Submitted to: Agricultural Experiment Station Publication
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/17/2004
Publication Date: 12/1/2004
Citation: Krishna, G.K., Zhang, J., Burrow, M., Pittman, R.N., Delikostadinov, S.G. 2004. Genetic diversity in valencia peanut (arachis hypogaea l.) using microsatellite markers. Cellular & Molecular Biology Letters. 9(4A):685-697 Interpretive Summary: In cultivated peanut, molecular markers have identified little variation or exotic lines. No polymorphism between Arachis hypogaea and A. monticola, while significant amount of variation has been reported among Arachis species and between botanical varieties of cultivated peanut using AFLP and DAF techniques. This investigation was carried out to identify genetic diversity in Valencia type peanuts belonging to the subspecies fastigiata variety fastigiata using the fluorescence-based SSR primers. Plant material consisted of 48 Valencia peanut genotypes from 20 different countries. Genomic DNA was isolated from green leaves of 25-day old seedlings. Leaves from 3-5 seedlings were pooled for DNA precipitation. Samples were analyzed using an agarose mixture of Metaphor and Agarose and those primer pairs showing polymorphism were florescently labeled and later analyzed for all genotypes. PCR reactions were prepared and amplified in a PE 97000 thermocycler. For sequencer band detection 2ul of amplified DNA and mixed with 0.3 ul of Gene Scan 350XL ROX standard except for primer 4-24 before loading. Samples were loaded on an ABI 377 sequencer. Electrophoretograms in the range of 75-500 bp were analayzed and compared using Gene Scan software. The results indicated that (1) Considerable genetic variation was discovered among the analyzed genotypes; (2) The f-SSR based clustering could identify the putative pedigree types of the Valencia types with diverse origins; and (3) the f-SSR in general is sufficient to obtain estimates of genetic divergence for the material in the study. The results are being utilized in the New Mexico peanut breeding program for parental selection and development of mapping population with linkage map construction. This study demonstrated the potential of SSR markers to reveal genetic polymorphism useful for genetic diversity analysis and genotyping individuals. This study with SSR's revealed the U.S. Valencia germplasm is not that narrow and that the European germplasm from Bulgaria is unique and form a separate group. The implication of this study that the current SSR markers could reveal genetic polymorphism in other botanical varieties of peanuts. Such information could be used to develop a linkage map and the markers could be used to assist in efficient breeding of various traits such as yield, flavor, oil quality, fatty acid content, and resistance to pest and diseases.
Technical Abstract: In cultivated peanut, RFLP, RAPD, and AFLP markers have identified little variation or exotic lines. This investigation was carried out to identify genetic diversity in Valencia type peanuts belonging to Arachis hypogaea fastigiata var. fastigiata using the florescence-based SSR. Plant materials consisted of 48 Valencia peanut genotypes from 20 different countries around the world. Levels of polymorphism per primer were very high; 100% in most primer pairs except in one primer pair which exhibited on 66.6% polymorphism among the genotypes screened. All the primer pairs were informative among which primer Lec 1 amplified 19 alleles. Eighty-six percent of the variation in the estimates of genetic similarity was explained by the first three components indicating the suitability of microsatellite based marker approaches for genetic clustering. The first Principal component explained approximately 80% of the variation and resolved the Valencia genotypes based on subspecies parental history. This investigation demonstrates the potential of SSR markers to reveal extensive genetic polymorphism useful for genetic diversity analysis and genotyping individuals. Thus, microsatellites have revealed that the U.S. germplasm is not that narrow and the European germplasm from Bulgaris is unique in that they form a separate group.