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

Abstract

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.

Copy Number Variation in Domestication

“…The results of experimental evolution experiments suggest that CNVs contribute to the rapid adaptation associated with domestication and during population expansion of the domesticated species. Advances in detection methodologies (summarized in Box 1), reduced sequencing costs, and proliferation of sequencing data have expanded CNV studies, and CNVs have been described in most major crop plant species, including rice, maize, potato, soybean, barley, cucumber, melon, apple, and grapevine ( Table 1, Key Table) [ [29][30][31][32][33][34][35][36][37]. Not surprisingly, they have also been examined in domesticated animal species, such as silkworm, sheep, goat, pig, chicken, cow, horse, and dog (Table 1) [22,[38][39][40][41][42][43].…”

Copy number variation and disease resistance in plants

“…Copy number variations related to disease resistance have also been identified in several plant species (Table 2), where disease resistance genes represent a significant fraction of genes in CNV regions and were significantly enriched for resistance gene models (Xu et al 2012;Lu et al 2012). For instance, Boocock et al (2015) have identified 876 CNV regions, which spanned 3.5% of the apple genome and were enriched for genes involved in disease resistance against apple scab. Bertioli et al (2003) showed that in peanut and legumes R-genes have undergone extensive copy number variation.…”

A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits inPopulustrees

“…Data so far have focused mostly on domesticated crops of agricultural importance and suggest that although present over thousands of sites, naturally occurring CNV occurs more frequently in gene-poor regions (12) and usually only encompasses a small proportion of the genome. For instance, in apple, maize, and barley, natural CNV has been detected only in 3.5, 10, and 14.9% of the genome, respectively (6,13,14), and therefore does not provide the power to systematically survey the effect of gene dosage variation on plant function.…”