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
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Cold stress is an emerging threat for rice production in Bangladesh particularly in Boro season (winter rice) at seedling stage. Cold stress during seedbed stage or early establishment stage at the main field induces severe seedling mortality that increases cost cultivation and delays crop establishment and ultimately entails into low yield. Development of sustainable cold tolerant high yielding rice varieties warrants an efficient and economic screening technique of germplasms and breeding population. The protocols for cold screening that so far have been used by the breeders and reported in literature are generally dependent on natural cool temperature and/or expensive climate chamber. In this paper, we report an in-house screening protocol that requires less than three weeks to complete the screening cycle and can be used all year round for mass screening of breeding population.
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