Application of Genotyping by Sequencing on Small Plant Genome Species Groups

Xingbo Wu, Tennessee State University


Genotyping by Sequencing (GBS) is an important approach for plant genetics and crop improvements. DNA polymorphisms in individual plants can be directly related to their phenotype differences for phenotypic predictions and plant selection, lead to key regulative genes that control agronomic traits, or indicate relationships/evolution between individuals in populations. However, this newly developed technology is widely applied to major plant species which usually possess large genome but are lack of use in small genome plant species. This study was undertaken to apply GBS in three small plant genome species, which are grain amaranth (Amaranthus), mung bean ( Vigna radiate L.) and cowpea (Vigna unguiculata) to develop single nucleotide polymorphism and use those makers to perform genetic diversity study in amaranth, conduct genome wide association mapping of mineral content in mung bean and compare the phylogenetic relationship between vegetable, grain cowpea and their wild relative. A total of 10,668 SNPs were discovered in 94 amaranth accessions with ApeKI complexity reduction and 10X genome coverage Illumina sequencing. The distance matrix based on shared alleles provided information on the close relationships of the two cultivated Central American species with each other and of the wild and cultivated South American species with each other, as distinguished from the outgroup with two wild species, A. powellii and A. retroflexus. The GBS data also distinguished admixture between each pair of species and the geographical origins and seed colors of the accessions. A total of 6, 488 SNPs were discovered in 95 mung bean accessions. Mineral study in 2015 and 2016 indicated a large mineral contents variation with genotypes and between two years. Genome wide association study has identified 24 SNPs associated with seven minerals in 2015 and 2016. 33 genes were found to be related to those SNPs. 9,948 SNPs were discovered in 78 cowpea accessions. Phylogenetic studies indicated the independent domestication of vegetable cowpea in Asia due to the geographic isolation. The SNPs we discovered here can be used for marker development for grain amaranth, mung bean and cowpea breeding program.

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Recommended Citation

Xingbo Wu, "Application of Genotyping by Sequencing on Small Plant Genome Species Groups" (2018). ETD Collection for Tennessee State University. Paper AAI10842576.