Abstract
BackgroundBuckwheat (Fagopyrum esculentum Moench.) is an annual crop that originated in southern China. The nutritious seeds are used in cooking much like cereal grains. Buckwheat is an outcrossing species with heteromorphic self-incompatibility due to its dimorphic (i.e., short- and long-styled) flowers and intra-morph infertility. The floral morphology and intra-morph incompatibility are both determined by a single S locus. Plants with short-styled flowers are heterozygous (S/s) and plants with long-styled flowers are homozygous recessive (s/s) at this locus, and the S/S genotype is not found. Recently, we built a draft genome assembly of buckwheat and identified the 5.4-Mb-long S-allele region harbored by short-styled plants.In this study, the first report on the genome-wide diversity of buckwheat, we used a genotyping-by-sequencing (GBS) dataset to evaluate the genome-wide nucleotide diversity within cultivated buckwheat landraces worldwide. We also investigated the utility of the S-allele region for phylogenetic analysis of buckwheat.ResultsBuckwheat showed high nucleotide diversity (0.0065), comparable to that of other outcrossing plants, based on a genome-wide simple nucleotide polymorphism (SNP) analysis. Phylogenetic analyses based on genome-wide SNPs showed that cultivated buckwheat comprises two groups, Asian and European, and revealed lower nucleotide diversity in the European group (0.0055) and low differentiation between the Asian and European groups.The nucleotide diversity (0.0039) estimated from SNPs in the S-allele region is lower than that in genome-wide SNPs. Phylogenetic analysis based on this region detected three diverged groups, S-1, S-2, and S-3.ConclusionThe SNPs detected using the GBS dataset were effective for elucidating the evolutionary history of buckwheat, and led to the following conclusions: (1) the low nucleotide diversity of the entire genome in the European group and low differentiation between the Asian and European groups suggested genetic bottlenecks associated with dispersion from Asia to Europe, and/or recent intensified cultivation and selection in Europe; and (2) the high diversification in the S-allele region was indicative of gene flows from wild to cultivated buckwheat, suggesting that cultivated buckwheat may have multiple origins.
Highlights
Buckwheat (Fagopyrum esculentum Moench.) is an annual crop that originated in southern China
The phylogenetic relationships among cultivated buckwheat were well associated with geographic distribution; samples from one country were phylogenetically closely related in the NJ tree (e.g., I8601 and I 8605 for India, N8323 and N8605 for Nepal, and T1F and X1F for Japan)
Phylogenetic analyses based on genome-wide Simple nucleotide polymorphisms (SNPs) showed that cultivated buckwheat is composed of two groups, Asian and European
Summary
Buckwheat (Fagopyrum esculentum Moench.) is an annual crop that originated in southern China. Buckwheat is an outcrossing species with heteromorphic self-incompatibility due to its dimorphic (i.e., short- and long-styled) flowers and intra-morph infertility. We built a draft genome assembly of buckwheat and identified the 5.4-Mb-long S-allele region harbored by short-styled plants. Buckwheat (Fagopyrum esculentum Moench.; 2n = 2x = 16), a member of the Polygonaceae family, is an annual crop that originated in southern China [1, 2]. To identify agronomically useful genes, buckwheat linkage maps have been constructed using various molecular markers, including isozyme variations [6], simple sequence repeats (SSRs) [7], and amplified fragment-length polymorphisms (AFLPs) [8]. A microarray marker system and a genome-wide linkage map for common buckwheat were developed [9]. The genetic tools for buckwheat breeding are highly developed
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