Rice Genetics IV - IRRI books - International Rice Research Institute

in rice. To this end, two high-density RFLP linkage maps were constructed to providea framework of markers for the detection of individual factors controlling complextraits (Causse et al 1994, Harushima et al 1998, reviewed by Nagamura et al 1997).Kurata et al (1997) have also achieved about 60% genome coverage of yeast artificialchromosome (YAC) clone contigs. P1-derived artificial chromosome (PAC) and bacterialartificial chromosome (BAC) libraries have also been constructed in rice genomesequencing activities (Sasaki and Burr 2000). These YAC, PAC, and BAC clonesare also very useful materials for developing region-specific genetic markers. Moreover,about 5,000 cDNA clones have already been mapped on YAC contigs that wereplaced on the genetic linkage map (Wu et al 2000). These cDNA clones can be used asa potential candidate for genetic markers in target chromosomal regions. Furthermore,the release of rice genome sequence data has begun (Sasaki and Burr 2000).Although completion of the sequencing of the rice genome will need additional efforts,the existing sequence data have already provided and will continue to providean effective basis for developing new region-specific genetic markers. These resourceswill become a launching pad for the analysis of naturally occurring allelic variationsin rice.Genetic dissection of complex traitsDetection of QTLs controlling heading dateWe have performed comprehensive analyses of heading date as a model trait for complextraits using the resources described above. Thirteen QTLs controlling headingdate have been identified by using several progeny derived from Nipponbare (japonica)and Kasalath (indica) (Fig. 2). Five QTLs, Hd1–Hd5, have been mapped based onanalysis of the F 2 population (Yano et al 1997) and an additional two, Hd7 and Hd11,have been detected by using BC 1 F 5 lines (Lin et al 1998). In addition, new loci involvingheading date—Hd6, Hd8–Hd10, Hd12, and Hd13—have been detected byusing advanced backcross progeny, such as BC 3 F 2 or BC 4 F 2 but not F 2 or BC 1 F 5(Yamamoto et al 2000, M. Yano, unpublished data). These results clearly indicate thatnot all factors involved in the target traits could be detected by using primary mappingpopulations, such as F 2 and recombinant inbred lines. One reason is the statisticallimitation of QTL analysis. It is often difficult to detect QTLs with small phenotypiceffects in the analysis of a primary population because of the noise of QTLswith a large effect or environmental variation (Tanksley 1993, Yano and Sasaki 1997).Another reason may be due to the existence of epistatic interaction among QTLs(Yamamoto et al 2000, Lin et al 2000). This point is described later.Fine mapping of QTLs using advanced backcross progenyBecause of the statistical nature of QTL analysis, the chromosomal location of a QTL isnot accurate and allows no information about the function of the genes. Populationsused in previous QTL analyses of rice were mainly F 2 , BCF 1 , recombinant inbred lines,or doubled-haploid lines (McCouch and Doerge 1995, Yano and Sasaki 1997). Thesepopulations, which segregate multiple genetic factors on the whole genome simulta-Naturally occurring allelic variations as a new resource . . . 229