Structural differences in the vicinity of the waxy locus among the Oryza species with the AA-genome: identification of variable regions

Abstract 

We constructed a fine physical map for a 260-kb rice BAC contig surrounding the waxy locus. In order to identify variable regions within this 260-kb as to the restriction fragments length polymorphisms and copy numbers, sixty overlapping fragments derived from the 260-kb contig were used as probes to compare their corresponding structures among the Oryza species with AA-genome. According to the hybridization patterns, each fragment was classified into four types; true single copy (class 1), single copy with a smear background (class 2), multiple copy without a smear background (class 3), and only a smear background (class 4). Out of 16 single copy (class 1 and class 2) regions obtained in this map, the one site corresponding to wx gave rise to remarkable polymorphisms among AA-genome species in Oryza. In most of the fragments observed as repetitive segments (class 4), we could not find obvious differences in the hybridization pattern. However, interestingly, one site sorted into class-3 showed copy numbers varying among the lines. The lines belonging to O. sativa O. rufipogon, O. meridionalis,and O. longistaminata possessed high-copy numbers of this fragment, whereas only a few bands were detected in the lines from O. glaberrima, O. barthii, and O. glumaepatula. The two variable regions found within the AA-genome species represented genomic dynamisms.