Rice Genetics IV - IRRI books - International Rice Research Institute

addition, some accessions of wild relatives have been used as donor parental lines todevelop chromosome segmental introgression lines at Kyushu University (Doi et al1997, Sobrizal et al 1999). A wide range of cross combinations will be very importantfor detecting naturally occurring allelic variations because wild relatives and ecotypesare adapted to specific environmental conditions and variations in genes give advantagesfor adaptation. We might find a wider range of allelic variation in these wildrelatives than in cultivated species.Future prospectsAlthough many mutants have contributed to our understanding of gene functions sofar, the application of mutational approaches in rice, compared with the model plantArabidopsis thaliana, is limited for several reasons, including large plant size, longlife cycle, and large seed size. As described in this chapter, the use of naturally occurringallelic variations will be an alternative resource for functional genomics in rice aswell as in Arabidopsis (Alonso-Blanco and Koornneef 2000).The use of naturally occurring allelic variations compared with mutational approacheshas several advantages. First, naturally occurring allelic variations may determinenot only the presence or absence of allele function but also leaky or weaklyfunctional alleles. This would be more informative for the analysis of an importantgene; for example, when the gene function is completely lost, the plant does not survive.Multicopy genes (redundant genes), whose function is always complementedby other members, cannot be easily analyzed by simple gene disruption analysis becausegenes with no or very small phenotypic effect cannot be analyzed genetically.On the other hand, various kinds of allele combinations of redundant genes will occurin the progeny of different ecotypes or wild relatives. Dramatic phenotypic changeswill be detected in this type of progeny, even if the frequency is very low. An exampleis gametic abortion causing seed sterility.Second, phenotype assays often require large-scale field or greenhouse experimentsand a long time period. Applications of these types of assays are limited tomutational approaches based on chemical, physical, and transposon mutagenesis. It iscurrently not possible to perform such large-scale assays on transgenic mutagenesis,such as T-DNA tagging or Ac/Ds mutagenesis. In contrast, the use of naturally occurringallelic variations needs the survey of only 100–200 lines or individuals from theprimary mapping population. This approach will be a very powerful strategy for analyzingyield performance, abiotic and biotic stress tolerance, eating and cooking qualities,and so on. Although the analysis of naturally occurring allelic variations hasseveral disadvantages compared with mutational analysis, such as small allelic differencesin phenotypes, the approach will complement mutational approaches in thefunctional analysis of rice genes.We are now employing this strategy to analyze several complex traits, such asseed shattering habit, plant height, seed size, and pollen sterility; tolerance for abioticstresses such as cold temperature and ultraviolet irradiation; and tolerance for nutrientimbalances. Only one cross combination has given us a wide range of resources for236 Yano