Parental Polymorphism Survey Research Articles

Identification of introgressed rice lines of Binadhan-7×FL-378 under salt stress through SSR markers

Thirty two rice lines of BC1F1 population (Binadhan-7/FL 378) were used to identify introgressed rice lines for salt tolerance using SSR markers at the Plant Breeding and Biotechnology Divisions of Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh. Seeds of BC1F1 population of Binadhan-7/FL-378 were collected from backcross population of F1 (Binadhan-7/FL 378). Salt tolerant genotype, FL-378 was crossed with high yielding variety, Binadhan-7. Randomly selected 32 BC1F1 progenies along with their two parents (Binadhan-7, FL-378) were genotyped with microsatellite or SSR markers for identification of introgressed rice lines. Parental polymorphism survey was assayed by 8 SSR markers and three polymorphic SSR markers viz., RM296, RM585 and OSR30 were selected to evaluate BC1F1 rice lines for salt tolerance. Primer RM585 indicated 16 lines as introgressed and 16 lines as susceptible in comparison with salt tolerant parent FL-378 and salt susceptible parent Binadhan-7. Primer RM296 identified 13 introgressed, and 19 susceptible lines. Nine introgressed and 23 susceptible lines were identified when BC1F1 lines were evaluated with marker OSR30. Line BC1F1-30, BC1F1-40, BC1F1-2, BC1F1-16 and BC1F1-34 were identified as introgressed in comparison with parent FL-378 (salt tolerant) when RM585 and RM296 markers were used but line BC1F1-1 and BC1F1-3 were identified as introgressed incase of 3 primers (RM585, RM296 and OSR30). Again the lines BC1F1-5, BC1F1-24, BC1F1-26, BC1F1-27, BC1F1-29, BC1F1-31, BC1F1-37 and BC1F1-38 were found susceptible as compared with parent Binadhan-7 when marker RM585, RM296 and OSR30 were used. The polymorphism information content (PIC) values ranged from 0.3290 to 0.3671 with an average of 0.3544. The overall gene diversity of SSR loci for the 32 BC1F1 rice lines along with two parents was 0.4614, ranging from 0.4152 to 0.4844. Positive correlations were found between the genetic diversity and the maximum number of repeats. Among the lines, all the loci were polymorphic and clearly distinct and the cluster analysis (NJ tree and UPGMA) showed nearly similar pattern of variation which could be used for improvement of salt tolerant rice lines of rice through SSR markers. DOI: http://dx.doi.org/10.3329/jbau.v10i2.14680 J. Bangladesh Agril. Univ. 10(2): 185–190, 2012

Marker-assisted Backcrossing for Identification of Salt Tolerant Rice Lines

SSR or microsatellite markers are proved to be ideal for making genetic maps, assisting selection and studying genetic diversity in germplasm. SSR markers are playing important role to identify gene for salt tolerance that can be helpful for plant breeders to develop new cultivars. The experiment was conducted during the period from July 2009 to November 2010 in the experimental field and Biotechnology Laboratory of Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh to identify salt tolerant rice line of BC1F1 progenies of Binadhan-5 x FL-478 using SSR markers. Salt tolerant genotype, FL-478 was crossed with high yielding variety, Binadhan-5. Randomly selected 40 BC1F1 progenies along with their two parents (Binadhan-5, FL-478 and F1) were genotyped with microsatellite or SSR markers for identification of salt tolerant rice lines. Parental polymorphism survey was assayed by 10 SSR markers and three polymorphic SSR markers viz., RM 336, RM 510, and RM 585 were selected to evaluate BC1F1 rice lines for salt tolerance. In respect of Primer RM 336, 11 lines were found as salt tolerant and 25 lines were heterozygous and 3 lines were susceptible. Primer RM 510 identified two tolerant, 14 heterozygous and 22 susceptible lines. And primer RM 585 identified 4 lines as tolerant and 35 lines as susceptible. Thus, these markers could be efficiently used in tagging salt tolerant genes, in marker-assisted selection and quantitative trait loci (QTL) mapping. The selected BC1F1 could be used for developing BC2F1 and BC2F2 and mapping genes for salinity tolerance. DOI: http://dx.doi.org/10.3329/ijarit.v2i2.14008 Int. J. Agril. Res. Innov. & Tech. 2 (2): 1-8, December, 2012

Identification of introgressed rice lines of Binadhan-7×FL-378 under salt stress through SSR markers

Thirty two rice lines of BC1F1 population (Binadhan-7/FL 378) were used to identify introgressed rice lines for salt tolerance using SSR markers at the Plant Breeding and Biotechnology Divisions of Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh. Seeds of BC1F1 population of Binadhan-7/FL-378 were collected from backcross population of F1 (Binadhan-7/FL 378). Salt tolerant genotype, FL-378 was crossed with high yielding variety, Binadhan-7. Randomly selected 32 BC1F1 progenies along with their two parents (Binadhan-7, FL-378) were genotyped with microsatellite or SSR markers for identification of introgressed rice lines. Parental polymorphism survey was assayed by 8 SSR markers and three polymorphic SSR markers viz., RM296, RM585 and OSR30 were selected to evaluate BC1F1 rice lines for salt tolerance. Primer RM585 indicated 16 lines as introgressed and 16 lines as susceptible in comparison with salt tolerant parent FL-378 and salt susceptible parent Binadhan-7. Primer RM296 identified 13 introgressed, and 19 susceptible lines. Nine introgressed and 23 susceptible lines were identified when BC1F1 lines were evaluated with marker OSR30. Line BC1F1-30, BC1F1-40, BC1F1-2, BC1F1-16 and BC1F1-34 were identified as introgressed in comparison with parent FL-378 (salt tolerant) when RM585 and RM296 markers were used but line BC1F1-1 and BC1F1-3 were identified as introgressed incase of 3 primers (RM585, RM296 and OSR30). Again the lines BC1F1-5, BC1F1-24, BC1F1-26, BC1F1-27, BC1F1-29, BC1F11F1-37 and BC1F1(PIC) values ranged from 0.3290 to 0.3671 with an average of 0.3544. The overall gene diversity of SSR loci for the 32 BC1F1 rice lines along with two parents was 0.4614, ranging from 0.4152 to 0.4844. Positive correlations were found between the genetic diversity and the maximum number of repeats. Among the lines, all the loci were polymorphic and clearly distinct and the cluster analysis (NJ tree and UPGMA) showed nearly similar pattern of variation which could be used for improvement of salt tolerant rice lines of rice through SSR markers.DOI: http://dx.doi.org/10.3329/jbau.v10i1.12039J. Bangladesh Agril. Univ. 10(1): 49–54, 2012

Identification of SSR markers associated with seed coat permeability and electrolyte leaching in soybean

Seed coat permeability and electrolyte leaching are the important traits that have been negatively associated with seed longevity in soybean. The objective of this study was to use SSR markers to identify genomic regions significantly associated with QTLs controlling seed coat permeability and electrolyte leaching in a segregating F2 population derived from a cross of Birsa soya-1 x JS 71-05. Parental polymorphism survey using 145 SSR markers identified 21 polymorphic ones, which were used to genotype 153 F2 individuals. Four independent markers (Satt434, Satt538, Satt281 and Satt598) were significantly (P=0.05) associated with seed coat permeability. One of these markers (Satt 281) also showed significant association with electrolyte leaching that partly supported the observed positive correlation (r = 0.425) between the two traits. Markers for seed coat permeability individually explained 3.9% to 4.5% of the total phenotypic variation, while the marker linked with electrolyte leaching explained 5.6% of the total variation.

Construction of Integrated Genetic Map between Various Existing DNA Markers and Newly Developed P450-related PBA Markers in Diploid Potato (Solanum tuberosum)

We have generated estimates of the genomic distribution of newly developed molecular markers, which are P450-based analogues (PBAs), in diploid potato (Solanum tuberosum, 2n = 2x = 24) based on functional genomics. A total of 401 markers, including 111 SSR, 33 RFLP, 87 RFLP-STS, 45 CAPS, 94 RAPD, 15 PBA, 9 AFLP, 3 RGL and 4 ISSR markers, were employed in a parental polymorphism survey. A total of 127 out of 401 markers (172 loci) displayed polymorphisms between parents and were confirmed to show segregation in partial progenies. These selected 127 markers were then tested for their possible use for a whole mapping population. The subsequent results of genetic mapping of the PBAs revealed that they were distributed on at least 8 chromosomes, suggesting that they have a significant potential not only as tools for assessing genetic diversity but also as effective markers to construct more detailed genetic maps of potato, in conjunction with existing identified genetic loci. To integrate the information from existing maps into our mapping study, we performed a comparative analysis between two representative maps (RFLP and SSR-based) with our PBA map. Based on the subsequent results, we predict that our map will be useful as a bridge between the existing genetic maps of potato and will enable to integrate information about different markers.