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PLoS One. 2014 Apr 11;9(4):e94150. doi: 10.1371/journal.pone.0094150. eCollection 2014.

Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes.

Author information

1
Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri, United States of America.
2
Department of Computer Science, University of Missouri, Columbia, Missouri, United States of America.
3
Division of Computing, McKendree University, Lebanon, Illinois, United States of America.
4
Department of Computer Science, University of Missouri, Columbia, Missouri, United States of America; National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, United States of America; Informatics Institute, University of Missouri, Columbia, Missouri, United States of America; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America.

Abstract

In this Genomics Era, vast amounts of next-generation sequencing data have become publicly available for multiple genomes across hundreds of species. Analyses of these large-scale datasets can become cumbersome, especially when comparing nucleotide polymorphisms across many samples within a dataset and among different datasets or organisms. To facilitate the exploration of allelic variation and diversity, we have developed and deployed an in-house computer software to categorize and visualize these haplotypes. The SNPViz software enables users to analyze region-specific haplotypes from single nucleotide polymorphism (SNP) datasets for different sequenced genomes. The examination of allelic variation and diversity of important soybean [Glycine max (L.) Merr.] flowering time and maturity genes may provide additional insight into flowering time regulation and enhance researchers' ability to target soybean breeding for particular environments. For this study, we utilized two available soybean genomic datasets for a total of 72 soybean genotypes encompassing cultivars, landraces, and the wild species Glycine soja. The major soybean maturity genes E1, E2, E3, and E4 along with the Dt1 gene for plant growth architecture were analyzed in an effort to determine the number of major haplotypes for each gene, to evaluate the consistency of the haplotypes with characterized variant alleles, and to identify evidence of artificial selection. The results indicated classification of a small number of predominant haplogroups for each gene and important insights into possible allelic diversity for each gene within the context of known causative mutations. The software has both a stand-alone and web-based version and can be used to analyze other genes, examine additional soybean datasets, and view similar genome sequence and SNP datasets from other species.

PMID:
24727730
PMCID:
PMC3984090
DOI:
10.1371/journal.pone.0094150
[Indexed for MEDLINE]
Free PMC Article

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