Identification of QTLs and possible candidate genes conferring sheath blight resistance in rice (Oryza sativa L.)

Abstract

Sheath blight, caused by the pathogenic fungus Rhizoctonia solani Kühn, is one of the most devastating diseases in rice. Breeders have always faced challenges in acquiring reliable and absolute resistance to this disease in existing rice germplasm. In this context, 40 rice germplasm including eight wild, four landraces, twenty- six cultivated and two advanced breeding lines were screened utilizing the colonized bits of typha. Except Tetep and ARC10531 which expressed moderate level of resistance to the disease, none could be found to be authentically resistant. In order to map the quantitative trait loci (QTLs) governing the sheath blight resistance, two mapping populations (F2 and BC1F2) were developed from the cross BPT-5204/ARC10531. Utilizing composite interval mapping analysis, 9 QTLs mapped to five different chromosomes were identified with phenotypic variance ranging from 8.40 to 21.76%. Two SSR markers namely RM336 and RM205 were found to be closely associated with the major QTLs qshb7.3 and qshb9.2 respectively and were attested as well in BC1F2 population by bulk segregant analysis approach. A hypothetical β 1–3 glucanase with other 31 candidate genes were identified in silico utilizing rice database RAP-DB within the identified QTL region qshb9.2. A detailed insight into these candidate genes will facilitate at molecular level the intricate nature of sheath blight, a step forward towards functional genomics.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-0954-2) contains supplementary material, which is available to authorized users.

Identification, Mapping and Pyramiding of Genes/Quantitative Trait Loci (QTLs) for Durable Resistance of Crops to Biotic Stresses

“…Similarly, Klarquist et al [8] used 151 F 2:5 RIL populations to identify and map QTLs involved in stripe rust resistance in wheat. Moreover, Perchepied et al [20] mapped two new pear resistance loci using three F 1 segregating populations (182, 144 and 81). Hence, it is important to decide the appropriate mapping population size required in locating chromosomal position of trait of interest, and generally the larger (>100) the mapping population, the better the map resolution would be [55].…”

“…Perchepied et al [20] targeted to identify and map new pear resistance loci against the fungal pathogen Venturia. As a procedure, they developed three F 1 segregating populations derived from the cross of: (1) Ange´lys (scab susceptible) × P3480 (scab-resistant), (2) Euras (resistant) × P2896 (susceptible) and (3) Euras × P3480.…”

“…DNA markers tightly linked (<5 cM) to the desired gene ( Figure 8) serve as chromosomal landmark, 'signs' or 'flags' [17] to track the introgression of the desired gene in progenies in a cross i.e., identification of the marker indicates presence of the desired gene. The use of molecular marker technology in breeding to select progenies with the desired genes is called marker assisted selection (MAS), marker-assisted breeding or 'smart breeding' [20].…”

“…For instance, Yadav et al [19] identified and mapped nine QTLs associated with sheath blight resistance in rice using MAS. Similarly, Perchepied et al [20] identified and mapped two new pear resistance loci against the fungal pathogen Venturia pirina using MAS. Moreover, molecular markers are widely used for successful pyramiding of several resistance genes Identification, Mapping and Pyramiding of Genes/Quantitative Trait Loci (QTLs) for Durable Resistance of Crops to Biotic Stresses the production of some "signal" molecule called elicitors (pathogenassociated molecular patterns (PAMPs)).…”

Current Applicable DNA Markers for Marker Assisted Breeding in Abiotic and Biotic Stress Tolerance in Rice (Oryza sativa L.)

“…There are about 50 ShB resistance QTLs that have been mapped to all the 12 rice chromosomes and pyramiding of diverse ShB resistance QTLs could help achieve higher levels of resistance to ShB (Yadav et al 2015). One study showed pyramiding of ShB resistance, qSB-9TQ and tiller angle TAC1TQ resulted to NILs carrying both QTLs showing more resistance than the NILs containing only one of them (Zuo et al 2014).…”