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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UKM Scientists Developed High Yielding Superior Red Rice

BANGI, 23 Feb. 2012 – After seven years of research UKM’s scientists with the cooperation of MARDI’s research officers have successfully produced a variety of rice which not only can increase padi yield but also has properties with low glycaemic index suitable for diabetics.

Its Plant Genetics and Biotechnology expert, from the Faculty of Science and Technology, Prof Dr. R. Wickneswari Ratnam assisted by some 14 other scientists from UKM, Malaysia Agricultural Research and Development Institute (MARDI), Universiti Putra Malaysia (UPM) , Malaysia Nuclear Agency (MNA) and UM had been doing research on this since 2002 and have succeeded in producing the new padi variant G33 named UKMRC9 which can increase local red rice production.

Prof Wickneswari described it as a superior red rice developed through conventional breeding involving controlled cross-breeding between cultivar MR219 and wild rice Oryza rufipogon. It involved the transfer of genes of the wild type to the common paddy produced by MARDI now extensively cultivated in the country.

She was assisted by Dr K K Sabu, Dr. Lim Li Sze, Dr. Atiqur Bhuiyan, Dr. Abdul Rahim Harun,  En. Parviz Fasahat, Puan Ngu Mee Siing, En. Abdullah M Zain, Puan Site Zuraini Abdul Rahman, Dr. Narimah Md Kairudin, Dr. Tilakavati Karupiah, Prof. Aminah Abdullah, Dr. Kharidah Muhammad, Chua Khun Aik and Tan Choon Heen in planning and carrying out the seven years of research.

In an interview with UKM News Portal, Prof Wickneswari said the cross-breeding was done manually. “We did not make any manipulation. We took pollen from the wild rice and pollinated it with the modern rice and used genetic markers to determine whether it was cross-bred or not.

“This was because there’s a possibility the cross-breeding did not materialise and we also wanted to know how much of the wild rice genes was transferred to the modern rice that we eat today,” she said.
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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

Development and evaluation of advanced backcross families of rice for agronomically important traits

ABSTRACT
Wild relatives of crop species may contain trait-enhancing genes. Our studies showed that grain yield in cultivated rice can be increased significantly using the genes found in common wild rice. Advanced backcross progenies (Oryza rufipogon IRGC105491 x O. sativa cv. MR219) exhibited higher values for most of the yield and yield-related traits analyzed in comparison to the cultivated parent, MR219. About 10% of the BC2F2 families exhibited 33.5% higher grain yield per plant in comparison to MR219. Even though there was an increase in empty grains per panicle, number of tillers per plant also increased considerably (41.5%). This resulted in higher grain yield per plant, which ranged from 52.4 to 77.5g for the selected families in contrast to 42.4g for MR219. Two families, viz., S163 and S165, were identified through GGE biplot analysis as most promising genotypes for cultivar development. The backcross families offer an efficient source of genetic diversity for future breeding programmes.

CITATION: Sabu, K.K., Abdullah, M.Z., Lim, L.S., Wickneswari, R. (2006). Development and evaluation of advanced backcross families of rice for agronomically important traits. Commun. Biometry Crop Sci. 1 (2), 111-123. 

Heritability and genetic variability in Oryza sativa x O. rufipogon cross

Analysis of heritability and genetic variability of agronomically important traits in Oryza sativa x O. rufipogon cross

Abstract
Heritability is a measure of possible genetic advancement under selection. Estimation of variance components could imply partitioning of genetic variability over different sources of variation. This article describes statistical methods applied and some of the observations made on results of heritability and analysis of environmental variances of grain yield and related traits of progenies derived from a cross between wild and cultivated rice. The study shed light on the genetic information of grain yield and related traits such as their heritability, genetic and environmental effects in the F1 progenies of a cross between O. sativa and O. rufipogon. A considerable amount of additive genetic variation was found in these families. The traits with high heritability, considerable phenotypic correlation and low seasonal variability can be used in further improvement of the F1 progenies. The results obtained were highly promising and can be utilized to develop new rice cultivars.

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Agronomy Research 7(1), 97-102, 2009

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.