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Genetic Analysis of Aromatic and Quality Rice Germplasm Using Microsatellite Markers

F. D. Shams
Department of Biotechnology, Bangladesh Agricultural University, Mymensingh

M. M. A. Kuddus
Department of Biotechnology, Bangladesh Agricultural University, Mymensingh

K. M. Nasiruddin
Department of Biotechnology, Bangladesh Agricultural University, Mymensingh

S. N. Begum
Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensing

M. M. Islam
Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensing

Abstract/ Executive Summary:

Twenty rice genotypes were analysed with three SSR primers viz., RM223, RM515 and RM342 for detection of the fgr gene responsible for aroma. The primers RM223 and RM515 identified eight and seven genotypes, respectively as having the fgr locus. Presence of the specific allele of the RM342 amplicon, also correlated with strong aroma in two and with weak aroma in five genotypes. The banding pattern for the primer RM342 was different in genotypes with no aroma. Among the three primers (RM223, RM515 and RM342), RM223 detected the highest number of fgr loci in the 20 rice genotypes. In total 11 genotypes were identified as having strong aroma genes by the three primers. These accessions also showed high yields and therefore may prove to be a good source for producing aromatic rice.

Keywords: Aromatic rice, Grain quality, Microsatellite marker

Location:

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Rice

Objectives:

The present experiment was carried out to select rice genotypes having aroma with fine grain and considerable seed yield. Microsatellite (SSR) markers were employed particularly for genotype selection.

Methodology:

Twenty rice germplasm with diverse origin were used in the present experiment. The origin of these germplasm was not Bangladesh. But these germplasm were available in Bangladesh and for this reason these were included in the present study. The germplasm under study were collected from International Network for Genetic Evaluation of Rice (INGER), IRRI, Philippines. DNA was extracted from the leaves of each genotype using the CTAB miniprep method (Stewart and Laura 1993) at Biotechnology laboratory, BINA, Mymensingh. The quality of the isolated DNA following this protocol was sufficient for PCR analysis. RM223, RM342 and RM515 were used to detect marker gene for aroma. These primers were used earlier by Begum (2006) for tagging the genes controlling grain quality traits and RM223 was found closely linked to extremely aromatic phenotypes (Lang and Buu 2008). The details of the primers are given in Table 1. The PCR reaction mixture contained 2 μl of 50 ng/μl template DNA, 8.25 μl ddH₂O, 1.5 μl 10 × PCR buffer, 0.75 μl of 1 mM dNTPs, 1 μl of 5 μM forward and reverse primers and 0.5 μl Taq polymerase (~2.5 units/μl). Template DNA was initially denatured at 94°C for 5 min followed by 30 cycles of PCR amplification following: 30 sec of denaturation at 94°C, 30 sec of primer annealing at 55°C and 1 min of primer extension at 72°C. Final 5 min incubation at 72°C was allowed for complete of primer extension. The amplified products were electrophoretically resolved on a 1.5% agarose gel in 0.5 × TBE and visualized under UV light after staining with ethidium bromide. The bands representing particular alleles at the microsatellite loci were scored manually on the basis of parental bands like aromatic type band (Basmati 370), non‐aromatic type (IR70) and heterozygotes type band (both).

Source of Information: Plant Tissue Cult. & Biotech. 22(1): 65-71, 2012 (June)

Article Link (Online Journal):

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

it was found that among the three primers, RM223 responded best in all the 20 rice genotypes because RM223 primer could identify aromatic and non‐aromatic germplasm effectively which supported the phenotypic result. In the light of the above discussion microsattelite has been shown to be appropriate as markers to evaluate the genetic variation among the rice germplasm. The germplasm that are used here have the potential to improve breeding programs for release of a new aromatic rice variety with better agronomic performance and better aroma.

Knowledge Management: Journal