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ABSTRACT: A novel method is introduced for producing molecular markers in plants using single 15- to 18-mer PCR primers designed from the short conserved consensus branch point signal sequences and standard agarose gel electrophoresis. This method was tested on cultivated peanut and verified to give good fingerprinting results in other plant species (mango, banana, and longan). These single primers, designed from relatively conserved branch point signal sequences within gene introns, should be universal across other plant species. The method is rapid, simple, and efficient, and it requires no sequence information of the plant genome of interest. It could be used in conjunction with, or as a substitute for, conventional RAPD or ISSR techniques for applications including genetic diversity analysis, phylogenetic tree construction, and quantitative trait locus mapping. This technique provides a new way to develop molecular markers for assessing genetic diversity of germplasm in diverse species based on conserved branch point signal sequences.
Biochemical Genetics 01/2011; 49(5-6):352-63. · 0.86 Impact Factor
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ABSTRACT: Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic diversity and relatedness among 20 accessions of four major botanical varieties of peanut. Of 36 primers screened, 18 primers could produce unambiguous and reproducible bands. All 18 primers generated a total of 157 fragments, with a mean of 8.72 ranging from 4 to 17 per primer. Of 157 bands, 60 (38.22%) were polymorphic. One to seven polymorphic bands were amplified per primer, with 3.33 polymorphic bands on average. Polymorphism per primer ranged from 14.29 to 66.67%, with an average of 36.76%. The results revealed that not all accessions of the same variety were grouped together and high genetic similarity was detected among the tested genotypes based on cluster analysis and genetic distance analysis, respectively. Further, accession-specific markers were observed in several accessions. All these results demonstrated the following: (1) start codon targeted polymorphism technique can be utilized to identify DNA polymorphisms and fingerprint cultivars in domesticated peanut, and (2) it possesses considerable potential for studying genetic diversity and relationships among peanut accessions.
Molecular Biology Reports 11/2010; 38(5):3487-94. · 2.93 Impact Factor
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ABSTRACT: Peanut (Arachis hypogaea L.) is an important source crop for edible oil and protein. It is important to identify the genetic diversity of peanut genetic resources for cultivar development and evaluation of peanut accessions. Thirty-four SSR markers were used to assess the genetic variation of four sets of twenty-four accessions each from the four botanical varieties of the cultivated peanut. Among the tested accessions, ten to sixteen pairs of SSR primers showed polymorphisms. The maximum differentiation index, which was defined as the degree of genetic differentiation, was as high as 0.992 in the tested accessions. Each accession could be discriminated by a specific set of polymorphic SSR primers, and the intra-variety genetic distance was determined among accessions, with an average of 0.59 in var. fastigiata 0.46 in var. hypogaea 0.38 in var. vulgaris and 0.17 in var. hirsuta. Dendrogrames based on genetic distances were constructed for the four botanical varieties, which revealed the existence of different clusters. It was concluded that there was abundant intra-variety SSR polymorphism, and with more and more SSR markers being developed, the intrinsic genetic diversity would be detected and the development of genetic map and marker-assisted selection for cultivated peanut would be feasible.
Journal of Genetics and Genomics 06/2007; 34(5):449-59. · 1.88 Impact Factor
