Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry

Abstract

SUMMARY Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of Prunus campanulata ‘Plena’ (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high‐quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome‐wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.

Chromosome-level genome assembly provides insights into the genetic diversity, evolution, and flower development of Prunus conradinae

“…To identify orthologous genes, the complete genome sequences of Atha (Zapata et al 2016 ), Parm (Groppi et al 2021 ), Pavi (Wang et al 2020b ), Pcam (Nie et al 2023 ), Pcer (Goeckeritz et al 2023 ), P. dulcis (Pdul; Alioto et al 2020 ), Pfru (Wöhner et al 2021 ), P. huminis (Phum; https://ngdc.cncb.ac.cn/search/?dbId=gwh&q=GWHBCKI00000000 ), Pmum (Zheng et al 2022 ), Pper (Tan et al 2021 ), Ppus (Jiu et al 2023 ), Pser (Yi et al 2020 ), Pyed (Baek et al 2018 ), Rosa chinensis (Rchi; Raymond et al 2018 ), and Vvin (Jaillon et al 2007 ) were retrieved for comparison with Pcon. Gene families were identified using OrthoFinder v.2.2.7 with default parameters.…”

“…The P. mume (Pmum) genome was sequenced and published in 2012, becoming the first Prunus fruit genome available (Zhang et al 2012 ). Subsequently, several genomes from subgenus Cerasus have been sequenced, including P. yedoensis (Pyed; Baek et al 2018 ), a Cerasus × yedoensis hybrid (“Somei-Yoshino”) (Shirasawa et al 2019 ), P. avium (Pavi; Wang et al 2020b ), C. serrulata (Yi et al 2020 ), P. fruticosa (Pfru; Wöhner et al 2021 ), P. pusilliflora (Ppus; Jiu et al 2023 ), and P. campanulata (Pcam; Nie et al 2023 ). These genomic resources have greatly enhanced our understanding of the origin, evolution, and genomic selection of Cerasus .…”

Genome-Wide Identified MADS-Box Genes in Prunus campanulata ‘Plena’ and Theirs Roles in Double-Flower Development

“…We downloaded the PCP genome data from the website http://tree-bio.hzau.edu.cn/ download/PCP/, accessed on 1 Fabruary 2022 [46]. Two strategies were used to identify the members of the MADS-box gene family in PCP.…”

Analysis on Genetic Diversity of 40 Flowering Cherry Cultivars and Construction of Molecular ID Based on SSR Markers

“…Cerasus, with 48 species and 10 varieties, accounting for nearly one-third of subg. Cerasus species [3] [4]. There are more than 300 cultivars in worldwide [5], about 70 cultivars are grown in China [6].…”