{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:55:16Z","timestamp":1753890916422,"version":"3.41.2"},"reference-count":36,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,3,6]],"date-time":"2024-03-06T00:00:00Z","timestamp":1709683200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p>Cattle contribute to the nutritional needs and economy of a place. The performance and fitness of cattle depend on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding, and availability of relevant reference genomes is essential. In the present study, the genome of a Vechur calf was sequenced on both short-read Illumina and long-read Nanopore sequencing platforms. The hybrid <jats:italic>de novo<\/jats:italic> assembly approach was deployed to obtain an average contig length of 1.97 Mbp and an N50 of 4.94 Mbp. By using a short-read genome sequence of the corresponding sire and dam, a haplotype-resolved genome was also assembled. In comparison to the taurine reference genome, we found 28,982 autosomal structural variants and 16,926,990 SNVs, with 883,544 SNVs homozygous in the trio samples. Many of these SNPs have been reported to be associated with various QTLs including growth, milk yield, and milk fat content, which are crucial determinants of cattle production. Furthermore, population genotype data analysis indicated that the present sample belongs to an Indian cattle breed forming a unique cluster of <jats:italic>Bos indicus<\/jats:italic>. Subsequent F<jats:sub>ST<\/jats:sub> analysis revealed differentiation of the Vechur cattle genome at multiple loci, especially those regions related to whole body growth and cell division, especially <jats:italic>IGF1<\/jats:italic>, <jats:italic>HMGA2<\/jats:italic>, <jats:italic>RRM2<\/jats:italic>, and <jats:italic>CD68<\/jats:italic> loci, suggesting a possible role of these genes in its small stature and better disease resistance capabilities in comparison with the local crossbreeds. This provides an opportunity to select and engineer cattle breeds optimized for local conditions.<\/jats:p>","DOI":"10.3389\/fgene.2024.1338224","type":"journal-article","created":{"date-parts":[[2024,3,6]],"date-time":"2024-03-06T11:25:00Z","timestamp":1709724300000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle \u2014 elucidating genetic variation"],"prefix":"10.3389","volume":"15","author":[{"given":"Poorvishaa V.","family":"Muthusamy","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajesh","family":"Vakayil Mani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shivani","family":"Kumari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manpreet","family":"Kaur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Balu","family":"Bhaskar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajeev","family":"Raghavan Pillai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thankappan","family":"Sajeev Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thapasimuthu Vijayamma","family":"Anilkumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nongmaithem Sadananda","family":"Singh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2024,3,6]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/gim.2017.105","article-title":"Genetic disruption of the oncogenic HMGA2\u2013PLAG1\u2013IGF2 pathway causes fetal growth restriction","volume":"20","author":"Abi Habib","year":"2018","journal-title":"Genet. Med."},{"key":"B2","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res."},{"key":"B4","doi-asserted-by":"publisher","first-page":"68","DOI":"10.3389\/fgene.2017.00068","article-title":"Signatures of selection for environmental adaptation and zebu \u00d7 taurine hybrid fitness in east african shorthorn zebu","volume":"8","author":"Bahbahani","year":"2017","journal-title":"Front. Genet."},{"key":"B5","doi-asserted-by":"publisher","first-page":"972","DOI":"10.2527\/2006.844972x","article-title":"Physiological responses of Bos taurus and Bos indicus cattle to prolonged, continuous heat and humidity","volume":"84","author":"Beatty","year":"2006","journal-title":"J. Anim. Sci."},{"key":"B6","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1093\/jhered\/esr153","article-title":"Genome sequence and assembly of Bos indicus","volume":"103","author":"Canavez","year":"2012","journal-title":"J. Hered."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.1007\/s13258-023-01401-w","article-title":"Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds","volume":"45","author":"Chakraborty","year":"2023","journal-title":"Genes Genomics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"B10","doi-asserted-by":"publisher","first-page":"21924","DOI":"10.1038\/s41598-021-01144-2","article-title":"Genome analyses revealed genetic admixture and selection signatures in Bos indicus","volume":"11","author":"Dixit","year":"2021","journal-title":"Sci. Rep."},{"key":"B11","doi-asserted-by":"publisher","first-page":"9412","DOI":"10.1038\/s41598-020-66272-7","article-title":"Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)","volume":"10","author":"Fernandes J\u00fanior","year":"2020","journal-title":"Sci. Rep."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa149","article-title":"GALLO: an R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci","volume":"9","author":"Fonseca","year":"2020","journal-title":"GigaScience"},{"key":"B13","doi-asserted-by":"publisher","first-page":"e0140749","DOI":"10.1371\/journal.pone.0140749","article-title":"A non-synonymous HMGA2 variant decreases height in shetland ponies and other small horses","volume":"10","author":"Frischknecht","year":"2015","journal-title":"PLOS ONE"},{"key":"B14","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.tig.2012.119","article-title":"The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation","volume":"29","author":"Hayes","year":"2013","journal-title":"Trends Genet."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1607","DOI":"10.1182\/blood.v81.6.1607.bloodjournal8161607","article-title":"Molecular cloning of CD68, a human macrophage marker related to lysosomal glycoproteins","volume":"81","author":"Holness","year":"1993","journal-title":"Blood"},{"key":"B16","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1017\/S2078633612000501","article-title":"Vechur cattle \u2013 from extinction to sustainability","volume":"52","author":"Iype","year":"2013","journal-title":"Anim. Genet. Resour. G\u00e9n\u00e9tiques Anim. Gen\u00e9ticos Anim."},{"key":"B17","doi-asserted-by":"publisher","first-page":"1174","DOI":"10.1038\/nbt.4277","article-title":"De novo assembly of haplotype-resolved genomes with trio binning","volume":"36","author":"Koren","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"jkab417","DOI":"10.1093\/g3journal\/jkab417","article-title":"Hmga2 deficiency is associated with allometric growth retardation, infertility, and behavioral abnormalities in mice","volume":"12","author":"Lee","year":"2022","journal-title":"G3 GenesGenomesGenetics"},{"key":"B19","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.gene.2018.04.027","article-title":"A case report and review of the literature indicate that HMGA2 should be added as a disease gene for Silver-Russell syndrome","volume":"663","author":"Leszinski","year":"2018","journal-title":"Gene"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.48550\/ARXIV.1303.3997","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013"},{"key":"B21","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/s0092-8674(05)80084-4","article-title":"Mice carrying null mutations of the genes encoding insulin-like growth factor I (Igf-1) and type 1 IGF receptor (Igf1r)","volume":"75","author":"Liu","year":"1993","journal-title":"Cell"},{"key":"B22","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1186\/s12864-021-07554-w","article-title":"Investigating the impact of reference assembly choice on genomic analyses in a cattle breed","volume":"22","author":"Lloret-Villas","year":"2021","journal-title":"BMC Genomics"},{"key":"B23","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s12711-021-00607-4","article-title":"On the use of whole-genome sequence data for across-breed genomic prediction and fine-scale mapping of QTL","volume":"53","author":"Meuwissen","year":"2021","journal-title":"Genet. Sel. Evol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"v","DOI":"10.1007\/978-1-60761-175-2","article-title":"Protein networks and pathway analysis. Preface","volume":"563","author":"Nikolsky","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"B27","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1080\/10495398.2017.1297719","article-title":"Evaluation of genetic diversity, population structure, and relationship between legendary vechur cattle and crossbred cattle of Kerala state, India","volume":"29","author":"Radhika","year":"2018","journal-title":"Anim. Biotechnol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"giaa021","DOI":"10.1093\/gigascience\/giaa021","article-title":"De novo assembly of the cattle reference genome with single-molecule sequencing","volume":"9","author":"Rosen","year":"2020","journal-title":"GigaScience"},{"key":"B29","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.mgene.2018.01.003","article-title":"Molecular characterization and differential mRNA expression profiling of Toll-like receptor-2 gene in Vechur (Bos indicus) and crossbred (Bos indicus X Bos taurus) cattle of Kerala in response to anthrax vaccination","volume":"16","author":"Shivakumara","year":"2018","journal-title":"Meta Gene"},{"key":"B30","doi-asserted-by":"publisher","first-page":"3437","DOI":"10.3168\/jds.s0022-0302(88)79949-x","article-title":"Relationships between body measurements, body weight, and productivity in Holstein dairy cows","volume":"71","author":"Sieber","year":"1988","journal-title":"J. Dairy Sci."},{"key":"B31","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"B32","doi-asserted-by":"publisher","first-page":"100673","DOI":"10.1016\/j.animal.2022.100673","article-title":"Animal board invited review: genomic-based improvement of cattle in response to climate change","volume":"16","author":"Strand\u00e9n","year":"2022","journal-title":"Animal"},{"key":"B33","doi-asserted-by":"publisher","first-page":"19378","DOI":"10.1073\/pnas.0809223105","article-title":"The hormonal action of IGF1 in postnatal mouse growth","volume":"105","author":"Stratikopoulos","year":"2008","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B34","doi-asserted-by":"publisher","first-page":"txaa166","DOI":"10.1093\/tas\/txaa166","article-title":"Cow efficiency: modeling the biological and economic output of a Michigan beef herd","volume":"4","author":"Thompson","year":"2020","journal-title":"Transl. Anim. Sci."},{"key":"B35","doi-asserted-by":"publisher","first-page":"731","DOI":"10.21105\/joss.00731","article-title":"qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots","volume":"3","author":"Turner","year":"2018","journal-title":"J. Open Source Softw."},{"key":"B36","doi-asserted-by":"publisher","first-page":"1358","DOI":"10.1111\/j.1558-5646.1984.tb05657.x","article-title":"ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE","volume":"38","author":"Weir","year":"1984","journal-title":"Evolution"}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2024.1338224\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,6]],"date-time":"2024-03-06T11:25:04Z","timestamp":1709724304000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2024.1338224\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,6]]},"references-count":36,"alternative-id":["10.3389\/fgene.2024.1338224"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2024.1338224","relation":{},"ISSN":["1664-8021"],"issn-type":[{"type":"electronic","value":"1664-8021"}],"subject":[],"published":{"date-parts":[[2024,3,6]]},"article-number":"1338224"}}