Gene presence-absence variation associates with quantitative Verticillium longisporum disease resistance in Brassica napus

Abstract

Andreas von tiedemann 2 , Rod J. Snowdon 1 & christian obermeier 1* Although copy number variation (CNV) and presence-absence variation (PAV) have been discovered in selected gene families in most crop species, the global prevalence of these polymorphisms in most complex genomes is still unclear and their influence on quantitatively inherited agronomic traits is still largely unknown. Here we analyze the association of gene PAV with resistance of oilseed rape (Brassica napus) against the important fungal pathogen Verticillium longisporum, as an example for a complex, quantitative disease resistance in the strongly rearranged genome of a recent allopolyploid crop species. Using Single Nucleotide absence Polymorphism (SNaP) markers to efficiently trace PAV in breeding populations, we significantly increased the resolution of loci influencing V. longisporum resistance in biparental and multi-parental mapping populations. Gene PAV, assayed by resequencing mapping parents, was observed in 23-51% of the genes within confidence intervals of quantitative trait loci (QTL) for V. longisporum resistance, and high-priority candidate genes identified within QTL were all affected by PAV. The results demonstrate the prominent role of gene PAV in determining agronomic traits, suggesting that this important class of polymorphism should be exploited more systematically in future plant breeding. Duplication of genes followed by diversification is a common process shaping the evolution of plant species by natural and artificial (breeding) selection 1. Genes can be duplicated by different mechanisms, including tandem duplication, transposon-mediated duplication, segmental duplication, or in the most extreme form by whole-genome duplication (WGD) or polyploidization. WGD is common in the evolutionary history of many wild and cultivated plant species. Different terms have been used frequently to describe short-and long-range genomic duplication and genome structural variation (SV), a term originally defined in reference to insertions, deletions and inversions greater than 1 kb in size 2-4. In contrast to small-scale insertion-deletion (InDel) polymorphisms, which are generally defined as small insertions or deletions of a few nucleotides (up to 50 bp), SV in the size range of genes (up to a few kb) can give rise to copy number variation (CNV) or presence/absence variation (PAV). The latter is an extreme form of CNV where fragments in the size range of genes are missing from the genomes of some investigated genotypes. Genes affected by duplications, InDels, CNVs and PAVs in diploid and polyploid plant species have been linked to local adaptation of wild populations 5 and to important agronomical traits in crops 1,3,6-8 for example flowering time and vernalization requirement in oilseed rape 9,10 and wheat 11 , abiotic stress tolerance in wheat 12,13 and biotic stress tolerance in tobacco 14. However, the strong impact of CNV and other forms of SV in polyploid crop genomes on evolution and trait selection was not recognized until the las...

The Genetic Basis of Tomato Aroma

“…For example, SV-based linkage mapping can be applied by genotyping mapping populations using SV markers that showed polymorphism in the parental lines [193]. Furthermore, SV studies may help to get more insight in the mechanisms leading to a certain phenotype [26,65,194,195], pinpointing the best donors for a certain allele cross. By providing a comprehensive set of candidate genes for tomato aroma, our review may guide researchers and breeders in the selection of the most interesting genes that can be investigated for structural variation.…”

Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

“…Gabur et al . (2020) reported gene presence–absence variations (PAV) in 23 to 51% genes within confidence intervals of QTL for V. longisporum resistance in B. napus . In a third case study related to a prominent disease resistance in oilseed rape, we investigated the impact of SV in resistance‐related genes co‐localizing with QTL for quantitative disease resistance in a bi‐parental cross between the sequenced accessions Express 617 and R53.…”

Optimization of the genotyping‐by‐sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

“…In particular, cape gooseberry represents a mixed-ploidy genome as has been shown by classic cytogenetic analyses [2,51]. In addition, the use of intermediate stringent parameters (mnLCov: 0.5 and mnScov: 0.7) was useful to decrease the missing data and the underestimation of diversity because of the presence-absence variations [52,53]. As a consequence, the selected intermediate strict parameters had a reliable effect on population clustering, as was verified by the grouping of the 95 technical replicates with high genetic distance congruence (70%).…”