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Evaluation of molecular markers linked to fragrance and genetic diversity in Indian aromatic rice

DNA-based markers have the potential to improve the efficiency and precision of breeding programs based on markerassisted selection. In the present study we evaluated the predictive abilities of previously reported PCR-based simple sequence repeat and functional markers related to fragrance in a set of 24 rice genotypes, including traditional basmatis, evolved basmatis, and aromatic indigenous landraces. | Turkish Journal of Botany http://journals.tubitak.gov.tr/botany/ Research Article Turk J Bot (2015) 39: 209-217 © TÜBİTAK doi:10.3906/bot-1405-117 Evaluation of molecular markers linked to fragrance and genetic diversity in Indian aromatic rice Ved Prakash RAI, Anil Kumar SINGH, Hemant Kumar JAISWAL*, Sheo Pratap SINGH, Ravi Pratap SINGH, Showkat Ahmad WAZA Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India Received: 31.05.2014 Accepted: 05.10.2014 Published Online: 16.03.2015 Printed: 10.04.2015 Abstract: DNA-based markers have the potential to improve the efficiency and precision of breeding programs based on markerassisted selection. In the present study we evaluated the predictive abilities of previously reported PCR-based simple sequence repeat and functional markers related to fragrance in a set of 24 rice genotypes, including traditional basmatis, evolved basmatis, and aromatic indigenous landraces. High-resolution melting analysis with 3 markers was also performed to detect the presence of SNPs and length polymorphism in monomorphic amplicons. All genotypes showed expected marker patterns according to their fragrance classification except 5 fragrant genotypes: Kalanamak 3119, Kasturi Basmati, Basmati LC 74-3, Thurunbhog, and Jeeraga Samba. The genetic diversity analysis based on fragrance locus grouped the genotypes broadly into 2 major clusters representing fragrant and nonfragrant genotypes. Kalanamak 3119, Kasturi Basmati, and Basmati LC 74-3 comprised the fragrant cluster, while Thurunbhog and Jeeraga Samba clustered with nonfragrant genotypes. None of the functional markers could identify these 5 genotypes as fragrant, which supports the assumption of the existence of a second gene for fragrance in rice. Our work validates previously identified markers, namely nksbad2, L06, BADEX7-5, and ESP + IFAP + INSP + EAP, suitable for use in marker-assisted selection programs. Key .