HUSCAP logo Hokkaido Univ. logo

Hokkaido University Collection of Scholarly and Academic Papers >
Graduate School of Agriculture / Faculty of Agriculture >
Peer-reviewed Journal Articles, etc >

A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits

Files in This Item:

The file(s) associated with this item can be obtained from the following URL:

Title: A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits
Authors: Hirakawa, Hideki Browse this author
Toyoda, Atsushi Browse this author
Itoh, Takehiko Browse this author
Suzuki, Yutaka Browse this author
Nagano, Atsushi J. Browse this author
Sugiyama, Suguru Browse this author
Onodera, Yasuyuki Browse this author →KAKEN DB
Keywords: spinach
resistance gene analogues
bolting timing
fruit/seed shape
Issue Date: Jun-2021
Publisher: Oxford University Press
Journal Title: DNA Research
Volume: 28
Issue: 3
Start Page: dsab004
Publisher DOI: 10.1093/dnares/dsab004
Abstract: Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N-50 = 11.3Mb) with a low proportion of undetermined nucleotides (Ns= 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing similar to 73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.
Type: article
Appears in Collections:農学院・農学研究院 (Graduate School of Agriculture / Faculty of Agriculture) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Export metadata:

OAI-PMH ( junii2 , jpcoar_1.0 )

MathJax is now OFF:


 - Hokkaido University