ARS | Publication request: Indica and Japonica crosses resulting in linkage block and recombination suppression on rice chromosome 12

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 16, 2012
Publication Date: August 17, 2012
Citation: Jia, Y., Jia, M.H., Wang, Z., Liu, G. 2012. Indica and Japonica crosses resulting in linkage block and recombination suppression on rice chromosome 12. PLoS One. 7(8):Article e43066.

Interpretive Summary: Large linkage blocks due to recombination suppression is a phenomenon that commonly observed in plant breeding. The molecular basis of linkage block size due to recombination suppression at the centromere of rice chromosome 12, where the effective rice blast resistance gene Pi-ta resides, has been unclear. A previous study indicated that large linkage blocks observed at the Pi-ta locus could be due to selection for blast resistance and incompatibility between indica and japonica. In the present study, we investigated how much recombination suppression at the centromere region of rice chromosome 12 was due to incompatibility between indica and japonica subspecies by using crosses derived from indica and japonica, japonica and japonica, and indica and indica cultivars. Simple sequence repeat markers spanning the entire chromosome 12 were used to detect recombination break points and to delimit the physical size of linkage blocks. Large linkage blocks ranging from 4.1 megabases to 10 megabases were identified from recombinant individuals derived from indica and japonica and their reciprocal crosses. However, significantly reduced blocks, from less than 800 kb to 2.1megabases, were identified from indica by indica crosses regardless of the existence of Pi-ta. We suggest that large linkage blocks at the centromere of rice chromosome 12 could be due to subspecies incompatibility.

Technical Abstract: Understanding linkage block size and molecular mechanisms of recombination suppression is important for plant breeding. Previously large linkage blocks ranging from 14 megabases to 27 megabases were observed around the rice blast resistance gene Pi-ta in rice cultivars and backcross progeny involving an indica and japonica cross. In the present study, the same linkage block was further examined using 456 random recombinant individuals derived from five crosses ranging from F2 to F10 generation derived from both indica and japonica germplasm with and without Pi-ta genomic regions. Simple sequence repeat markers spanning the entire chromosome 12 were used to detect recombination break points and to delimit the physical size of the linkage blocks. Large linkage blocks ranging from 4.1 megabases to 10 megabases were predicted from recombinant individuals involving genomic regions of indica and japonica and their reciprocal crosses. However, significantly reduced blocks, from less than 800 kb to 2.1megabases, were identified from crosses of indica with indica cultivars regardless of the existence of Pi-ta. These findings suggest that crosses of indica and japonica rice have significant recombination suppression near the centromere on chromosome 12