Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean
Annual wild soybean (<i>G. soja</i>) is the ancestor of the cultivated soybean (<i>G. max</i>). To reveal the genetic changes from <i>soja</i> to <i>max</i>, an improved wild soybean chromosome segment substitution line (CSSL) population, <i>Soja...
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MDPI AG
2021-02-01
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| Series: | International Journal of Molecular Sciences |
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| author | Cheng Liu Xianlian Chen Wubin Wang Xinyang Hu Wei Han Qingyuan He Hongyan Yang Shihua Xiang Junyi Gai |
| author_facet | Cheng Liu Xianlian Chen Wubin Wang Xinyang Hu Wei Han Qingyuan He Hongyan Yang Shihua Xiang Junyi Gai |
| author_sort | Cheng Liu |
| collection | DOAJ |
| description | Annual wild soybean (<i>G. soja</i>) is the ancestor of the cultivated soybean (<i>G. max</i>). To reveal the genetic changes from <i>soja</i> to <i>max</i>, an improved wild soybean chromosome segment substitution line (CSSL) population, <i>SojaCSSLP5</i>, composed of 177 CSSLs with 182 SSR markers (SSR-map), was developed based on <i>SojaCSSLP1</i> generated from <i>NN1138-2</i>(<i>max</i>)×<i>N24852</i>(<i>soja</i>). The <i>SojaCSSLP5</i> was genotyped further through whole-genome resequencing, resulting in a physical map with 1366 SNPLDBs (SNP linkage-disequilibrium blocks), which are composed of more markers/segments, shorter marker length and more recombination breakpoints than the SSR-map and caused 721 new wild substituted segments. Using the SNPLDB-map, two loci co-segregating with seed-coat color (SCC) and six loci for days to flowering (DTF) with 88.02% phenotypic contribution were identified. Integrated with parental RNA-seq and DNA-resequencing, two SCC and six DTF candidate genes, including three previously cloned (<i>G</i>, <i>E2</i> and <i>GmPRR3B</i>) and five newly detected ones, were predicted and verified at nucleotide mutant level, and then demonstrated with the consistency between gene-alleles and their phenotypes in <i>SojaCSSLP5</i>. In total, six of the eight genes were identified with the parental allele-pairs coincided to those in 303 germplasm accessions, then were further demonstrated by the consistency between gene-alleles and germplasm phenotypes. Accordingly, the CSSL population integrated with parental DNA and RNA sequencing data was demonstrated to be an efficient platform in identifying candidate wild vs. cultivated gene-alleles. |
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| spelling | doaj.art-c4806f7aecbe4945a2bf5972f58df2ab2023-12-03T12:20:21ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-02-01224155910.3390/ijms22041559Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in SoybeanCheng Liu0Xianlian Chen1Wubin Wang2Xinyang Hu3Wei Han4Qingyuan He5Hongyan Yang6Shihua Xiang7Junyi Gai8Soybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaSoybean Research Institute & MOA National Center for Soybean Improvement & MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General) & State Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, ChinaAnnual wild soybean (<i>G. soja</i>) is the ancestor of the cultivated soybean (<i>G. max</i>). To reveal the genetic changes from <i>soja</i> to <i>max</i>, an improved wild soybean chromosome segment substitution line (CSSL) population, <i>SojaCSSLP5</i>, composed of 177 CSSLs with 182 SSR markers (SSR-map), was developed based on <i>SojaCSSLP1</i> generated from <i>NN1138-2</i>(<i>max</i>)×<i>N24852</i>(<i>soja</i>). The <i>SojaCSSLP5</i> was genotyped further through whole-genome resequencing, resulting in a physical map with 1366 SNPLDBs (SNP linkage-disequilibrium blocks), which are composed of more markers/segments, shorter marker length and more recombination breakpoints than the SSR-map and caused 721 new wild substituted segments. Using the SNPLDB-map, two loci co-segregating with seed-coat color (SCC) and six loci for days to flowering (DTF) with 88.02% phenotypic contribution were identified. Integrated with parental RNA-seq and DNA-resequencing, two SCC and six DTF candidate genes, including three previously cloned (<i>G</i>, <i>E2</i> and <i>GmPRR3B</i>) and five newly detected ones, were predicted and verified at nucleotide mutant level, and then demonstrated with the consistency between gene-alleles and their phenotypes in <i>SojaCSSLP5</i>. In total, six of the eight genes were identified with the parental allele-pairs coincided to those in 303 germplasm accessions, then were further demonstrated by the consistency between gene-alleles and germplasm phenotypes. Accordingly, the CSSL population integrated with parental DNA and RNA sequencing data was demonstrated to be an efficient platform in identifying candidate wild vs. cultivated gene-alleles.https://www.mdpi.com/1422-0067/22/4/1559annual wild soybean (<i>G. soja</i> Sieb. and Zucc.)chromosome segment substitution line (CSSL)cultivated soybean (<i>G. max</i> (L.) Merr.)days to floweringseed coat colorSNP linkage disequilibrium block (SNPLDB) |
| spellingShingle | Cheng Liu Xianlian Chen Wubin Wang Xinyang Hu Wei Han Qingyuan He Hongyan Yang Shihua Xiang Junyi Gai Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean International Journal of Molecular Sciences annual wild soybean (<i>G. soja</i> Sieb. and Zucc.) chromosome segment substitution line (CSSL) cultivated soybean (<i>G. max</i> (L.) Merr.) days to flowering seed coat color SNP linkage disequilibrium block (SNPLDB) |
| title | Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean |
| title_full | Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean |
| title_fullStr | Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean |
| title_full_unstemmed | Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean |
| title_short | Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean |
| title_sort | identifying wild versus cultivated gene alleles conferring seed coat color and days to flowering in soybean |
| topic | annual wild soybean (<i>G. soja</i> Sieb. and Zucc.) chromosome segment substitution line (CSSL) cultivated soybean (<i>G. max</i> (L.) Merr.) days to flowering seed coat color SNP linkage disequilibrium block (SNPLDB) |
| url | https://www.mdpi.com/1422-0067/22/4/1559 |
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