2024-03-29T05:30:30Zhttps://eprints.lib.hokudai.ac.jp/dspace-oai/requestoai:eprints.lib.hokudai.ac.jp:2115/843382022-11-17T02:08:08Zhdl_2115_20046hdl_2115_138A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traitsHirakawa, HidekiToyoda, AtsushiItoh, TakehikoSuzuki, YutakaNagano, Atsushi J.Sugiyama, SuguruOnodera, Yasuyukispinachresistance gene analoguesbolting timingfruit/seed shape610Spinach (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.Oxford University PressJournal Articlehttp://hdl.handle.net/2115/843381340-2838DNA Research283dsab0042021-06enginfo:doi/10.1093/dnares/dsab004none