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ARS Home » Southeast Area » Stuttgart, Arkansas » Harry K. Dupree Stuttgart National Aquaculture Research Cntr » Research » Publications at this Location » Publication #287520
Title: Efficiency of the inbreeding coefficient f and other estimators in detecting null alleles, as revealed by empirical data of locus oke3 across 65 populations of chum salmon Oncorhynchus keta

Author
item ZHIVOTOVSKY, LEV - State Research Institute Of Genetics And Selection Of Industrial Microorganisms (GENETIKA)
item KORDICHEVA, SVETLANA - State Research Institute Of Genetics And Selection Of Industrial Microorganisms (GENETIKA)
item SHAIKHAEV, EVGENY - State Research Institute Of Genetics And Selection Of Industrial Microorganisms (GENETIKA)
item RUBTSOVA, GALINA - State Research Institute Of Genetics And Selection Of Industrial Microorganisms (GENETIKA)
item SHITOVA, MARINA - State Research Institute Of Genetics And Selection Of Industrial Microorganisms (GENETIKA)
item Fuller, Adam
item GHARRETT, ANTHONY - University Of Alaska
item SHAIKHAEV, GADZHIRAMAZAN - State Research Institute Of Genetics And Selection Of Industrial Microorganisms (GENETIKA)
item AFANASIEV, KONSTANTIN - State Research Institute Of Genetics And Selection Of Industrial Microorganisms (GENETIKA)

Submitted to: Journal of Fish Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/24/2014
Publication Date: 1/1/2015
Citation: Zhivotovsky, L.A., Kordicheva, S.Y., Shaikhaev, E.G., Rubtsova, G.A., Shitova, M.V., Fuller, S.A., Gharrett, A.J., Shaikhaev, G.O., Afanasiev, K. 2015. Efficiency of the inbreeding coefficient f and other estimators in detecting null alleles, as revealed by empirical data of locus oke3 across 65 populations of chum salmon Oncorhynchus keta. Journal of Fish Biology. 86:402-408.

Interpretive Summary: Some DNA markers may be removed from data analyses if the researcher suspects there may be a problem with the marker, such as if the marker shows a lack of variation in a population, possibly due to the presence of a null allele. Null alleles, identified as a reaction that does not generate sufficient copies of the DNA to be able to analyze due to a mutation, result in the misidentification of a genetic marker’s "true" score. This can become a problem if multiple markers are suspected of having reaction failures, necessitating "throwing out" the marker, as it reduces the amount of information available to researchers. Because these problems may occur often in only a small part of the species' range, studies in different geographic areas may encounter a higher number of these issues. A survey of 65 populations of chum salmon across the species' range, revealed fully 1/3 of the suspected problematic marker scores actually were caused by these mutations, and many were specific to geographically distinct groups of fish. This large difference among populations can alter estimates of population genetics parameters. This study demonstrated the lack of variation in markers across populations is a reliable indicator of null alleles and demonstrates useful methods to improve estimates of population statistics.

Technical Abstract: Polymorphic DNA markers, e.g. mini- or microsatellite (SSR) loci, are often removed from data analyses if an excess of homozygosity, presumably an indication of null alleles, is observed. However, exclusion of such loci can reduce available information if multiple loci carry null alleles. Because null alleles may be abundant in part of the species range, studies in different geographic areas often include different suites of loci and are incompatible for broader studies. Here we provide chum salmon as an example for which many Asian collections have homozygosity excesses at the minisatellite locus Oke3. A survey of 65 populations across the species range, revealed 947 homozygotes in 2976 fish. We designed additional PCR primers for Oke3, selected new forward and reverse primers, and discovered that 328 of the homozygotes were actually heterozygotes. A SNP and one deletion produced several different null alleles, which had population frequencies ranging between 0 and 0.13 in different populations; some null alleles were specific to geographically distinct stocks. Moreover, the large frequency differences in null alleles among populations can alter estimates of population genetics parameters. This study demonstrated that significant homozygosity excesses across populations is a reliable indicator of null alleles and that developing alternative set(s) of PCR primers for SSR loci may: avoid the exclusion of DNA markers from population data sets; resolve mutations in the primer zone, which can provide additional population markers; and amplify cryptic SSR alleles, which can improve estimates of population statistics, e.g. allelic richness, allele diversity, and genetic distances.