Deletion of the miR172 target site in a TOE‐type gene is a strong candidate variant for dominant double‐flower trait in Rosaceae

Abstract

Double flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants, including Prunus persica (peach), a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in five segregating progenies delimited Di2 to an interval spanning 150 858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic resequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait, and we showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co-segregated with the phenotype in 621 progenies, accounting for the dominant inheritance of the Di2 locus. Further corroborating the results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double-flower roses. Phylogenetic analysis showed that these two genes belong to a TARGET OF EAT (TOE)-type clade not represented in Arabidopsis, indicating a divergence of gene functions between AP2-type and TOE-type factors in Arabidopsis and other species. The identification of orthologous candidate genes for the double-flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.

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

“…We found that the most significant association signals were almost in the same genome regions between the two datasets; however, GWAS using SV data link traits to large genome variations, which are more likely to alter gene functions. For the 11 qualitative traits analyzed in this study, candidate genes have been previously found for four of them, namely fruit hairiness [15], flesh color [14], double flower shape [16], and pendulous branches [17], and we also identified these candidate causal DNA variations using GWAS with the SV data (Additional file 2: Fig. S7, S8, S10, S12, Additional file 1: Table S12).…”

“…However, only a few studies in plants to date have described GWAS using SVs [8,32]. There is considerable evidence from peach genetic and molecular studies that SVs can cause major phenotypic variance [10,[15][16][17], suggesting that SVs may represent a valuable source of variation for GWAS in peach. In order to characterize causal SVs, GWAS were performed separately using SNPs and SVs (including small variations < 50 bp) with MAF > 0.01.…”

“…Furthermore, most GWAS analyses to date have been based on SNP data, while many phenotypes are associated with SVs. In peach, all reported genes that might be responsible for target traits have been associated with SVs [10,[15][16][17]. A pioneer study using SV data for GWAS in plants was reported in cucumber, where a large duplication controlling the reproductive morphology trait was detected [8].…”

“…Peach is the fourth largest deciduous fruit crop in the world (FAO, http://faostat.fao.org ) and is regarded as a model plant for the Rosaceae family, thanks to its small genome and relatively short juvenile period [ 13 ]. Linkage analysis in peach has identified candidate genes for traits such as fruit flesh color [ 14 ], fruit hairiness [ 15 ], fruit flesh texture [ 10 ], double flower shape [ 16 ], and pendulous branches [ 17 ]; however, the genetic basis of these and other agronomic traits still remains largely unexplored. Genome-wide association studies (GWAS) represent an efficient method for mapping candidate genes and have been applied in peach to identify genome regions and/or genes associated with important traits, using genome-wide single nucleotide polymorphism (SNP) data [ 18 – 20 ].…”

In the name of the rose: a roadmap for rose research in the genome era

“…Silencing it decreased the number of petals 90 . It was proposed that the insertion of a TE in the eight intron is responsible for transcription of a messenger RNA without a miR172 binding site, leading to a deregulation of the APETALA2/TOE homologue 91,92 .…”