Rice Genetics IV - IRRI books - International Rice Research Institute

tion of the parental lines; (3) enforced massive gene flow through maximum introductionof diversity from the primary rice gene pool into elite genetic backgrounds bybackcrossing and phenotypic selection and developing many sets of near-isogenicintrogression lines (NIILs) in the elite genetic backgrounds; (4) simultaneous identification,mapping, and transfer of large numbers of desirable QTLs for target traitsusing DNA markers and the NIILs; (5) development of new improved cultivars andlarge numbers of near-isogenic line sets for the core rice germplasm by using markeraidedQTL pyramiding; and (6) establishment of a molecular and phenotypic databasefor core rice germplasm.Future perspectivesWe conclude that QTLs are real and may include different kinds of genes or groups ofgenes that have varied and appreciable effects on complex phenotypes. Informationon QTL epistasis and QE interactions is particularly lacking, thus limiting the applicationof the results from past QTL mapping efforts to MAS for genetic improvementof quantitative traits. In addition, major challenges remain regarding what genes underliebiochemical pathways and the physiology causing quantitative trait variation,even though a couple of successful cases in QTL cloning have been reported (Yano etal 2000, Zamir et al 2000). Fortunately, several recent developments in rice genomeresearch will provide tremendous opportunities to solve these problems. These includecomplete physical maps of the rice genome, DNA sequence data of almost allrice expressed sequence tags (genes), and the complete genomic sequence data ofindividual rice chromosomes and the whole rice genome. The immediate results ofthese developments are new high-throughput functional genomic tools such asmicroarray and gene chips for large-scale gene expression studies and the availabilityof a virtually unlimited number of PCR-based DNA markers (SSRs and SNPs) coveringthe whole rice genome. All of these developments prophesy a golden era of ricefunctional genomics to connect DNA sequences to gene functions and to phenotypes,and applying this to rice improvement. Nevertheless, fine-QTL mapping and accuratephenotyping using unique genetic stocks such as near-isogenic lines will remainvital elements for the discovery and full understanding of the genes underlying biochemicalpathways and physiology related to complex phenotypes.ReferencesAllard RW. 1988. Future directions in plant population genetics, evolution and breeding. In:International Symposium for Population Genetics and Germplasm Resources in Crop Improvement.Suppl. Vol.:9-18.Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC,Harrington SE, Second G, McCouch SR, Tanksley SD. 1994. Saturated molecular map ofthe rice genome based on an interspecific backcross population. Genetics 138:1251-1274.Cho YG, McCouch SR, Kuiper M, Kang MR, Pot J, Groenen JTM, Eun MY. 1998. Integratedmap of AFLP, SSLP, and RFLP markers using a recombinant inbred population of rice(Oryza sativa L.). Theor. Appl. Genet. 97:370-380.168 Zhi-Kang Li