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Molecular Characterization of Parental Lines of Rice Aiming to Address High Yield and Nutritional Quality Under Drought and Cold Stress Condition

Nomita Das
Jahangirnagar University, Savar, Dhaka, Bangladesh

Partha S. Biswas
Bangladesh Rice Research Institute, Gazipur, Bangladesh

Abstract/ Executive Summary:

Abiotic stresses limit crop growth at different growth stages resulting low yield of rice. Molecular characterization of parental materials gives precise information on the extent of genetic diversity that exists between them. A set of 60 SSRs randomly distributed over 12 chromosomes were used to analyze eight cultivars intend to be used as parents in breeding programs to address cold and drought tolerance, and the nutritional quality of rice. A total of 300 alleles were detected across the cultivars for 51 polymorphic markers with 5.88 alleles per loci. On average 30.6% of the genotypes shared a common allele at any given locus. UPGMA cluster analysis showed that 67% of common alleles were shared by the cultivars. The cultivars were clearly grouped into two distinct clusters at 67.0% genetic similarity. Hbj. BVI showing high tolerance to cold stress at seedling stage differed from cold susceptible BR1, BRRI dhan28, and BRRI dhan29 by 33% alleles while BR18 that showed moderately cold tolerance differed by 29.0 - 29.9% alleles which indicated that only 3-4% alleles difference caused higher cold tolerance in Hbj. BVI. The moderate genetic distance between cold-tolerant Hbj. BVI and high yielding BRRI dhan28 and BRRI dhan29 indicated that there is a higher possibility of obtaining high yielding cold-tolerant segregants from the crosses between them. On the other hand, Kalobokri, which had 31.7 mg zinc a kilogram of polished rice differed by 33.0% alleles from the drought-tolerant rainfed low varieties BRRI dhan56 and BRRI dhan57 having a moderate level of zinc (~20 mg/kg), which also indicated that crosses between them might produce progenies with higher nutritional quality under drought environment.

Keywords: Drought, Cold, Grain zinc content, Genetic diversity, SSR, Rice.

Location: Bangladesh Rice Research Institute, Gazipur, Bangladesh

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Drought, Rice

Objectives:

To measure the extent of genotypic differences, genetic relationships and to assist in broadening the germplasm base of future drought and cold tolerance rice breeding programs.

Methodology:

A total of eight rice cultivars having diverged trait benefits, like drought tolerance, cold tolerance, enhanced grain zinc content, short duration, and high yielding were analyzed using 60 SSR markers randomly distributed over the rice genome. Among the eight cultivars, BR1, BR18, BRRI dhan28, BRRI dhan29, and Hbj.B.VI were evaluated against artificial cold treatment for seedling stage cold tolerance following the protocol described in Khatun, et al. Cold tolerance was estimated based on leaf discoloration (LD) score following SES of IRRI, % Survival plants at the day of scoring, and % Recovery of plants after seven days of cold stress withdrawal. BRRI dhan56 and BRRI dhan57, two drought-tolerant varieties showing no significant yield losses even when the groundwater table remained 70-80 cm below the surface at the reproductive stage were included in this study. All the genotypes except Hbj.BVI was analyzed for polished grain zinc content using the X-Ray Fluorescence method in X-Supreme 8000. For SSR analysis, DNA was extracted from young and actively growing fresh leaves using miniprep modified CTAB method as described by Virk, et al. Polymerase chain reaction (PCR) was performed in 10µl volume containing 2µl of genomic DNA, 5.3µl of DDH₂O, 1µl of 1X PCR buffer, 1µl of 0.1mM dNTP mix, 0.5µl of 0.25uM of each primer, 2µl of Taq polymerase of 1U. The temperature cycles were programmed at 94°C for 5 min(initial denaturation), 94°C for 30 sec (denaturation), 55°C for 30sec (primer annealing), 72°C for 60sec (extension), 72°C for 5 min (final extension) and 10°C forever (storage). The PCR products were detected using 6% polyacrylamide gel electrophoresis. DNA bands were visualized in a UV transilluminator with ethidium bromide staining. The molecular weight of a clearly resolved and unambiguous band was determined by comparing it with the known-sized marker DNA using Alpha Ease FC 4.0. Polymorphic Information Content (PIC) values were calculated for each SSR loci using Power Marker V3.25 based on the formula developed by Anderson, et al.

Source of Information: Current Research in Agricultural Sciences, 2017, 4(2): 51-60

Article Link (Online Journal): DOI: 10.18488/journal.68.2017.42.51.60

Funding Source:

Budget:

Total Budget (Tk.) :

Achievement/Findings:

The larger range of similarity values for cultivars revealed by the SSR markers provides greater confidence for the assessment of genetic diversity and relationships, which can be used in future breeding programs. With the aid of the SSR markers used in this study, beneficial traits (cold or drought tolerance and nutritional quality) from Hbj.BVI, BRRI dhan56 or Kalobokri could be combined with modern HYVs by intercrossing. Furthermore, genetic mapping, population structure or kinships could be explored by increasing marker resolution.

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