Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple

Abstract

Background: Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes.

Results: We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome.

Conclusion: We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species.

Figure 1

Co-segregation between the MdMYB10 marker and red core and foliage. The marker developed for MdMYB10 (indel) was screened over a subset of the A194 population (16 individuals) and both parents. Lanes 1 and 20, and lanes 2 and 19 correspond to the parents 'Sciros' and 91.136 B6-77, respectively. Three phenotypes were observed for fruit flesh colouration in the progeny: a/red cortex and core (lanes 3 to 6); b/white core and red cortex (lanes 7 to 10); c/white cortex and core (lanes 11 to 18). All the fruit with red core were borne on red foliage trees and showed a 786 bp band for the MdMYB10 marker, the two other types are green-leafed and lacked the 786 bp band. A 1,182 bp PCR product was used as a positive control for PCR amplification. 1 Kb Plus DNA ladder (Invitrogen, Carlsbad, CA, USA) was run alongside the PCR products.

Figure 2

Genetic map of apple linkage group 09 showing the position of Rni and MdMYB10. The genetic maps of 'Discovery' (left) [36] and 91.136 B6-77 (right) aligned with three common microsatellite markers (green). Rni (red) and MdMYB10 (blue) are located at the bottom of the linkage group. NZms_EB115198 is unpublished (E. Rikkerink, S. Gardiner, K. Zuiderdin, D. Chagné, J-M. Celton).