Study of total seed storage protein in indigenous Brassica species based on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)

Genetic diversity was studied in 234 accessions of locally collected Brassica species for total seed protein content through sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). These accessions were collected from different locations of Pakistan. After the study of these accessions on SDS-PAGE, 28 reproducible bands were used for cluster analysis and with the help of these bands, genetic diversity were estimated. Out of 28, four major bands were observed. Dendogram was constructed and the accessions were divided into two main groups comprising 11 clusters. The results obtained from these clusters showed minimum genetic diversity in these accessions on SDS-PAGE level. Due to low genetic diversity on SDS-PAGE level, it is suggested that two dimensional (2D)- electrophoresis can be used for protein study.Key words: Genetic variation, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), protein electrophoresis, cluster analysis, brassica

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice ( Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection

Molecular characterization of traditional and improved rice cultivars based on random amplified polymorphic DNAs (RAPDs) markers

Information of genetic similarities and diversity among superior rice cultivars is needed for potential rice breeding programs and origin of plant lines. Genetic polymorphism and relationships among 35 commercial varieties and primitive cultivars of Rice (Oryza sativa L.) were established by using random amplified polymorphic DNAs (RAPDs) primers. Polymerase chain reaction (PCR) with 14 primers produced a total of 126 different marker bands, of which 82.5% were polymorphic. The size range of the amplified DNAs was mostly between 0.2 and 3.63 kbp. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the cultivars. Cluster analysis placed most of the aromatic cultivars close to each other showing a high level of genetic relatedness. Lower levels of polymorphism in aromatic cultivars of rice indicated that there is a basic similarity among basmati cultivars used in this study, which is to be expected due to their same ancestors and selection for similar characteristics. The RAPD analysis offered a simple and quick method for the assessment of variability between different cultivars.Key words: Random amplified polymorphic DNAs (RAPDs), un-weighted pair-group method with arithmetic averages (UPGMA), rice (Oryza sativa L.)

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice (Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the *Corresponding author short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice ( Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection

Monitoring Expression Profiles of Rice Genes under Cold, Drought, and High-Salinity Stresses and Abscisic Acid Application Using cDNA Microarray and RNA Gel-Blot Analyses

To identify cold-, drought-, high-salinity-, and/or abscisic acid (ABA)-inducible genes in rice (Oryza sativa), we prepared a rice cDNA microarray including about 1,700 independent cDNAs derived from cDNA libraries prepared from drought-, cold-, and high-salinity-treated rice plants. We confirmed stress-inducible expression of the candidate genes selected by microarray analysis using RNA gel-blot analysis and finally identified a total of 73 genes as stress inducible including 58 novel unreported genes in rice. Among them, 36, 62, 57, and 43 genes were induced by cold, drought, high salinity, and ABA, respectively. We observed a strong association in the expression of stress-responsive genes and found 15 genes that responded to all four treatments. Venn diagram analysis revealed greater cross talk between signaling pathways for drought, ABA, and high-salinity stresses than between signaling pathways for cold and ABA stresses or cold and high-salinity stresses in rice. The rice genome database search enabled us not only to identify possible known cis-acting elements in the promoter regions of several stress-inducible genes but also to expect the existence of novel cis-acting elements involved in stress-responsive gene expression in rice stress-inducible promoters. Comparative analysis of Arabidopsis and rice showed that among the 73 stress-inducible rice genes, 51 already have been reported in Arabidopsis with similar function or gene name. Transcriptome analysis revealed novel stress-inducible genes, suggesting some differences between Arabidopsis and rice in their response to stress