The haplotype-phased genome assembly facilitated the deciphering of the bud dormancy-related QTLs in Prunus mume.

Autor:	Hsiang TF; Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan., Yamane H; Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan., Yuan-Jui L; Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan., Sugimori M; Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan., Nishiyama S; Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan., Nagasaka K; Experimental Farm, Graduate School of Agriculture, Kyoto University, Kyoto 619-0218, Japan., Nakano R; Experimental Farm, Graduate School of Agriculture, Kyoto University, Kyoto 619-0218, Japan., Ryutaro T; Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
Jazyk:	angličtina
Zdroj:	DNA research : an international journal for rapid publication of reports on genes and genomes [DNA Res] 2024 Dec 04. Date of Electronic Publication: 2024 Dec 04.
DOI:	10.1093/dnares/dsae034
Abstrakt:	Bud dormancy is a vital physiological process in woody perennials, facilitating their adaptation to seasonal environmental changes. Satisfying genotype-specific chilling requirements (CR) and heat requirements (HR) through exposure to specific chilling and warm temperatures is essential for dormancy release and the subsequent resumption of growth. The genetic mechanisms regulating bud dormancy traits in Prunus mume remain unclear. In this study, we first assembled the genome of 'Nanko', the leading P. mume cultivar in Japan, in a haplotype-resolved manner. Using an F1 segregating population from a cross between 'Nanko' (high-chill) and 'SC' (low-chill), a cultivar adapted to subtropical conditions, we identified quantitative trait loci (QTLs) for vegetative bud dormancy traits on chromosome 4 (LG4 QTLs) in the 'Nanko' genome and for CR and HR on chromosome 7 (LG7 QTL) in the 'SC' genome. A notable 5.6 Mb chromosome inversion was overlapped with LG4 QTL interval in one of the 'Nanko' haplotypes. We also identified candidate genes based on haplotyping, differential expression between the parents or the presence of trait-correlated variants in coding regions. Notably, genes such as PmuMAIN, PmuNAC2, PmuDOG1, PmuSUI1, PmuATG8CL, PmubZIP44, and PmuSAUR50 were identified. This study provides valuable insights into the genetic regulation of vegetative bud dormancy in Prunus species. (© The Author(s) 2024. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)
Databáze:	MEDLINE
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