Genetic diversity among perennial wild rice Oryza rufipogon Griff., in the Mekong Delta

Abstract

Oryza rufipogon Griff. is a perennial species of wild rice widely distributed along the channels and rivers of the Mekong Delta, Vietnam. This study attempted to find centers of diversity among wild rice populations in this area and their inter-relationships. The highest genetic diversity was found in the Dong Thap population and the lowest in the Can Tho population. Maternal diversity evaluated using chloroplast INDELs detected ten plastid types, five of which were novel relative to other Asian countries. The mitochondrial genome suggested two unique deletions. One 699-bp deletion via short tandem repeats was accompanied by another deletion including orf153. All accessions carrying the mitochondrial type were found in a particular plastid type. This unique maternal lineage was confined to specific channels where it showed vigorous vegetative growth in comparison to upstream areas where various maternal lineages and maximum genetic diversity occurred. This area along the Mekong Delta is a center of not only nuclear but also maternal diversity.

Keywords: Mekong Delta; Oryza rufipogon; clonal propagation; maternal lineage; mitochondrial rearrangement.

Figure 1

Collection sites for the wild rice Oryza rufipogon in the Mekong Delta, Vietnam. (a) Location of the Mekong Delta in southwest Vietnam. (b) Four populations of wild rice collected along the Mekong River, including Dong Thap as an upstream area, My Tho as a downstream area, Vinh Long as an intermediate area, and Can Tho as a flooding area. Dots and triangles indicate collection sites

Figure 2

Compositions of maternal lineages among the Dong Thap, My Tho, and Intermediate populations

Figure 3

Unique deletions detected in the mitochondrial genome of wild rice, Oryza rufipogon, in the Mekong Delta. (a) Location of the presumed deletion around orf153. (b) Another deletion involving simple direct repeats. (c) INDEL pattern for the orf153 deletion. (d) INDEL pattern of the 669‐bp deletion. DNA templates were Nipponbare (lane 1), W0107, and W0108 for O. rufipogon originating in India (lanes 2 and 3). P75‐2 in the Can Tho population (lane 4).P36‐3 in the Intermediate population (lane 5). (d) INDEL pattern of the deletion spanning the bp 328,592 to bp 329,291 stretch. From left to right, Nipponbare, W0107, W0108, P75‐2, and P36‐3. (e) Southern blot showing the orf153 deletion in the P75‐1 and P75‐2 wild rice accessions from the Can Tho population. (f) Southern blot showing higher rearrangement around atp6 when probed with 2.5f‐5r (probe 1). (g) Location of Probe 1 as 2.5f‐5r between 231,946‐239,055nt in Nipponbare genome. Probe 2 is indicated as black box corresponding to orf153

Figure 4

Banding pattern of cpINDEL and mitochondrial deletion showing accessions carrying the deletions is shared by an identical plastid type, Type 15. Template DNA from left to right: Nipponbare, P36‐3 (plastid type 9), P59‐2 (plastid type 2), P46‐4 (plastid type16), P75‐1, P36‐1, P53‐1, and P46‐2 belonging to plastid type 15. Markers from top downwards are listed beside each figure

Figure 5

Phylogenetic tree of Vietnamese wild rice Oryza rufipogon categorized using 20 SSR markers. (a) Phylogenetic tree between four populations. (b) Phylogenetic tree among all subpopulations