 48 QTLs, including nine significant QTLs detected by multiple methods and in multiple environments. Meanwhile, genotyping of all lines using the SoySNP660k BeadChip produced 54,836 non-redundant single-nucleotide polymorphism (SNP) genotypes. We used five multi-locus genome-wide association analysis methods to locate 10 quantitative trait nucleotides (QTNs), four of which overlap with previously located QTLs. Five candidate genes related to plant height are predicted to lie within 200 kb of these four QTNs. We identified 19 homologous genes in Arabidopsis, two of which may be associated with plant height. These findings further our understanding of the multi-gene regulatory network and genetic determinants of soybean plant height, which will be important for breeding high-yielding soybean.https://www.frontiersin.org/article/10.3389/fpls.2020.00009/fullsoybeanplant heightquantitative trait nucleotidesmulti-locus genome-wide association studieslinkage analysis |
| spellingShingle | Yanlong Fang Shulin Liu Quanzhong Dong Kaixin Zhang Zhixi Tian Xiyu Li Wenbin Li Zhongying Qi Yue Wang Xiaocui Tian Jie Song Jiajing Wang Chang Yang Sitong Jiang Wen-Xia Li Hailong Ning Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height Frontiers in Plant Science soybean plant height quantitative trait nucleotides multi-locus genome-wide association studies linkage analysis |
| title | Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height |
| title_full | Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height |
| title_fullStr | Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height |
| title_full_unstemmed | Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height |
| title_short | Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height |
| title_sort | linkage analysis and multi locus genome wide association studies identify qtns controlling soybean plant height |
| topic | soybean plant height quantitative trait nucleotides multi-locus genome-wide association studies linkage analysis |
| url | https://www.frontiersin.org/article/10.3389/fpls.2020.00009/full |
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