High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum

Abstract

Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5–1 Mya) multiplied TEs (“transposon burst”) and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.

Biotechnological Methods for Buckwheat Breeding

“…Ethyl-methane sulphonate (EMS)-induced mutant pools of buckwheat for these genes are now being screened for the development of SC lines with highly valuable agronomical traits, for instance, low amylose and low-allergen lines [85]. Recently, single-molecule real-time (SMRT) long reads were used together with Illumina short reads for de novo assembly of the common buckwheat genome with 39 times better N50 score (~180 kb) [172] than that of [75]. A transcriptome map, based on the newly assembled genome, was constructed and made publicly available on the TraVA database (http://travadb.org/browse/Species=Fesc/, accessed on 10 March 2021).…”

Buckwheat in Tissue Culture Research: Current Status and Future Perspectives

“…Draft genome sequences for common and Tartary buckwheat will help in gaining understanding of genetic mechanisms and regulation of specific traits, proteomic, transcriptomic, metabolomics and epigenomic approaches. For example, Penin et al [127] characterised 1.5 Gb genome along with the reference assembly of common buckwheat. This will lead to opportunities to determine functions that will help in the population improvement programmes as well as to examine their mechanisms.…”

“…This will lead to opportunities to determine functions that will help in the population improvement programmes as well as to examine their mechanisms. These authors used the draft genome in order to reference it with genotyping-by-sequencing (GBS) analysis and discover the location of the 5.4 Mbp S-allelic region along with candidate genes responsible for controlling buckwheat heteromorphic self-incompatibility [127].…”

Genetic basis of maturity time is independent from that of flowering time and contributes to ecotype differentiation in common buckwheat (Fagopyrum esculentum Moench)

“…(1) GRAS-Di mapping-based genotyping with Buckwheat Genome DataBase (BGDB) [28] as a reference, (2) GRAS-Di mapping-based genotyping with 'Dasha' [29] as a reference, and (3) GRAS-Di co-dominant genotyping (GRAS-Di-CDG) in Cross A (Table 1). Because the total number of usable markers and average marker distance of the GRAS-Di-CDG system were better than those of both mapping-based genotyping systems, we used the GRAS-Di-CDG system to construct linkage maps in Crosses A and B_1.…”

“…Because the GRAS-Di system mainly provides information for dominant genotyping, GRAS-Di combined with a mapping-based genotyping method applied to a high-quality reference genome is reportedly efficient for obtaining information for co-dominant genotyping, constructing a linkage map, and detecting quantitative trait loci (QTLs) [26,27]. Although a draft genome sequence (N50 = 25 kb, 387,594 scaffolds) [28] and a recently published reference genome of the Russian cultivar 'Dasha' (N50 = 188 kb, 85,178 scaffolds) [29] are available for buckwheat, the large number of scaffolds hampers mapping-based analysis.…”