Microsatellite diversity within Oryza sativa with emphasis on indica–japonica divergence

Abstract

The molecular evolution of cultivated rice Oryza sativa L. has long been a subject of rice evolutionists. To investigate genetic diversity within and differentiation between the indica and japonica subspecies, 22 accessions of indica and 35 of japonica rice were examined by five microsatellite loci from each chromosome totalling 60 loci. Mean gene diversity value in the indica rice (H=0.678) was 1.18 times larger than in the japonica rice (H=0.574). Taking the sampling effect into consideration, average allele number in the indica rice was 1.40 times higher than that in the japonica rice (14.6 vs 10.4 per variety). Chromosome-based comparisons revealed that nine chromosomes (1, 2, 3, 4, 5, 8, 9, 10 and 11) harboured higher levels of genetic diversity within the indica rice than the japonica rice. An overall estimate of F(ST) was 0.084-0.158, indicating that the differentiation is moderate and 8.4-15.8% of the total genetic variation resided between the indica and japonica groups. Our chromosome-based comparisons further suggested that the extent of the indica-japonica differentiation varied substantially, ranging from 7.62% in chromosome 3 to 28.72% in chromosome 1. Cluster analyses found that most varieties formed merely two clusters for the indica and japonica varieties, in which two japonica varieties and five indica varieties were included in the counterpart clusters, respectively. The 12 chromosome-based trees further showed that 57 rice varieties cannot be clearly clustered together into either the indica or japonica groups, but displayed relatively different clustering patterns. The results suggest that the process of indica japonica differentiation may have proceeded through an extensive contribution by the alleles of the majority in the rice genome.

Genetic diversity analysis of Cuban traditional rice (Oryza sativa L.) varieties based on microsatellite markers

“…The number of alleles per microsatellite loci ranged from 4 in the RM-18 to 8 in the RM-4, RM-167 and RM-202 (Table 3). In accordance with previous studies (Wu and Tanksley, 1993;Ni et al, 2002;Lu et al, 2005), the average number of alleles per locus was 6.6, a value higher than that reported by Xiao et al (1996b) surveying elite inbred lines but slightly lower than those found by Yang et al (1994), Xu et al (2004) and Gao et al (2005) studying a larger sample of landraces and/or commercial varieties.…”

“…Rexoro, Blue Bonnet and Nira) previously assigned to this subspecies group by Lu et al (2005). To gain more insight into this relationship further research needs to be carried out including some international japonica control strains such as the Nipponbare cultivar and an additional set of microsatellite markers with proved diagnose value for differentiation between the indica and japonica subspecies groups (Ni et al, 2002;Coburn et al, 2002;Gao et al, 2005). We have previously shown that the improved varieties in the Cuban rice breeding program, here included in group II, are indica genotypes (Fuentes et al, 1999(Fuentes et al, , 2004(Fuentes et al, , 2005.…”

“…Moreover, multiplex microsatellite marker panels have been designed for high throughput analyses and semi-automated genotyping (Coburn et al, 2002). The application of microsatellites markers in rice include characterization of the genetic structure of the cultivated rice O. sativa at both the inter and intra-varietal level (Olufowote et al, 1997;Garris et al, 2005), genetic diversity and/or evolutionary analyses of landraces, weedy and wild rice germplasm (Yang et al, 1994;Vaughan et al, 2001;Ni et al, 2002;Gao, 2004Gao, , 2005Gao et al, 2005), determination of the purity of breeding material or seed stocks (Olufowote et al, 1997), prediction of hybrid performance and heterosis (Xiao et al, 1996a) and the analyses and tagging of valuable quantitative trait loci (QTL) and genes (Xiao et al, 1996b;Zou et al, 2000).…”

Genome-wide multilocus analysis of intraspecific differentiation in Oryza rufipogon Griff. from China and the influence of introgression from O. sativa L.

“…This differentiation between indica and japonica resulted from genome-wide DNA changes such as DNA rearrangements, base substitutions, InDels, translocations, and inversions (Feng et al, 2002;Gao et al, 2005). The completion of the whole genome sequences of O. sativa japonica Nipponbare and indica 9311 (Goff et al, 2002;Yu et al, 2002) revealed a large number of InDels and InDel polymorphisms between indica and japonica (Shen et al, 2004;Gao et al, 2005;Mei et al, 2007). Shen et al (2004) indicated that 90% of InDels between Nipponbare and 9311 could be used as molecular markers and that 68 to 89% of these InDel markers showed polymorphisms between three japonica cultivars (Nipponbare, 9522, and Zhonghua 11) and three indica cultivars (9311, GLA4, and Longtepu B).…”

Molecular Genetic Diversity of Landraces, Cultivars and Wild Relatives of Rice of Goa

“…However, an in-depth knowledge on local germplasm of rice could not be provided. Hence, various local rice germplasm studies have been taken up at the national or state level to understand the genetic diversity of rice in a particular area [4][5][6][7][8] . Molecular markers have been used as an important tool for assessing the genetic relations, identification and for the desirable genotype selection in breeding programmes and germplasm conservation 9 .…”