Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

Abstract

Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.

Draft genome sequence of an inbred line ofChenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties

“…As the first step of our quinoa genome project, we estimated the genome size using the frequency distribution curve of 17-mer obtained from Illumina short reads, as successfully reported in previous studies 35 , 65 . The k-mer frequency distribution curve (k-mer =17) using paired-ends (PEs) with a 185-bp insert size is shown in Supplementary Figure S1.…”

Important agronomic characteristics of yielding ability in common buckwheat; ecotype and ecological differentiation, preharvest sprouting resistance, shattering resistance, and lodging resistance

“…Furthermore, we consider that by fixing the photoperiod sensitivity genes, it is thought that ecotype breeding could be carried out more efficiently even in allogamous buckwheat. In recent years, data required for molecular breeding of common buckwheat, such as the draft genome (Yasui et al 2016), buckwheat genome database (http://buckwheat.kazusa.or.jp), and a high-density linkage map (Yabe et al 2014), have been used to increase the yielding ability by genomic selection (Yabe et al 2018). and several previous studies.…”

Development of co-dominant markers linked to a hemizygous region that is related to the self-compatibility locus (<i>S</i>) in buckwheat (<i>Fagopyrum esculentum</i>)

“…be a transcription factor, has been identified as a candidate gene for the I s or G gene; it is expressed only in the style of thrum plants and is linked to the S locus with no recombination in buckwheat (Yasui et al 2012). Using genome assembly analysis with next-generation sequencing (NGS), we have developed a buckwheat genome database (BGDB) and also found that the region that includes this locus is absent in the genome of pin plants (Yasui et al 2016). The S h alleles have a deletion of a nucleotide in the S-ELF3 locus, which causes a frame shift.…”

“…Because the region of the S-ELF3 locus is missing in the genome of s plants (Yasui et al 2016), we needed to detect the flanking regions of the S h alleles that would be present in the s genome. In this study, we used NGS analysis in combination with bulked segregant analysis of segregating progeny of a cross between SI and SC plants.…”