1Bioinformatics Section, CCS Haryana Agricultural University, Hisar 125 004.
2Department of Plant Breeding, Cornell University, 240 Emerson Hall, Ithaca, NY 14853-1901, USA
Department of Biotechnology and Molecular Biology
*Corresponding author's e-mail: sunitajain60@gmail.com
Published by Indian Society of Genetics & Plant Breeding, F2, First Floor, NASC Complex, PB#11312, IARI, New Delhi 110 012.
Molecular markers provide novel tools for varietal identification, diversity analysis and assessing phylogenetic relationships among various rice groups in genus Oryza. A DNA fingerprint database has been developed for 50 rice genotypes representative of the traditional Basmati (TB), cross-bred Basmati, indica, japonica and wild rice groups using fifty SSR and thirty transposable element (TE) based markers. The salient features of marker data analyzed using various clustering algorithms, principal component analysis and Mantel test are as given below: (i) SSR generated higher levels of polymorphism (mean PIC value = 0.698) than TE based markers (PIC = 0.258), (ii) a total of 341 alleles were generated with an average of 6.8 allele per locus using SSR markers of which 40 were rare/unique alleles being present in only one of 50 genotypes with 17 unique alleles in the nine wild rice genotypes, (iii) analysis of SSR database clearly exhibited the formation of four distinct groups of Basmati, indica, japonica and wild rice genotypes, (iv) traditional Basmati rice varieties except Basmati 217 were genetically distinct from indica, japonica and wild rice types and invariably formed a separate cluster, (v) twelve Basmati rice varieties developed from indica x Basmati crosses/backcrosses were scattered between the traditional Basmati and indica rice groups with CSR30, Super, Kasturi and Pusa Basmati 1 being closer to theTB, (vi) genetic relationships assessed using TE based markers (mPing and Dasheng) were essentially the same as obtained using SSRs except that it also differentiated between the temperate and tropical japonica rice genotypes into separate clusters, and (vii) SSR and TE based marker data-set showed high levels of positive correlation (Mantel test, r= 0.655). The study demonstrate that SSRs are best for differentiating between the closely related Basmati, indica or japonica rice varieties, while TE based markers may provide vital clues about evolution/speciation in rice.
Basmati, microsatellite, Dasheng, mPing, Oryza sativa L
