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Distribution and SNPs of the rice CMS-related gene in AA-genome of Oryza species

DUAN Shi-Hua1,2, LI Shao-Qing1, LI Yang-Sheng1, XIONG Yun3, ZHU Ying-Guo1 1. Ministry of Education Key Laboratory for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China; 2. College of Life Science, Jinggangshan University, Ji’an 343009, China; 3. Management Bureau of Prison, Hubei Province, Wuhan 430006, China  
The moiety of a chimeric gene in mitochondrial genome, orf79 and orfH79, probably related to BT-type and HL-type CMS of rice respectively, has 98% homology and only 4 nucleotide variation in DNA sequence. Of which, the former comes from Oryza sativa L., and the latter originates from Oryza rufipogon Griff. That means the orf79/ orfH79 may widely exist in Oryza species with AA genome. In order to investigate the distribution and difference of orf79/ orfH79 in the Oryza species, 190 cultivated rice accessions (including O. sativa and O. glaberrima) and 104 accessions of AA-genomeOryza wild species (including O. nivara, O. rufipogon, O. barthii, O. longistaminlata, O. glumaepatula, and O. meridionalis) were detected with PCR amplification. Of which, 31 accessions mainly from AA-genome Oryza species were found to share the special amplified fragment with the control of Yuetai A and Shijin A. The special amplified fragments were all recovered and sequenced. Phylogenetic analysis based on DNA sequences showed that the 31 accessions were fallen into two groups, correspondingly representing HL-type and BT-type cytoplasm group. Further, the results revealed that the HL-type cytoplasm distributed mainly in annual O. nivara, and the BT-type cytoplasm centered in cultivated varieties or perennial O. rufipogon.
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