Comparative evaluation of within-cultivar variation of rice (Oryza sativaL.) using microsatellite and RFLP markers

Abstract

The objective of this study was to determine an efficient way of detecting within-cultivar variation in rice varieties obtained from national and international germplasm collections. Seventy-one rice cultivars were evaluated for within-cultivar variation using a combination of phenotypic, RFLP, and microsatellite or simple sequence length polymorphism (SSLP). Variation between individuals within and accession and between duplicate accessions within a cultivar was detected even in cultivars that had been purified by phenotypic evaluation. Landrace cultivars were more heterogeneous and displayed a larger number of both RFLP and SSLP alleles than did modern cultivars. Microsatellite markers detected a greater number of alleles and were able to discriminate between even closely related individuals more efficiently than RFLPs. Some microsatellite markers were more informative than others for assessing genetic diversity. Single markers revealed 5.6-61.1% of the total variation detected by the 10 SSLP markers. Some marker combinations were complementary, providing more information than others. Several combinations of 4 SSLP markers detected as much as 94% of the total within-cultivar variation detected by the 10 SSLP markers. These results suggest that the use of four well-chosen microsatellites would be an efficient method for evaluating the heterogeneity of rice accessions.

Genetic Structure and Diversity in Oryza sativa L.

“…A greater proportion of ries for the world population (World Rice Statistics, diversity is expected to reside in differences between hohttp://www.irri.org; FAOSTAT, http://apps.fao.org). As mozygous lines within a heterogenous landrace in rice a model organism with a fully sequenced genome, rice (Olufowote et al 1997) compared to the distribution of affords unique opportunities to use genomic approaches diversity among heterozygous individuals within a landrace to study its domestication, adaptive diversity, and the of maize (Labate et al 2003). In addition, evidence sughistory of crop improvement.…”

Computational and Experimental Analysis of Microsatellites in Rice (Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential

“…Previous studies in rice have contributed to the development of several hundred microsatellite markers and a genetic map consisting of 320 SSRs (Wu and Tanksley 1993;Akagi et al 1996;Panaud et al 1996;Chen et al 1997;Temnykh et al 2000). These markers have been used to analyze diversity (Yang et al 1994;Olufowote et al 1997;Cho et al 2000;Harrington 2000) and to locate genes and QTLs on rice chromosomes using both intra-and interspecific crosses (Xiao et al 1998;Bao et al 2000;Zou et al 2000;Bres-Patry et al 2001;Moncada et al 2001). SSRs are increasingly useful for integrating the genetic, physical, and sequence-based maps of rice, and they simultaneously provide breeders and geneticists with an efficient tool to link phenotypic and genotypic variation.…”

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

“…Studies that have investigated the genetic basis of intracultivar heterogeneity have primarily reported on the rates of molecular marker polymorphisms within cultivars and inbred lines of crops such as barley (Hordeum vulgare), maize, rice (Oryza sativa), sunflower (Helianthus annuus), and wheat (Zhang et al, 1995;Olufowote et al, 1997;Gethi et al, 2002;Rö der et al, 2002;Sjakste et al, 2003;Soleimani et al, 2005;Giarrocco et al, 2007). However, the number and types of markers applied in these studies limited their throughput and ability to resolve major features of structural variation, including large-scale deletions, duplications, and more complicated genomic rearrangements.…”