Signatures of Selection in Indigenous Chinese Cattle Genomes Reveal Adaptive Genes and Genetic Variations to Cold Climate

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

PLINK: a tool set for whole-genome association and population-based linkage analyses.

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works

Fast model-based estimation of ancestry in unrelated individuals

Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898 · see citing works

The Ensembl Variant Effect Predictor

McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099 · see citing works

Climate change and evolutionary adaptation

Hoffmann, A. A., & Sgrò, C. M. (2011) · Nature · doi:10.1038/nature09670 · Cited by 3,262 · see citing works

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

Lefort, V., Desper, R., & Gascuel, O. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv150 · Cited by 1,792 · see citing works

Using ggtree to Visualize Data on Tree‐Like Structures

Yu, G. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.96 · Cited by 1,388 · see citing works

Central control of thermogenesis in mammals

Morrison, S. F., Nakamura, K., & Madden, C. J. (2008) · Experimental Physiology · doi:10.1113/expphysiol.2007.041848 · Cited by 424 · see citing works

Whole-Genome Resequencing Reveals World-Wide Ancestry and Adaptive Introgression Events of Domesticated Cattle in East Asia

Chen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., Hu, S., Huang, S., Zhang, H., Zheng, Z., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04737-0 · Cited by 403 · see citing works

Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations

Fariello, M. I., Boitard, S., Naya, H., SanCristobal, M., & Servin, B. (2013) · Genetics · doi:10.1534/genetics.112.147231 · Cited by 343 · see citing works

The Second Report on the State of the World’s Animal Genetic Resources for Food and Agriculture

(2015) · FAO eBooks · doi:10.4060/i4787e · Cited by 300 · see citing works

Heart rate measurements as an index of energy expenditure and energy balance in ruminants: A review1

Brosh, A. (2007) · Journal of Animal Science · doi:10.2527/jas.2006-298 · Cited by 152 · see citing works

Adaptation to environmental stress at different timescales

Kristensen, T. N., Ketola, T., & Kronholm, I. (2018) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13974 · Cited by 139 · see citing works

Cold-induced lipid dynamics and transcriptional programs in white adipose tissue

Xu, Z., You, W., Zhou, Y., Chen, W., Wang, Y., & Shan, T. (2019) · BMC Biology · doi:10.1186/s12915-019-0693-x · Cited by 127 · see citing works

Signatures of Selection Reveal Candidate Genes Involved in Economic Traits and Cold Acclimation in Five Swedish Cattle Breeds

Ghoreishifar, S. M., Eriksson, S., Johansson, A. M., Khansefid, M., Moghaddaszadeh-Ahrabi, S., Parna, N., Davoudi, P., & Javanmard, A. (2020) · Genetics Selection Evolution · doi:10.1186/s12711-020-00571-5 · Cited by 126 · see citing works

Scans for Signatures of Selection in Russian Cattle Breed Genomes Reveal New Candidate Genes for Environmental Adaptation and Acclimation

Yurchenko, A. A., Daetwyler, H. D., Yudin, N., Schnabel, R. D., Vander Jagt, C. J., Soloshenko, V., Lhasaranov, B., Popov, R., Taylor, J. F., & Larkin, D. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-31304-w · Cited by 117 · see citing works

Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis

Bahbahani, H. M., Clifford, H., Wragg, D., Mbole-Kariuki, M. N., Tassell, C. P. V., Sonstegard, T. S., Woolhouse, M. E. J., & Hanotte, O. (2015) · Scientific Reports · doi:10.1038/srep11729 · Cited by 110 · see citing works

Mitochondrial stress-activated cGAS-STING pathway inhibits thermogenic program and contributes to overnutrition-induced obesity in mice

Bai, J., Cervantes, C., He, S., He, J., Plasko, G., Wen, J., Li, Z., Yin, D., Zhang, C., Liu, M., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-0986-1 · Cited by 100 · see citing works

The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment

Shin, S. C., Ahn, D., Kim, S. J., Pyo, C., Lee, H., Kim, M.-K., Lee, J., Lee, J., Detrich, H. W., Postlethwait, J. H., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0468-1 · Cited by 99 · see citing works

Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep

Ahbara, A., Bahbahani, H. M., Almathen, F. S., Al‐Abri, M., Agoub, M. O., Abeba, A., Kebede, A., Musa, H. H., Mastrangelo, S., Pilla, F., et al. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2018.00699 · Cited by 99 · see citing works

Climate change effects on livestock in the Northeast US and strategies for adaptation

Hristov, A. N., Degaetano, A., Rotz, C. A., Hoberg, E. P., Skinner, R. H., Felix, T. L., Li, H., Patterson, P. H., Roth, G. W., Hall, M. H., et al. (2017) · Climatic Change · doi:10.1007/s10584-017-2023-z · Cited by 96 · see citing works

Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions

Weldenegodguad, M., Popov, R. G., Pokharel, K., Ammosov, I., Ming, Y., Ivanova, Z., & Kantanen, J. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2018.00728 · Cited by 95 · see citing works

Demography and Rapid Local Adaptation Shape Creole Cattle Genome Diversity in the Tropics

Pitt, D., Bruford, M. W., Barbato, M., Orozco‐terWengel, P., Martínez, R., & Sevane, N. (2019) · Evolutionary Applications · doi:10.1111/eva.12641 · Cited by 79 · see citing works

BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures

Chen, N., Fu, W., Zhao, J., Shen, J., Chen, Q., Zheng, Z., Chen, H., Sonstegard, T. S., Lei, C., & Jiang, Y. (2020) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2019.03.007 · Cited by 78 · see citing works

Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

Freitas, P. H. F., Wang, Y., Yan, P., de Oliveira, H. R., Schenkel, F. S., Zhang, Y., Xu, Q., & Brito, L. F. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.604823 · Cited by 77 · see citing works

Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia

Buggiotti, L., Yurchenko, A. A., Yudin, N. S., Jagt, C. J. V., Vorobieva, N. V., Kusliy, M. A., Vasiliev, S. K., Rodionov, A. N., Boronetskaya, O. I., Zinovieva, N. A., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab078 · Cited by 63 · see citing works

Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

Shen, J., Hanif, Q., Cao, Y., Yu, Y., Lei, C., Zhang, G., & Zhao, Y. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00094 · Cited by 53 · see citing works

Genomic selection strategies for breeding adaptation and production in dairy cattle under climate change

Strandén, I., Kantanen, J., Russo, I. M., Orozco‐terWengel, P., & Bruford, M. W. (2019) · Heredity · doi:10.1038/s41437-019-0207-1 · Cited by 51 · see citing works

Brown adipose tissue development and metabolism in ruminants1

Smith, S. B., Carstens, G. E., Randel, R. D., Mersmann, H. J., & Lunt, D. K. (2004) · Journal of Animal Science · doi:10.2527/2004.823942x · Cited by 49 · see citing works

Production, reproduction and some adaptation characteristics of Boran cattle breed under changing climate: A systematic review and meta-analysis

Bayssa, M., Yigrem, S., Betsha, S., & Tolera, A. Y. (2021) · PLoS ONE · doi:10.1371/journal.pone.0244836 · Cited by 44 · see citing works

Transcriptomic plasticity in brown adipose tissue contributes to an enhanced capacity for nonshivering thermogenesis in deer mice

Velotta, J. P., Jones, J., Wolf, C. J., & Cheviron, Z. A. (2016) · Molecular Ecology · doi:10.1111/mec.13661 · Cited by 42 · see citing works

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

Igoshin, A. V., Yurchenko, A. A., Belonogova, N. M., Petrovsky, D. V., Aitnazarov, R. B., Soloshenko, V. A., Yudin, N. S., & Larkin, D. M. (2019) · BMC Genetics · doi:10.1186/s12863-019-0725-0 · Cited by 42 · see citing works

cAMP-inducible coactivator CRTC3 attenuates brown adipose tissue thermogenesis

Yoon, Y., Tsai, W., de Velde, S. V., Chen, Z., Lee, K., Morgan, D. A., Rahmouni, K., Matsumura, S., Wiater, E., Song, Y., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1805257115 · Cited by 35 · see citing works

Ontogenic development of brown adipose tissue in Angus and Brahman fetal calves

Landis, M. D., Carstens, G. E., McPhail, E. G., Randel, R. D., Green, K. K., Slay, L. J., & Smith, S. B. (2002) · Journal of Animal Science · doi:10.2527/2002.803591x · Cited by 32 · see citing works

Egr1 deficiency induces browning of inguinal subcutaneous white adipose tissue in mice

Milet, C., Bléher, M., Allbright, K., Orgeur, M., Coulpier, F., Duprez, D., & Havis, E. (2017) · Scientific Reports · doi:10.1038/s41598-017-16543-7 · Cited by 28 · see citing works

Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle

Wang, X., Ju, Z., Jiang, Q., Zhong, J., Liu, C., Wang, J., Hoff, J. L., Schnabel, R. D., Zhao, H., Gao, Y., et al. (2021) · Genomics · doi:10.1016/j.ygeno.2021.03.023 · Cited by 23 · see citing works

Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Igoshin, A., Yudin, N., Aitnazarov, R., Yurchenko, A. A., & Larkin, D. M. (2021) · Life · doi:10.3390/life11090959 · Cited by 19 · see citing works

Population genomics reveals that natural variation in PRDM16 contributes to cold tolerance in domestic cattle

Yan, C., Lin, J., Lin, J., Huang, Y.-Y., Gao, Q., Piao, Z.-Y., Yuan, S., Chen, L., Ren, X., Ye, R.-C., et al. (2022) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2021.360 · Cited by 19 · see citing works

Genomic Diversity and Selection Signatures for Weining Cattle on the Border of Yunnan-Guizhou

Liu, Y., Cheng, H., Wang, S., Luo, X., Ma, X., Sun, L., Chen, N., Zhang, J., Qu, K., Wang, M., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.848951 · Cited by 18 · see citing works

Introgression, admixture and selection facilitate genetic adaptation to high-altitude environments in Chinese cattle

Huang, J., Wang, X., ZhiHua, J., Jiang, Q., Zhong, J., Liu, C., Wang, J. W., Hoff, J. L., Schnabel, R., Zhao, H., et al. (2022) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5061/dryad.15dv41nvs · Cited by 1 · see citing works

Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations

Xu, S., Akhatayeva, Z., Liu, J., Feng, X., Yu, Y., Badaoui, B., Esmailizadeh, A., Kantanen, J., Amills, M., Lenstra, J. A., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2744-4 · Cited by 29 · see citing works

Genomic responses to climatic challenges in beef cattle: A review

Colombi, D., Perini, F., Bettini, S., Mastrangelo, S., Abeni, F., Conte, G., Marletta, D., Cassandro, M., Bernabucci, U., Ciampolini, R., et al. (2024) · Animal Genetics · doi:10.1111/age.13474 · Cited by 24 · see citing works

Potential Genetic Markers Associated with Environmental Adaptability in Herbivorous Livestock

Liu, X., Peng, Y., Zhang, X., Chen, W., Chen, Y., Wei, L., Zhu, Q., Khan, M. Z., & Wang, C. (2025) · Animals · doi:10.3390/ani15050748 · Cited by 15 · see citing works

Leveraging Whole-Genome Resequencing to Uncover Genetic Diversity and Promote Conservation Strategies for Ruminants in Asia

Wang, Q., Lu, Y. C., Li, M., Gao, Z., Li, D., Gao, Y., Deng, W., & Wu, J. (2025) · Animals · doi:10.3390/ani15060831 · Cited by 10 · see citing works

Selection signatures associated with adaptation in South African Drakensberger, Nguni, and Tuli beef breeds

Gomo, M., van Marle-Köster, E., Lashmar, S. F., & Visser, C. (2024) · Tropical Animal Health and Production · doi:10.1007/s11250-024-04265-8 · Cited by 6 · see citing works

Selection signatures in Gir and Holstein cattle

Braga, L. G., Schenkel, F. S., Chud, T. C. S., Rodrigues, J. L., Saada, B., Machado, M. A., Panetto, J. C. D. C., da Silva, M. V. G. B., & Munari, D. P. (2025) · Journal of Dairy Science · doi:10.3168/jds.2024-26147 · Cited by 6 · see citing works

Whole-Genome Resequencing Reveals Genetic Diversity and Growth Trait-Related Genes in Pinan Cattle

Bo, D., Feng, Y., Bai, Y., Li, J., Wang, Y., You, Z., Shen, J., & Bai, Y. (2024) · Animals · doi:10.3390/ani14152163 · Cited by 5 · see citing works

Whole-Genome Sequencing Unveils the Uniqueness of Yushu Yaks (Bos grunniens)

Cai, B., Wu, X., Shi, Y., Kang, Y., Ding, Z., Guo, S., Cao, M., Hu, L., Zhang, B., Wang, X., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26083879 · Cited by 4 · see citing works

Genome‐wide analysis of genetic diversity and selection signatures in Fuzhou cattle

Wang, N., Li, Y., Li, X., Li, H., Bian, C., Chen, X., Jafari, H., Chen, N., & Lei, C. (2025) · Animal Genetics · doi:10.1111/age.70015 · Cited by 4 · see citing works

Characterization of runs of homozygosity islands in American mink using whole‐genome sequencing data

Davoudi, P., Do, D. N., Rathgeber, B. M., Colombo, S. M., Sargolzaei, M., Plastow, G. S., Wang, Z., & Miar, Y. (2024) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12859 · Cited by 3 · see citing works

Local Ancestry and Adaptive Introgression in Xiangnan Cattle

Yan, H., Li, J., Zhang, K., Duan, H., Sun, A., Zhang, B., Li, F., Chen, N., Lei, C., & Yi, K. (2024) · Biology · doi:10.3390/biology13121000 · Cited by 3 · see citing works

Whole-genome sequencing reveals genetic structure and adaptive genes in Nepalese buffalo breeds

Dhakal, A., Si, J., Sapkota, S., Pauciullo, A., Han, J., Gorkhali, N. A., Zhao, X., & Zhang, Y. (2024) · BMC Genomics · doi:10.1186/s12864-024-10993-w · Cited by 2 · see citing works

The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution

Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works

Genomic Characterization of Crossbred-Driven Adaptation in the Endangered Yangba Cattle of China

Cai, B., Kang, Y., Ding, Z., Guo, S., Cao, M., Hu, L., Zhang, B., Wang, X., Pei, J., Ge, Q., et al. (2025) · Animals · doi:10.3390/ani15071065 · Cited by 1 · see citing works

Fertility of indigenous “Atlas Brown” Algerian cattle under different heat stress levels

Ferag, A., Gherissi, D. E., Khenenou, T., Boughanem, A., Moussa, H. H., Maamour, A., & Hanzen, C. (2025) · International Journal of Environmental Studies · doi:10.1080/00207233.2025.2507444 · Cited by 1 · see citing works

Whole-genome sequencing reveals genomic diversity and selection signatures for adaptation in South African Afrikaner and Bonsmara cattle

Alberts, D., van Marle-Köster, E., Joubert, F., & Berry, D. P. (2026) · Frontiers in Genetics · doi:10.3389/fgene.2026.1717538 · Cited by 1 · see citing works

Runs of homozygosity reveal population dynamics and selection across global cattle

Ma, J., Liu, X., Gao, X., Wei, D., Zhang, Z., Muhammad, A., Chen, N., Xia, X., Ma, Y., Wang, E., et al. (2026) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-026-01403-0 · Cited by 1 · see citing works

Availability and seasonal dynamics of feed sources for Ladakhi cattle breed in the cold arid region of Ladakh and future scope under increasing growing degree days

Youdol, T., Mishra, A. K., Raghuwanshi, M. S., Ram, H., Bhattacharjee, S., Apurva, A., & Saxena, A. (2024) · Biological Rhythm Research · doi:10.1080/09291016.2024.2357221 · Cited by 1 · see citing works

Candidate genes and genomic regions relevant for adaptation to extreme climates in livestock

Cheruiyot, E. K., Negussie, E., Tarekegn, G. M., & Haile‐Mariam, M. (2025) · CABI Reviews · doi:10.1079/cabireviews.2025.0052 · Cited by 1 · see citing works

Cattle Ancestry, Domestication and Carnivores

Campbell, M. O. (2025) · Springer eBooks · doi:10.1007/978-3-031-97363-5_3

From selection signatures in cattle to functional validation in mice: HSPA12B negatively regulates adipose browning and thermogenesis

Gao, Y., Wang, J., Jiang, Q., Wang, X., Ju, Z., Yang, C., Wei, X., Zhang, Y., Xiao, Y., & Huang, J. (2026) · Journal of Animal Science · doi:10.1093/jas/skag016

Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle

Zhao, C., Teng, J., Chen, Y., Yang, C., Zhang, X., Ning, C., Wang, H., Yang, Q., Lv, W., Wang, D., et al. (2026) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-026-01451-6

Dietary triple-strain Bacillus -based probiotic improves growth performance by modulating intestinal barrier function and gut microbiota in weaned pigs

Zhou, A., Huang, Y., Yu, J., Liu, Z., Luo, Z., Zheng, H., Zhou, Y., Zhu, W., & Pan, L. (2026) · Journal of Animal Science · doi:10.1093/jas/skag230

Comparative analysis of cattle of different craniological types based on whole genome sequencing

Abdel’manova, A. S., Deniskova, T. E., Dotsev, A. V., & Сержевна, Ф. М. (2025) · Achievements of Science and Technology in Agro-Industrial Complex · doi:10.53859/02352451_2025_39_7_60

Genetic Architecture and Introgression Signatures Underlying Complex Coat Color Variation in Lufeng CattlePreprint

Wei, Y., Tan, S., Chen, N., Luo, X., Zhang, L., Luo, W., khan, N., Jafari, H., Jin, J., Li, Y., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-10520900/v1

Genome-wide identification of candidate breed-specific markers and selection signatures in Kalmyk cattle

Bochkaeva, Z., Abdelmanova, A. S., Deniskova, T. E., Убушиева, В. С., Ubushieva, A., Chimidova, N., Khakhlinov, A. I., Болаев, Б. К., Salaev, B. K., & Zinovieva, N. A. (2026) · Veterinary World · doi:10.14202/vetworld.2026.4498-4528

Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle

Zhao, C., Teng, J., Chen, Y., Yang, C., Zhang, X., Ning, C., Wang, H., Yang, Q., Lv, W., Wang, D., et al. (2026) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-026-01451-6

Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity characteristics in three Chinese cattle breeds

Wu, X., Pei, J., Xiong, L., Ge, Q., Bao, P., Liang, C., Yan, P., & Guo, X. (2025) · BMC Genomics · doi:10.1186/s12864-025-11328-z · Cited by 10 · see citing works

Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Igoshin, A., Yudin, N., Aitnazarov, R., Yurchenko, A. A., & Larkin, D. M. (2021) · Life · doi:10.3390/life11090959 · Cited by 19 · see citing works

Whole Genome Scan and Selection Signatures for Climate Adaption in Yanbian Cattle

Shen, J., Hanif, Q., Cao, Y., Yu, Y., Lei, C., Zhang, G., & Zhao, Y. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00094 · Cited by 53 · see citing works

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

Igoshin, A. V., Yurchenko, A. A., Belonogova, N. M., Petrovsky, D. V., Aitnazarov, R. B., Soloshenko, V. A., Yudin, N. S., & Larkin, D. M. (2019) · BMC Genetics · doi:10.1186/s12863-019-0725-0 · Cited by 42 · see citing works