Genomic differences between cultivated soybean, G. max and its wild relative G. soja

BMC Genomics

Proceedings

Henry T Nguyen¹  Trupti Joshi²  Dong Xu²  Jeng-Hung Wu³  Suk-Ha Lee⁴  Babu Valliyodan⁵ 

[1] Christopher S. Bond Life Sciences Center, University of Missouri, 65211, Columbia, MO, USA;National Center for Soybean Biotechnology, University of Missouri, 65211, Columbia, MO, USA;Division of Plant Sciences, University of Missouri, 65211, Columbia, MO, USA;Department of Computer Science, University of Missouri, 65211, Columbia, MO, USA;Christopher S. Bond Life Sciences Center, University of Missouri, 65211, Columbia, MO, USA;National Center for Soybean Biotechnology, University of Missouri, 65211, Columbia, MO, USA;Informatics Institute, University of Missouri, 65211, Columbia, MO, USA;Department of Medicine, National Yang-Ming University, Taipei, Taiwan, R.O.C;Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea;Plant Genomics and Breeding Institute, Seoul National University, 151-921, Seoul, Korea;National Center for Soybean Biotechnology, University of Missouri, 65211, Columbia, MO, USA;Division of Plant Sciences, University of Missouri, 65211, Columbia, MO, USA;

关键词: Seed Development;    Unique Gene;    Unique Locus;    Wild Soybean;    Signal Recognition Particle;   

DOI  :  10.1186/1471-2164-14-S1-S5

来源: Springer

【 摘 要 】

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 http://soykb.org/GSoja.

【 授权许可】

Unknown   
© Joshi et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.