Assessing the Effect of Phenotyping Scoring Systems and SNP Calling and Filtering Parameters on Detection of QTL Associated with Reaction of Brassica napus to Sclerotinia sclerotiorum

Abstract

The polyploid nature of canola (Brassica napus) represents a challenge for the accurate identification of single nucleotide polymorphisms (SNPs) and the detection of quantitative trait loci (QTL). In this study, combinations of eight phenotyping scoring systems and six SNP calling and filtering parameters were evaluated for their efficiency in detection of QTL associated with response to Sclerotinia stem rot, caused by Sclerotinia sclerotiorum, in two doubled haploid (DH) canola mapping populations. Most QTL were detected in lesion length, relative areas under the disease progress curve (rAUDPC) for lesion length, and binomial-plant mortality data sets. Binomial data derived from lesion size were less efficient in QTL detection. Inclusion of additional phenotypic sets to the analysis increased the numbers of significant QTL by 2.3-fold; however, the continuous data sets were more efficient. Between two filtering parameters used to analyze genotyping by sequencing (GBS) data, imputation of missing data increased QTL detection in one population with a high level of missing data but not in the other. Inclusion of segregation-distorted SNPs increased QTL detection but did not impact their R2 values significantly. Twelve of the 16 detected QTL were on chromosomes A02 and C01, and the rest were on A07, A09, and C03. Marker A02-7594120, associated with a QTL on chromosome A02 was detected in both populations. Results of this study suggest the impact of genotypic variant calling and filtering parameters may be population dependent while deriving additional phenotyping scoring systems such as rAUDPC datasets and mortality binary may improve QTL detection efficiency.

Genome-Wide Association Mapping and Genomic Prediction for Adult Stage Sclerotinia Stem Rot Resistance in Brassica Napus (L) Under Field Environments

“…1d). The diversity of phenotypic responses observed in this study is consistent with observations made by other researchers [18][19][20]22,24 and reinforce the notion that resistance to sclerotinia infections is quantitatively inherited and controlled by multiple genes. The combENV BLUEs of the top ve promising source of resistance ranged between 2.6 to 4.2 cm for LL, from 23.7 to 40.6% for LW, and had between 2 to 10% PM_14D, and between 16 to 37% PM_21D.…”

“…To mimic the natural sclerotinia infections on rapeseed/canola plants, we used agar-plug stem inoculation method to challenge the plants. This screening method has been implemented successfully by other researchers for the effective identi cation of SSR resistance 20,24,62 . Plants were inoculated during the owering, because this is the most prevalent stage for SSR infection in natural eld conditions 22 .…”

“…Since, plant mortality is directly related to yield performance, therefore it may be necessary to record plant mortality in addition to the other associated traits for sclerotinia phenotyping. Plant mortality has successfully been used by Shahoveisi et al 24 . Li et al 62 evaluated 42 B. napus and 12 B. juncea genotypes for SSR resistance for PM at 21 dpi under eld conditions and did not nd any signi cant differences among the genotypes.…”

“…In this study, we used S. sclerotiorum isolate WM031 for all inoculations. This isolate has been used in previous studies because of its high virulence to canola 24 . The isolate was cultured on autoclaved potato dextrose agar medium (24 gL -1 potato dextrose broth and 1.5 gL -1 agar) at 22-24℃ for 48h.…”

“…QTL mapping using bi-parental populations have detected several QTLs for SSR resistance, and the majority of them located on chromosomes A09, C02, and C06. However, in very few instances common markers have been detected in different mapping populations 24 , which makes it di cult to identify the overlapping QTLs. The availability of the B. napus reference genome sequence 25 offers an opportunity to determine the physical location of the previously identi ed QTLs by aligning the QTL primers with the B. napus genome.…”