Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) Landraces
Soybean [<i>Glycine max</i> (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing...
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MDPI AG
2023-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/1/873 |
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| author | Seong-Hoon Kim Rupesh Tayade Byeong-Hee Kang Bum-Soo Hahn Bo-Keun Ha Yoon-Ha Kim |
| author_facet | Seong-Hoon Kim Rupesh Tayade Byeong-Hee Kang Bum-Soo Hahn Bo-Keun Ha Yoon-Ha Kim |
| author_sort | Seong-Hoon Kim |
| collection | DOAJ |
| description | Soybean [<i>Glycine max</i> (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing crops that are resistant to climatic extremes and produce viable yields under predicted climatic conditions will be essential in the coming decades. To develop such crops, it will be necessary to gain a thorough understanding of the genetic basis of agronomic and plant root traits. As plant roots generally lie beneath the soil surface, detailed observations and phenotyping throughout plant development present several challenges, and thus the associated traits have tended to be ignored in genomics studies. In this study, we phenotyped 357 soybean landraces at the early vegetative (V2) growth stages and used a 180 K single-nucleotide polymorphism (SNP) soybean array in a genome-wide association study (GWAS) conducted to determine the phenotypic relationships among root traits, elucidate the genetic bases, and identify significant SNPs associated with root trait-controlling genomic regions/loci. A total of 112 significant SNP loci/regions were detected for seven root traits, and we identified 55 putative candidate genes considered to be the most promising. Our findings in this study indicate that a combined approach based on SNP array and GWAS analyses can be applied to unravel the genetic basis of complex root traits in soybean, and may provide an alternative high-resolution marker strategy to traditional bi-parental mapping. In addition, the identified SNPs, candidate genes, and diverse variations in the root traits of soybean landraces will serve as a valuable basis for further application in genetic studies and the breeding of climate-resilient soybeans characterized by improved root traits. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T09:58:16Z |
| publishDate | 2023-01-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ce87c19d8b9941ed885367094107f1aa2023-11-16T15:39:42ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-01-0124187310.3390/ijms24010873Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) LandracesSeong-Hoon Kim0Rupesh Tayade1Byeong-Hee Kang2Bum-Soo Hahn3Bo-Keun Ha4Yoon-Ha Kim5National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Republic of KoreaDepartment of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of KoreaDepartment of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of KoreaNational Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Republic of KoreaDepartment of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of KoreaDepartment of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of KoreaSoybean [<i>Glycine max</i> (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing crops that are resistant to climatic extremes and produce viable yields under predicted climatic conditions will be essential in the coming decades. To develop such crops, it will be necessary to gain a thorough understanding of the genetic basis of agronomic and plant root traits. As plant roots generally lie beneath the soil surface, detailed observations and phenotyping throughout plant development present several challenges, and thus the associated traits have tended to be ignored in genomics studies. In this study, we phenotyped 357 soybean landraces at the early vegetative (V2) growth stages and used a 180 K single-nucleotide polymorphism (SNP) soybean array in a genome-wide association study (GWAS) conducted to determine the phenotypic relationships among root traits, elucidate the genetic bases, and identify significant SNPs associated with root trait-controlling genomic regions/loci. A total of 112 significant SNP loci/regions were detected for seven root traits, and we identified 55 putative candidate genes considered to be the most promising. Our findings in this study indicate that a combined approach based on SNP array and GWAS analyses can be applied to unravel the genetic basis of complex root traits in soybean, and may provide an alternative high-resolution marker strategy to traditional bi-parental mapping. In addition, the identified SNPs, candidate genes, and diverse variations in the root traits of soybean landraces will serve as a valuable basis for further application in genetic studies and the breeding of climate-resilient soybeans characterized by improved root traits.https://www.mdpi.com/1422-0067/24/1/873soybeanroot traitGWASSNPcandidate gene |
| spellingShingle | Seong-Hoon Kim Rupesh Tayade Byeong-Hee Kang Bum-Soo Hahn Bo-Keun Ha Yoon-Ha Kim Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) Landraces International Journal of Molecular Sciences soybean root trait GWAS SNP candidate gene |
| title | Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) Landraces |
| title_full | Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) Landraces |
| title_fullStr | Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) Landraces |
| title_full_unstemmed | Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) Landraces |
| title_short | Genome-Wide Association Studies of Seven Root Traits in Soybean (<i>Glycine max</i> L.) Landraces |
| title_sort | genome wide association studies of seven root traits in soybean i glycine max i l landraces |
| topic | soybean root trait GWAS SNP candidate gene |
| url | https://www.mdpi.com/1422-0067/24/1/873 |
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