Anupama Mukherjee

Sabyasachi Mukherjee

Zexi Cai

Frontiers in Genetics

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Editorial: Application of genomicsin livestock populations underselection or conservationAnupama Mukherjee1†, Zexi Cai2† and Sabyasachi Mukherjee1*†1ICAR-National Dairy Research Institute, Karnal, Haryana, India, 2Center for Quantitative Genetics andGenomics, Aarhus University, Aarhus, DenmarkKEYWORDSlivestock genomics, selection, conservation, WGS, GWAS, genotypingEditorial on the Research TopicApplication of genomics in livestock populations under selection orconservationGenomics is one of the newest branches of biology that has progressed tremendouslyduring the last decades. Genomics deals with the molecular structures, functions, evolution,andmapping of the genomes of any species and has significantly generated new informationthat has improved our understanding of the complex biology and genetic mechanisms ofanimal production systems. The advancement of genomics is linked with a number of keydevelopments, which include the rapid expansion of next-generation sequencing and chip-based genotyping assays. Large-scale genomics data are now utilized more and more due tothe dwindling cost of such sequencing and genotyping techniques. Livestock breedingprograms, including selection and conservation efforts, have attained huge success due toaffordable genomic prediction, particularly in dairy cattle. It is expected that there will befurther reduction in the cost of these high-throughput genomic data generation platformsand more development of precise estimation methodologies. Multi-disciplinaryinvolvement is going to further benefit the genomics community with the advancementof robust and reliable tools in the field of bioinformatics and their use in livestock breeding.Keeping these developments in the area of livestock genomics in mind, the presentResearch topic of the Frontiers in Genetics titled “Application of Genomics in LivestockPopulations under Selection or Conservation” was aptly selected with several major themesthat highlighted the usage of genomics for conservation, current methods of genomics,application of whole-genome- and genome-wide-based techniques, and use of differentbioinformatics tools and pipelines for the processing of genomic data. The resulting effortscontributed to the publication of a total 19 research papers in the current volume,comprising major focal points in the area of genomics of livestock and other specieswith the concerns of the present day. However, the ocean of genomics is too vast, and eventhis wide-array of published articles could hardly justify an ounce of that vastness!Nonetheless, genuine efforts were made to include articles in this volume on thosecentral themes of genomics that comprise the major skills and techniques employed invarious animal populations for selection and conservation issues. These include genome-wide association studies (GWAS), differential gene expression utilizing transcriptome data,and analysis of selection signatures through whole-genome sequencing and high-densitygenotyping datasets, which are utilized for discovering genes and genomic variants thatcontrol significant traits of importance in livestock species.OPEN ACCESSEDITED AND REVIEWED BYMartino Cassandro,University of Padua, Italy*CORRESPONDENCESabyasachi Mukherjee,sabayasachimukherje@gmail.com†These authors have contributed equally tothis workRECEIVED 31 December 2023ACCEPTED 17 January 2024PUBLISHED 24 January 2024CITATIONMukherjee A, Cai Z and Mukherjee S (2024),Editorial: Application of genomics in livestockpopulations under selection or conservation.Front. Genet. 15:1363839.doi: 10.3389/fgene.2024.1363839COPYRIGHT© 2024 Mukherjee, Cai and Mukherjee. This isan open-access article distributed under theterms of the Creative Commons AttributionLicense (CC BY). The use, distribution orreproduction in other forums is permitted,provided the original author(s) and thecopyright owner(s) are credited and that theoriginal publication in this journal is cited, inaccordance with accepted academic practice.No use, distribution or reproduction ispermitted which does not comply with theseterms.Frontiers in Genetics frontiersin.org01TYPE EditorialPUBLISHED 24 January 2024DOI 10.3389/fgene.2024.1363839Terefe et al. in African cattle, Naji et al. in Austrian and Chinesecattle, Karam et al. in sobaity seabream, Heidaritabar et al. incrossbred and purebred pigs, Li et al. in yak populations, Chenet al. in buffaloes, and Liu et al. in Chinese Qaidam cattle utilizedwhole-genome-sequenced datasets for the analysis of variant calling,selection signatures, and genomic copy number variations toidentify genes related to major economic traits of importance,including production, growth, immunity, and adaptability, inthese livestock species. Terefe et al. provided possible examples ofconvergent selection between cattle and humans through theidentification of unique selection signatures in African cattleliving in the Ethiopian highlands.Liu et al. generated skin transcriptome data from cashmere goatsand identified key pathways and six hub genes (PDGFRA, WNT5A,PPP2R1A, BMPR2, BMPR1A, and SMAD1) that regulate cashmeredevelopment in these goats that are mediated by exogenousmelatonin. This study is expected to provide a foundation forunderstanding the mechanism of melatonin-regulated cashmeregrowth. Liu et al. identified LTBP2 gene polymorphisms andtheir association with the thoracolumbar vertebrae number, bodysize, and carcass traits in Dezhou donkeys, which will be useful as amolecular marker to improve the production performance in thisdonkey population.Genomic selection (GS) is another potential breeding tool thatcan reduce the generation interval, improve the accuracy ofselection, and bring genetic improvement and, therefore, hasbeen successfully employed in many farm animals for more thana decade now (Hayes et al., 2009; Gorjanc et al., 2015; de Koning,2016; Meuwissen et al., 2016; Wiggans et al., 2017; Yang et al., 2020).Ning et al. studied various marker densities and designed severalstatistical models to increase the accuracy of genomic selection forwool traits in Angora rabbits. They are the first to estimate genomicheritability in Angora rabbits and showed that their work will be ableto provide key strategies to optimize GS using 50k marker density inrabbits for early selection of various wool traits. Wiggans andCarrillo reviewed the progress of GS in the United States andfound that the dairy genomic selection program has doubled therate of annual genetic gain since 2010, with a rapid increase in thenumber of genotype evaluations for over 50 traits. The use ofgenomic information has enabled us to determine the value ofanimals at a much earlier age and has contributed to a dramaticincrease in the rate of genetic improvement.Culver and Labow (2002) mentioned that genomics is a multi-disciplinary field of biology that focuses on the structure,function, evolution, mapping, and editing of genomes. Unlikegenetics, which refers to the study of individual genes having arole in inheritance and variation, genomics targets the combinedcharacterization of all of an organism’s genes, their combinedinheritance, and variation on the organism (WHO, 2020).Genomics also includes studies of various within-the-genomephenomena such as epistasis (the effect of one gene on another),pleiotropy (one gene affecting more than one trait), heterosis orhybrid vigor, and the different interplay of loci and alleles withinthe genome (Pevsner, 2009). Since the domain of genomics isquite broad, it is unlikely that the coverage of the presentResearch Topic will be able to encompass all. Nonetheless, the19 articles did cover a great number of aspects of genomics andtheir application in various animal populations for selection andconservation. Given that these articles are interesting and timely,we agree that there is still scope for improvement inincorporating genomics Research Topic for the selection ofcomplex traits, i.e., the selection for traits with low heritabilityand disease resistance in farm animals and other species. High-throughput phenotyping or phenomics and precision farming aresuch tools that are being applied along with genomics in mostadvanced countries for livestock breeding programs (Pedrosaet al., 2023). We sincerely hope that a future Research Topic ongenomics may well embrace many other emerging areas withingenomics, i.e., phenomics, epigenomics, and metagenomics,utilized not only for genetic improvement programs but alsofor the sustainability of livestock production systems.Author contributionsAM: Writing–original draft, Writing–review and editing,Conceptualization. ZC: Writing–original draft, Writing–reviewand editing, Conceptualization. SM: Writing–original draft,Writing–review and editing.FundingThe author(s) declare that no financial support was received forthe research, authorship, and/or publication of this article.AcknowledgmentsThe authors acknowledge the Directors, ICAR-NDRI, Karnal,India, and the Center for Quantitative Genetics and Genomics,Aarhus University, Aarhus, Denmark, for all the facilities to carryout this work.Conflict of interestThe authors declare that the research was conducted in theabsence of any commercial or financial relationships that could beconstrued as a potential conflict of interest.Publisher’s noteAll claims expressed in this article are solely those of the authorsand do not necessarily represent those of their affiliatedorganizations, or those of the publisher, the editors and thereviewers. Any product that may be evaluated in this article, orclaim that may be made by its manufacturer, is not guaranteed orendorsed by the publisher.Frontiers in Genetics frontiersin.org02Mukherjee et al. 10.3389/fgene.2024.1363839ReferencesCulver, K. W., and Labow, M. A. (2002). “Genomics,” in Genetics. EditorR. Robinson (New York, NY: Macmillan Science Library, MacmillanReference USA).de Koning, D. J. (2016). Meuwissen et al. on Genomic Selection. Genetics 203 (1), 5–7.doi:10.1534/genetics.116.189795Gorjanc, G., Cleveland, M. A., Houston, M. D., and Hickey, J. M. (2015). Potential ofgenotyping-by-sequencing for genomic selection in livestock populations. Genet. Sel.Evol. 47, 12. doi:10.1186/s12711-015-0102-zHayes, B. J., Bowman, P. J., Chamberlain, A. J., and Goddard, M. E. (2009). Invitedreview: genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 92 (2),433–443. doi:10.3168/jds.2008-1646Meuwissen, T. H., Hayes, B., and Goddard, T. (2016). Genomic selection: aparadigm shift in animal breeding. Anim. Front. 6, 6–14. doi:10.2527/af.2016-0002Pedrosa, V. B., Boerman, J. P., Gloria, L. S., Chen, S. Y., Montes, M. E., Doucette, J. S.,et al. (2023). Genomic-based genetic parameters for milkability traits derived fromautomatic milking systems in North American Holstein cattle. J. Dairy Sci. 106,2613–2629. doi:10.3168/jds.2022-22515Pevsner, J. (2009). Bioinformatics and functional genomics. 2nd Edn. Hoboken, NJ:Wiley-Blackwell.WHO (2020).WHO definitions of genetics and genomics. World Health Organization,20. Archived from the original on December.Wiggans, G. R., Cole, J. B., Hubbard, S. M., and Sonstegard, T. S. (2017). Genomicselection in dairy cattle: the USDA experience. Annu. Rev. Anim. Biosci. 5, 309–327.doi:10.1146/annurev-animal-021815-111422Yang, C. J., Sharma, R., Gorjanc, G., Hearne, S., Powell, W., and Mackay, I. (2020). Originspecific genomic selection: a simple process to optimize the favorable contribution of parentsto progeny. G3 Genes| Genomes| Genet. 10 (7), 2445–2455. doi:10.1534/g3.120.401132Frontiers in Genetics frontiersin.org03Mukherjee et al. 10.3389/fgene.2024.1363839

Editorial: Application of genomics in livestock populations under selection or conservation

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Editorial: Application of genomics in livestock populations under selection or conservation

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