Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool
In this study, we performed a genotyping-by-sequencing analysis and a genome-wide association study of a soybean mutant diversity pool previously constructed by gamma irradiation. A GWAS was conducted to detect significant associations between 37,249 SNPs, 11 agronomic traits, and 6 phytochemical tr...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-09-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/18/10441 |
| _version_ | 1797487399800930304 |
|---|---|
| author | Dong-Gun Kim Jae Il Lyu Jung Min Kim Ji Su Seo Hong-Il Choi Yeong Deuk Jo Sang Hoon Kim Seok Hyun Eom Joon-Woo Ahn Chang-Hyu Bae Soon-Jae Kwon |
| author_facet | Dong-Gun Kim Jae Il Lyu Jung Min Kim Ji Su Seo Hong-Il Choi Yeong Deuk Jo Sang Hoon Kim Seok Hyun Eom Joon-Woo Ahn Chang-Hyu Bae Soon-Jae Kwon |
| author_sort | Dong-Gun Kim |
| collection | DOAJ |
| description | In this study, we performed a genotyping-by-sequencing analysis and a genome-wide association study of a soybean mutant diversity pool previously constructed by gamma irradiation. A GWAS was conducted to detect significant associations between 37,249 SNPs, 11 agronomic traits, and 6 phytochemical traits. In the merged data set, 66 SNPs on 13 chromosomes were highly associated (FDR <i>p</i> < 0.05) with the following 4 agronomic traits: days of flowering (33 SNPs), flower color (16 SNPs), node number (6 SNPs), and seed coat color (11 SNPs). These results are consistent with the findings of earlier studies on other genetic features (e.g., natural accessions and recombinant inbred lines). Therefore, our observations suggest that the genomic changes in the mutants generated by gamma irradiation occurred at the same loci as the mutations in the natural soybean population. These findings are indicative of the existence of mutation hotspots, or the acceleration of genome evolution in response to high doses of radiation. Moreover, this study demonstrated that the integration of GBS and GWAS to investigate a mutant population derived from gamma irradiation is suitable for dissecting the molecular basis of complex traits in soybeans. |
| first_indexed | 2024-03-09T23:47:05Z |
| format | Article |
| id | doaj.art-c0fcf768448f4b5f98c43a5e41e5c902 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:47:05Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-c0fcf768448f4b5f98c43a5e41e5c9022023-11-23T16:41:45ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-0123181044110.3390/ijms231810441Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity PoolDong-Gun Kim0Jae Il Lyu1Jung Min Kim2Ji Su Seo3Hong-Il Choi4Yeong Deuk Jo5Sang Hoon Kim6Seok Hyun Eom7Joon-Woo Ahn8Chang-Hyu Bae9Soon-Jae Kwon10Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaAdvanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaAdvanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaAdvanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaAdvanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaDepartment of Horticultural Science, Chungnam National University, Daejeon 34134, KoreaAdvanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaDepartment of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin 17104, KoreaAdvanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaDepartment of Life Resources, Graduate School, Sunchon National University, Suncheon 57922, KoreaAdvanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, KoreaIn this study, we performed a genotyping-by-sequencing analysis and a genome-wide association study of a soybean mutant diversity pool previously constructed by gamma irradiation. A GWAS was conducted to detect significant associations between 37,249 SNPs, 11 agronomic traits, and 6 phytochemical traits. In the merged data set, 66 SNPs on 13 chromosomes were highly associated (FDR <i>p</i> < 0.05) with the following 4 agronomic traits: days of flowering (33 SNPs), flower color (16 SNPs), node number (6 SNPs), and seed coat color (11 SNPs). These results are consistent with the findings of earlier studies on other genetic features (e.g., natural accessions and recombinant inbred lines). Therefore, our observations suggest that the genomic changes in the mutants generated by gamma irradiation occurred at the same loci as the mutations in the natural soybean population. These findings are indicative of the existence of mutation hotspots, or the acceleration of genome evolution in response to high doses of radiation. Moreover, this study demonstrated that the integration of GBS and GWAS to investigate a mutant population derived from gamma irradiation is suitable for dissecting the molecular basis of complex traits in soybeans.https://www.mdpi.com/1422-0067/23/18/10441soybeangenotyping-by-sequencinggenome-wide association study |
| spellingShingle | Dong-Gun Kim Jae Il Lyu Jung Min Kim Ji Su Seo Hong-Il Choi Yeong Deuk Jo Sang Hoon Kim Seok Hyun Eom Joon-Woo Ahn Chang-Hyu Bae Soon-Jae Kwon Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool International Journal of Molecular Sciences soybean genotyping-by-sequencing genome-wide association study |
| title | Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool |
| title_full | Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool |
| title_fullStr | Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool |
| title_full_unstemmed | Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool |
| title_short | Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool |
| title_sort | identification of loci governing agronomic traits and mutation hotspots via a gbs based genome wide association study in a soybean mutant diversity pool |
| topic | soybean genotyping-by-sequencing genome-wide association study |
| url | https://www.mdpi.com/1422-0067/23/18/10441 |
| work_keys_str_mv | AT donggunkim identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT jaeillyu identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT jungminkim identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT jisuseo identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT hongilchoi identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT yeongdeukjo identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT sanghoonkim identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT seokhyuneom identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT joonwooahn identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT changhyubae identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool AT soonjaekwon identificationoflocigoverningagronomictraitsandmutationhotspotsviaagbsbasedgenomewideassociationstudyinasoybeanmutantdiversitypool |