Genomic Variation in Rice: Genesis of Highly Polymorphic Linkage Blocks during Domestication

Abstract

Genomic regions that are unusually divergent between closely related species or racial groups can be particularly informative about the process of speciation or the operation of natural selection. The two sequenced genomes of cultivated Asian rice, Oryza sativa, reveal that at least 6% of the genomes are unusually divergent. Sequencing of ten unlinked loci from the highly divergent regions consistently identified two highly divergent haplotypes with each locus in nearly complete linkage disequilibrium among 25 O. sativa cultivars and 35 lines from six wild species. The existence of two highly divergent haplotypes in high divergence regions in species from all geographical areas (Africa, Asia, and Oceania) was in contrast to the low polymorphism and low linkage disequilibrium that were observed in other parts of the genome, represented by ten reference loci. While several natural processes are likely to contribute to this pattern of genomic variation, domestication may have greatly exaggerated the trend. In this hypothesis, divergent haplotypes that were adapted to different geographical and ecological environments migrated along with humans during the development of domesticated varieties. If true, these high divergence regions of the genome would be enriched for loci that contribute to the enormous range of phenotypic variation observed among domesticated breeds.

Molecular Evolution of thePi-taGene Resistant to Rice Blast in Wild Rice (Oryza rufipogon)

“…Some genes of this group show a hybrid pattern possibly caused by introgression (Tang et al 2006;Rakshit et al 2007). Two groups of highly diversified haplotypes have consistently been identified in the 10 selected unlinked loci of the AA-genome group of Oryza.…”

“…Two groups of highly diversified haplotypes have consistently been identified in the 10 selected unlinked loci of the AA-genome group of Oryza. This was suggested to have been caused by recent admixture, possibly as a result of human migration coupled with evolving agricultural practices (Tang et al 2006). Two groups of divergent haplotypes also occurred in the Pi-ta gene in O. rufipogon and O. barthii (Figures 1 and 2).…”

“…Furthermore, recent surveys of genomewide polymorphism in O. rufipogon also showed that the data do not fit standard neutral models. Examples such as the average 10 reference genes (Tang et al 2006), 9 of 10 nuclear loci (Zhu et al 2007), and 111 randomly chosen gene fragments (Caicedo et al 2007) all had negative Tajima's D values (Table 6). There is a systematic shift across the genome toward lower-than-expected allelic frequencies, further supporting the scenario of population expansion.…”

“…Tang et al (2006) also reported an average p silent of 0.00583 for 10 reference loci of O. rufipogon. This lowvariation average is comparable with that of O. sativa, which has a nucleotide diversity (p silent ) in the range of 0.0011-0.0035 (Tang et al 2006;Zhu et al 2007). The nucleotide polymorphism of the coding region (p ¼ 0.00089) was shown to be much lower than that of the noncoding region (p ¼ 0.00345, Table 3).…”

Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte

“…Geneticists are just now beginning to understand the consequences of domestication and breeding history of a crop species (Hamblin et al 2006;Hyten et al 2006;Tang et al 2006). One such consequence is that useful genetic variation may have been lost during the domestication process.…”