Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean
Vegetable soybeans are one of the most important vegetable types in East Asia. The yield of vegetable soybeans is considerably influenced by the size of their pods. To facilitate the understanding of the genetic basis of the pod length and width in vegetable soybeans, we conducted a genome-wide asso...
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2024-11-01
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| author | Dongqing Dai Lu Huang Xiaoyan Zhang Jinyang Liu Shiqi Zhang Xingxing Yuan Xin Chen Chenchen Xue |
| author_facet | Dongqing Dai Lu Huang Xiaoyan Zhang Jinyang Liu Shiqi Zhang Xingxing Yuan Xin Chen Chenchen Xue |
| author_sort | Dongqing Dai |
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| description | Vegetable soybeans are one of the most important vegetable types in East Asia. The yield of vegetable soybeans is considerably influenced by the size of their pods. To facilitate the understanding of the genetic basis of the pod length and width in vegetable soybeans, we conducted a genome-wide association study (GWAS) and transcriptome sequencing. Four quantitative trait loci, namely, <i>qGPoL1</i>, <i>qGPoL2</i>, <i>qGPoW1</i>, and <i>qGPoW2</i>, were mapped via GWAS analysis. Through the integration of gene function annotation, transcriptome sequencing, and expression pattern analysis, we identified <i>Glyma.06G255000</i> and <i>Glyma.13G007000</i> as the key determinants of the pod length and width in vegetable soybeans, respectively. Furthermore, two kompetitive allele-specific polymerase chain reaction (KASP) markers, namely, S06-42138365 (A/T) and S13_628331 (A/T), were developed and effectively validated in 27 vegetable soybean accessions. Overall, our research identified genes that regulate the pod length and width and determined KASP markers for molecular marker-assisted selection breeding. These findings have crucial implications for the improvement of soybean crops and can contribute to the development of efficient breeding strategies. |
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| institution | Kabale University |
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| language | English |
| publishDate | 2024-11-01 |
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| spelling | doaj-art-a779fcabe5f54089858b2c9b561d7fa42024-11-26T17:44:52ZengMDPI AGAgronomy2073-43952024-11-011411265410.3390/agronomy14112654Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable SoybeanDongqing Dai0Lu Huang1Xiaoyan Zhang2Jinyang Liu3Shiqi Zhang4Xingxing Yuan5Xin Chen6Chenchen Xue7Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaInstitute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, ChinaVegetable soybeans are one of the most important vegetable types in East Asia. The yield of vegetable soybeans is considerably influenced by the size of their pods. To facilitate the understanding of the genetic basis of the pod length and width in vegetable soybeans, we conducted a genome-wide association study (GWAS) and transcriptome sequencing. Four quantitative trait loci, namely, <i>qGPoL1</i>, <i>qGPoL2</i>, <i>qGPoW1</i>, and <i>qGPoW2</i>, were mapped via GWAS analysis. Through the integration of gene function annotation, transcriptome sequencing, and expression pattern analysis, we identified <i>Glyma.06G255000</i> and <i>Glyma.13G007000</i> as the key determinants of the pod length and width in vegetable soybeans, respectively. Furthermore, two kompetitive allele-specific polymerase chain reaction (KASP) markers, namely, S06-42138365 (A/T) and S13_628331 (A/T), were developed and effectively validated in 27 vegetable soybean accessions. Overall, our research identified genes that regulate the pod length and width and determined KASP markers for molecular marker-assisted selection breeding. These findings have crucial implications for the improvement of soybean crops and can contribute to the development of efficient breeding strategies.https://www.mdpi.com/2073-4395/14/11/2654vegetable soybeansGWASpod lengthpod widthKASP |
| spellingShingle | Dongqing Dai Lu Huang Xiaoyan Zhang Jinyang Liu Shiqi Zhang Xingxing Yuan Xin Chen Chenchen Xue Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean Agronomy vegetable soybeans GWAS pod length pod width KASP |
| title | Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean |
| title_full | Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean |
| title_fullStr | Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean |
| title_full_unstemmed | Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean |
| title_short | Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean |
| title_sort | detection of candidate genes and development of kasp markers for pod length and pod width by combining genome wide association and transcriptome sequencing in vegetable soybean |
| topic | vegetable soybeans GWAS pod length pod width KASP |
| url | https://www.mdpi.com/2073-4395/14/11/2654 |
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