We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
SNP deserts of Asian cultivated rice: genomic regions under domestication.
- Authors
Wang, L.; Hao, L.; Li, X.; Hu, S.; Ge, S.; Yu, J.
- Abstract
When performing a genome-wide comparison between indica (93-11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these ‘SNP deserts’, experimentally confirmed genes show increased Ka/ Ks that indicate adaptive selection. To further elucidate this connection, we survey the level and pattern of genetic variation in both cultivated and wild rice groups, using 155 noncoding regions located within SNP deserts. The results suggest that cultivated rice has greatly reduced genetic variation within SNP deserts as compared to either the nondesert or corresponding genomic regions in wild rice. Consistent with this reduction in genetic variation, we find a biased distribution of derived allele frequency in the cultivated group, indicative of positive selection. Furthermore, over half of the confirmed, domestication-related genes are found within SNP deserts, also suggesting that SNP deserts are strongly related to domestication, and might be the key sites in the process of domestication.
- Subjects
GENOTYPE-environment interaction; DOMESTICATION of plants; RICE genetics; PLANT genetics; PLANT genomes; GENETIC polymorphisms
- Publication
Journal of Evolutionary Biology, 2009, Vol 22, Issue 4, p751
- ISSN
1010-061X
- Publication type
Article
- DOI
10.1111/j.1420-9101.2009.01698.x