ORIGINAL PAPER 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 & Md. Zain Abdullah # Springer-Verlag 2012 Abstract A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC 2 F 2 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 micro- satellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map gen- erated 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 map- ping (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 BC 2 F 2 fami- lies, 26 advanced backcross breeding lines (BC 2 F 5 ) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC 2 F 3 and BC 2 F 4 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 BC 2 F 5 generation whereas 29 QTLs were detected in BC 2 F 2 generation of the same pop- ulation. 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 BC 2 F 5 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. Keyword Backcross breeding . Composite interval mapping . Oryza rufipogon . Oryza sativa . QTL identification . QTL validation . Trait-based marker analysis Introduction The Asian cultivated rice (Oryza sativa L.) is an economically important crop that is a staple food for more than one-half of the world’ s population. The world’ s rice production is inade- quate and has been on a plateau in recent years despite many advances in conventional rice breeding. Domestication and later on intensive breeding have further caused a genetic bottleneck of modern rice cultivars. The wild relatives in the genus Oryza represent a valuable source of novel genetic variation in rice that can be used to broaden the genetic background of cultivated rice in breeding programs (Brar and Khush 1997; Tanksley and McCouch 1997). Inter- specific hybridization of genetically divergent parents offers a way of widening the gene pool of cultivated rice and R. Wickneswari (*) : M. A. R. Bhuiyan : L. S. Lim : M. K. Narimah School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia e-mail: wicki@ukm.my S. Kalluvettankuzhy K. Jawaharlal Nehru Tropical Botanic Garden & Research Institute (JNTBGRI), Palode, Thiruvananthapuram 695562, India M. J. Thomson Crop and Environmental Sciences Division, International Rice Research Institute, Los Baños, Laguna, Philippines M. Z. Abdullah Universiti Malaysia Terengganu (UMT), 21030 Kuala Terengganu, Terengganu, Malaysia Plant Mol Biol Rep DOI 10.1007/s11105-011-0404-4