Heading date is one of the most important quantitative traitsresponsible for the domestication of rice. We compared a 155kb reference segment of the O. sativa ssp. japonica cv. Nipponbaregenome surrounding Hd1, a major heading date gene in rice, toorthologous regions from nine diploid Oryza species that divergedover a relatively short time frame (16 MY) in order to studysequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare andcontrast the evolution in a more distant relative of rice. Consistentwith other observations at the adh1/adh2, monoculm1 and sh2/a1loci in grass species we found high gene colinearity in the Hd1 region amidst size differences that were lineage-specificand LTR-retrotransposon driven. Unexpectedly, the Hd1 gene wasdeleted in O. glaberrima, while the O. rufipogon and O. punctatacopies had degenerative mutations, suggesting that other headingdate loci might compensate for the loss or non-functionalityof Hd1 in these species. Compared to the japonica Hd1 region,the orthologous region in sorghum exhibited micro-rearrangementsincluding gene translocations, seven additional genes and agene triplication and truncation event predating the divergencefrom Oryza.

Key Words: Comparative genomics • microsynteny • genome evolution • transposons

 

Heading date is one of the most important quantitative traitsresponsible for the domestication of rice. We compared a 155kb reference segment of the O. sativa ssp. japonica cv. Nipponbaregenome surrounding Hd1, a major heading date gene in rice, toorthologous regions from nine diploid Oryza species that divergedover a relatively short time frame (16 MY) in order to studysequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare andcontrast the evolution in a more distant relative of rice. Consistentwith other observations at the adh1/adh2, monoculm1 and sh2/a1loci in grass species we found high gene colinearity in the Hd1 region amidst size differences that were lineage-specificand LTR-retrotransposon driven. Unexpectedly, the Hd1 gene wasdeleted in O. glaberrima, while the O. rufipogon and O. punctatacopies had degenerative mutations, suggesting that other headingdate loci might compensate for the loss or non-functionalityof Hd1 in these species. Compared to the japonica Hd1 region,the orthologous region in sorghum exhibited micro-rearrangementsincluding gene translocations, seven additional genes and agene triplication and truncation event predating the divergencefrom Oryza.

Key Words: Comparative genomics • microsynteny • genome evolution • transposons

 

Heading date is one of the most important quantitative traitsresponsible for the domestication of rice. We compared a 155kb reference segment of the O. sativa ssp. japonica cv. Nipponbaregenome surrounding Hd1, a major heading date gene in rice, toorthologous regions from nine diploid Oryza species that divergedover a relatively short time frame (16 MY) in order to studysequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare andcontrast the evolution in a more distant relative of rice. Consistentwith other observations at the adh1/adh2, monoculm1 and sh2/a1loci in grass species we found high gene colinearity in the Hd1 region amidst size differences that were lineage-specificand LTR-retrotransposon driven. Unexpectedly, the Hd1 gene wasdeleted in O. glaberrima, while the O. rufipogon and O. punctatacopies had degenerative mutations, suggesting that other headingdate loci might compensate for the loss or non-functionalityof Hd1 in these species. Compared to the japonica Hd1 region,the orthologous region in sorghum exhibited micro-rearrangementsincluding gene translocations, seven additional genes and agene triplication and truncation event predating the divergencefrom Oryza.

Key Words: Comparative genomics • microsynteny • genome evolution • transposons