Gene flow signature in the S-allele region of cultivated buckwheat

Abstract

Background: Buckwheat (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.

Results: Buckwheat 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.

Conclusion: The 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.

Keywords: Buckwheat; Crop evolution; GBS; Heteromorphic self-incompatibility.

Fig. 1

Neighbor-joining (NJ) tree of 46 cultivars of common buckwheat based on 7.15 Mbp including 255,517 SNPs. Red and blue represent short- and long-styled plants, respectively. Numbers above branches show bootstrap values based on 100 replicates (those less than 80% are not shown) and red asterisks indicate bootstrap values of 95% or over. The scale bar corresponds to 0.001 substitutions per nucleotide site

Fig. 2

Principal-component analysis (PCA) of 46 cultivars of common buckwheat based on GBS data mapped on all genome scaffolds. Graph of the first two axes (x-axis for PC1 and y-axis for PC2) from PCA. The proportion of variance explained by each component is given in parentheses along each axis. Red and blue represent short- and long-styled plants, respectively

Fig. 3

Neighbor-joining (NJ) tree based on GBS sequences (60.1 Kbp) mapped on 332 S-allelic scaffolds. All 23 samples are short-styled plants harboring an S allele (genotype, S/s). Numbers above branches show bootstrap values based on 100 replicates (those less than 80% were not shown). The scale bar corresponds to 0.001 substitutions per nucleotide site