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Most of the chloroplast genome in higher plants is highly conserved. However, two hypervariable regions have been identified in the alfalfa (Medicago sativa L) chloroplast genome. The hypervariable regions are being used as a means to assess the degree of relationship among the accessions of the perennial alfalfa core collection. Genetic distance was measured as the proportion of hypervariable fragments not in common among two plant accessions; 24 plants are assayed from each accession. The country of origin of each PI was determined from the USDA Germplasm Resources Information Network (GRIN) system (http://www.ars-grin.gov). The average distance of each accession to all other accessions was calculated and used to calculate average between-country-of-origin distances (Table 1). The likely basic germplasm source (Barnes et al., 1977) of each PI was determined from the country of origin and its position on the basic germplasm source map. The average genetic distances of each of the basic germplasm sources to all other germplasm sources are shown in Table 2. Mean genetic distances ranged from 0.33 to 0.99 with a mean of 0.46. A larger average genetic distance was interpreted to indicate a more distinctive population, i.e.the PIs from that group (country or germplasm source) were most unlike the other PIs. By this criterion, the most distinctive PIs were of the African and Chilean germplasm sources (Table 2). Interestingly, the most distinctive PIs grouped by country of origin tended to be from countries which are not considered to be part of the basic germplasm origins, such as China and parts of the Great Plains of the US (Table 1). These results indicate that the hypervariable regions of the chloroplast DNA provide a means to distinguish accessions and populations, and to provide a quantitative measure of relatedness.
Barnes, DK, Bingham, ET, Murphy, RP, Hunt, OJ, Beard, DF, Skrdla WH, and Teuber, LR. 1977. Alfalfa Germplasm in the United States: Genetic Vulnerability, Use, Improvement and Maintenance. U.S. Department of Agriculture, U.S. Printing Office. Technical Bulletin No. 1571.
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