Sel’skokhozyaistvennaya Biologiya [Agricultural Biology], 2015, Vol. 50, № 5, pp. 571-578.

doi: 10.15389/agrobiology.2015.5.571eng

UDC 575.17:575.118.5:575.162:57.087.1

Supported in part by Russian Foundation for Basic Research (grant № 13-04-00128-а)

EVALUATION OF THE MEASURE OF POLYMORPHISM INFORMATION OF GENETIC DIVERSITY

Yu.V. Chesnokov, A.M. Artemyeva

Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources, Federal Agency of Scientific Organizations,
42-44, ul. Bol’shaya Morskaya, St. Petersburg, 190000 Russia,
e-mail yu.chesnokov@vir.nw.ru

Received February 26, 2015

 

Gene identification and mapping are one of the main goals of plant and animal genetics. Upon verifying genetic linkage it is usually found which marker loci (markers) possess alleles co-segregated with the alleles of the desired locus. Marker utility for these purposes depends on the number of alleles, which the marker possesses, and their relative rates. There are two indexes, or measures, usually used for the polymorphism degree evaluation. They are the heterozygosity (Н) for which the evaluation method and variability formula are well known (M. Nei et al., 1974, 1979), and polymorphism information content (PIC) (D. Botstein et al., 1980). Based on published data, we described the statistical approaches which are used for analysis of polymorphism information. Herein, the value of polymorphism information content, heterozygosity and some associated values detected upon evaluation of genetic diversity on interspecific and intraspecific population levels are considered. PIC shows haw the marker can indicate the population polymorphism depending on the number and frequency of the alleles (D. Botstein et al., 1980). So the PIC reflects a discriminating ability of the marker and, in fact, depends on the number of known alleles and their frequency distribution, thus being equal to genetic diversity. PIC maximal value for dominant markers is 0.5. Note, that for the markers with equal distribution in the population the PIC values are higher. They are much higher for markers with multiple alleles, and, however, also depend on the frequency distribution of the alleles. Using 135 SSR (simple sequence repeats) and 123 S-SAP (sequence specific amplified polymorphism) primers, we found 135 SSR и 123 S-SAP polymorphic markers among 96 Brassica rapa L. samples from the VIR (N.I. Vavilov Institute of Plant Genetic Resources) core collection. The PIC values for both markers, SSR and S-SAP markers were 0.316, 0.257 and 0.379 (50 % higher on average), respectively. Expected heterozigosity (HE) is usually used to describe the genetic diversity because it is less sensitive to the sample size compared to observed heterozigosity (HO). The  crossings in the population are occasional, if HO and HE are similar (i.e., no reliable differences found). They are related as HO < HE in inbred population, and as HO > HE in case of occasional crossing prevailing compared with inbreeding. Effective multiplex ratio (EMR) is calculated as total number of polymorphic loci per primer multiplied by the rate of polymorphic loci from their total number (W. Powell с соавт., 1996; J. Nagaraju с соавт., 2001). Marker index (MI) is a statistical parameter used to estimate total utility of the maker system; the higher MI, the better method is used) (W. Powell et al., 1996; J. Nagaraju et al., 2001). Resolving power (Rp) is a parameter characterizing ability of the primer/marker combination to detect differences between large numbers of genotypes (J.E. Gilbert et al., 1999; A. Prevost et al., 1999). The information about some software which can be used for calculation of polymorphism information content value and heterozygosity is also summarized. The formula for effective multiplex ratio, marker index calculation, and resolving power calculation are shown.  

Keywords: heterozygosity, polymorphism information content value, effective multiplex ratio, marker index, resolving power, software.

 

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