An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population

被引:179
作者
Hauser, Lorenz [1 ]
Baird, Melissa [1 ]
Hilborn, Ray [1 ]
Seeb, Lisa W. [1 ]
Seeb, James E. [1 ]
机构
[1] Univ Washington, Sch Aquat & Fishery Sci, Seattle, WA 98195 USA
基金
美国国家科学基金会;
关键词
Cervus; Colony; kinship; microsatellites; parentage; single nucleotide polymorphisms; MAXIMUM-LIKELIHOOD-ESTIMATION; REPRODUCTIVE SUCCESS; MULTIPLE PATERNITY; GENOTYPING ERRORS; SIBSHIP INFERENCE; COMPUTER-PROGRAM; ATLANTIC SALMON; GENETIC-MARKERS; RELATEDNESS; LOCI;
D O I
10.1111/j.1755-0998.2010.02961.x
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Because of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high-throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites-that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs (H-E = 0.30, 80 independent alleles) and 11 microsatellites (H-E = 0.85, 192 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, although Cervus and SNPPIT detected more parent pairs. Identification of full-sib groups without parental information from relatedness measures was possible using both marker systems, although explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles.
引用
收藏
页码:150 / 161
页数:12
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