In silico integration of disease resistance QTL, genes and markers with the Brassica juncea physical map

Abstract

Brassica juncea (AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences for B. juncea has made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be identified by co-localization with genetically mapped disease resistance quantitative trait loci (QTL). Here we identify and characterise disease resistance gene analogs (RGAs), including nucleotide-binding site–leucine-rich repeat (NLR), receptor-like kinase (RLK) and receptor-like protein (RLP) classes, and investigate their association with disease resistance QTL intervals. The molecular genetic marker sequences for four white rust (Albugo candida) disease resistance QTL, six blackleg (Leptosphaeria maculans) disease resistance QTL and BjCHI1, a gene cloned from B. juncea for hypocotyl rot disease, were extracted from previously published studies and used to compare with candidate RGAs. Our results highlight the complications for the identification of functional resistance genes, including the duplicated appearance of genetic markers for several resistance loci, including Ac2(t), AcB1-A4.1, AcB1-A5.1, Rlm6 and PhR2 in both the A and B genomes, due to the presence of homoeologous regions. Furthermore, the white rust loci, Ac2(t) and AcB1-A4.1, mapped to the same position on chromosome A04 and may be different alleles of the same gene. Despite these challenges, a total of nine candidate genomic regions hosting 14 RLPs, 28 NLRs and 115 RLKs were identified. This study facilitates the mapping and cloning of functional resistance genes for applications in crop improvement programs.

In silico prediction and analysis of transmembrane‐coiled‐coil resistance gene analogues in 27Brassicaceaespecies

“…The TM-CC positions in Brassica crop genomes were compared with known disease resistance QTLs in Brassica crops to identify possible candidate genes. The number of colocalized TM-CCs here were smaller compared to the identified colocalized RGAs (RLPs, RLKs and NLRs) in previous disease resistance QTLs in Brassicaceae crops (Bayer et al, 2019;Dolatabadian et al, 2020;Fu et al, 2019;Inturrisi et al, 2022;Stotz et al, 2018). This is probably because TM-CCs do not have a subtype compared to NLRs with seven subtypes and RLKs and RLPs with three subtypes each (Li et al, 2016).…”

“… a 1, Stotz et al (2018); 2, Inturrisi et al (2022); 3, Lee et al (2015); 4, Ferdous, Hossain, Park, Kim, et al (2020); 5, Hossain et al (2020); 6, Ferdous, Hossain, Park, Robin, et al (2020); 7, Ferdous et al (2019); 8, Chang et al (2019); 9, Yang et al (2021); 10, Raman et al (2021). …”

“…sativa species underwent WGT (Beilstein et al, 2010; Kagale, Koh, et al, 2014; Liu et al, 2014; Lysak et al, 2005). Tandem duplication is probably a factor for the clustering of TM‐CCs here and other RGAs or cloned disease R gene homologues in Brassicaceae crops (Cantila, Neik, et al, 2022; Cantila, Thomas, et al, 2022; Fu et al, 2019; Inturrisi et al, 2022; Yang et al, 2020) as these genes have common resistance domains (Leister, 2004; Michelmore & Meyers, 1998). The clustering of genes with resistance domains opens opportunity to identify novel R genes.…”

Supporting crop plant resilience during climate change

“…Genetic markers are heritable and abundantly distributed throughout a genome. During genomics‐assisted breeding, the identification of genetic markers and other variations is essential to perform downstream analyses, such as linkage mapping, QTL analysis, and association studies, thereby identifying genes of interest to assist breeding (Inturrisi et al., 2022). Different methods are applied to facilitate the identification of genotypes, among which genotyping by sequencing (GBS) has been increasingly used.…”

Selection of Powdery Mildew Resistant Brassica Genotypes Based on Disease Indexing and Microsatellite Markers

“…Mustard is susceptible to disease attacks owing to the genetic homogeneity among all grown types [22]. "Among various biotic factors responsible for severe yield loss in mustard powdery mildew causes serious damage worldwide" [23,24].…”