Department of Computer Science, University of Missouri, Columbia, MO 65211, USA.
BMC Genomics. 2013;14 Suppl 1(Suppl 1):S5. doi: 10.1186/1471-2164-14-S1-S5. Epub 2013 Jan 21.
Glycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild soybean), both became available in 2010. This opened the door for comprehensive comparative genomics studies between the two varieties.
We have further analysed the sequences and identified the 425 genes that are unique to G. max and unavailable in G. soja. 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 G. max. 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 G. soja.
The comparisons between genome sequences of G. max and G. soja 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 http://soykb.org/GSoja.
大豆是一种经济上重要的作物，全世界有许多不同的大豆品种。2010 年，栽培大豆（大豆）和野生大豆（野大豆）的基因组草图和基因模型首次问世，为两者之间的综合比较基因组学研究开辟了道路。
我们进一步分析了这些序列，鉴定出了 425 个仅存在于大豆而不存在于野大豆中的基因。我们进一步研究了上游区域具有大量非同义 SNP 的基因。在种子发育、油脂和蛋白质浓度方面，有 12 个基因、3 个基因和 6 个基因是大豆特有的。大量特有的基因与包括种子、油和蛋白质在内的三个性状的 QTL 区域重叠。我们还开发了一个图形染色体可视化工具，作为大豆知识库（SoyKB）分子育种工具的一部分，用于分析和可视化野大豆缺失和 SNP 与多个性状重叠的 QTL 区域。
大豆和野大豆基因组序列的比较显示，两者的基因组组成存在显著差异。这些差异也突出了两者在种子发育、油脂和蛋白质性状方面的表型差异。这些重要的结果已经整合到 SoyKB 资源中，并在 http://soykb.org/GSoja 上供用户浏览。
