Assessment of genetic diversity among Pakistani wheat (Triticum aestivum L) advanced breeding lines using RAPD and SDS-PAGE

Genetic diversity was assessed among 32 advanced wheat breeding lines included in the National Uniform Wheat Yield Trials (2006-07) of Pakistan using molecular (DNA) and biochemical (SDS-PAGE) markers. Of the 72 RAPD primers used for initial screening, 15 were found polymorphic. A total of 140 bands (61.4 percent polymorphic) were generated by the 15 random decamer primers. Genetic similarity coefficients ranged from 0.81 to 0.94 for rainfed and from 0.70 to 0.93 for the normal seeding date group. Cluster analysis using the unweighted pair group method of arithmetic averages (UPGMA) clustered the 32 advanced wheat breeding lines into one major and three small groups. Maximum level of polymorphism (90 percent) was observed for the primer OPA-05. Lines N9 and N11 showed the least genetic similarities (0.70-0.82 and 0.71-0.83, respectively) with rest of the lines studied. Line RF1 had the maximum similarity (0.81-0.94) with other lines. Wheat lines included in the normal seeding date were relatively distantly related than those in the rainfed group. Seed storage protein analysis produced 19 subunits ranging from 29-120KDa. Similarity coefficients ranged from 0.53 to 1.0 for the normal seeding date and from 0.47 to 1.0 for the rainfed group. High molecular weight subunits (particularly 120KDa) showed greater polymorphism than the lower molecular weight subunits. Narrow genetic base was observed in wheat lines included in the rainfed group. DNA fingerprinting of advanced breeding lines may help to avoid release of varieties with narrow genetic base in the future.

Assessment of genetic variation within Indian mustard (Brassica juncea) germplasm using random amplified polymorphic DNA markers.

Genetic diversity among 45 Indian mustard (Brassica juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession 'Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.

Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L. ) using RAPD markers

The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. Information on genetic diversity and relationships among rice genotypes from Pakistan is currently very limited. The objective of this study was to evaluate the genetic polymorphisms and identities of 10 traditional, 28 improved and 2 Japanese cultivars of rice using the random amplified polymorphic DNA technique. Twenty-five decamer-primers could generate a total of 208 RAPD fragments, of which 186 or 89.4 percent were polymorphic. The number of amplification products produced by each primer varied from 4 to 16 with an average of 8.3 bands primer-1. The size of amplified fragments were ranged from 200 to 4000 bp. Pair-wise Nei and Li's similarity had estimated the range of 0.50 to 0.96 between rice cultivars. Based on analysis performed on a similarity matrix using UPGMA, 40 cultivars were grouped into 3 main clusters corresponding to aromatic, non-aromatic and japonica group. There were a few of independent cultivars. The cluster analysis had placed most of the aromatic cultivars into a close relation showing a high level of genetic relatedness. However, the clusters formed by the aromatic cultivars were distinct from those of non-aromatic and japonica types. Interestingly, a number of improved and traditional cultivars originating from diverse sources did not form well defined groups and were interspersed, indicating no association between the RAPD patterns and the geographic origin of the cultivars. The information generated from this study can be used to maximize selection of diverse parents and broaden the germplasm base in the future of rice breeding programs.