Insights from Initial Variant Detection by Sequencing Single Sperm in Cattle

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dc.contributor.authorYang, Liu
dc.contributor.authorGao, Yahui
dc.contributor.authorBoschiero, Clarissa
dc.contributor.authorLi, Li
dc.contributor.authorZhang, Hongping
dc.contributor.authorMa, Li
dc.contributor.authorLiu, George E.
dc.date.accessioned2023-10-30T16:33:17Z
dc.date.available2023-10-30T16:33:17Z
dc.date.issued2021-11-15
dc.description.abstractMeiotic de novo mutation (DNM) is one of the important phenomena contributing to gamete genome diversity. However, except for humans and a few model organisms, they are not well studied in livestock, including cattle. Moreover, bulk sperm samples have been routinely utilized in experiments, which include millions of single sperm cells and only report high-frequency variants. In this study, we isolated and sequenced 143 single sperms from two Holstein bulls and identified hundreds of candidate DNM events in ten sperms with deep sequencing coverage. We estimated DNM rates ranging from 1.08 × 10−8 to 3.78 × 10−8 per nucleotide per generation. We further validated 12 out of 14 selected DNM events using Sanger sequencing. To our knowledge, this is the first single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of point mutations and male fertility. Our preliminary results pointed out future research directions and highlighted the importance of uniform whole genome amplification, deep sequence coverage, and dedicated software pipelines for genetic variant detection using single-cell sequencing data.
dc.description.urihttps://doi.org/10.3390/dairy2040050
dc.identifierhttps://doi.org/10.13016/dspace/n5qf-rnny
dc.identifier.citationYang, L.; Gao, Y.; Boschiero, C.; Li, L.; Zhang, H.; Ma, L.; Liu, G.E. Insights from Initial Variant Detection by Sequencing Single Sperm in Cattle. Dairy 2021, 2, 649-657.
dc.identifier.urihttp://hdl.handle.net/1903/31186
dc.language.isoen_US
dc.publisherMDPI
dc.relation.isAvailableAtCollege of Agriculture & Natural Resourcesen_us
dc.relation.isAvailableAtAnimal & Avian Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectcattle
dc.subjectsingle sperm sequencing
dc.subjectde novo mutation
dc.subjectvariant detection
dc.titleInsights from Initial Variant Detection by Sequencing Single Sperm in Cattle
dc.typeArticle
local.equitableAccessSubmissionNo

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