Characterization of Japanese Plum (Prunus salicina) PsMYB10 Alleles Reveals Structural Variation and Polymorphisms Correlating With Fruit Skin Color

Abstract

The red to blue hue of plant organs is caused due to anthocyanins, which are water-soluble flavonoid pigments. The accumulation of these pigments is regulated by a complex of R2R3-MYB transcription factors (TFs), basic-helix-loop-helix (bHLH), and WD-repeat (WDR) proteins (MBW complex). In Rosaceae species, R2R3-MYBs, particularly MYB10 genes, are responsible for part of the natural variation in anthocyanin colors. Japanese plum cultivars, which are hybrids of Prunus salicina, have high variability in the color hue and pattern, going from yellow-green to red and purple-blue, probably as a result of the interspecific hybridization origin of the crop. Because of such variability, Japanese plum can be considered as an excellent model to study the color determination in Rosaceae fruit tree species. Here, we cloned and characterized the alleles of the PsMYB10 genes in the linkage group LG3 region where quantitative trait loci (QTLs) for the organ color have been mapped to other Prunus species. Allele segregation in biparental populations as well as in a panel of varieties, combined with the whole-genome sequence of two varieties with contrasting fruit color, allowed the organization of the MYB10 alleles into haplotypes. With the help of this strategy, alleles were assigned to genes and at least three copies of PsMYB10.1 were identified in some varieties. In total, we observed six haplotypes, which were able to characterize 91.36% of the cultivars. In addition, two alleles of PsMYB10.1 were found to be highly associated with anthocyanin and anthocyanin-less skin. Their expression during the fruit development confirms their role in the fruit skin coloration. Here, we provide a highly efficient molecular marker for the early selection of colored or non-colored fruits in Japanese plum breeding programs.

PpMYB36 Encodes a MYB-Type Transcription Factor That Is Involved in Russet Skin Coloration in Pear (Pyrus pyrifolia)

“…Furthermore, pear cultivar breeding is a lengthy process, largely because the trees have long juvenile stages. The MAS approach would improve the efficiency of pear breeding ( Kumar et al, 2019 ; Fiol et al, 2021 ). The mapped region of the pear genome containing PpRus , which contains two PpRus -linked SSR marker loci, is useful for future pear breeding programs.…”

Research Progress on Genetic Basis of Fruit Quality Traits in Apple (Malus × domestica)

“…Comparative genomics analysis of 148 apple populations and a segregated hybrid population revealed that a gypsy-like long terminal repeat retrotransposon (designated redTE) was inserted 3297 bp upstream of MdMYB1 , thereby activating the expression of MdMYB1 and controlling the redness of the skin ( Figure 2A ; Zhang et al, 2019 ). In Japanese plums, high levels of variability in the intronic and intergenic regions of the MYB10 LG3 cluster were also closely associated with polymorphisms in their skin color ( Fiol et al, 2021 ). These results reveal the important function of MYB1 as a major gene in regulating fruit coloration, and its function is affected by extensive variation in gene regions and intergenic regions.…”

An efficient CRISPR-Cas9 enrichment sequencing strategy for characterizing complex and highly duplicated genomic regions. A case study in the Prunus salicina LG3-MYB10 genes cluster

“…The objective of this study was to evaluate the potential of CRISPR-Cas9 enrichment to identify the variability (in particular SV) in highly complex regions using a pool of DNA of highly diverse varieties. The region selected was the Japanese plum ( Prunus salicina ) MYB10 region located on linkage group 3 (LG3), found recently to contain at least three MYB10.1 ( MYB10.1a , MYB10.1b and MYB10.c ) genes, one MYB10.2 gene and one MYB10.3 gene, while additional copies could not be discarded [ 26 ]. A marker system designed in this region was able to characterize the LG3- PsMYB10 allelic organization in Japanese plum varieties and progenies into six haplotypes (H1 to H6), each with a different combination of the MYB10.1–3 alleles [ 26 ].…”