Bulked Segregant Analysis Coupled with Whole-Genome Sequencing (BSA-Seq) Mapping Identifies a Novel pi21 Haplotype Conferring Basal Resistance to Rice Blast Disease

Abstract

Basal or partial resistance has been considered race-non-specific and broad-spectrum. Therefore, the identification of genes or quantitative trait loci (QTLs) conferring basal resistance and germplasm containing them is of significance in breeding crops with durable resistance. In this study, we performed a bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) to identify QTLs controlling basal resistance to blast disease in an F2 population derived from two rice varieties, 02428 and LiXinGeng (LXG), which differ significantly in basal resistance to rice blast. Four candidate QTLs, qBBR-4, qBBR-7, qBBR-8, and qBBR-11, were mapped on chromosomes 4, 7, 8, and 11, respectively. Allelic and genotypic association analyses identified a novel haplotype of the durable blast resistance gene pi21 carrying double deletions of 30 bp and 33 bp in 02428 (pi21-2428) as a candidate gene of qBBR-4. We further assessed haplotypes of Pi21 in 325 rice accessions, and identified 11 haplotypes among the accessions, of which eight were novel types. While the resistant pi21 gene was found only in japonica before, three Chinese indica varieties, ShuHui881, Yong4, and ZhengDa4Hao, were detected carrying the resistant pi21-2428 allele. The pi21-2428 allele and pi21-2428-containing rice germplasm, thus, provide valuable resources for breeding rice varieties, especially indica rice varieties, with durable resistance to blast disease. Our results also lay the foundation for further identification and functional characterization of the other three QTLs to better understand the molecular mechanisms underlying rice basal resistance to blast disease.

Fine Mapping and Candidate Gene Identification of a White Flower Gene BrWF3 in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

“…BSA-seq has been widely deployed for mapping agronomical traits in crops (Wang et al, 2017;Lee et al, 2020;Liang et al, 2020). In most cases, the genes controlling the target agronomic traits are located on the candidate regions detected by BSA-seq analysis.…”

Rapid identification of mutations caused by fast neutron bombardment in Medicago truncatula

“…In order to identify the associated deletions linked to the mutants’ phenotypes, the mutants are usually backcrossed to the wild-type plants. Backcrossing not only purifies the background, but also creates a segregating population that can be used for Bulked Segregant Analysis coupled with Whole-Genome Sequencing (BSA-Seq) [ 16 , 17 ]. For BSA-Seq, if the F 1 plants show wild-type like phenotype and the ratio of mutant to wild-type like phenotype is 1:3 in F 2 progeny, then the mutant is likely to be recessive.…”

Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis

“…Michelmore et al (1991) for the first time used the BSA method to screen three markers closely associated with the downy mildew resistance gene DM5/8 in an isolated lettuce population. With the development of high-throughput sequencing technology, BSA-seq analysis has been applied in wheat (Yin et al, 2018), soybean (Song et al, 2017), tomato (Zhao et al, 2016), rice (Ma et al, 2018;Liang et al, 2020), groundnut (Pandey et al, 2017), pepper (Lee et al, 2020), and cotton (Chen et al, 2015;Zhu et al, 2017;Zhao et al, 2018) for the rapid mining of QTLs and screening of candidate genes. However, the method has not been used in research related to VW resistance of cotton.…”