A free lunch: microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster.

IF 2.1 3区生物学 Q3 GENETICS & HEREDITY

G3: Genes|Genomes|Genetics Pub Date : 2024-12-19 DOI:10.1093/g3journal/jkae280

Neil F Thompson, Ben J G Sutherland, Timothy J Green, Thomas A Delomas

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引用次数: 0

Abstract

Amplicon panels using genotyping by sequencing methods are now common, but have focused on characterizing SNP markers. We investigate how microhaplotype (MH) discovery within a recently developed Pacific oyster (Magallana gigas) amplicon panel could increase the statistical power for relationship assignment. Trios (offspring and two parents) from three populations in a newly established breeding program were genotyped on a 592 locus panel. After processing, 92% of retained amplicons contained polymorphic MH variants and 85% of monomorphic SNP markers contained MH variation. The increased allelic richness resulted in substantially improved power for relationship assignment with much lower estimated false positive rates. No substantive differences in assignment accuracy occurred between SNP and MH datasets, but using MHs increased the separation in log-likelihood values between true parents and highly related potential parents (aunts and uncles). A high number of Mendelian incompatibilities among trios were observed, likely due to null alleles. Further development of a MH panel, including removing loci with high rates of null alleles, would enable high-throughput genotyping by reducing panel size and therefore cost for Pacific oyster research and breeding programs.

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来源期刊

G3: Genes|Genomes|Genetics GENETICS & HEREDITY-

CiteScore

5.10

自引率

3.80%

发文量

305

审稿时长

3-8 weeks

期刊介绍： G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.