Pms1, a locus for photoperiod sensitive genic male sterility in rice, was identified and mapped to chromosome 7 in previous studies. Here we report an effort to identify the candidate genes for Pms1 by comparative sequencing of BAC clones from two cultivars Minghui 63 and Nongken 58, the parents for the initial mapping population. Annotation and comparison of the sequences of the two clones resulted in a total of five potential candidates which should be functionally tested. We also conducted com-parative analysis of sequences of these two cultivars with two other cultivars, Nipponbare and 93-11, for which sequence data were available in public databases. The analysis revealed large differences in sequence composition among the four genotypes in the Pms1 region primarily due to retroelement activity leading to rapid recent growth and divergence of the genomes. High levels of polymorphism in the forms of indels and SNPs were found both in intra- and inter-subspecific comparisons. Dating analysis using LTRs of the retroelements in this region showed that the substitution rate of LTRs was much higher than reported in the literature. The results provided strong evidence for rapid genomic evolution of this region as a consequence of natural and artificial selection.
YU JinSheng FAN YouRong LIU Nan SHAN Yan LI XiangHua ZHANG QiFa
Using a cDNA microarray consisting of 9198 expressed sequence tags,we surveyed the gene expression profiles in shoots and roots of a rice hybrid,Liangyoupei 9 and its parents Peiai 64s and 93-11 at 72 h after germination. A total of 8587 sequences had detectable signals in both shoots and roots of the three genotypes. A total of 1571 sequences exhibited significant (P<0.01) expression differences in shoots or roots among the three genotypes,of which 121 showed expression poly-morphisms in both shoots and roots,and 870 revealed significant expression differences between the hybrid and one of the parents. The expression polymorphism of the sequences was associated with the functional categories of the sequences. They occurred more frequently in categories of carbohy-drate,energy and lipid metabolisms and stress response than expected,while less frequently in categories of amino acid metabolism,transcription and translation regulation,and signal transduction. A total of 214 sequences exhibited significant (P<0.05) mid-parent heterosis in expression,of which 117 had homology to genes with known functions,assigned in the categories of basic metabolism,genetic information processing,cell growth and death,signal transduction,transportation and stress response. The results may provide useful information for exploring the relationship between gene expression polymorphism and phenotypic variation,and for characterizing the molecular mechanism of seedling development and heterosis in rice.
HUANG Yi LI Lihua CHEN Ying LI Xianghua XU Caiguo WANG Shiping ZHANG Qifa
