An integrated peach genome structural variation map uncovers genes associated with fruit traits

Abstract

Background Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored. Results Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation. Conclusions The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.

A subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1γ, confers flat fruit abortion in peach by regulating sugar and starch metabolism

“…2b). Gene expression pattern was consistent with their genotypes, as fruit abortion trait was recessive [6,8]. As well, tissue speci c analysis showed that this gene was mostly expressed in seed and fruit ( Fig.…”

“…In order to elucidate the genetic basis for at fruit abortion, candidate gene identi cation was carried out. We have already identi ed a 1.67-Mb chromosome inversion co-segregated with at fruit shape and validated it in 336 peach accessions [8] (Fig. 2a).…”

“…It was reported that quite a few fruits could be abnormally mature with no seeds and cracking fruit phenotypes in these aborting at peach progenies [11]. In addition, overexpression the at shape gene, PpOFP1, did not result in fruit abortion in tomato [8] and Arabidopsis [12]. These results indicated that PpOFP1 was the at shape gene and the at fruit abortion trait should be controlled by the adjacent Af gene locus.…”

“…We have already analyzed the four genes around the two breakpoints of this inversion, and found that the expression levels of Prupe.6G290900 (PpOFP1, at fruit shape gene) and Prupe.6G323700 were both related to the allelic genotypes of at and round peach [8]. Given that the close position between at shape and at fruit abortion locus, and the recessive trait, Prupe.6G323700 was hypothesized as the candidate gene responsible for at fruit abortion, which was annotated as γ subunit of SNF1-related protein kinase.…”

How the pan-genome is changing crop genomics and improvement

“…Likewise, GWAS based on the graph soybean pan-genome identified a PAV associated with variation in seed luster [ 24 ]. In peach, candidate causative SVs for early fruit maturity, flesh color around the stone, fruit shape, and flat shape formation have also been observed [ 121 ]. However, our understanding of the importance of SVs to phenotypic trait variation is still in its infancy.…”