Sequences analysis
The entire sequence of the atp H genes of B810S and 810S were determined by comparisons with those of other previously reported rices (GenBank accession number NC_031333). The atpH gene sequences of B810S’, 810S’ and other rices (downloaded from Genebank)were aligned by the computer program Clustal X 1.81. To calculate the sequence differences between B810S and 810S, the formula D = 1 - (M/L ) was used. In the formula, different capitals represent different means, where M is the number of alignment positions at which the two sequences have a common base , and L is the total number of alignment positions over which the two sequences are compared. The Megalign procedure within DNAStar 5.0 (Burland, 2000) was used to analyze sequence similarities of B810S and other rices which included 810S and other rice gene sequences which are downloaded from Genebank. Also, to align the variable sites of B810S and 810S, and calculate their haplotype (Hd) and nucleotide diversity (Pi), the computer program Dna SP 5.0 was used with default parameters.
Phylogenetic analysis
To infer the phylogenetic relationship of B810S, 810S and other rices, a phylogenetic tree was re-constructed using the maximum likelihood (ML) method. ML analyses were performed using PhyML 3.0 (Guindon et al. 2010), and the GTR+I model with its parameters determined by JModeltest (Posada, 2008). Bootstrap support (BS) for the ML tree was calculated using 100 bootstrap replicates. In the tree, B810S, 810S and other members of the Oryzais genus(e.g.,(O.sativa (MK348618),O.coarctata (MG383937), O. longistaminata (KF359907),O.meridionalis (KF359906), O.barthii (KF359904), O. glaberrima
(KF359903), O. rufipogon (KF359902), O. glumipatula (KR364803), O. nivara (AP006728),O.rhizomatis (KX085497), O.eichingeri (KX085496),O.latifolia (MF401451), O. alta (KF359913) andO.officinalis (KF359910)) were considered as the inside-group, andTriticum aestivum was considered as the out-group. Tree View program version 1.65 was used to draw the phylogenetic tree (Page, 1996).