Identification and Characterization of a Large Effect QTL from Oryza glumaepatula Revealed Pi68(t) as Putative Candidate Gene for Rice Blast Resistance

Abstract

Background: Field resistance is often effective and durable as compared to vertical resistance. The introgression line (INGR15002) derived from O. glumaepatula has proven broad spectrum field resistance for both leaf and neck blast. Results: Quantitative Trait Loci (QTL) analysis of INGR15002, led to the identification of two major QTL-qBL3 contributing about 34% and 32% phenotypic variance towards leaf and neck blast resistance, respectively and qBL7 contributing about 25% of phenotypic variance for leaf blast. Further, qBL3 was fine mapped, narrowed down to 300 kb region and a linked SNP maker was identified. By combining mapping with microarray analysis, a candidate gene, Os03g0281466 (malectin-serine threonine kinase), was identified in the fine mapped region and named as Pi68(t). The nucleotide variations in the coding as well as upstream region of the gene was identified through cloning and sequence analysis of Pi68(t) alleles. These significant variations led to the non-synonymous changes in the protein as well as variations (presence/absence) in four important motifs (W-box element; MYC element; TCP element; BIHD1OS) at promoter region those are associated with resistance and susceptible reactions. The effect of qBL3 was validated by its introgression into BPT5204 (susceptible variety) through marker-assisted selection and progeny exhibiting resistance to both leaf and neck blast was identified. Further, the utility of linked markers of Pi68(t) in the blast breeding programs was demonstrated in elite germplasm lines. Conclusions: This is the first report on the identification and characterization of major effect QTL from O. glumaepatula, which led to the identification of a putative candidate gene, Pi68(t), which confers field resistance to leaf as well as neck blast in rice.

Marker Assisted Gene Pyramiding (MAGP) for bacterial blight and blast resistance into mega rice variety “Tellahamsa”

“…Estimated yield loss due to blast can be more than 50% when the disease occurs in epidemic proportions [12] and severe cases, it can reach up to 60-100% [13]. Till now, more than 100 distinctive blast resistance genes have been identified [14] and out of them, 21 genes have been cloned [15]. Two dominant resistance genes (Pi54 and Pi1) are known to confer resistance against the major virulent races of the pathogen in India and widely used by different research groups [16].…”

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

“…Molecular markers for genes Pi54, Pib, Piz, Piz-t, Pik, Pi-kh, Pik-p, PikmPik-h, Pita/Pita-2, Pi2, Pi9, Pi1, and Pi5 were utilized in this investigation. Recently in Oryza glumaepatula, characterization of a wide effect QTL showed Pi68(t) as a potential gene for field resistance and neck blast in rice (Devi et al, 2020). Another very recent study focused on the meta-analysis of QTL with multiple disease resistance in rice (Kumar and Nadarajah, 2020).…”

Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi

“…)显著关联位点, 这些位点都与染色体上已经 定位的基因(pi66(t) [43] (22.92 Mb~27.89 Mb)和 Pi68 [44] (9.33 Mb~9.78 Mb)在 3 号染色体上; Pi10 [45] (14.52…”