Genetic analysis of RG28 locus for aroma using molecular markers in rice
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Date
2005
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Publisher
CCSHAU
Abstract
Twenty-five rice genotypes belonging to traditional Basmati, cross-bred
Basmati, indica and japonica rice varieties and a F5 population derived
from the cross between CSR10 (salt tolerant, indica and HBC19 (Taraor
Basmati) using single seed descent method, were assessed for genetic
diversity in RG28 region, where a major gene for aroma has been
mapped, using 10 SSR/aroma specific markers. A total of 30 alleles were
detected among 25 rice genotypes. The number of alleles ranged from
one (Fgr-04, SCUO-17 and RM325A) to six (SCUO-15) with an average of
3.0 alleles per locus. The overall size of amplified products ranged from
133 (RM284 and RM210) to 491 bp (Fgr-04). A total of 7 rare alleles were
observed at 3 of 10 SSR loci. On an average, 65.6% of the rice genotypes
shared a common allele at any given locus. PIC value, which is indicative
of genetic diversity, ranged from 0 to 0.787 depending upon the marker
employed, with an average of 0.423 per locus. NTSYS - PC cluster tree
analysis led to the grouping of 25 varieties in two major groups at a
similarity coefficient of 0.10. The smaller major group comprised of all
the Basmati rice varieties (Basmati 370, HBC19, HKR94-416, HKR228,
Super, SB3000, Pusa Basmati 1, Kasturi and Karnal local) except
Basmati 217, HKR93-401. Group II had rest of the 15 rice genotypes
including all of the indica, japonica and a few atypical Basmati rice
varieties. The results indicate Basmati rice varieties are quite distinct
from those belonging to indica and japonica rice groups.
The frequency of CSR10 and HBC19 specific alleles in F5 plants
ranged from 1 to 6. At three SSR loci, new/ recombinant alleles were
obtained which indicate the active recombination between genome of two
rice varieties. Cluster tree analysis and two dimensional PCA
demonstrate high level of diversity between CSR10 and HBC19 with 48
CSR10 X HBC19 F5 plants interspersed between them. The marker
based analysis of CSR10 X HBC19 F5 population shows a %
homozygosity of 88.90% which is close to expected value of 96.6%.
Molecular marker analysis showed that RM42 and RM223 are
significantly correlated to aroma and may be used for marker-assisted
selection for aroma in rice.