{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T18:04:44Z","timestamp":1789495484418,"version":"build-2803163510"},"reference-count":102,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2021-38420-34945"],"award-info":[{"award-number":["2021-38420-34945"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010576","name":"Iowa Pork Producers Association","doi-asserted-by":"publisher","award":["22015"],"award-info":[{"award-number":["22015"]}],"id":[{"id":"10.13039\/100010576","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2022-67015-36298"],"award-info":[{"award-number":["2022-67015-36298"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>Mammalian ejaculates contain heterogeneous sperm subpopulations that differ in subcellular architecture and developmental history, despite appearing morphologically uniform. The extent to which this cellular heterogeneity reflects underlying nuclear genomic structure within a sire remains largely unexplored. Mitochondrial architecture in sperm is established during spermatogenesis, with final assembly and organization occurring during spermiogenesis under nuclear genomic control, positioning variation in mitochondrial abundance and organization as a potential phenomic indicator of within-sire allelic segregation. Here, we tested whether sperm subpopulations defined by differing mitochondrial abundance exhibit systematic differences in nuclear allele representation. Boar sperm were resolved into low and high mitochondrial subpopulations using fluorescence-activated cell sorting based on MitoTracker\u2122 Green fluorescence while excluding debris, doublets, and non-viable cells. Epifluorescence microscopy confirmed that high MitoTracker\u2122 Green fluorescence sperm possessed longer mitochondrial sheaths, validating a structural distinction between subpopulations. Whole-genome sequencing of paired mitochondrial subpopulations from three boars was performed, and allelic ratio distortion was evaluated relative to heterozygous baseline populations. Analyses across heterozygous loci genome-wide identified candidate allele frequency shifts between mitochondrial-defined subpopulations, suggesting non-random segregation of alleles within ejaculates. Using a minimum sequencing depth of 30 reads in both sorted fractions, 182 candidate SNPs were identified with evidence of allele-frequency differences between mitochondrial fluorescence-defined subpopulations. These findings suggest that sperm mitochondrial abundance can potentially serve as an indirect, high-throughput marker of nuclear genomic heterogeneity within sires. This proof-of-concept framework establishes a foundation for future studies integrating sperm phenotyping, genome-wide allele-frequency analysis and functional validation to better characterize gamete-level heterogeneity.<\/jats:p>","DOI":"10.1371\/journal.pone.0358219","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T17:32:27Z","timestamp":1789493547000},"page":"e0358219","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Sperm subpopulations differing in mitochondrial abundance show divergent nuclear allele frequencies"],"prefix":"10.1371","volume":"21","author":[{"given":"Tyler","family":"Weide","sequence":"first","affiliation":[{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Department of Animal Science"]},{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Interdepartmental Genetics and Genomics"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Koltes","sequence":"additional","affiliation":[{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Department of Animal Science"]},{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Interdepartmental Genetics and Genomics"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Steibel","sequence":"additional","affiliation":[{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Department of Animal Science"]},{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Interdepartmental Genetics and Genomics"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7425-0131","authenticated-orcid":true,"given":"Karl","family":"Kerns","sequence":"additional","affiliation":[{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Department of Animal Science"]},{"name":"Iowa State University","place":["Ames, Iowa, United States of America"],"department":["Interdepartmental Genetics and Genomics"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"issue":"4","key":"pone.0358219.ref001","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1111\/j.1439-0531.2010.01725.x","article-title":"\u201cIn vitro\u201d capacitation and acrosome reaction are concomitant with specific changes in mitochondrial activity in boar sperm: evidence for a nucleated mitochondrial activation and for the existence of a capacitation-sensitive subpopulational structure","volume":"46","author":"L Rami\u00f3-Lluch","year":"2011","journal-title":"Reprod Domest Anim"},{"issue":"2","key":"pone.0358219.ref002","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1111\/j.1365-2605.2011.01218.x","article-title":"The role of mitochondria in energy production for human sperm motility","volume":"35","author":"P Piomboni","year":"2012","journal-title":"Int J Androl"},{"key":"pone.0358219.ref003","doi-asserted-by":"crossref","unstructured":"Barbagallo F, La Vignera S, Cannarella R, Aversa A, Calogero AE, Condorelli RA. Evaluation of sperm mitochondrial function: a key organelle for sperm motility. https:\/\/doi.org\/10.3390\/jcm9020363","DOI":"10.3390\/jcm9020363"},{"issue":"1","key":"pone.0358219.ref004","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1002\/jemt.10319","article-title":"Ubiquitin-dependent proteolysis in mammalian spermatogenesis, fertilization, and sperm quality control: killing three birds with one stone","volume":"61","author":"P Sutovsky","year":"2003","journal-title":"Microsc Res Tech"},{"issue":"2","key":"pone.0358219.ref005","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1111\/andr.12320","article-title":"Molecular changes and signaling events occurring in spermatozoa during epididymal maturation","volume":"5","author":"MG Gervasi","year":"2017","journal-title":"Andrology"},{"issue":"5","key":"pone.0358219.ref006","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1095\/biolreprod59.5.1037","article-title":"Relative impact of oxidative stress on the functional competence and genomic integrity of human spermatozoa","volume":"59","author":"RJ Aitken","year":"1998","journal-title":"Biol Reprod"},{"issue":"3","key":"pone.0358219.ref007","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1042\/BJ20102121","article-title":"Regulation of spermiogenesis, spermiation and blood-testis barrier dynamics: novel insights from studies on Eps8 and Arp3","volume":"435","author":"CY Cheng","year":"2011","journal-title":"Biochem J"},{"issue":"5","key":"pone.0358219.ref008","doi-asserted-by":"crossref","first-page":"726","DOI":"10.4103\/1008-682X.155255","article-title":"Epididymosomes: a heterogeneous population of microvesicles with multiple functions in sperm maturation and storage","volume":"17","author":"R Sullivan","year":"2015","journal-title":"Asian J Androl"},{"issue":"2","key":"pone.0358219.ref009","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1093\/humupd\/dmn055","article-title":"New insights into epididymal biology and function","volume":"15","author":"GA Cornwall","year":"2009","journal-title":"Hum Reprod Update"},{"issue":"2","key":"pone.0358219.ref010","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1111\/brv.12569","article-title":"Post-ejaculatory modifications to sperm (PEMS)","volume":"95","author":"S Pitnick","year":"2020","journal-title":"Biol Rev Camb Philos Soc"},{"key":"pone.0358219.ref011","doi-asserted-by":"crossref","first-page":"72","DOI":"10.3389\/fcell.2018.00072","article-title":"Molecular basis of human sperm capacitation","volume":"6","author":"LC Puga Molina","year":"2018","journal-title":"Front Cell Dev Biol"},{"issue":"1","key":"pone.0358219.ref012","doi-asserted-by":"crossref","DOI":"10.1002\/rmb2.12614","article-title":"Molecular mechanisms of mammalian sperm capacitation, and its regulation by sodium-dependent secondary active transporters","volume":"23","author":"GL Takei","year":"2024","journal-title":"Reprod Med Biol"},{"issue":"5","key":"pone.0358219.ref013","doi-asserted-by":"crossref","DOI":"10.1530\/REP-13-0178","article-title":"Mitochondria functionality and sperm quality","volume":"146","author":"A Amaral","year":"2013","journal-title":"Reproduction"},{"issue":"2","key":"pone.0358219.ref014","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1152\/physrev.00025.2007","article-title":"Transcriptional paradigms in mammalian mitochondrial biogenesis and function","volume":"88","author":"RC Scarpulla","year":"2008","journal-title":"Physiol Rev"},{"issue":"2","key":"pone.0358219.ref015","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/S0005-2728(98)00161-3","article-title":"The mitochondrial genome: structure, transcription, translation and replication","volume":"1410","author":"JW Taanman","year":"1999","journal-title":"Biochim Biophys Acta"},{"issue":"3","key":"pone.0358219.ref016","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1002\/cm.970190306","article-title":"Metabolic regulation in mammalian sperm: mitochondrial volume determines sperm length and flagellar beat frequency","volume":"19","author":"RA Cardullo","year":"1991","journal-title":"Cell Motil Cytoskeleton"},{"key":"pone.0358219.ref017","article-title":"Sperm mitochondrial sheath formation \u2014 how and why?","author":"ML Graffeo","year":"2025","journal-title":"Nature Reviews Urology"},{"issue":"2","key":"pone.0358219.ref018","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1016\/0012-1606(75)90411-X","article-title":"The mammalian spermatozoon","volume":"44","author":"DW Fawcett","year":"1975","journal-title":"Dev Biol"},{"issue":"2","key":"pone.0358219.ref019","doi-asserted-by":"crossref","first-page":"230","DOI":"10.4103\/1008-682X.135123","article-title":"Oxidative phosphorylation versus glycolysis: what fuel do spermatozoa use?","volume":"17","author":"SS du Plessis","year":"2015","journal-title":"Asian J Androl"},{"issue":"10","key":"pone.0358219.ref020","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1002\/mrd.22871","article-title":"Reactive oxygen species as mediators of sperm capacitation and pathological damage","volume":"84","author":"RJ Aitken","year":"2017","journal-title":"Mol Reprod Dev"},{"issue":"4","key":"pone.0358219.ref021","doi-asserted-by":"crossref","DOI":"10.1096\/fj.202301957RR","article-title":"Mitochondrial function and reactive oxygen species production during human sperm capacitation: unraveling key players","volume":"38","author":"PA Irigoyen","year":"2024","journal-title":"FASEB J"},{"key":"pone.0358219.ref022","doi-asserted-by":"crossref","first-page":"767161","DOI":"10.3389\/fcell.2021.767161","article-title":"Capacitation-induced mitochondrial activity is required for sperm fertilizing ability in mice by modulating hyperactivation","volume":"9","author":"MM Giaccagli","year":"2021","journal-title":"Front Cell Dev Biol"},{"issue":"5","key":"pone.0358219.ref023","doi-asserted-by":"crossref","first-page":"563","DOI":"10.3390\/genes11050563","article-title":"Mitochondrial protein quality control mechanisms","volume":"11","author":"P Jadiya","year":"2020","journal-title":"Genes (Basel)"},{"issue":"3","key":"pone.0358219.ref024","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/ng0398-231","article-title":"Mitochondrial transcription factor a is necessary for mtDNA maintenance and embryogenesis in mice","volume":"18","author":"NG Larsson","year":"1998","journal-title":"Nat Genet"},{"issue":"4","key":"pone.0358219.ref025","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1002\/jemt.20785","article-title":"Surfing the wave, cycle, life history, and genes\/proteins expressed by testicular germ cells. Part 4: intercellular bridges, mitochondria, nuclear envelope, apoptosis, ubiquitination, membrane\/voltage-gated channels, methylation\/acetylation, and transcription factors","volume":"73","author":"L Hermo","year":"2010","journal-title":"Microsc Res Tech"},{"issue":"48","key":"pone.0358219.ref026","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2118020118","article-title":"Mitochondria-cytoskeleton interactions in mammalian sperm revealed by cryoelectron tomography","volume":"118","author":"H Wang","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"pone.0358219.ref027","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.3390\/antiox9111033","article-title":"Relationship between the length of sperm tail mitochondrial sheath and fertility traits in boars used for artificial insemination","volume":"9","author":"K Kerns","year":"2020","journal-title":"Antioxidants"},{"key":"pone.0358219.ref028","doi-asserted-by":"crossref","unstructured":"Parameters and Probes. Practical Flow Cytometry. 2003. 273\u2013410.","DOI":"10.1002\/0471722731.ch7"},{"key":"pone.0358219.ref029","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1111\/j.1439-0531.2010.01622.x","article-title":"Probes and techniques for sperm evaluation by flow cytometry","author":"F Mart\u00ednez-Pastor","year":"2010","journal-title":"Reprod Domest Anim"},{"issue":"4","key":"pone.0358219.ref030","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1017\/S0967199415000490","article-title":"Simultaneous evaluation of plasma membrane integrity, acrosomal integrity, and mitochondrial membrane potential in bovine spermatozoa by flow cytometry","volume":"24","author":"C Kanno","year":"2016","journal-title":"Zygote"},{"issue":"6","key":"pone.0358219.ref031","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1002\/cyto.a.21061","article-title":"Cytometric assessment of mitochondria using fluorescent probes","volume":"79","author":"C Cottet-Rousselle","year":"2011","journal-title":"Cytometry A"},{"key":"pone.0358219.ref032","doi-asserted-by":"crossref","first-page":"213","DOI":"10.2527\/1999.77suppl_2213x","article-title":"The Beltsville sperm sexing technology: high-speed sperm sorting gives improved sperm output for in vitro fertilization and AI","author":"LA Johnson","year":"1999","journal-title":"J Anim Sci"},{"key":"pone.0358219.ref033","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1017\/S1751731114000202","article-title":"Update on sexed semen technology in cattle","volume":"8","author":"GE Seidel","year":"2014","journal-title":"Animal"},{"issue":"8","key":"pone.0358219.ref034","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1016\/j.theriogenology.2008.06.009","article-title":"Functional integrity of sex-sorted, frozen-thawed boar sperm and its potential for artificial insemination","volume":"70","author":"R Bathgate","year":"2008","journal-title":"Theriogenology"},{"issue":"1","key":"pone.0358219.ref035","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1111\/rda.12640","article-title":"Flow cytometric chromosomal sex sorting of stallion spermatozoa induces oxidative stress on mitochondria and genomic DNA","volume":"51","author":"CM Balao da Silva","year":"2016","journal-title":"Reprod Domest Anim"},{"issue":"4","key":"pone.0358219.ref036","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1016\/j.theriogenology.2006.01.063","article-title":"Effect of sex-sorting on the ability of fresh and cryopreserved bull sperm to undergo an acrosome reaction","volume":"66","author":"E Moc\u00e9","year":"2006","journal-title":"Theriogenology"},{"issue":"1","key":"pone.0358219.ref037","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.theriogenology.2004.11.010","article-title":"Effect of staining and sorting on boar sperm membrane integrity, mitochondrial activity and in vitro blastocyst development","volume":"64","author":"M Spinaci","year":"2005","journal-title":"Theriogenology"},{"issue":"1","key":"pone.0358219.ref038","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.theriogenology.2008.09.044","article-title":"Sex-sorting sperm by flow cytometry in pigs: issues and perspectives","volume":"71","author":"JM Vazquez","year":"2009","journal-title":"Theriogenology"},{"key":"pone.0358219.ref039","article-title":"Impact of sorting and catch media on porcine sperm motility, capacitation, and viability","author":"T Weide","year":"2026","journal-title":"Andrology"},{"issue":"1","key":"pone.0358219.ref040","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1534\/genetics.112.139576","article-title":"Evaluating the evidence for transmission distortion in human pedigrees","volume":"191","author":"WK Meyer","year":"2012","journal-title":"Genetics"},{"issue":"8089","key":"pone.0358219.ref041","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1038\/s41586-025-09448-3","article-title":"Sperm sequencing reveals extensive positive selection in the male germline","volume":"647","author":"MDC Neville","year":"2025","journal-title":"Nature"},{"issue":"5","key":"pone.0358219.ref042","doi-asserted-by":"crossref","DOI":"10.1093\/dnares\/dsaa019","article-title":"Whole genome sequencing identifies allelic ratio distortion in sperm involving genes related to spermatogenesis in a swine model","volume":"27","author":"M G\u00f2dia","year":"2020","journal-title":"DNA Res"},{"issue":"8","key":"pone.0358219.ref043","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1002\/jemt.20457","article-title":"Three dimensional rendering of the mitochondrial sheath morphogenesis during mouse spermiogenesis","volume":"70","author":"H-C Ho","year":"2007","journal-title":"Microsc Res Tech"},{"issue":"5","key":"pone.0358219.ref044","doi-asserted-by":"crossref","first-page":"129845","DOI":"10.1016\/j.bbagen.2021.129845","article-title":"Mitochondrial fission factor (Mff) is required for organization of the mitochondrial sheath in spermatids","volume":"1865","author":"G Varuzhanyan","year":"2021","journal-title":"Biochim Biophys Acta Gen Subj"},{"issue":"1","key":"pone.0358219.ref045","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1002\/ar.1092220106","article-title":"Development of mitochondrial helical sheath in the middle piece of the mouse spermatid tail: regular dispositions and synchronized changes","volume":"222","author":"H Otani","year":"1988","journal-title":"Anat Rec"},{"issue":"8","key":"pone.0358219.ref046","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1016\/j.bbamcr.2013.03.010","article-title":"Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA","volume":"1833","author":"M Sato","year":"2013","journal-title":"Biochim Biophys Acta"},{"issue":"2","key":"pone.0358219.ref047","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1262\/jrd.2018-136","article-title":"Glycerol kinase 2 is essential for proper arrangement of crescent-like mitochondria to form the mitochondrial sheath during mouse spermatogenesis","volume":"65","author":"K Shimada","year":"2019","journal-title":"J Reprod Dev"},{"issue":"6","key":"pone.0358219.ref048","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2018355118","article-title":"ARMC12 regulates spatiotemporal mitochondrial dynamics during spermiogenesis and is required for male fertility","volume":"118","author":"K Shimada","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pone.0358219.ref049","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1111\/andr.12889","article-title":"Tsga10 is essential for arrangement of mitochondrial sheath and male fertility in mice","volume":"9","author":"G Luo","year":"2021","journal-title":"Andrology"},{"issue":"14","key":"pone.0358219.ref050","doi-asserted-by":"crossref","first-page":"7919","DOI":"10.3390\/ijms25147919","article-title":"Metabolic shift in porcine spermatozoa during sperm capacitation-induced zinc flux","volume":"25","author":"T Weide","year":"2024","journal-title":"Int J Mol Sci"},{"issue":"1","key":"pone.0358219.ref051","doi-asserted-by":"crossref","first-page":"2061","DOI":"10.1038\/s41467-018-04523-y","article-title":"Zinc ion flux during mammalian sperm capacitation","volume":"9","author":"K Kerns","year":"2018","journal-title":"Nat Commun"},{"issue":"12","key":"pone.0358219.ref052","doi-asserted-by":"crossref","first-page":"4097","DOI":"10.3390\/ijms19124097","article-title":"Zinc: A necessary ion for mammalian sperm fertilization competency","volume":"19","author":"K Kerns","year":"2018","journal-title":"Int J Mol Sci"},{"issue":"1","key":"pone.0358219.ref053","doi-asserted-by":"crossref","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"pone.0358219.ref054","unstructured":"Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. 2010."},{"issue":"19","key":"pone.0358219.ref055","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"P Ewels","year":"2016","journal-title":"Bioinformatics"},{"issue":"7424","key":"pone.0358219.ref056","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/nature11622","article-title":"Analyses of pig genomes provide insight into porcine demography and evolution","volume":"491","author":"MAM Groenen","year":"2012","journal-title":"Nature"},{"key":"pone.0358219.ref057","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-ME. 2013. https:\/\/doi.org\/10.48550\/arXiv.1303.3997"},{"issue":"16","key":"pone.0358219.ref058","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence alignment\/map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pone.0358219.ref059","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","author":"R Poplin","year":"2018","journal-title":"bioRxiv"},{"issue":"9","key":"pone.0358219.ref060","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Res"},{"issue":"2","key":"pone.0358219.ref061","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"P Danecek","year":"2021","journal-title":"Gigascience"},{"issue":"2","key":"pone.0358219.ref062","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"P Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"issue":"1","key":"pone.0358219.ref063","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society Series B: Statistical Methodology"},{"issue":"8","key":"pone.0358219.ref064","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1093\/bioinformatics\/btp101","article-title":"ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks","volume":"25","author":"G Bindea","year":"2009","journal-title":"Bioinformatics"},{"issue":"11","key":"pone.0358219.ref065","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res"},{"issue":"2","key":"pone.0358219.ref066","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1002\/cyto.a.20033","article-title":"Efficacy of MitoTracker Green and CMXrosamine to measure changes in mitochondrial membrane potentials in living cells and tissues","volume":"61","author":"W Pendergrass","year":"2004","journal-title":"Cytometry A"},{"issue":"5","key":"pone.0358219.ref067","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.24272\/j.issn.2095-8137.2023.373","article-title":"Cadherin-18 loss in prospermatogonia and spermatogonial stem cells enhances cell adhesion through a compensatory mechanism","volume":"45","author":"X-X Li","year":"2024","journal-title":"Zool Res"},{"issue":"8","key":"pone.0358219.ref068","doi-asserted-by":"crossref","first-page":"5236","DOI":"10.1074\/jbc.272.8.5236","article-title":"Identification of human cadherin-14, a novel neurally specific type II cadherin, by protein interaction cloning","volume":"272","author":"T Shibata","year":"1997","journal-title":"J Biol Chem"},{"issue":"21","key":"pone.0358219.ref069","doi-asserted-by":"crossref","first-page":"8264","DOI":"10.3390\/ijms21218264","article-title":"The central role of cadherins in gonad development, reproduction, and fertility","volume":"21","author":"RA-O Piprek","year":"2020","journal-title":"Int J Mol Sci"},{"issue":"14","key":"pone.0358219.ref070","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1071\/RD23084","article-title":"Classical cadherins in the testis: how are they regulated?","volume":"35","author":"HT Nguyen","year":"2023","journal-title":"Reproduction Fertility and Development"},{"issue":"4","key":"pone.0358219.ref071","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1095\/biolreprod66.4.992","article-title":"Dynamic testicular adhesion junctions are immunologically unique. II. Localization of classic cadherins in rat testis","volume":"66","author":"KJ Johnson","year":"2002","journal-title":"Biology of Reproduction"},{"issue":"9","key":"pone.0358219.ref072","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1242\/jcs.200758","article-title":"Intraflagellar transport protein IFT52 recruits IFT46 to the basal body and flagella","volume":"130","author":"B Lv","year":"2017","journal-title":"J Cell Sci"},{"issue":"2","key":"pone.0358219.ref073","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.ydbio.2012.04.028","article-title":"STIM1 is required for Ca2+ signaling during mammalian fertilization","volume":"367","author":"K Lee","year":"2012","journal-title":"Dev Biol"},{"issue":"10","key":"pone.0358219.ref074","doi-asserted-by":"crossref","first-page":"2682","DOI":"10.1074\/mcp.M115.049569","article-title":"Quantitative proteomics reveals the essential roles of stromal interaction molecule 1 (STIM1) in the testicular cord formation in mouse testis","volume":"14","author":"B Zheng","year":"2015","journal-title":"Mol Cell Proteomics"},{"issue":"5","key":"pone.0358219.ref075","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0062882","article-title":"LIN9, a subunit of the DREAM complex, regulates mitotic gene expression and proliferation of embryonic stem cells","volume":"8","author":"J Esterlechner","year":"2013","journal-title":"PLOS ONE"},{"issue":"8","key":"pone.0358219.ref076","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1009753","article-title":"Nuclear translocation of MTL5 from cytoplasm requires its direct interaction with LIN9 and is essential for male meiosis and fertility","volume":"17","author":"X Zhang","year":"2021","journal-title":"PLoS Genet"},{"issue":"12","key":"pone.0358219.ref077","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1128\/MCB.00028-10","article-title":"Lin9, a subunit of the mammalian DREAM complex, is essential for embryonic development, for survival of adult mice, and for tumor suppression","volume":"30","author":"N Reichert","year":"2010","journal-title":"Mol Cell Biol"},{"issue":"2","key":"pone.0358219.ref078","doi-asserted-by":"crossref","first-page":"100891","DOI":"10.1016\/j.repbio.2024.100891","article-title":"Identification of a novel mutation in chibby family member 2 in a non-obstructive azoospermic patient","volume":"24","author":"G Zhang","year":"2024","journal-title":"Reprod Biol"},{"key":"pone.0358219.ref079","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S0925-4773(02)00217-4","article-title":"Nurit, a novel leucine-zipper protein, expressed uniquely in the spermatid flower-like structure","volume":"117","author":"E Feige","year":"2002","journal-title":"Mech Dev"},{"issue":"1","key":"pone.0358219.ref080","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s12964-020-00696-6","article-title":"Slit\/Robo signaling regulates Leydig cell steroidogenesis","volume":"19","author":"E Martinot","year":"2021","journal-title":"Cell Commun Signal"},{"issue":"5","key":"pone.0358219.ref081","doi-asserted-by":"crossref","first-page":"1902","DOI":"10.3390\/ijms21051902","article-title":"Gene polymorphisms in boar spermatozoa and their associations with post-thaw semen quality","volume":"21","author":"A Ma\u0144kowska","year":"2020","journal-title":"Int J Mol Sci"},{"issue":"3","key":"pone.0358219.ref082","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0001737","article-title":"The human TPR protein TTC4 is a putative Hsp90 co-chaperone which interacts with CDC6 and shows alterations in transformed cells","volume":"3","author":"G Crevel","year":"2008","journal-title":"PLoS One"},{"issue":"7","key":"pone.0358219.ref083","article-title":"Differential impact of tetratricopeptide repeat proteins on the steroid hormone receptors","volume":"5","author":"J-P Sch\u00fclke","year":"2010","journal-title":"PLoS One"},{"issue":"1","key":"pone.0358219.ref084","article-title":"Genetic and genomic analyses of testicular hypoplasia in Nellore cattle","volume":"14","author":"HHR Neves","year":"2019","journal-title":"PLoS One"},{"key":"pone.0358219.ref085","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1242\/jcs.093849","article-title":"PINK1- and Parkin-mediated mitophagy at a glance","volume":"125","author":"SM Jin","year":"2012","journal-title":"J Cell Sci"},{"issue":"1","key":"pone.0358219.ref086","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1080\/15548627.2021.1888244","article-title":"Regulation of PRKN-independent mitophagy","volume":"18","author":"P Tere\u0161ak","year":"2022","journal-title":"Autophagy"},{"issue":"4","key":"pone.0358219.ref087","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.3390\/ijms19041252","article-title":"SPAG17 is required for male germ cell differentiation and fertility","volume":"19","author":"E Kazarian","year":"2018","journal-title":"Int J Mol Sci"},{"key":"pone.0358219.ref088","doi-asserted-by":"crossref","unstructured":"Ericsson V, Elam M, Sapao P, Nguyen LMT, Gill ME, Chodavarapu S, et al. Regulation of female reproductive aging by the Spag17 gene. 2025;2025:01.640648. https:\/\/doi.org\/10.1101\/2025.03.01.640648","DOI":"10.1101\/2025.03.01.640648"},{"issue":"3","key":"pone.0358219.ref089","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1111\/andr.13685","article-title":"A novel homozygous LRRC6 mutation causes male infertility with asthenozoospermia and primary ciliary dyskinesia in humans","volume":"13","author":"S Shi","year":"2025","journal-title":"Andrology"},{"issue":"9","key":"pone.0358219.ref090","doi-asserted-by":"crossref","DOI":"10.1111\/and.14517","article-title":"Polymorphisms in the HSF2, LRRC6, MEIG1 and PTIP genes correlate with sperm motility in idiopathic infertility","volume":"54","author":"N Gupta","year":"2022","journal-title":"Andrologia"},{"issue":"4","key":"pone.0358219.ref091","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1007\/s00109-009-0449-0","article-title":"Elovl6: a new player in fatty acid metabolism and insulin sensitivity","volume":"87","author":"T Matsuzaka","year":"2009","journal-title":"J Mol Med (Berl)"},{"issue":"1","key":"pone.0358219.ref092","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s12711-015-0111-y","article-title":"Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs","volume":"47","author":"J Corominas","year":"2015","journal-title":"Genet Sel Evol"},{"issue":"1","key":"pone.0358219.ref093","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0053687","article-title":"Polymorphism in the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs","volume":"8","author":"J Corominas","year":"2013","journal-title":"PLoS One"},{"issue":"11","key":"pone.0358219.ref094","doi-asserted-by":"crossref","first-page":"7786","DOI":"10.3168\/jds.2022-23062","article-title":"Transmission ratio distortion regions in the context of genomic evaluation and their effects on reproductive traits in cattle","volume":"106","author":"S Id-Lahoucine","year":"2023","journal-title":"J Dairy Sci"},{"issue":"11","key":"pone.0358219.ref095","doi-asserted-by":"crossref","first-page":"101012","DOI":"10.1016\/j.animal.2023.101012","article-title":"Transmission ratio distortion detection by neutral genetic markers in the Pura Raza Espa\u00f1ola horse breed","volume":"17","author":"DI Perdomo-Gonz\u00e1lez","year":"2023","journal-title":"Animal"},{"issue":"1","key":"pone.0358219.ref096","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyab192","article-title":"Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line","volume":"220","author":"D Arends","year":"2022","journal-title":"Genetics"},{"issue":"9","key":"pone.0358219.ref097","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.3390\/genes11091050","article-title":"Maternal transmission ratio distortion in two iberian pig varieties","volume":"11","author":"M V\u00e1zquez-G\u00f3mez","year":"2020","journal-title":"Genes"},{"issue":"6","key":"pone.0358219.ref098","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1093\/molbev\/msw036","article-title":"R2d2 Drives selfish sweeps in the house mouse","volume":"33","author":"JP Didion","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"4","key":"pone.0358219.ref099","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1534\/genetics.114.169607","article-title":"A flexible bayesian model for testing for transmission ratio distortion","volume":"198","author":"J Casellas","year":"2014","journal-title":"Genetics"},{"key":"pone.0358219.ref100","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1146\/annurev-genet-112618-043905","article-title":"Standard deviations: the biological bases of transmission ratio distortion","volume":"53","author":"L Fishman","year":"2019","journal-title":"Annu Rev Genet"},{"key":"pone.0358219.ref101","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cellsig.2018.03.003","article-title":"Distinct signalling properties of insulin receptor substrate (IRS)-1 and IRS-2 in mediating insulin\/IGF-1 action","volume":"47","author":"A Rabiee","year":"2018","journal-title":"Cell Signal"},{"key":"pone.0358219.ref102","doi-asserted-by":"crossref","first-page":"286","DOI":"10.3389\/fcell.2020.00286","article-title":"Insulin-like growth factor binding protein-3 (IGFBP-3): unraveling the role in mediating IGF-independent effects within the cell","volume":"8","author":"S Varma Shrivastav","year":"2020","journal-title":"Front Cell Dev Biol"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0358219","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T17:32:46Z","timestamp":1789493566000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0358219"}},"subtitle":[],"editor":[{"given":"Suresh","family":"Yenugu","sequence":"first","affiliation":[{"name":"University of Hyderabad","place":["INDIA"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,15]]},"references-count":102,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0358219","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,15]]}}}