Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

Qiuping Tan,Dongmei Li,Wei Xiao,Ling Li,Yuzheng Zhang,Binbin Wen,Yong Wang,Shan Jiang,Xiude Chen,Sen Li,Min Chen,Xiling Fu,Hongyu Wu

doi:10.1038/s41438-021-00648-2

Abstract

Prunus species include many important perennial fruit crops, such as peach, plum, apricot, and related wild species. Here, we report de novo genome assemblies for five species, including the cultivated species peach (Prunus persica), plum (Prunus salicina), and apricot (Prunus armeniaca), and the wild peach species Tibetan peach (Prunus mira) and Chinese wild peach (Prunus davidiana). The genomes ranged from 240 to 276 Mb in size, with contig N50 values of 2.27−8.30 Mb and 25,333−27,826 protein-coding gene models. As the phylogenetic tree shows, plum diverged from its common ancestor with peach, wild peach species, and apricot ~7 million years ago (MYA). We analyzed whole-genome resequencing data of 417 peach accessions, called 3,749,618 high-quality SNPs, 577,154 small indels, 31,800 deletions, duplications, and inversions, and 32,338 insertions, and performed a structural variant-based genome-wide association study (GWAS) of key agricultural traits. From our GWAS data, we identified a locus associated with a fruit shape corresponding to the OVATE transcription factor, where a large inversion event correlates with higher OVATE expression in flat-shaped accessions. Furthermore, a GWAS revealed a NAC transcription factor associated with fruit developmental timing that is linked to a tandem repeat variant and elevated NAC expression in early-ripening accessions. We also identified a locus encoding microRNA172d, where insertion of a transposable element into its promoter was found in double-flower accessions. Thus, our efforts have suggested roles for OVATE, a NAC transcription factor, and microRNA172d in fruit shape, fruit development period, and floral morphology, respectively, that can be connected to traits in other crops, thereby demonstrating the importance of parallel evolution in the diversification of several commercially important domesticated species. In general, these genomic resources will facilitate functional genomics, evolutionary research, and agronomic improvement of these five and other Prunus species. We believe that structural variant-based GWASs can also be used in other plants, animal species, and humans and be combined with deep sequencing GWASs to precisely identify candidate genes and genetic architecture components.

Highlights

Introduction TheRosaceae family includes many genera with different types of fruit, of which the Prunus genus containsTan et al Horticulture Research (2021)8:213 species have considerable economic value, the genetic mechanisms underlying favorable traits are poorly understood
Genome assembly In this study, we de novo assembled the plum, Prunus mira, and Prunus davidiana genomes for the first time and improved the peach and apricot genomes by integrating single-molecule real-time (SMRT) long-read sequencing (PacBio), short high-quality Illumina paired-end sequencing, and Hi-C technology
The single nucleotide polymorphism (SNP)/indel and structural variants (SVs) datasets used for genome-wide association study (GWAS) were all analyzed (Fig. S8), we identified a small indel located upstream of the candidate Prupe.5G005400 gene that showed the strongest association with this trait, which is a different locus from the candidate reported by a previous study[17] and encodes a switch subunit three protein

Summary

Introduction

Tan et al Horticulture Research (2021)8:213 species have considerable economic value, the genetic mechanisms underlying favorable traits are poorly understood This lack of understanding is, to some extent, attributed to the scarcity of genomic resources, which severely limits efforts to improve Prunus crops, for plum, Prunus mira, and Prunus davidiana. Owing to their small genome sizes (~250 Mb) and relatively short juvenile periods (2−3 years), most of the aforementioned Prunus species are promising candidates for functional and evolutionary studies of the Rosaceae family, peach[1], which originated in China, was domesticated. The single nucleotide polymorphism (SNP)-based GWAS approach uses LD to relate the top associated SNPs to flanking genes and directly or indirectly identifies candidate genes and genetic architecture components[15]

Methods

Results

Conclusion