Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences

Abstract

Tartary buckwheat is an important edible crop as well as medicinal plant in China. More and more research is being focused on this minor grain crop because of its medicinal functions, but there is a paucity of molecular markers for tartary buckwheat due to the lack of genomics. In this study, a genome survey was carried out in tartary buckwheat, from which SSR markers were developed for analysis of genetic diversity. The survey generated 21.9 Gb raw sequence reads which were assembled into 348.34 Mb genome sequences included 204,340 contigs. The genome size was estimated to be about 497 Mb based on K-mer analysis. In total, 24,505 SSR motifs were identified and characterised from this genomic survey sequence. Most of the SSR motifs were dinucleotide (67.14 %) and tri-nucleotide (26.05 %) repeats.AT/AT repeat motifs were the most abundant, accounting for 78.60 % of di-nucleotide repeat motifs. SSR fingerprinting of 64 accessions yielded 49.71 effective allele loci from a total of 63 with the 23 polymorphic SSR primer combinations. Analyses of the population genetic structure using SSR data strongly suggested that the 64 accessions of tartary buckwheat clustered into two separate subgroups. One group was mainly distributed in Nepal, Bhutan and the Yunnan-Guizhou Plateau regions of China; the other group was mainly derived from the Loess Plateau regions, Hunan and Hubei of China and USA. The cluster analysis of these accession's genetic similarity coefficient by UPMGA methods strongly supported the two subgroup interpretation. However accessions from Qinghai of China could be grouped into either of the two subgroups depending on which classification method was used. This region is at the intersection of the two geographical regions associated with the two subgroups. These results and information could be used to identify and utilize germplasm resources for improving tartary buckwheat breeding.

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes

“…From our genome survey data, the estimated genome size of L. cylindrica was 789.97 Mb using all of the clean data for K-mer analysis, which was almost two times of Cucumis melo L. and three times of Cucumis sativus L. Genome data of L. cylindrica can be improved by the additional sequencing of larger insert libraries to increase the contig and scaffold sizes. With the development of NGS technologies, genome sequencings of horticultural plants, such as L. cylindrica , not only help easily understand genome organization and critical gene associated with important traits, but also help conveniently design more highly polymorphic molecular markers for subsequent application in molecular breeding [ 22 ]. In addition, these data here contribute to genomic research of sponge.…”

Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability

“…Further, the sequence survey resulted in the identification of 24,505 SSR motifs. The researchers further carried out SSR fingerprinting of 64 accessions and predicted the population structure of tartary buckwheat (Hou et al, 2016).…”

Morphological, physiological, cytological and phytochemical studies in diploid and colchicine-induced tetraploid plants of Fagopyrum tataricum (L.) Gaertn

“…Buckwheat originates from China and is widely distributed in Asia and Europe (Hou et al 2016). The tartary buckwheat ( Fagopyrum tataricum (L.) Gaertn), a diploid species (2n = 2x = 16), belongs to the big-achene group of genus Fagopyrum (Chen et al 2004; Sheng et al 2011).…”