Rice grain quality is an important factor that has a great influence on its market value and consumer acceptance. It is determined by three parameters controlling the cooking and eating qualities of rice (amylose content, gelatinization temperature and gel consistency) and by the aroma, which becomes a criterion increasingly preferred by consumers. Molecular characterization of specific genomic regions of rice genotypes by trait specific markers can help in the development of suitable breeding program. This study was conducted at AfricaRice Regional station, Saint-Louis, Senegal. 30 rice genotypes commonly used in Africa were evaluated using eight simple sequence repeat (SSR) markers linked to the cooking, eating properties, and the aroma. The total number of alleles was 45 with an average of 5.63 allele per locus. The number of alleles per marker varied from three for RM204 to eight for RM190 and RM342A and the effective number of alleles varied from 1.66 for RM204 to 6.16 for RM342A. The polymorphic information content (PIC) varied from 0.39 to 0.83 and the allele frequency ranged from 0.015 to 0.75. A maximum genetic similarity of 1 was observed between Gambiaka Kokoum and Gambiaka Burkina Faso, Basmati 270 and Basmati 370, Sahel 108 and Sahel 201, Sahel 108 and Sahel 208, Sahel 201 and Sahel 208, Sahel 202 and Sahel 209, and Sahel 305 and Sahel 317. The Sahel varieties found with maximum genetic similarity have the same amylose content, but different gelatinization temperature except Sahel 305 and Sahel 317 which have the same cooking and eating properties. Therefore, more markers are needed to discriminate those varieties. Minimum genetic similarity was observed between traditional aromatic rice Basmati 370 and the landrace Gambiaka Nigeria. The unweighted pair-groups method using arithmetic averages (UPGMA) cluster analysis of these cultivars enabled the classification of our varieties in five major groups with additional sub-clusters in groups 2, 3 and 4. Groups 1 and 2 composed of aromatics varieties, group 3 gathered the three improved Sahel aromatic varieties, group 4 was the most diversified group with three sub-clusters and group 5 corresponded to the traditional varieties Gambiaka. The results of this study indicated that the use of trait specific SSR markers enabled to group the varieties according to their cooking and eating quality and the aroma and therefore can be very useful in breeding rice varieties harboring good cooking and eating quality traits and aroma in rice breeding program.
Key words: Grain quality, cooking and eating properties, aroma, cluster analysis, simple sequence repeat (SSR), rice.
RM, Rice microsatellite; SSR, simple sequence repeats; UPGMA, unweighted pair group method with arithmetic averages.
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