Identification of quantitative trait loci for blast resistance in BC2F3 and BC2F5 advanced backcross families of rice

Genet. Mol. Res. 11 (3): 3277 - 3289

DOI: 10.4238/2012.September.12.11

Authors: H.A. Rahim, M.A.R. Bhuiyan, L.S. Lim, K.K. Sabu, A. Saad, M. Azhar, R. Wickneswari
Abstract:
Advanced backcross families derived from Oryza sativa cv MR219/O. rufipogon IRGC105491 were utilized for identification of quantitative trait loci (QTL) for blast resistance using simple sequence repeat markers. Two hundred and sixty-one BC2F3 families were used to construct a linkage map, using 87 markers, which covered 2375.2 cM of 12 rice chromosomes, with a mean density of 27.3 cM. The families were evaluated in a greenhouse for resistance to blast disease caused by pathotypes P7.2 and P5.0 of Magnaporthe oryzae. Five QTLs (qBL5.1, qBL5.2, qBL6.1, qBL8.1, and qBL10.1) for pathotype P5.0 and four QTLs (qBL5.3, qBL5.4, qBL7.1, and qBL8.2) for pathotype P7.2 were identified using the BC2F3 families. Another linkage map was also constructed based on 31 BC2F5 families, using 63 SSR markers, which covered 474.9 cM of 9 rice chromosomes, with a mean density of 8.01 cM. Five suggestive QTLs (qBL11.2, qBL11.3, qBL12.1, qBL12.2, qBL12.3) and one putative QTL (qBL2.1) were identified for pathotype P7.2. Also, seven suggestive QTLs (qBL1.1, qBL2.2, qBL4.1, qBL4.2, qBL5.3, qBL8.3, and qBL11.1) were detected for pathotype P5.0. We conclude that there is a non-race-specific resistance spectrum of O. rufipogon against M. oryzae pathotypes.

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Association Mapping in Plants

Association (linkage disequilibrium [LD]) studies represent a novel powerful approach to evaluate candidate genes regulating plant phenotype and identify alleles of key interest at these genes. It is based on correlation between gene sequence and plant performance for target traits, and represent a powerful approach to evaluate candidate genes regulating the plant phenotype.

This new technique takes into account the thousands of genes to evaluate for QTL effect and is a more efficient approach that does not require generation of segregating populations/large numbers of progeny. As it can utilize all of the historic recombination events in a diverse population of individuals it can generate higher resolution genetic maps and, is needed to complement current map based cloning methods.

Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219

Ratnam Wickneswari, M. A. R. Bhuiyan, Sabu Kalluvettankuzhy K., Li Sze Lim, Michael J. Thomson, Md. Kairudin Narimah and Md. Zain Abdullah

Abstract 
A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC2F2 population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16.2 cM, spanning 1,553.4 cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3.0). The O. rufipogon allele was favourable for 59% of QTLs detected through CIM. Of 261 BC2F2 families, 26 advanced backcross breeding lines (BC2F5) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC2F3 and BC2F4 generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC2F5 generation whereas 29 QTLs were detected in BC2F2 generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R 2 values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC2F5 population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization. [More details]

Keywords
Backcross breeding – Composite interval mapping – Oryza rufipogon – Oryza sativa – QTL identification – QTL validation – Trait-based marker analysis

Postdoc research: Improvement of rice yield through molecular breeding

ABSTRACT
This research was conducted to identify possible trait enhancing quantitative trait loci (QTLs) from common wild rice, Oryza rufipogon. Two hundred and sixty-six BC2F2 families were developed from an interspecific cross between O. rufipogon accession no. IRGC 105491 and O. sativa cv. ‘MR219’during 2002-2003. Field evaluation of the BC2F2 families for 18 yield and yield related traits was carried out in 2004 at Malaysian Agricultural Research and Development Institute, Seberang Perai. Ninety three SSR (simple sequence repeat) markers were used to create a genetic linkage map spanning the twelve rice chromosomes. Ninety one QTLs were detected by means of marker regression with a significance level of p < 0.01. Among the putative QTLs, 21 were significant and 70 were suggestive. QTLs having favourable effects were noticed for days to heading (decrease heading period up to 6%), grain filling (increased filled grains plant-1 up to 12%), grain yield (increased grain yield plant-1 up to 10%), resistance to bacterial leaf blight (increased resistance by 13%), and tolerance to brown planthopper infection (increased tolerance by 40%). Quantitative data analysis suggests that about 10% of the total of 266 BC2F2 families demonstrated nearly 27% higher yield potential in comparison to the parental cultivar ‘MR219’. This increase is mostly due to higher tillering ability which is characteristic of O. rufipogon. These families also showed a considerable increase in tolerance against bacterial leaf blight and brown plant hopper infestation. The selected BC2F2 families can offer an efficient source of genetic diversity for future breeding programmes. The study concludes that even though wild rice is inferior to most of the agronomic traits, they could positively contribute to the overall yield enhancement in cultivated rice.