Development, inheritance and evaluation of 55 novel single nucleotide polymorphism markers for parentage assignment in the Pacific oyster (Crassostrea gigas)

Autor: Yu-Lin Jin, Hong Yu, Lingfeng Kong, Qi Li
Rok vydání: 2013
Předmět:
Zdroj: Genes & Genomics. 36:129-141
ISSN: 2092-9293
1976-9571
DOI: 10.1007/s13258-013-0150-0
Popis: Expressed sequence tags (ESTs) are essential to ascertain gene function, but also to identify polymorphic gene-associated single nucleotide polymorphisms (SNPs) (type I markers) suitable for map construction and population analysis in the Pacific oyster (Crassostrea gigas). In this study, a total of 48,769 putative SNPs were detected from 46,171 ESTs of the Pacific oyster. Fifty-five gene-derived SNPs were isolated and characterized by means of high resolution melting analysis. The observed and expected heterozygosities ranged from 0.063–0.563 and 0.091–0.448, with an average of 0.284 and 0.279, respectively. The SNPs were tested on 6 families of C. gigas for examination of inheritance mode of SNPs. One hundred and thirty-two tests of segregation ratios at 48 loci revealed 30 (22 %) significant departures from expected Mendelian ratios, but no null allele was detected. The power of these SNPs in parentage assignment was evaluated, and the real data demonstrated that 17 % of all real offspring were unambiguously assigned parents with 30 SNPs, and 100 % of the offspring were correctly allocated to their parents when 40 or more SNPs were used. The results obtained in this study suggest that gene-derived SNPs will complement the currently available microsatellite markers and may be useful for comparative mapping, marker-assisted selection and evolutionary studies.
Databáze: OpenAIRE
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