Genetic diversity of the genus Malus and implications for linkage mapping with SNPs

Abstract

Knowledge about the sequence-based genetic diversity of a crop species is important in order to develop highly informative genotyping assays, which will eventually positively impact breeding practice. Diversity data were obtained from two pools of 185 and 75 accessions each, representing most of the species belonging to the genus Malus, by re-sequencing 27 gene-specific amplicons and by screening 237 Malus × domestica SNPs using the multiplex genotyping technology SNPlex™. Nucleotide diversity and insertion/deletion rates in M. × domestica were estimated as π=0.0037 and 1/333 bp, respectively. The SNP frequency was estimated as 0.0194 (1 SNP/52 bp) while within a single apple cultivar an average of one SNP in every 455 bp was found. We also investigated transferability (T SNP ) of the heterozygous state of SNPs across the species M. × domestica and the genus Malus. Raw re-sequencing showed that 12-15% of M. × domestica SNPs are transferable to a second M. × domestica cultivar, however T SNP rose to ∼41% with SNPs selected for high minor allele frequency. T SNP of chosen SNPs averaged ∼27% in the two M. × domestica-related species, Malus sieversii and Malus sylvestris, but was much lower in more distantly related species. On the basis of T SNP , simulations, and empirical results, we calculated that a close-design, multiplexed genotyping array with at least 2,000 SNPs is required for building a highly saturated linkage maps within any M. × domestica cross. The same array would gradually lose informativeness in increasingly phylogenetically distant Malus species.

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

“…Although, probabilistically, the expected proportion between transitions and transversions is 1:2, a bias towards transitions is frequently observed, probably as a consequence of greater purifying selection against transversions (Keller et al 2007) that may vary for different organisms (Strandberg and Salter 2004). The transition/transversion ratio observed here (1.77) is similar to that observed in grape (1.56 by Salmaso et al 2004 and1.46 by Lijavetzky et al 2007) and potato (1.5 by Simko et al 2006) and higher than that observed in apple (1.27 by Micheletti et al 2011). The number of polymorphic sites in polymorphic loci (including SNPs and indels) varied from one to six, with an average of 2.3 (Table 4).…”

“…2). This contrasts with allele frequencies observed in species more variable than peach, such as apple, with 26-42 % of alleles with MAF>0.2 after re-sequencing two different sets of M. x domestica germplasm (Micheletti et al 2011). Our results suggest that a large proportion of the SNPs discovered on sequencing peach occidental germplasm will be useful for association mapping purposes, where MAF is usually set at ≥5 %, as well as for inclusion in large-scale genotyping platforms, where only robust SNPs are desired.…”

“…Nucleotide variation was observed in seven out of the 23 sequenced fragments (30 %), with 14 SNPs and two indels, corresponding to one SNP every 598 bp and one indel every 4,189 bp. As expected, variability in non-coding regions was higher than in coding regions (Ching et al 2002;Lijavetzky et al 2007;Micheletti et al 2011), with one SNP every 390 non-coding bp versus one in 1,850 bp in coding DNA. According to these data, the proportion of fragments found with at least one polymorphism is much lower than that in other species also subjected to bottlenecks and strong selection, such as sugarcane where sequencing projects have found 86-94 % of the fragments (depending on the sample set) to be polymorphic (Bundock et al 2009).…”

Towards genomic selection in apple (Malus × domestica Borkh.) breeding programmes: Prospects, challenges and strategies

“…Sequencing of the complex heterozygous genome of the apple cultivar 'Golden Delicious' ) has led to the discovery of many thousands of DNA polymorphisms (about 4.4 single nucleotide polymorphisms (SNPs) per kilobase (kb)). Some other recent reports indicated an occurrence of one SNP every 149 bp within coding sequences of 'Royal Gala' , and one SNP every 52 bp in the wider Malus germplasm (Micheletti et al 2011). A practical goal of sequencing was to accelerate the breeding of this economically important perennial crop species.…”

Identification of SNPs linked to eight apple disease resistance loci

“…Research was initiated to define the position of resistances that had not been fine-mapped satisfactorily (Rvi2, Rvi4 and Rvi11), and to develop cost-effective genetic markers for high-throughput screening of all the resistances listed. For this last purpose, SNP markers seemed most suitable because of their high frequency (between 4.5 and 20 markers/ kbp) in the apple genome (Velasco et al 2010;Micheletti et al 2011) and coupled with the availability of technologies enabling the simultaneous genotyping from a few to thousands of markers per DNA sample. The resistance genes Rvi6, Rvi15, Pl2 and FB_MR5 have been cloned in the last decade (Belfanti et al 2004;Schouten et al 2014;Rikkerink et al 2007;Broggini et al 2014), while for FB_E, positional cloning is in progress (Parravicini et al 2011).…”