A search for null alleles at the microsatellite locus of chum salmon (Oncorhynchus keta Walbaum)

Kordicheva, S. Yu.; Рубцова, Г. А.; Shitova, M. A.; Shaikhaev, G. O.; Afanasiev, K. I.; Zhivotovsky, Lev A.

doi:10.1134/s1022795410080168

Cited by 12 publications

(9 citation statements)

References 10 publications

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“…Using these primers for allele sequencing, the nucleotide sequences of the One103 [15], One109 [15], OMM1037 [16], and Ots102 [17] were determined in all of the analyzed species. In addition, the primers developed were used for sequencing of the Oke3 locus [18] in all of the species of interest, except taimen [19]. Furthermore, using the NCBI BLAST program (http://blast.ncbi.nlm.…”

Section: Methodsmentioning

confidence: 99%

The evolution of microsatellite loci in salmonid fishes

Шайхаев

Zhivotovsky

2014

Russ J Genet

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In ten species of salmonid fishes, sequences of five microsatellite loci were determined. Consid erable differences in the structure of the same microsatellites in different species were found. It was demon strated that the evolution of microsatellites was a complex process, including changes in the copy number, point mutations, and extended deletions and insertions, leading either to the formation of microsatellites or to their loss.

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Section: Methodsmentioning

confidence: 99%

The evolution of microsatellite loci in salmonid fishes

Шайхаев

Zhivotovsky

2014

Russ J Genet

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“…Essa é uma situação muito comum para marcadores microssatélites, que pode levar a erros de genotipagem (Kordicheva et al, 2010).…”

Section: Resultsunclassified

“…O desequilíbrio de Hardy-Weinberg pode ser causado por diversos motivos, como: endogamia, mistura de várias populações com diferentes frequências de alelos, endocruzamento, excesso de homozigose e presença de alelos nulos (Romana-Eguia et al, 2005;Kordicheva et al, 2010). No presente estudo, o desequilíbrio observado nos resultados pode ser explicado pelo endocruzamento na formação das gerações.…”

Section: Resultsunclassified

Caracterização genética de gerações de tilápia Gift por meio de marcadores microssatélites

Rodríguez-Rodríguez

Lopera-Barrero

Vargas

et al. 2013

Pesq. agropec. bras.

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O objetivo deste trabalho foi caracterizar a variabilidade genética nos parentais (G0) e em três gerações consecutivas (G1, G2 e G3) de tilápia Gift (genetically improved farmed tilapia), por meio de marcadores microssatélites. Trezentos e sessenta indivíduos, provenientes do programa de melhoramento da Universidade Estadual de Maringá, foram selecionados quanto ao ganho de peso. O total de 21 alelos foi encontrado nos cinco loci microssatélites polimórficos (G12292, UNH140; G12311, UNH159; G12312, UNH160; G12314, UNH162; e G12315, UNH163), com número médio entre três e cinco alelos por locus. As frequências alélicas variaram de 0,017 (UNH160 - G2) a 0,750 (UNH160 - G0). A heterozigosidade média observada foi de 0,501, 0,391, 0,531 e 0,503 para G0, G1, G2 e G3, respectivamente. O coeficiente de endogamia médio foi 0,192 (G0), 0,401 (G1), 0,230 (G2) e 0,301 (G3). Todas as gerações apresentaram desvio no equilíbrio de Hardy-Weinberg, com desequilíbrio de ligação na maioria dos loci. Exceto para a G1, a heterozigosidade foi mantida nas gerações G2 e G3, o que indica que não há perda significativa de variabilidade genética no programa de melhoramento.

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“…The practice of excluding loci, however, may be difficult to extend to large‐scale population studies because some populations may be free of null alleles at a given locus whereas other populations may have them. For example, in multiple samples of chum salmon Oncorhynchus keta (Walbaum 1792), taken from the Columbia River, U.S.A., no deviation from Hardy–Weinberg expectations at the SSR locus oke3 were observed (Small et al , ), whereas a strong deviation attributable to oke3 null alleles was observed in the Kuril Islands, Russia, O. keta (Kordicheva et al , ).…”

Section: Frequencies Of Null Alleles At Locus Oke3 That Were Revealedmentioning

confidence: 99%

“…The approach was to evaluate variability at the SSR locus oke3 with two sets of primers: (1) the original described for the locus, which has a varying number of identical 13-nucleotide repeats (Bucholz et al, 2001) and (2) new primers re-designed to resolve PCR products for all alleles at this locus (Kordicheva et al, 2010). Collections from 65 population samples (a total of 2954 fish) were sampled from spawning runs in 32 rivers across a large part of the range of O. keta (Fig.1).…”

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confidence: 99%

Efficiency of the inbreeding coefficientfand other estimators in detecting null alleles, as revealed by empirical data of locusoke3across 65 populations of chum salmonOncorhynchus keta

Zhivotovsky

Kordicheva

Шайхаев

et al. 2014

Journal of Fish Biology

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A survey of 65 populations of chum salmon Oncorhynchus keta across the species range revealed homozygote excess (947 homozygotes in 2954 fish) at a polymerase chain reaction (PCR)-based simple sequence repeat (SSR) locus oke3 with multiple alleles, whereas re-designed PCR primers indicated that 328 of these homozygotes were actually heterozygotes. Statistically significant high positive values of inbreeding coefficients, f, in multiple populations appeared to be a reliable predictor of null alleles. Based on these data, three methods were checked for their ability to estimate null-allele frequencies.

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A search for null alleles at the microsatellite locus of chum salmon (Oncorhynchus keta Walbaum)

Cited by 12 publications

References 10 publications

The evolution of microsatellite loci in salmonid fishes

The evolution of microsatellite loci in salmonid fishes

Caracterização genética de gerações de tilápia Gift por meio de marcadores microssatélites

Efficiency of the inbreeding coefficientfand other estimators in detecting null alleles, as revealed by empirical data of locusoke3across 65 populations of chum salmonOncorhynchus keta

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