Rice Genetics IV - IRRI books - International Rice Research Institute

Naturally occurring allelic variationsas a new resource for functionalgenomics in riceM. YanoRecent progress in rice genome analysis has made it possible to analyzenaturally occurring allelic variation underlying complex traits. Using headingdate as a model for complex traits, we detected and characterized quantitativetrait loci (QTLs) and identified genes at QTLs at the molecular level. QTLsfor heading date were mapped by using several types of progeny derived froma cross between varieties Nipponbare and Kasalath. Nine QTLs were mappedprecisely as single Mendelian factors by the use of advanced backcross progeny.Nearly isogenic lines of QTLs were also developed by marker-assistedselection and were used to identify the function of each detected QTL. Combiningtwo QTLs into the genetic background of Nipponbare allowed us toinvestigate epistatic gene interactions among QTLs. We analyzed a large segregatingpopulation by genetic and physical mapping to narrow down candidategenomic regions for target QTLs. These analyses revealed 10- to 50-kbregions as candidate regions for the target genes. We identified genes of themost probable candidates for the photoperiod-sensitivity loci Hd1 and Hd6.Naturally occurring allelic variation could be a new resource for the functionalanalysis of rice genes.Structural analysis of the rice genome has progressed much in the past decade. Morethan 40,000 expressed sequence tags (ESTs) have been sequenced and deposited inthe public DNA databases (Sasaki et al 1994, Yamamoto and Sasaki 1997). Moreover,a high-density restriction fragment length polymorphism (RFLP) linkage map hasbeen constructed and about 60% genome coverage of yeast artificial chromosome(YAC) clone contigs has been achieved (Harushima et al 1998, Kurata et al 1997).This progress has allowed us to embark on the sequencing of the whole rice genome(Sasaki and Burr 2000). Resources—genetic markers, sequence data, and genomicclones—derived from such efforts will be used for the functional analysis of ricegenes in the next decade. Although artificially induced variations, such as mutants,have been used mainly for genetic and physiological studies in rice and other plantspecies, the development of DNA markers has allowed access to naturally occurringallelic variations underlying complex traits (Tanksley 1993, Paterson 1995, Yano andNaturally occurring allelic variations as a new resource . . . 227