Abstract
Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools. We utilized a wild Brassicaceae species with excellent resistance against stem rot to develop a set of B. juncea - B. fruticulosa introgression lines (ILs). These were assessed for resistance using a highly reproducible stem inoculation technique against a virulent pathogen isolate. Over 40% of ILs showed higher levels of resistance. IL-43, IL-175, IL-215, IL-223 and IL-277 were most resistant ILs over three crop seasons. Sequence reads (21x) from the three most diverse ILs were then used to create B. juncea pseudomolecules, by replacing SNPs of reference B. juncea with those of re-sequenced ILs. Genotyping by sequencing (GBS) was also carried out for 88 ILs. Resultant sequence tags were then mapped on to the B. juncea pseudomolecules, and SNP genotypes prepared for each IL. Genome wide association studies helped to map resistance responses to stem rot. A total of 13 significant loci were identified on seven B. juncea chromosomes (A01, A03, A04, A05, A08, A09 and B05). Annotation of the genomic region around identified SNPs allowed identification of 20 candidate genes belonging to major disease resistance protein families, including TIR-NBS-LRR class, Chitinase, Malectin/receptor-like protein kinase, defensin-like (DEFL), desulfoglucosinolate sulfotransferase protein and lipoxygenase. A majority of the significant SNPs could be validated using whole genome sequences (21x) from five advanced generation lines being bred for Sclerotinia resistance as compared to three susceptible B. juncea germplasm lines. Our findings not only provide critical new understanding of the defensive pathway of B. fruticulosa resistance, but will also enable development of marker candidates for assisted transfer of introgressed resistant loci in to agronomically superior cultivars of crop Brassica.
Highlights
Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools
Many of these marker trait associations (MTA’s) were consistent across crop seasons and explained significant phenotypic variation (7.34% to 16.04%), and helped to predict 20 candidate genes belonging to major disease resistance protein families
Continuous phenotypic variations for stem rot resistance confirmed the quantitative nature of Sclerotinia stem rot resistance in B. juncea - B. fruticulosa introgression lines (ILs)
Summary
Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools. High levels of disease resistances are present in genetically diverse wild allies of the family Brassicaceae such as Erucastrum gallicum, Capsella bursa-pastoris, E. cardaminoides, Diplotaxis tenuisiliqua, B. fruticulosa and B. oleracea Many of these have been utilized in recent research into stem rot resistance in B. napus and B. juncea[16,17,18]. This generated large numbers of marker trait associations (MTA’s) and highlighted 49 significant SNPs corresponding to thirteen loci on chromosomes A01, A03, A04, A05, A08, A09 and B05 Many of these MTA’s were consistent across crop seasons and explained significant phenotypic variation (7.34% to 16.04%), and helped to predict 20 candidate genes belonging to major disease resistance protein families. We discuss how discovery of such novel SNP marker associations to Sclerotinia stem rot resistance will facilitate novel candidates contributing to mustard immune response, but will enable development of breeder-friendly markers for assisted introgression of resistant loci into agronomically superior cultivars of crop Brassica against Sclerotinia stem rot
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