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Screening of Aromatic Rice Lines by Phenotypic and Molecular Markers

K. KIBRIA
Department of Biotechnology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh

M. M. ISLAM
Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh-2200, Bangladesh.

S. N. BEGUM
Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh-2200, Bangladesh.

Abstract/ Executive Summary:

To improve the yield potential of local aromatic variety Kalizira, a segregating population was developed from a cross between Y-1281 (high yielding mutant variety) and Kalizira. Thirty two F7 rice lines were used to evaluate agronomic characteristics, aroma detection through sensory test and genotypic analysis using microsatellite markers. Highly significant negative association was found between aroma and grain yield. Nine, 12 and 17 pedigree lines (PLs) having fragrance gene (fgr) locus were found using three SSR markers RM223, RM342A and RM515, respectively as homozygous condition in 32 rice lines. The marker RM515 detected highest number of fgr locus in PLs. Fourteen promising lines were identified with aroma genes having higher yield with good agronomic performance and other grain quality traits. These SSR markers could be utilized in marker-assisted selection (MAS) and would have a great impact on identifying fgr locus in rice genotypes.

Keywords: Aromatic rice, Grain quality, Microsatellite marker

Location: Department of Biotechnology, Bangladesh Agricultural University, Mymensingh

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Rice

Objectives:

SSR or microsatellite markers behave as a co-dominant marker which was used for this study to select rice lines having aroma with fine grain and good seed yield.

Methodology:

Plant materials: A segregating population was developed by crossing Y-1281 (a high yielding variety) with Kalizira (a local aromatic variety) for developing superior quality of aromatic rice lines at the Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh. Thirty two F7 pedigree lines along with their parents and a check variety, BRRI dhan38 were used for phenotypic and genotypic study. Phenotyping of rice germplasm: Five randomly selected plants of each genotype were used for agronomic data analysis. Data on plant height (cm), number of effective tillers/plant, panicle length (cm), number of filled grains/panicle, 1000 seed weight (g), days to maturity and grain yield/plant (g) were recorded and subjected to statistical analyses using MSTATC software. After harvesting the seeds of each genotype were dehulled for evaluation of the grain quality viz. grain size (grain length), grain shape (grain length-breadth ratio) and aroma. The grains were classified into different types based on their dimension according to Dela Cruz and Khush (1989). Forty grains of each genotype were soaked in 10 ml 1.7% KOH solution at room temperature in a covered conical flask for about 1 h. The samples were scored on 1-4 scale with 1, 2, 3 and 4 corresponding to absence of aroma, slight aroma, moderate aroma and strong aroma, respectively. The score for each sample was recorded by a panel of five experts who have experience in aromatic rice breeding and quality evaluation. Molecular marker analysis: DNA isolation was carried out using the mini preparation CTAB method (IRRI 1997). Three SSR markers RM223, RM342A and RM515 (linked to aroma) were used to confirm the presence of fgr gene as described by Garland et al. (2000) and Begum (2006). The PCR reaction mixture contained 2µl of 50 ng/μl template DNA, 8.25 µl ddH2O, 1.5 μl 10X 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^oC for 5 min followed by 30 cycles of PCR amplification following: 30 sec of denaturation at 94^oC, 30 sec of primer annealing at 55^oC and 1 min of primer extension at 72^oC. Final 5 min incubation at 72^oC was allowed for complete of primer extension. The amplified products were electrophoretically resolved on a 1.5% agarose gel in 0.5xTBE 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 (Kalizira), non-aromatic type (Y-1281) and heterozygotes type band (both).

Source of Information: Bangladesh J. Bot. 37(2): 141-147, 2008 (December)

Article Link (Online Journal):

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

Based on the study, 14 lines (PL1, PL3, PL5, PL6, PL9, PL10, PL11, PL16, PL19, PL20, PL21, PL22, PL31 and PL32) having good aroma and superior agronomic performance have been selected in F7 generation. The result having aroma in selected rice lines were confirmed by both phenotypic and genotypic analysis. These selected pedigree lines could be used as donors for future breeding programmes that aim to develop aromatic rice varieties.

Knowledge Management: Journal