Topics and Trends in Most Cited Genetic and phenotypic traits in livestock Papers

Ranked by citations 18 months after publication

Class of 2026 (Papers Published in 2024)

What topics and trends defined most-cited Genetic and phenotypic traits in livestock research in the Class of 2026?

The Class of 2026 is defined by a surge in high-resolution multi-omics and single-cell RNA sequencing, moving beyond traditional genomic selection. Research increasingly targets specific breeds like Hu and Tibetan sheep, emphasizing high-altitude adaptation and microbiome interactions to unravel complex phenotypic traits.

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At a glance

Field
Genetic and phenotypic traits in livestock
Cohort label
Class of 2026 (2024 publications)
Papers analyzed
7,294
Papers ranked
20
Top topics in ranked papers
Whole-genome sequencing, GWAS, and multi-omics integration
Publication window
Jan 1, 2024 – Dec 31, 2024
Eligibility
Research articles; reviews excluded
Citation window
18 months post-publication
18m citation range
18–118
Data source
OpenAlex · Retrieved July 2026
License
CC BY 4.0

Rankings

20 papers ranked by 18-month citation count

#1 of 7,294
11818m citations

A compendium of genetic regulatory effects across pig tissues

Jinyan Teng, Yahui Gao, Hongwei Yin, Zhonghao Bai, Shuli Liu, Haonan Zeng et al.Nature Genetics202410.1038/s41588-023-01585-7

Zhe Zhang, Albert Tenesa, Kui Li, George E. LiuSouth China Agricultural University, China

FarmGTEx projectPigGTExgenotype imputation panelExpression quantitative trait locus (eQTL)Whole-genome sequencingRNA sequencingtissue specificity of regulatory effectsMulti-omics integrationtranscriptomic phenotypescomplex phenotype mapping in pigsgene expression regulatory variantsgenetic resource conservationpig as human biomedical modelcross-species comparative genomicsMolecular quantitative trait locus (molQTL)genotype-phenotype associationanimal breeding genomicsgene regulationcomparative gene regulation (pig vs human)complex trait genetics
#2 of 7,294
5118m citations

Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds

Giorgio Chessari, Andrea Criscione et al.Scientific Reports202410.1038/s41598-023-49125-x

Andrea CriscioneUniversity of Catania, Italy

heterozygosity-rich regionsIllumina GoatSNP50k BeadChipSliding Window detection methodConsecutive Runs detection methodruns of homozygosityItalian goat breedsMontecristo feral goatbalancing selectioninbreedinginter-breed genetic relationshipsEuropean vs non-European breed divergencenorth-south genetic gradientCHI1CHI11CHI12CHI18Pearson correlationClimate adaptationanthropogenic selectiongenome modelling
#3 of 7,294
3918m citations

Integrated multi-omics reveals the relationship between growth performance, rumen microbes and metabolic status of Hu sheep with different residual feed intakes

Yanzhen Zhang et al.Animal nutrition202410.1016/j.aninu.2024.04.021

Lingling Sun, Chong WangZhejiang A&F University, China

residual feed intake (RFI)Hu sheepfeed efficiencyhigh RFI (HRFI) grouplow RFI (LRFI) grouprumen microbiome16S rRNA sequencingPrevotellarumen metabolomeplasma metabolomevolatile fatty acidsacetatepropionatevaleratecitrate cyclepyruvate metabolismalanine, aspartate and glutamate metabolismmalic acidoxoglutaric acidcitric acid
#4 of 7,294
3018m citations

Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep

Xiaolong Liang, Qijiao Duan, Bowen Li et al.Proceedings of the National Academy of Sciences202410.1073/pnas.2322291121

Xiaolong Liang, Qijiao Duan, Bowen Li, Jianquan Liu, Eviatar Nevo, Kexin LiLanzhou University, China

Structural variationTibetan sheepHu sheepHigh-altitude adaptationQinghai-Tibet plateauEPAS1 genePAPSS2PTPRDcis-acting effectsSingle-cell RNA sequencingluciferase reporter assaychromosomal inversionchromatin architectureintramuscular adipogenesisangiogenesisDNA repair genescardiac function genestissue-specific gene expressionheart protection genescirculation-associated genes
#5 of 7,294
2518m citations

Genomic prediction using machine learning: a comparison of the performance of regularized regression, ensemble, instance-based and deep learning methods on synthetic and empirical data

Vanda M Lourenço et al.BMC Genomics202410.1186/s12864-023-09933-x

Vanda M LourençoNOVA SST, Portugal

genomic predictiongenomic selectionmolecular markersregularized regressionensemble learninginstance-based learningdeep learningadaptive regularizationgroup regularizationlinear mixed modelbreeding valuehigh dimensional datacomputational performancePredictive accuracysimulated animal breeding datasetempirical maize breeding datasetscommercial breeding programtarget trait dependencemodel complexitysupervised machine learning methods
#6 of 7,294
2518m citations

Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

Ji Yang, Dong-Feng Wang, Jia-Hui Huang et al.Genome biology202410.1186/s13059-024-03288-6

Meng-Hua LiChina Agricultural University, China

Structural variationchromosome-level genome assemblyAsiatic mouflonconvergent evolutiondomesticationsheep genomesgoat genomesBMPR1BBMPR2RALYLCOL21A1LRP1Bfecundity traitswool/hair finenessmeat productionmilk productiontransposable elementsQTL associationSelection signatureDEL00067921 deletion
#7 of 7,294
2518m citations

Genome-wide variation study and inter-tissue communication analysis unveil regulatory mechanisms of egg-laying performance in chickens

Dandan Wang et al.Nature Communications202410.1038/s41467-024-50809-9

Hong Li, Yiqiang Zhao, Xiangtao Kang, Xiaojun LiuHenan Agricultural University, China

egg productionTFPI2CAMK2DOSTNGnRH secretionFSHβLHβgranulosa cell proliferationsex steroid hormonesAPOA4ANGPTL2hypothalamic-pituitary-ovarian axisinter-tissue crosstalkhepatokineadipokineMulti-omics integrationgenome-wide variationhypothalamic neuron cellspituitary cellsavian reproduction
#8 of 7,294
2418m citations

The Population History of Domestic Sheep Revealed by Paleogenomes

Damla Kaptan et al.Molecular Biology and Evolution202410.1093/molbev/msae158

Damla KaptanMiddle East Technical University, Turkey

paleogenomicssheep domesticationNeolithic West EurasiaSouthwest Asia domestication originCentral AnatoliaEpipaleolithic wild sheepAnatolian MouflonCyprian MouflonIranian mouflonFertile Crescentadmixture eventspopulation replacement eventsPontic Steppe-related ancestry expansionpost-Bronze Age gene flowAsia-related allelesancient DNAOvis ariesNeolithic IberiaNeolithic Francezooarchaeological record
#9 of 7,294
2318m citations

Insights into left-right asymmetric development of chicken ovary at the single-cell level

Tao Wang et al.Journal of genetics and genomics/Journal of Genetics and Genomics202410.1016/j.jgg.2024.08.002

Diyan Li, Zhuanjian LiChengdu University, China

left-right asymmetric ovarian developmentchicken (Gallus gallus) embryonic ovarySingle-cell RNA sequencingcortex cellszygotene germ cellspre-granulosa cellsmeiotic transcriptome clusteringgerm cell meiosis stagesdifferential gene expression analysiscell type-specific marker genesintercellular signaling pathwayspre-granulosa-germ cell communicationspatial transcriptomicssecreted signaling moleculesleft ovary functional dominanceright ovary regressionembryonic developmentgonadal single-cell RNA sequencingavian reproductive asymmetry
#10 of 7,294
2318m citations

Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds

Suthar Teerath Kumar et al.Animals202410.3390/ani14243560

Yuan Zhao, Shumin ZhangJilin Agricultural University, China

Songliao Black PigLarge White × Landrace Piglongissimus dorsi muscleMarblingBackfat thicknesslipidomicsdocosahexaenoic acidtranscriptomicsmetabolomicsprotein-protein interaction networkPPP1R3BPPARGC1AFASNinsulin signaling pathwayfructose and mannose metabolismgene-metabolite associationMYOGNR4A3fat depositionMeat quality
#11 of 7,294
2218m citations

Analysis of 206 whole‐genome resequencing reveals selection signatures associated with breed‐specific traits in Hu sheep

Fuping Zhao et al.Evolutionary Applications202410.1111/eva.13697

Yang Liu, Lixian WangChinese Academy of Agricultural Sciences, China

Hu sheepWhole-genome sequencingSelection signaturecomposite likelihood ratiointegrated haplotype scoreruns of homozygosityBMPR1BGNRH2HOXA gene clusterhigh fertilitywavy lambskinhair follicle developmentLAMTOR3EEF1A2fat tail formationKCNQ2fat depositionJAZF1 genefeed intakeCandidate genes
#12 of 7,294
2118m citations

Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds

Tao Zhong, Dunying Hou et al.BMC Genomics202410.1186/s12864-024-10396-x

Tao ZhongSichuan Agricultural University, China

Hu sheepFecB mutationWhole-genome sequencingFSTXP-CLRCC2D1B geneMissense mutationLinkage disequilibrium (LD)BMPR1BPPM1KRHEBHSPA2PPP1CCHVCN1CCDC63high fecundity mechanismsSelection signaturehaplotype analysisreproductive traits in sheep
#13 of 7,294
2018m citations

Integrating genome‐ and transcriptome‐wide association studies to uncover the host–microbiome interactions in bovine rumen methanogenesis

Wei Wang et al.iMeta202410.1002/imt2.234

Fuyong Li, Shengru Wu, Yu WangNorthwest A&F University, China

Genome-wide association study (GWAS)Transcriptome-wide association study (TWAS)rumen microbiomemethanogenic archaeamethanogenesisHolstein-Friesian cattleheritabilityhost-microbe interactionvolatile fatty acidssubstrate hydrogen metabolismmicrobial abundance variancerumen transcriptomegreenhouse gas emission mitigationmethane emission mitigationMulti-omics integration
#14 of 7,294
1918m citations

Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle

Hengwei Yu et al.Journal of Agricultural and Food Chemistry202410.1021/acs.jafc.3c07844

Gong Cheng, Linsen ZanNorthwest A&F University, China

intramuscular adipogenesisQinchuan cattleNanyang cattleJapanese black cattletranscriptomicsmetabolomicsWeighted gene coexpression network analysisITGB1fatty acid metabolism pathwayunsaturated fatty acid metabolismfatty acid elongationinsulin signaling pathwaycreatinelysineglutamineMeat qualitybeef flavor formationcattle breed improvement
#16 of 7,294
1918m citations

Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens

Linyong Shen, Xue Bai, Liru Zhao et al.Nature Communications202410.1038/s41467-024-53692-6

Hui Li, Hui ZhangNortheast Agricultural University, China

abdominal fat depositionchickendivergent selection linesGenome-wide association study (GWAS)3D genomicschromatin interaction networkepigenomicstranscriptomicsrs734209466allele-specific enhancerIGFBP2IGFBP5IRF4transcription factor bindingintramuscular adipogenesispoultry breedingmolecular targets for selective breedinggene regulationHi-C
#17 of 7,294
1918m citations

Single-cell transcriptomic and cross-species comparison analyses reveal distinct molecular changes of porcine testes during puberty

Xiaoyan Wang, Yang Wang, Yu Wang, Yifei Guo et al.Communications Biology202410.1038/s42003-024-07163-9

Chunsheng Han, Jingtao Guo, Jianguo ZhaoInstitute of Zoology, China

Single-cell RNA sequencingBama pigporcine testicular developmentcross-species comparisonmeiosis onset timingspermatogonial stem cellstranscriptome state 0myoid cell progenitorsLeydig cell steroidogenesisestrogen synthesisSertoli cell maturationspermatogenesispubertyfetal to adult developmental trajectorylivestock model organismtranslational medicine applicationtesticular cell lineage differentiationproliferating progenitor cellshuman-mouse-pig comparisonreproductive biology
#18 of 7,294
1818m citations

Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle

Alexander S Leonard et al.Genome Research202410.1101/gr.278267.123

Alexander S LeonardETH Zurich, Switzerland

Pangenome graph constructionHiFi haplotype-resolved assembliesPanGenie genotypingstructural variant genotyping from short readsDeepVariantexpression quantitative trait loci (eQTL) mappingsplicing quantitative trait loci (sQTL) mappingcattle testis transcriptometransposable elementsSTN1MYH7CEP89ASAH2linkage disequilibrium between SVs and small variantscausal candidate structural variantsminor allele frequency filtering (MAF > 0.1)short-read alignment limitations for SV detectionmedium coverage HiFi validation16 cattle assemblies pangenome307 short-read sample cohort
#19 of 7,294
1818m citations

Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep

Buying Han et al.Molecular Biology and Evolution202410.1093/molbev/msae058

Buying HanChinese Academy of Sciences, China

Tibetan sheepBMPR1BPAPPAlitter sizelambing intervalGenome-wide association study (GWAS)Single-cell RNA sequencingmural granulosa cell subtypeovarian follicular developmentsteroidogenesismutually exclusive exons3D protein structure predictioncoimmunoprecipitationmonotocous sheeppolytocous sheepMulti-omics integrationtranscriptomicsproteomicsmetabolomicsfecundity gene
#20 of 7,294
1818m citations

Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation

Meilin Jin, Huihua Wang et al.Genetics Selection Evolution202410.1186/s12711-024-00880-z

Lixin Du, Caihong WeiChinese Academy of Agricultural Sciences, China

Whole-genome sequencingChinese indigenous sheepClimate adaptationSelection signaturePopulation structureKazakh sheepMongolian sheepTibetan sheepYunnan sheepTBXT geneTG geneHOXA1 geneDYSF geneEPAS1 geneJAZF1 genePDGFDNF1 geneTSHR geneABCD4Missense mutation
Methodology

PRI identifies high-impact research using a transparent, topic-agnostic framework applied consistently across scientific domains. Bibliographic records are drawn from OpenAlex, including publication dates, citation relationships, and document types.

This ranking covers the Class of 2026 cohort: journal articles published in 2024. Reviews and other non-article document types are excluded to ensure comparability.

Research impact is quantified with an 18-month post-publication citation window—the number of citing works published within 18 months of each paper's publication date. This metric captures early impact while controlling for publication age.

An LLM-based relevance classifier then reviews each candidate's title and abstract to confirm substantive alignment with the target domain. Only papers classified as relevant appear in the final ranking.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459

Cite this ranking

Pepkio Research Index (PRI). Topics and Trends in Most Cited Genetic and phenotypic traits in livestock Papers, Class of 2026. https://pri.pepkio.com/top-papers/genetic-and-phenotypic-traits-in-livestock/2026. Accessed 2026-07-15.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459