Identification of QTLs Containing Resistance Genes for Sclerotinia Stem Rot in Brassica napus Using Comparative Transcriptomic Studies

Abstract

Sclerotinia stem rot is a major disease in Brassica napus that causes yield losses of 10-20% and reaching 80% in severely infected fields. SSR not only causes yield reduction but also causes low oil quality by reducing fatty acid content. There is a need to identify resistant genetic sources with functional significance for the breeding of SSR-resistant cultivars. In this study, we identified 17 QTLs involved in SSR resistance in three different seasons using SNP markers and disease lesion development after artificial inoculation. There were no common QTLs in all 3 years, but there were three QTLs that appeared in two seasons covering all seasons with a shared QTL. The QTLs identified in the 2 years were SRA9a, SRC2a and SRC3a with phenotypic effect variances of 14.75 and 11.57% for SRA9a, 7.49 and 10.38% for SRC3a and 7.73 and 6.81% for SRC2a in their 2 years, respectively. The flowering time was also found to have a negative correlation with disease resistance, i.e., early-maturing lines were more susceptible to disease. The stem width has shown a notably weak effect on disease development, causing researchers to ignore its effect. Given that flowering time is an important factor in disease resistance, we used comparative RNA-sequencing analysis of resistant and susceptible lines with consistent performance in 3 years with almost the same flowering time to identify the resistance genes directly involved in resistance within the QTL regions. Overall, there were more genes differentially expressed in resistant lines 19,970 than in susceptible lines 3936 compared to their mock-inoculated lines, demonstrating their tendency to cope with disease. We identified 36 putative candidate genes from the resistant lines that were upregulated in resistant lines compared to resistant mock and susceptible lines that might be involved in resistance to SSR.

Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination

“…RNA-seq analysis can quickly identify differently expressed genes (DEGs) between different samples. Up to now, RNA-seq has facilitated the identification of DEGs in rapeseed under abiotic stresses such as drought [ 5 ], freezing [ 6 ] and salinity [ 7 ], as well as some candidate genes related to sclerotinia [ 8 ], seed aging [ 9 ], seed coat color [ 10 ], and flowering time [ 11 ]. Some studies on herbicide stress to plants were also carried out using RNA-seq.…”

Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement in Brassica juncea

“…They concluded that all QTLs worked cumulatively for disease and the lines having all three QTLs showed the highest resistant level. Qasim et al (2020) identified three major QTLs through comparative transcriptomic studies harboring 36 putative candidate genes from resistant B. napus lines that might actively involved in SSR resistance. Wu et al (2013) identified 10 and 3 QTLs for stem and leaf resistance in B. napus , respectively.…”

Status and advances in mining for blackleg (Leptosphaeria maculans) quantitative resistance (QR) in oilseed rape (Brassica napus)

“…In another study, the exaptation of a transposable element (TE) enabled a duplicated iron-stress gene (CYP82C2) to function in plant defence biosynthetic pathways (Barco et al 2019). Crosstalk between biotic and abiotic response pathways has been reported in Brassica-pathosystems, including blackleg (Tortosa et al 2019;Qasim et al 2020) and it is tempting to speculate that common genes in these pathways might have undergone exaptation to function from one stress condition to another. Gene exaptation presents an interesting view of how QR may have evolved in response to pathogen pressure.…”