Identification of SNPs linked to eight apple disease resistance loci

Jänsch, Melanie; Broggini, Giovanni A. L.; Weger, J.; Bus, Vincent G. M.; Gardiner, Susan E.; Bassett, H.; Patocchi, Andrea

doi:10.1007/s11032-015-0242-4

Cited by 43 publications

(34 citation statements)

References 43 publications

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“…In the more studied crop, apple, an example of development of a set of reliable markers for MAS, SNPs, has been recently reported (Jänsch et al 2015). Eight loci, robustly associated with resistance to three diseases (apple scab, powdery mildew, and fire blight), were the focus of this work.…”

Section: Resultsmentioning

confidence: 99%

Genetic mapping and pyramiding of two new pear scab resistance QTLs

et al. 2015

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Scab is one of the major fungal diseases infecting pear trees, causing the greatest economic losses. Identifying and pyramiding scab resistance factors should help in breeding new resistant pear cultivars. We have identified and mapped two new pear resistance loci against the fungal pathogen Venturia pirina. The first locus, mapped both as a major gene and as a QTL, is located on linkage group (LG) 01 of the hybrid P3480, deriving from the European pear cultivar 'Wilder.' It colocalizes with the Vnk resistance gene found in the Asian pear cultivar 'Kinchaku' against Venturia nashicola. A second locus, mapped as a QTL, is located on LG04 of the interspecific cultivar 'Euras.' In a small 'Euras' 9 P3480 progeny, seven seedlings carrying the resistant alleles at both loci have been selected using SSR markers.

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Section: Resultsmentioning

confidence: 99%

Genetic mapping and pyramiding of two new pear scab resistance QTLs

et al. 2015

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“…A study investigating QTLs associated with bud phenology in apple identified a candidate E3 ubiquitin protein encoding gene present as a tandem array of 14 copies in 'Golden Delicious', making it a putative CNV [49]. More recently, a study that was performed to design SNP markers for eight major disease resistance loci, encountered two problems that can be explained by the occurrence of CNV in these regions [51]. Firstly, for the Rvi2, Rvi4 and Rvi11 loci conferring resistance to apple scab (Venturia inaequalis), the presence of paralogs made it difficult to design primers for the SNPs linked to the respective loci, which amplified alleles only at the specific region of interest, without coamplifying the paralogous sequences.…”

Section: Discussionmentioning

confidence: 99%

“…This would be expected if resistance were conferred by the insertion of a segment of DNA, which contains the SNPs that failed to amplify, and is absent from susceptible individuals [51].…”

Section: Discussionmentioning

confidence: 99%

“…A CNVR on chromosome 11 contains the likely location of the marker FBsnPl2-2, which co-segregates with this trait. This CNVR is located at positions 3,506,106 to 3,509,841 and contains a predicted R gene (MDP000021232) [51].…”

Section: Cnvr Co-location With Apple Qtlsmentioning

confidence: 99%

“…Seven R genes (MDP000057795, MDP0000478441, MDP0000522693, MDP0000563856, MDP0000466397, MDP0000458576, and MDP0000746482) are found within this cluster of CNVRs ( Figure 6 & Figure 7). Sequences linked to Rvi4/Vh4 [52] (KM105054) and Rvi15/Vr2 [53] (KM105120) for which genetic markers tightly linked to these resistances have been developed are located within this region [51].…”

Section: Cnvr Co-location With Apple Qtlsmentioning

confidence: 99%

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The distribution and impact of common copy-number variation in the genome of the domesticated apple,MalusxdomesticaBorkh

Boocock

Chagné

Merriman

et al. 2015

Preprint

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Background: Copy number variation (CNV) is a common feature of eukaryotic genomes, and a growing body of evidence suggests that genes affected by CNV are enriched in processes that are associated with environmental responses. Here we use next generation sequence (NGS) data to detect copy-number variable regions (CNVRs) within the Malus x domestica genome, as well as to examine their distribution and impact. Methods: CNVRs were detected using NGS data derived from 30 accessions of M. x domestica analyzed using the read-depth method, as implemented in the CNVrd2 software. To improve the reliability of our results, we developed a quality control and analysis procedure that involved checking for organelle DNA, not repeat masking, and the determination of CNVR identity using a permutation testing procedure. Results: Overall, we identified 876 CNVRs, which spanned 3.5 % of the apple genome. To verify that detected CNVRs were not artifacts, we analyzed the B-allele-frequencies (BAF) within a single nucleotide polymorphism (SNP) array dataset derived from a screening of 185 individual apple accessions and found the CNVRs were enriched for SNPs having aberrant BAFs (P < 1e-13, Fisher's Exact test). Putative CNVRs overlapped 845 gene models and were enriched for resistance (R) gene models (P < 1e-22, Fisher's exact test). Of note was a cluster of resistance gene models on chromosome 2 near a region containing multiple major gene loci conferring resistance to apple scab. Conclusion:We present the first analysis and catalogue of CNVRs in the M. x domestica genome. The enrichment of the CNVRs with R gene models and their overlap with gene loci of agricultural significance draw attention to a form of unexplored genetic variation in apple. This research will underpin further investigation of the role that CNV plays within the apple genome.

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