Copy Number Variation among Resistance Genes Analogues in Brassica napus

Abstract

Copy number variations (CNVs) are defined as deletions, duplications and insertions among individuals of a species. There is growing evidence that CNV is a major factor underlining various autoimmune disorders and diseases in humans; however, in plants, especially oilseed crops, the role of CNVs in disease resistance is not well studied. Here, we investigate the genome-wide diversity and genetic properties of CNVs in resistance gene analogues (RGAs) across eight Brassica napus lines. A total of 1137 CNV events (704 deletions and 433 duplications) were detected across 563 RGAs. The results show CNVs are more likely to occur across clustered RGAs compared to singletons. In addition, 112 RGAs were linked to a blackleg resistance QTL, of which 25 were affected by CNV. Overall, we show that the presence and abundance of CNVs differ between lines, suggesting that in B. napus, the distribution of CNVs depends on genetic background. Our findings advance the understanding of CNV as an important type of genomic structural variation in B. napus and provide a resource to support breeding of advanced canola lines.

Pan-genome of pear provides insights into the fruit quality traits differentiation between Asian and European pears

“…Our high-quality genome assemblies also enable a comprehensive structural variation discovery among genomes of different pear species, leading to the identification of 6,341 highconfident SVs (7 inversions, 15 translocations, 3,989 deletions, and 2,330 insertions). Along with previous studies of Brassicaceae (Dolatabadian et al, 2022) and soybean (Bayer et al, 2021), we found that deletions detected in Pco, Pdr and PsbF genomes result in a complete loss of two copies of disease-resistance related genes, reflecting the differentiation of disease resistance in pear species. Hence, these two high-quality reference genomes provide valuable genomic resources for detecting genomic variations in diverse pear species.…”

“…This inverted region contains 27 gene models in the PsbM genome, including two proline-serine-threonine phosphatase-interacting protein genes ( PsbM013G02206 and PsbM013G02206 ) functionally associated with cell division and chromosome partitioning and located in the inversion breakpoint at around 119Kb distance from the distal breakpoint ( Table S9 ). Moreover, deletions and insertions were reported to be related to adaptation to varying pathogen pressures within different growing environments (Dolatabadian et al, 2022; Hu et al, 2022; Zmienko et al, 2014). In this study, we identified that 2 insertions and 9 deletions were overlapped with the exon regions of genes which were functionally associated with disease resistance ( Table S9 ).…”

Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies

“…In rice, the CNV of 28 functional genes was identified to be involved in insect resistance and response to salt stress 43 . In Brassica napus , 563 resistance genes experienced 1137 CNV events including 704 deletions and 433 duplications 46 . Based on the phylogenetic clustering, a total of 43 HIS1 genes were further clustered into five subclasses including HIS1 (9), HSL1 (4), HSL2 (5), HSL3 (9), and HLS4 (16) (Fig.…”

Duplicated Copy Number Variant of the Maize 9-Lipoxygenase ZmLOX5 Improves 9,10-KODA-Mediated Resistance to Fall Armyworms

“…The growing evidence indicates that CNVs are among the major reasons for maize phenotypic diversity [27]. CNVs result from the genomic rearrangements that lead to gains or losses of DNA segments [28,29]. In our search for a superior ZmLOX5 locus, we have sequenced around 1.3 Kb of the ZmLOX5 gene spanning the last two exons in close to 400 inbred lines that represent the maize diversity panel [30].…”