Fingerprinting temperate japonica and tropical indica rice genotypes by comparative analysis of DNA markers

Abstract

This paper describes the relative efficiency of three marker systems, RAPD, ISSR, and AFLP, in terms of fingerprinting 14 rice genotypes consisting of seven temperate japonica rice cultivars, three indica near-isogenic lines, three indica introgression lines, and one breeding line of japonica type adapted to high-altitude areas of the tropics with cold tolerance genes. Fourteen RAPD, 21 ISSR, and 8 AFLP primers could produce 970 loci, with the highest average number of loci (92.5) generated by AFLP. Although polymorphic bands in the genotypes were detected by all marker assays, the AFLP assay discriminated the genotypes effectively with a robust discriminating power (0.99), followed by ISSR (0.76) and RAPD (0.61). While significant polymorphism was detected among the genotypes of japonica and indica through analysis of molecular variance (AMOVA), relatively low polymorphism was detected within the genotypes of japonica rice cultivars. The correlation coefficients of similarity were significant for the three marker systems used, but only the AFLP assay effectively differentiated all tested rice lines. Fingerprinting of backcross-derived resistant progenies using ISSR and AFLP markers easily detected progenies having a maximum rate of recovery for the recurrent parent genome and suggested that our fingerprinting approach adopting the 'undefined-element-amplifying' DNA marker system is suitable for incorporating useful alleles from the indica donor genome into the genome of temperate japonica rice cultivars with the least impact of deleterious linkage drag.Abbreviations: RAPD, randomly amplified polymorphic DNA; ISSR, inter-simple sequence repeat; AFLP, amplified fragment length polymorphism; AMOVA, analysis of molecular variance; MAB, marker-assisted backcrossing

Characterisation of downy mildew resistant and susceptible pearl millet (Pennisetum glaucum(L.) R.Br.) genotypes using isozyme, protein, randomly amplified polymorphic DNA and inter-simple sequence repeat markers

“…However, ISSR has been used successfully to construct a genetic linkage map in common bean (Phaseolus vulgaris) containing nine QTL comprising resistance to one bacterial, three fungal and two viral pathogen of bean (Miklas et al 2000) and for identification of leaf rust resistant gene (Lr 3/3 bg) in common wheat (Purnhauser et al 2000). Several reports are available showing application of ISSR markers, for study of variation among wild barley populations from West Turkey (Tanyolac 2003), differentiation of Japonica and tropical Indica rice genotypes (Jeung et al 2005) and genetic analysis of CMS, restorer, hybrid and open-pollinated genotypes of Indian pearl millet (Yadav et al 2007).…”

Assessment of Genetic Diversity in Contrasting Sugarcane Varieties Using Inter-Simple Sequence Repeat (ISSR) Markers

“…The 100 bp DNA ladder plus molecular weight marker was used to compare the molecular weight of amplified products. Twelve ISSR primers previously selected for Poaceae species, common cordgrass [21], barley [22] and rice [23] were chosen and ordered from MWG-Biotech for application on sugarcane varieties ( Table 2).…”

Assessment of Rice Sorts and Hybrids on the Salt Tolerance Using Laboratory Methods

“…But often it is difficult to transfer the salt tolerance genes in the high-yield sorts by the usual selection methods because of undesirable adhesion of genes that affect productivity and seed quality and occurs in hybrid posterity [15]. We also observed the very low frequency of segregation from the hybrid population of homozygous forms with the dominant Saltol allelesnear 7 % instead of expected 25 %.…”