Decoding the genetic mechanisms underlying disease resistance is of great importance for crop improvement. Rice false smut (RFS) is a major fungal disease caused by Ustilaginoidea virens that hampers the grain quality and yield of rice worldwide. It causes 2.8-49% global yield loss depending upon disease severity and varieties grown. In India, the severity of yield loss ranged from 2-75%. Keeping the economic importance of this disease, identi cation of the genes/QTLs governing disease resistance is of prime importance for the development of the linked markers and cloning of the genes. Here, we report mapping of QTLs using a recombinant inbred line (RIL) population derived from a cross between resistant line, RYT2668, and a highly susceptible variety, PR116. The population was evaluated for rice false smut disease under eld conditions for three cropping seasons 2013, 2015, and 2016. A total of seven QTLs were mapped on rice chromosomes 2, 4, 5, 7, and 9 of rice using 2326 single nucleotide polymorphism (SNP) markers. Among them, a novel QTL qRFSr9.1 affecting total smut ball (TSB)/panicle on chromosome 9 exhibited the largest phenotypic effect. The prediction of putative candidate genes within the qRFSr9.1 spanned in 994.1Kb revealed four NBS-LRR domain-containing disease resistance proteins. We identi ed SNPs/Indels associated with the disease resistance which could be used for accelerating breeding programs using marker-assisted selection. In summary, our ndings mark the 'hot-spot' region on rice chromosomes along with the identi cation of disease resistance genes in conferring resistance to the rice false smut disease.
Brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most destructive pests of rice accounting for 52% of annual yield loss. Under severe conditions, BPH cause "hopper burn" leading to drying and lodging of the matured plant. Utilization of host-plant resistance from diverse germplasm is considered a cost-effective and environment-friendly approach for its management. The current study reports the identi cation and mapping of a novel source of resistance from wild species of rice O. ru pogon accession CR100441 against the BPH biotype 4. Genetic analysis was performed using 276 BC 2 F 2 and 233 BC 2 F 3 populations derived from a cross of O. ru pogon accession CR100441 and highly susceptible cultivar PR122. The segregation of susceptible to resistant plants 3:1 ratio (210:66, χ 2 c = 0.17 ≤ χ 2 0.05,1 = 3.84) indicates the presence of a single major recessive gene. Genotyping using polymorphic microsatellite markers between PR122 and O.ru pogon acc.CR100441 spanning all the 12 chromosomes of rice was done. A total of 537 SSR markers were used to map a BPH resistance gene (designated as bph42) on the short arm of chromosome 4 between RM16282 and RM16335. QTL analysis identi ed a peak marker RM16335 contributing 29% of the phenotypic variance at 40.76 LOD. This marker co-segregates with the bph42 which could be e ciently used for marker-assisted selection (MAS) to transfer the traits into elite rice cultivars.
Decoding the genetic mechanisms underlying disease resistance is of great importance for crop improvement. Rice false smut (RFS) is a major fungal disease caused by Ustilaginoidea virens that hampers the grain quality and yield of rice worldwide. It causes 2.8-49% global yield loss depending upon disease severity and varieties grown. In India, the severity of yield loss ranged from 2-75%. Keeping the economic importance of this disease, identification of the genes/QTLs governing disease resistance is of prime importance for the development of the linked markers and cloning of the genes. Here, we report mapping of QTLs using a recombinant inbred line (RIL) population derived from a cross between resistant line, RYT2668, and a highly susceptible variety, PR116. The population was evaluated for rice false smut disease under field conditions for three cropping seasons 2013, 2015, and 2016. A total of seven QTLs were mapped on rice chromosomes 2, 4, 5, 7, and 9 of rice using 2326 single nucleotide polymorphism (SNP) markers. Among them, a novel QTL qRFSr9.1 affecting total smut ball (TSB)/panicle on chromosome 9 exhibited the largest phenotypic effect. The prediction of putative candidate genes within the qRFSr9.1 spanned in 994.1Kb revealed four NBS-LRR domain-containing disease resistance proteins. We identified SNPs/Indels associated with the disease resistance which could be used for accelerating breeding programs using marker-assisted selection. In summary, our findings mark the ‘hot-spot’ region on rice chromosomes along with the identification of disease resistance genes in conferring resistance to the rice false smut disease.
Background Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by a soil-borne fungus Rhizoctonia solani Kühn (R. solani). It limits global rice productivity by causing ~50% yield loss every year. Broad host range, rapid resurgence of new pathogen races, and the lack of highly resistant germplasm are the major caveat to managing this disease. Therefore, continuous scouting of new germplasm resources resistance to R. solani is urgently required. Results In this report, we identified a very promising resistance source O. nivara accession IRGC81941A which displays partial resistance across the five years of screening against R. solani. Quantitative trait loci (QTL) mapping was performed in F2 populations that identified a total of 29 QTLs with the total phenotypic variance explained (PVE) ranged from 4.70 to 48.05%. A cluster of four QTL qRLH1.1, qRLH1.2, qRLH1.5, and qRLH1.8 stably detected which showed consistent resistant response against R. solani. The size of these QTL ranging from 0.096-420.1 Kb, based on the rice reference genome harboring several important disease resistant genes such as Ser/Thr protein kinase, auxin-responsive protein, Protease inhibitor/seed storage/LTP family protein, MLO domain-containing protein, disease responsive protein, Thaumatin-like protein, Avr9/Cf9 eliciting protein, and many transcription factors. A simple sequence repeat (SSR) marker RM212 co-segregates with this QTL cluster. Conclusion Our finding suggests that a highly stable QTL cluster confers resistance to sheath blight disease. Effective transferring of this cluster as a single unit through backcross breeding marked the identification of three agronomically superior resistant lines. These promising germplasms could be an important pre-breeding material for varietal development. PCR-based SSR marker linked to these QTLs could facilitate efficient transfer of the QTLs into rice cultivars through marker-assisted selection programs.
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