Genome-wide association study and Genomic Prediction of spot blotch disease in wheat (Triticum aestivum L.) using genotyping by sequencing

Abstract

Background Spot blotch caused by Bipolaris sorokiniana is a major constraint in wheat production in tropics and subtropics. There is limited information available on GWAS and study on genomic prediction is completely lacking. To reveal the genetic markers associated with disease resistance, we performed a genome-wide association study (GWAS) for spot blotch disease in 141 spring wheat lines. Results Based on the testing under natural infection in three years at hot spots location in Pusa, India and Jamalpur, Bangladesh, the genotypes showed significant genetic variation for disease severity. Using Genotyping-by-Sequencing (GBS) based 18637 polymorphic SNP markers and phenotyping from diverse environments, we identified 23 genomic regions across the genome ( p < 0.001) on 14 chromosomes associated with disease scores. Consistent with the previous reports, a most stable genomic region on chromosome 2B, 5B and 7D were detected across the environments. The new genomic region on chromosome 3D was also identified. We performed functional annotation with wheat genome assembly annotation (IWGSC Ref Seq v1.0) and identified NBS-LRR and 35 other plant defense-related protein families across multiple chromosome regions. Using a five-fold cross-validation scheme, we observed moderate prediction accuracy for 3 of 4 environments indicated that our model was able to successfully capture the quantitative variation underlying the SB variation in our population. Conclusions The GWAS based on the phenotypic data from PUSA India and BARI Bangladesh resulted in a total of 23 genomic regions on 14 chromosomes. The new genomic region appeared on chromosome 3D associated with Zinc finger protein that play important role in plant disease resistance. The genomic prediction model for spot blotch disease resistance in wheat was tested and obtained moderate prediction accuracy.

New QTLs for Spot Blotch Disease Resistance in Wheat (Triticum aestivum L.) Using Genome-Wide Association Mapping

“…The technical support provided by Manish Kumar, Dr. Prashanth N. Suravajhala, and Dr. Raj Kumar Jat is duly acknowledged. This manuscript has been released as a pre-print at ( https://www.researchsquare.com/article/rs-13392/v1 ), [ Tomar et al (2020) Genome-wide association study and genomic prediction of spot blotch disease in wheat ( Triticum aestivum L.). doi: 10.21203/rs.2.22818/v1].…”

Potential of Genomic Selection and Integrating “Omics” Data for Disease Evaluation in Wheat

“…Besides enhancing prediction accuracy, GS + GWAS does not require additional data because the same phenotypic and genotypic data set is used, and it can be more accessible to breeders as it does not require extensive knowledge of the underlying genetics of a trait of interest [68]. The benefits of integrating GWAS with GS to further improve the accuracy of GS in wheat are confirmed for rusts [69,70], Septoria tritici blotch [71,72], and yield [73]. Particularly, Daetwyler et al [69] and Rutkoski et al [70] demonstrated the advantage of including markers linked to large to moderate effect genes or loci previously found to affect the traits of interest.…”

Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat

“…Another 141 spring wheat lines were collected for GWAS on spot blotch resistance. A total of 23 genomic loci were identified, including several stable QTLs on chromosomes 2B, 5B, and 7D, and a novel QTL on chromosome 3D ( Tomar et al, 2020 ).…”