STUDIES ON ESTABLISHING MOLECULAR IDENTITY FOR GENETIC PURITY ASSESSMENT OF POPULAR RICE (Oryza sativa L.) VARIETIES USING EST-SSR MARKERS
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Date
2009
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ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY, RAJENDRANAGAR, HYDERABAD
Abstract
The present investigation was carried out with an objective to identify
distinguishable EST-SSR (Expressed Sequence Tag derived Simple Sequence Repeat)
alleles to assess the genetic diversity and genetic purity for twelve popular rice
varieties, to validate the utility of EST-SSR markers in seed genetic purity
assessment. A set of 12 morphological traits were used for GOT and 98 hyper
variable EST-SSR markers were used for molecular marker analysis. The study was
also intended to develop molecular fingerprints or IDs for these varieties using locus
specific EST-SSR markers and to test their utility in seed genetic purity assessment.
A set of 98 EST-SSR markers across the 12 chromosome were employed for
fingerprinting the chosen varieties. Based on the polymorphic status, 24 EST-SSR
markers were found to be informative for discriminating the genotypes. A set of six
EST-SSR markers (RMES5-1, RMES5-2, RMES6-1, RMES7-1, JGT06-6.9 and
JGT07-25.2) was adequate for discriminating medium slender fine grain varieties
(BPT 5204, Swarna, JGL 384 and JGL 1798) from other grain types. The primer pairs
JGT11-15.3 and JGT10-0.3 distinguished long grain type varieties from other types.
A set of nine EST-SSR markers (RMES2-1, RMES2-2, RMES7-2, RMES12-2,
JGT03-29.2, JGT07-22.8, JGT07-25.2, JGT10-5.7 and JGT 12-18.6) exhibited unique
alleles for seven varieties (Swarna, MTU 1001, Tella Hamsa, Krishna Hamsa JGL
384, JGL 1798 and Vikas), which can serve as molecular IDs for these varieties.
The cluster analysis based on Jaccard’s similarity coefficient using UPGMA
(Unweighted Pair Group Method with Arithmetic Averages) grouped the varieties
into four clusters. The genetic similarity between the genotypes ranged from 0.3 to
0.92. Principal component analysis (PCA) revealed that the 12 varieties were
scattered into three distinct clusters.
To validate utility of EST-SSR markers in genetic purity assessment,
foundation seed lots of MTU 1001, Tella Hamsa, Krishna Hamsa and Vikas were
assessed for their genetic purity using both morphological and EST-SSR markers. The
impurities detected in the EST-SSR marker analysis were 2-3% higher as compared to
those detected based on morphological characters.
Utility of EST-SSR marker alleles as molecular IDs in monitoring genetic
purity of seeds was established. The results indicated the practical usefulness of ESTSSR
markers in assessing genetic purity of rice varieties and diversity among them
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Keywords
STUDIES, ESTABLISHING, MOLECULAR, IDENTITY, GENETIC, PURITY, ASSESSMENT, POPULAR, RICE, VARIETIES, USING, EST-SSR, MARKERS