Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program

Abstract

One hundred and ninety three parental lines obtained from 26 countries for an international rice molecular breeding program were evaluated using 101 well-distributed simple sequence repeat (SSR) markers. An overall genetic diversity of 0.68 and an average of 6.3 alleles per locus were revealed, indicating a high level of genetic variation in these lines. Cluster analysis of the 193 accessions showed three major groups and nine subgroups. Group I corresponded to the classical indica subspecies, whereas groups II and III belong to the japonica subspecies. Indica and japonica differentiation accounted for only 6.5% of the total variation in the entire sample and 93.5% was due to within-subspecies diversity. Differentiation among eco-geographic regions accounted for 24% of the diversity within the subspecies. Larger amounts of the eco-geographical differentiation were resolved within japonica than within indica. The largest indica-japonica differentiation based on the single locus level was detected by markers on chromosomes 9 and 12, while the smallest differentiation was detected by markers on chromosomes 4 and 8. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between indica and japonica and among the main geographic regions. The multilocus analysis in genetic diversity showed a higher proportion of variation caused by predominant non-random associations of different loci within and among the classified subspecies and geographic subdivisions. The results suggest that selection for eco-geographical adaptation on multilocus associations was largely responsible for the maintenance of the extensive variation in the primary gene pool of rice.

Genetic Diversity Studies on Selected Rice (Oryza sativa L.) Genotypes based on Gel Consistency and Alkali Digestion

“…Similar findings have been reported in Pakistan basmati and non-basmati genotypes [27]. However, these results were less than what is reported by other studies using different genotypes and SSR markers [28,29]. This could be as a result of use of different rice germplasm accessions and the selection of SSR markers.…”

Microsatellite Analysis of Genetic Variation and Population Genetic Differentiation in Autotetraploid and Diploid Rice

“…Consequently, the codominant SSR banding patterns were scored as AA or BB (for homozygote) and AB (for heterozygote) genotypes, corresponding to the alleles identified in the Gramene Database (Song et al 2003). SSR genotypes were determined based on their migration relative to the DNA marker and four varieties (Minghui63, Gang46B, IR36, and CDR22) loaded in each gel as references (Yu et al 2003). For genetic similarity estimates and cluster analysis, the allelic data were converted to a binary format, with the presence of a specific allele (band) scored as 1 and its absence as zero (Yu et al 2003).…”

“…SSR genotypes were determined based on their migration relative to the DNA marker and four varieties (Minghui63, Gang46B, IR36, and CDR22) loaded in each gel as references (Yu et al 2003). For genetic similarity estimates and cluster analysis, the allelic data were converted to a binary format, with the presence of a specific allele (band) scored as 1 and its absence as zero (Yu et al 2003). The experiments were repeated to confirm cases of null alleles or multiple alleles.…”

Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo

“…The genetic diversity of cultivated rice germplasm on a global scale has been well characterized using molecular markers (Caicedo et al 2007;Garris et al 2005;Glaszmann 1987;Yang et al 1994;Yu et al 2003). To encompass the entire range of rice diversity, these studies have sampled rice varieties from many different rice-growing countries around the world.…”