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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We have identified the <it>Rni </it>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 <it>Rni </it>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 <it>Rni </it>locus and is on Linkage Group (LG) 09 of the apple genome.</p> <p>Conclusion</p> <p>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 <it>Rni</it>. We have shown that the transcription factor MdMYB10 may be the gene underlying <it>Rni </it>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.</p

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.)

The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial cultivars at a very early stage. Thus GS has the potential to accelerate breeding efficiency significantly because of decreased generation interval or increased selection intensity. We evaluated the accuracy of GS in a population of 1120 seedlings generated from a factorial mating design of four females and two male parents. All seedlings were genotyped using an Illumina Infinium chip comprising 8,000 single nucleotide polymorphisms (SNPs), and were phenotyped for various fruit quality traits. Random-regression best liner unbiased prediction (RR-BLUP) and the Bayesian LASSO method were used to obtain GEBV, and compared using a cross-validation approach for their accuracy to predict unobserved BLUP-BV. Accuracies were very similar for both methods, varying from 0.70 to 0.90 for various fruit quality traits. The selection response per unit time using GS compared with the traditional BLUP-based selection were very high (>100%) especially for low-heritability traits. Genome-wide average estimated linkage disequilibrium (LD) between adjacent SNPs was 0.32, with a relatively slow decay of LD in the long range (r2 = 0.33 and 0.19 at 100 kb and 1,000 kb respectively), contributing to the higher accuracy of GS. Distribution of estimated SNP effects revealed involvement of large effect genes with likely pleiotropic effects. These results demonstrated that genomic selection is a credible alternative to conventional selection for fruit quality traits

Estimates of SNP effects (in additive genetic standard deviation) obtained using Bayesian LASSO for various traits: Fruit firmness (FF); Soluble solids (SSC); Russet; Weighted cortex intensity (WCI); Astringency (AST); Titratable acidity (TA).

<p>Effects are shown for each linkage group (LG: 1 to 17) across the genome.</p

Relative size of linkage groups (LG) (assuming the genome size of 1300 cM), and the number of single nucleotide polymorphisms (SNPs) retained on each LG after various quality checks.

<p>The average distance and the maximum distance between adjacent SNP pairs are also shown for each LG.</p

Relative efficiency of GEBV-based selection compared with the conventional BLUP-based selection for various traits: fruit firmness (FF), soluble solids (SSC), russet, weighted cortex intensity (WCI), astringency (AST), titratable acidity (TA).

<p>Estimates of narrow-sense heritability (<i>h</i>²) are also shown for each trait.</p>*<p>Estimated correlation was outside parameter space (>1.0), so constrained to 1.0.</p

Average linkage disequilibrium (LD) measured as <i>r</i>², for pairs of single nucleotide polymorphisms (SNPs) in increments of 10,000 bp, according to the distance between SNPs.

<p>Average linkage disequilibrium (LD) measured as <i>r</i>², for pairs of single nucleotide polymorphisms (SNPs) in increments of 10,000 bp, according to the distance between SNPs.</p

Distribution of linkage disequilibrium (LD), measured with <i>r</i>², among adjacent single nucleotide polymorphisms (SNPs) pairs in the training population.

<p>Distribution of linkage disequilibrium (LD), measured with <i>r</i>², among adjacent single nucleotide polymorphisms (SNPs) pairs in the training population.</p

Relationship between single nucleotide polymorphisms (SNPs) effects obtained from RR-BLUP and Bayesian LASSO for various traits.

<p>A: Fruit firmness (FF), soluble solids (SSC), and Russet; B: Weighted cortex intensity (WCI), astringency (AST), and titratable acidity (TA).</p

Average predicted accuracy (correlation) and bias (regression) of Bayesian LASSO (BL) and RR-BLUP methods for various traits: fruit firmness (FF), soluble solids (SSC), russet, weighted cortex intensity (WCI), astringency (AST), titratable acidity (TA).

<p>Standard errors are shown in parentheses.</p