Genetic structure and diversity in Oryza sativa L.

The population structure of domesticated species is influenced by the natural history of the populations of predomesticated ancestors, as well as by the breeding system and complexity of the breeding practices exercised by humans. Within Oryza sativa, there is an ancient and well-established divergence between the two major subspecies, indica and japonica, but finer levels of genetic structure are suggested by the breeding history. In this study, a sample of 234 accessions of rice was genotyped at 169 nuclear SSRs and two chloroplast loci. The data were analyzed to resolve the genetic structure and to interpret the evolutionary relationships between groups. Five distinct groups were detected, corresponding to indica, aus, aromatic, temperate japonica, and tropical japonica rices. Nuclear and chloroplast data support a closer evolutionary relationship between the indica and the aus and among the tropical japonica, temperate japonica, and aromatic groups. Group differences can be explained through contrasting demographic histories. With the availability of rice genome sequence, coupled with a large collection of publicly available genetic resources, it is of interest to develop a population-based framework for the molecular analysis of diversity in O. sativa.

Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.).

To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice.

High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice ( Oryza sativa L.).

The xa5 resistance gene from rice provides recessive, race-specific resistance to bacterial blight of rice caused by the pathogen Xanthomonas oryzae pv oryzae. A high-resolution genetic map of the chromosomal region surrounding xa5 was developed by placing 44 DNA markers on the distal end of rice chromosome 5. The basis for mapping was a PCR-based screening of 1,016 F(2) individuals derived from a cross between a near-isogenic line (NIL) and its corresponding recurrent parent to identify recombinants in the region. Recombinant F(2) individuals were progeny tested using F(3) families inoculated with the Philippine strain PXO 61 of bacterial blight pathogen. The xa5 gene was mapped to a 0.5-cM interval between the markers RS7 and RM611, which spanned an interval of approximately 70 kb and contained a total of 11 open reading frames. Sequence data for the locus was generated from an Indica (the IR24 isoline, IRBB21) BAC covering part of the region and compared to other overlapping Indica (cv 93-11) and Japonica (cv Nipponbare) sequences. Candidate-gene analysis revealed that a basal transcription factor (TFIIa), an ABC transporter, a tRNA synthase, a MAP kinase and a cysteine protease, as well as four unknown, hypothetical or putative proteins, are encoded at the locus and could be potential candidates for the resistance gene product. The mechanism by which these genes could provide recessive, race-specific resistance will be elucidated by map-based cloning of the xa5 gene.