Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it>
<p>Abstract</p> <p>Background</p> <p><it>Glycine max </it>is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of <it>G. max </it>(domesticated soybean) as wel...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2013-01-01
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| Series: | BMC Genomics |
| _version_ | 1818392113141776384 |
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| author | Joshi Trupti Valliyodan Babu Wu Jeng-Hung Lee Suk-Ha Xu Dong Nguyen Henry T |
| author_facet | Joshi Trupti Valliyodan Babu Wu Jeng-Hung Lee Suk-Ha Xu Dong Nguyen Henry T |
| author_sort | Joshi Trupti |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Glycine max </it>is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of <it>G. max </it>(domesticated soybean) as well as <it>G. soja </it>(wild soybean), both became available in 2010. This opened the door for comprehensive comparative genomics studies between the two varieties.</p> <p>Results</p> <p>We have further analysed the sequences and identified the 425 genes that are unique to <it>G. max </it>and unavailable in <it>G. soja</it>. We further studied the genes with significant number of non-synonymous SNPs in their upstream regions. 12 genes involved in seed development, 3 in oil and 6 in protein concentration are unique to <it>G. max</it>. A significant number of unique genes are seen to overlap with the QTL regions of the three traits including seed, oil and protein. We have also developed a graphical chromosome visualizer as part of the Soybean Knowledge Base (SoyKB) tools for molecular breeding, which was used in the analysis and visualization of overlapping QTL regions for multiple traits with the deletions and SNPs in <it>G. soja</it>.</p> <p>Conclusions</p> <p>The comparisons between genome sequences of <it>G. max </it>and <it>G. soja </it>show significant differences between the genomic compositions of the two. The differences also highlight the phenotypic differences between the two in terms of seed development, oil and protein traits. These significant results have been integrated into the SoyKB resource and are publicly available for users to browse at <url>http://soykb.org/GSoja</url>.</p> |
| first_indexed | 2024-12-14T05:24:15Z |
| format | Article |
| id | doaj.art-5a306275251e481d8c4c74eb492b980b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T05:24:15Z |
| publishDate | 2013-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5a306275251e481d8c4c74eb492b980b2022-12-21T23:15:34ZengBMCBMC Genomics1471-21642013-01-0114Suppl 1S510.1186/1471-2164-14-S1-S5Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it>Joshi TruptiValliyodan BabuWu Jeng-HungLee Suk-HaXu DongNguyen Henry T<p>Abstract</p> <p>Background</p> <p><it>Glycine max </it>is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of <it>G. max </it>(domesticated soybean) as well as <it>G. soja </it>(wild soybean), both became available in 2010. This opened the door for comprehensive comparative genomics studies between the two varieties.</p> <p>Results</p> <p>We have further analysed the sequences and identified the 425 genes that are unique to <it>G. max </it>and unavailable in <it>G. soja</it>. We further studied the genes with significant number of non-synonymous SNPs in their upstream regions. 12 genes involved in seed development, 3 in oil and 6 in protein concentration are unique to <it>G. max</it>. A significant number of unique genes are seen to overlap with the QTL regions of the three traits including seed, oil and protein. We have also developed a graphical chromosome visualizer as part of the Soybean Knowledge Base (SoyKB) tools for molecular breeding, which was used in the analysis and visualization of overlapping QTL regions for multiple traits with the deletions and SNPs in <it>G. soja</it>.</p> <p>Conclusions</p> <p>The comparisons between genome sequences of <it>G. max </it>and <it>G. soja </it>show significant differences between the genomic compositions of the two. The differences also highlight the phenotypic differences between the two in terms of seed development, oil and protein traits. These significant results have been integrated into the SoyKB resource and are publicly available for users to browse at <url>http://soykb.org/GSoja</url>.</p> |
| spellingShingle | Joshi Trupti Valliyodan Babu Wu Jeng-Hung Lee Suk-Ha Xu Dong Nguyen Henry T Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it> BMC Genomics |
| title | Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it> |
| title_full | Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it> |
| title_fullStr | Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it> |
| title_full_unstemmed | Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it> |
| title_short | Genomic differences between cultivated soybean, <it>G. max </it>and its wild relative <it>G. soja</it> |
| title_sort | genomic differences between cultivated soybean it g max it and its wild relative it g soja it |
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