Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to study the DNA polymorphism in elite blackgram genotypes. A total of 25 random and 16 ISSR primers were used. Amplification of genomic DNA of the 18 genotypes, using RAPD analysis, yielded 104 fragments that could be scored, of which 44 were polymorphic, with an average of 1.8 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from two (OPA-13) to nine (OPK-4) and varied in size from 200 bp to 2,500 bp. Percentage polymorphism ranged from 16.6% (OPK-7) to a maximum of 66.6% (OPE-5, OPH-2, and OPK-8), with an average of 42.7%. The 16 ISSR primers used in the study produced 101 bands across 18 genotypes, of which 55 were polymorphic. The number of amplified bands varied from two (ISSR 858) to ten (ISSR 810), with a size range of 200-2,200 bp. The average numbers of bands per primer and polymorphic bands per primer were 6.3 and 3.4, respectively. Percentage polymorphism ranged from 25% (ISSR 885) to 100% (ISSR 858), with an average percentage polymorphism of 57.5% across all the genotypes. The 3'-anchored primers based on poly(GA) and poly(AG) motifs produced high average polymorphisms of 54.98% and 58.32%, respectively. ISSR markers were more efficient than the RAPD assay, as they detected 57.4% polymorphic DNA markers in Vigna mungo as compared to 42.7% for RAPD markers. The Mantel test between the two Jaccard's similarity matrices gave r=0.32, showing low correlation between RAPD- and ISSR-based similarities. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in ISSR and combined data of RAPD and ISSR.

A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers

Advances in Arachis genomics for peanut improvement

Kompetitive allele-specific polymerase chain reaction (KASP) assays have emerged as cost-effective marker assays especially for molecular breeding applications. Therefore, a set of 96 informative single nucleotide polymorphisms (SNPs) was used to develop KASP assays in groundnut or peanut (Arachis spp.). Developed assays were designated as groundnut KASP assay markers (GKAMs) and screened on 94 genotypes (validation set) that included parental lines of 27 mapping populations, seven synthetic autotetraploid and amphidiploid lines, and 19 wild species accessions. As a result, 90 GKAMs could be validated and 73 GKAMs showed polymorphism in the validation set. Validated GKAMs were screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships. Cluster analysis of marker allelic data grouped accessions according to their genome type, subspecies, and botanical variety. The subspecies Arachis hypogaea L. subsp. fastigiata Waldron and A. hypogaea subsp. hypogaea formed distinct cluster; however, some overlaps were found indicating their frequent intercrossing during the course of evolution. The wild species, having diploid genomes, were grouped into a single cluster. The average polymorphism information content value for polymorphic GKAMs was 0.32 in the validation set and 0.31 in the reference set. These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species. P

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Single Nucleotide Polymorphism-based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost-Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays

Background
The genus Arachis is native to a region that includes Central Brazil and neighboring countries Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp) is essential to develop strategies of collection, conservation and use of the germplasm in variety development The identity of the ancestor progenitor species of cultivated peanut has also been of great interest Several species have been suggested as putative AA and BB genome donors to allotetraploid A hypogaea Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, and highly polymorphic genetic markers, appropriate for genetic diversity studies Microsatellite markers may also, to some extent, support phylogenetic inferences Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A hypogea and its wild relatives

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Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome.

A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers

Assessment of genetic diversity in a crop species is prerequisite to its improvement. The use of germplasm with distinct DNA profiles will help to generate genetically diversified breeding populations. The aims of the present experiment were to study molecular diversity among selected groundnut accessions and identify those with distinct DNA profiles for mapping and genetic enhancement. Twenty-six accessions and eight primers of a 10-mer were selected for random amplified polymorphic DNA assay. The genetic similarity (Sij) ranged from 59.0% to 98.8%, with an average of 86.2%. Both multidimensional scaling and unweighted pair-group method with arithmetic averages (UPGMA) dendrograms revealed the existence of five distinct clusters. However, this classification could not be related to known biological information about the accessions falling into different clusters. Some accessions with diverse DNA profiles (ICG 1448, 7101, and 1471, and ICGV 99006 and 99014) were identified for mapping and genetic enhancement in groundnut

/pdf/assessment-of-genetic-diversity-among-selected-groundnut-56sj4wg5ce.pdf

W. Yuejin

Papers

Assessment of genetic diversity among selected groundnut germplasm. I. RAPD analysis.