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BMC Genomics

, 14:S5

First Online: 21 January 2013DOI: 10.1186-1471-2164-14-S1-S5

Cite this article as: Joshi, T., Valliyodan, B., Wu, JH. et al. BMC Genomics 2013 14Suppl 1: S5. doi:10.1186-1471-2164-14-S1-S5


BackgroundGlycine 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.

ResultsWe 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.

ConclusionsThe 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

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-S1-S5 contains supplementary material, which is available to authorized users.

Trupti Joshi, Babu Valliyodan contributed equally to this work.

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Autor: Trupti Joshi - Babu Valliyodan - Jeng-Hung Wu - Suk-Ha Lee - Dong Xu - Henry T Nguyen


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