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Hokkaido University Collection of Scholarly and Academic Papers >
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Peer-reviewed Journal Articles, etc >
A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits
| 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 |
| URI: | http://hdl.handle.net/2115/84338 |
| 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)
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