Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus
Open accessAbstract
BACKGROUND: India harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome. RESULTS: Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics 'linked-read' technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance. CONCLUSIONS: This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
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Azam et al. identified 7.5 Mb of high-confidence non-reference unique insertions and 41 Mb of non-reference novel sequences in Indian cattle, enriched in immune-related gene clusters.
“Similarly, Azam et al. [185,186] identified 7.5 Mb of high-confidence non-reference unique insertions (NUIs) and 41Mb of non-reference novel sequences in Indian cattle. These insertions are enriched in immune-related gene clusters, further highlighting that indicine immune systems possess a genomic repertoire distinct from the taurine reference genome [186].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [186]
The Abstract Results report 6,844 high-confidence NUIs spanning 7.57 Mb in Indian Bos indicus breeds, supporting the 7.5 Mb figure. They report 8 Mb and 17.7 Mb of novel sequence by two methods, not 41 Mb. The Results section on the functional impact of common insertions reports enrichment for synaptic transmission, cell organization and adhesion, not immune-related gene clusters. (LLM, conf=0.90)
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STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
fastp: an ultra-fast all-in-one FASTQ preprocessor
(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074 · see citing works
Twelve years of SAMtools and BCFtools
Danecek, P., Bonfield, J., Liddle, J., Marshall, J., Ohan, V., Pollard, M., Whitwham, A., Keane, T., McCarthy, S., Davies, R. M., et al. (2021) · GigaScience · doi:10.1093/gigascience/giab008 · Cited by 15,314 · see citing works
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T.-C., Mendell, J. T., & Salzberg, S. L. (2015) · Nature Biotechnology · doi:10.1038/nbt.3122 · Cited by 14,118 · see citing works
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEMPreprint
Li, H. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1303.3997 · Cited by 9,540 · see citing works
Finding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336 · see citing works
Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
Meuwissen, T. H. E., Hayes, B. J., & Goddard, M. E. (2001) · Genetics · doi:10.1093/genetics/157.4.1819 · Cited by 7,917 · see citing works
REVIGO summarizes and visualizes long lists of gene ontology terms
Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021800 · Cited by 6,264 · see citing works
Long non-coding RNAs: insights into functions
Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2521 · Cited by 5,654 · see citing works
Genome Regulation by Long Noncoding RNAs
Rinn, J. L., & Chang, H. Y. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051410-092902 · Cited by 4,011 · see citing works
10 Years of GWAS Discovery: Biology, Function, and Translation
Visscher, P. M., Wray, N. R., Zhang, Q., Sklar, P., McCarthy, M. I., Brown, M. A., & Yang, J. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.06.005 · Cited by 3,719 · see citing works
Mash: fast genome and metagenome distance estimation using MinHash
(2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373 · see citing works
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems
Md, V., Misra, S., Li, H., & Aluru, S. (2019) · IEEE International Parallel and Distributed Processing Symposium (IPDPS) · doi:10.1109/ipdps.2019.00041 · Cited by 3,108 · see citing works
SRplot: A free online platform for data visualization and graphing
Tang, D., Chen, M., Huang, X., Zhang, G., Zeng, L., Zhang, G., Wu, S., & Wang, Y. (2023) · PLoS ONE · doi:10.1371/journal.pone.0294236 · Cited by 2,592 · see citing works
jvenn: an interactive Venn diagram viewer
Bardou, P., Mariette, J., Escudié, F., Djemiel, C., & Klopp, C. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-293 · Cited by 2,506 · see citing works
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. H. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn013 · Cited by 2,423 · see citing works
Sambamba: fast processing of NGS alignment formats
Tarasov, A., Vilella, A. J., Cuppen, E. P. J. G., Nijman, I. J., & Prins, P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv098 · Cited by 2,339 · see citing works
Chen, Y., Lun, A. T. L., & Smyth, G. K. (2016) · F1000Research · doi:10.12688/f1000research.8987.2 · Cited by 1,247 · see citing works
Comparative genomics: the bacterial pan-genome
Tettelin, H., Riley, D., Cattuto, C., & Medini, D. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.006 · Cited by 1,120 · see citing works
Mapping genes for complex traits in domestic animals and their use in breeding programmes
Goddard, M. E., & Hayes, B. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2575 · Cited by 1,100 · see citing works
Improved pairwise alignment of genomic dna
Harris, R. S. (2007) · Cited by 903 · see citing works
SAMBLASTER : fast duplicate marking and structural variant read extraction
Faust, G. G., & Hall, I. M. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu314 · Cited by 880 · see citing works
Current perspectives and the future of domestication studies
Larson, G., Piperno, D. R., Allaby, R. G., Purugganan, M. D., Andersson, L., Arroyo‐Kalin, M., Barton, L., Vigueira, C. C., Denham, T. P., Dobney, K. M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323964111 · Cited by 868 · see citing works
Variation graph toolkit improves read mapping by representing genetic variation in the reference
Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4227 · Cited by 821 · see citing works
Evidence for Two Independent Domestications of Cattle
Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M., & Cunningham, P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.7.2757 · Cited by 812 · see citing works
Direct determination of diploid genome sequences
Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M., & Jaffe, D. B. (2017) · Genome Research · doi:10.1101/gr.214874.116 · Cited by 803 · see citing works
<i>De novo</i> assembly of the cattle reference genome with single-molecule sequencing
Rosen, B. D., Bickhart, D. M., Schnabel, R. D., Koren, S., Elsik, C. G., Tseng, E., Rowan, T. N., Low, W. Y., Zimin, A., Couldrey, C., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa021 · Cited by 802 · see citing works
Gilbert, M., Nicolas, G., Cinardi, G., Boeckel, T. P. V., Vanwambeke, S., Wint, W., & Robinson, T. P. (2018) · Scientific Data · doi:10.1038/sdata.2018.227 · Cited by 739 · see citing works
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
Li, Y., Zhou, G., Ma, J., Jiang, W., Jin, L., Zhang, Z., Guo, Y., Zhang, J., Sui, Y., Zheng, L., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2979 · Cited by 703 · see citing works
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Zheng, G. X. Y., Lau, B. T., Schnall-Levin, M., Jarosz, M. V., Bell, J., Hindson, C. M., Kyriazopoulou-Panagiotopoulou, S., Masquelier, D. A., Merrill, L., Terry, J. M., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3432 · Cited by 678 · see citing works
Bickhart, D. M., Rosen, B. D., Koren, S., Sayre, B. L., Hastie, A. R., Chan, S., Lee, J., Lam, E. T., Liachko, I., Sullivan, S. T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3802 · Cited by 620 · see citing works
Self-citationDe novo assembly of haplotype-resolved genomes with trio binning
Koren, S., Rhie, A., Walenz, B. P., Dilthey, A., Bickhart, D. M., Kingan, S. B., Hiendleder, S., Williams, J. L., Smith, T. P. L., & Phillippy, A. M. (2018) · Nature Biotechnology · doi:10.1038/nbt.4277 · Cited by 494 · see citing works
Hayes, B. J., & Daetwyler, H. D. (2018) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-115024 · Cited by 467 · see citing works
Pseudogenes: Pseudo-functional or key regulators in health and disease?
Pink, R. C., Wicks, K., Caley, D. P., Punch, E. K., Jacobs, L. A., & Carter, D. R. F. (2011) · RNA · doi:10.1261/rna.2658311 · Cited by 459 · see citing works
The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455 · see citing works
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., et al. (2019) · Science · doi:10.1126/science.aav6202 · Cited by 441 · see citing works
Challenges and standards in integrating surveys of structural variation
Scherer, S. W., Lee, C., Birney, E., Altshuler, D., Eichler, E. E., Carter, N. P., Hurles, M. E., & Feuk, L. (2007) · Nature Genetics · doi:10.1038/ng2093 · Cited by 410 · see citing works
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
Predicting Genes in Single Genomes with AUGUSTUS
Hoff, K. J., & Stanke, M. (2018) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.57 · Cited by 401 · see citing works
Assembly of a pan-genome from deep sequencing of 910 humans of African descent
Sherman, R. M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N. M., Boorgula, M. P., Chavan, S., Vergara, C., Ortega, V. E., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0273-y · Cited by 359 · see citing works
Human Genomic Deletions Mediated by Recombination between Alu Elements
Sen, S. K., Han, K., Wang, J., Lee, J., Wang, H., Callinan, P. A., Dyer, M. D., Cordaux, R., Liang, P., & Batzer, M. A. (2006) · The American Journal of Human Genetics · doi:10.1086/504600 · Cited by 337 · see citing works
hnRNP A1 Relocalization to the Stress Granules Reflects a Role in the Stress Response
Guil, S., Long, J. C., & Cáceres, J. F. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.00224-06 · Cited by 318 · see citing works
Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement
Khan, A. W., Garg, V., Roorkiwal, M., Golicz, A. A., Edwards, D., & Varshney, R. K. (2019) · Trends in Plant Science · doi:10.1016/j.tplants.2019.10.012 · Cited by 314 · see citing works
On the Origin of Cattle: How Aurochs Became Cattle and Colonized the World
Ajmone‐Marsan, P., Garcia, J. F., & Lenstra, J. A. (2010) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.20267 · Cited by 287 · see citing works
Li, N., He, Q., Wang, J., Wang, B.-K., Zhao, J.-T., Huang, S.-Y., Yang, T., Tang, Y., Yang, S., Aisimutuola, P., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01340-y · Cited by 265 · see citing works
Resolving the full spectrum of human genome variation using Linked-ReadsPreprint
Marks, P., Garcia, S., Barrio, Á. M., Belhocine, K., Bernate, J., Bharadwaj, R., Bjornson, K. P., Catalanotti, C., Delaney, J., Fehr, A. N., et al. (2019) · Genome Research · doi:10.1101/gr.234443.118 · Cited by 252 · see citing works
Pervasive introgression facilitated domestication and adaptation in the Bos species complex
Wu, D., Ding, X., Wang, S., Wójcik, J. M., Zhang, Y., Tokarska, M., Li, Y., Wang, M.-S., Faruque, O., Nielsen, R., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0562-y · Cited by 233 · see citing works
Domestication of Cattle: Two or Three Events?
Pitt, D., Sevane, N., Nicolazzi, E. L., MacHugh, D. E., Park, S. D. E., Colli, L., Martinez, R., Bruford, M. W., & Orozco‐terWengel, P. (2019) · Evolutionary Applications · doi:10.1111/eva.12674 · Cited by 195 · see citing works
Low, W. Y., Tearle, R. G., Bickhart, D. M., Rosen, B. D., Kingan, S. B., Swale, T., Thibaud‐Nissen, F., Murphy, T. D., Young, R. A., Lefèvre, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08260-0 · Cited by 165 · see citing works
Self-citationPan-genome analyses of model fungal species
McCarthy, C. G. P., & Fitzpatrick, D. A. (2019) · Microbial Genomics · doi:10.1099/mgen.0.000243 · Cited by 122 · see citing works
Genome Sequence and Assembly of Bos indicus
Canavez, F., Luche, D. D., Stothard, P., Leite, K. R. M., de Sousa-Canavez, J. M., Plastow, G. S., Meidânis, J., Souza, M. A., Feijão, P., Moore, S. S., et al. (2012) · Journal of Heredity · doi:10.1093/jhered/esr153 · Cited by 120 · see citing works
CirGO: an alternative circular way of visualising gene ontology terms
Kuznetsova, I., Lugmayr, A. R., Siira, S. J., et al. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2671-2 · Cited by 114 · see citing works
Transposable element insertions have strongly affected human evolution
Britten, R. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014330107 · Cited by 112 · see citing works
Alu Recombination-Mediated Structural Deletions in the Chimpanzee Genome
Han, K., Lee, J., Meyer, T. J., Wang, J., Sen, S. K., Srikanta, D., Liang, P., & Batzer, M. A. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030184 · Cited by 103 · see citing works
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms
Scalzitti, N., Jeannin‐Girardon, A., Collet, P., Poch, O., & Thompson, J. (2020) · BMC Genomics · doi:10.1186/s12864-020-6707-9 · Cited by 102 · see citing works
Novel Functional Sequences Uncovered through a Bovine Multiassembly Graph
Crysnanto, D., Leonard, A. S., Fang, Z.-H., & Pausch, H. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101056118 · Cited by 96 · see citing works
Sigdel, A., Abdollahi-Arpanahi, R., Aguilar, I., & Peñagaricano, F. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00928 · Cited by 95 · see citing works
Maiorano, A. M., Lourenco, D. A. L., Tsuruta, S., Ospina, A. M. T., Stafuzza, N. B., Masuda, Y., Filho, A. E. V., Cyrillo, J. N. D. S. G., Curi, R. A., & Silva, J. A. I. D. V. (2018) · PLoS ONE · doi:10.1371/journal.pone.0200694 · Cited by 93 · see citing works
Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition
Zhuang, Y., Wang, X., Li, X., Hu, J., Fan, L., Landis, J. B., Cannon, S. B., Grimwood, J., Schmutz, J., Jackson, S. A., et al. (2022) · Nature Plants · doi:10.1038/s41477-022-01102-4 · Cited by 93 · see citing works
A genomic map of climate adaptation in Mediterranean cattle breeds
Flori, L., Moazami‐Goudarzi, K., Alary, V., Araba, A., Boujenane, I., Boushaba, N., Casabianca, F., Casu, S., Ciampolini, R., d’Acier, A. C., et al. (2018) · Molecular Ecology · doi:10.1111/mec.15004 · Cited by 89 · see citing works
Zhou, Y., Yang, L., Han, X., Han, J., Hu, Y., Li, F., Xia, H., Peng, L., Boschiero, C., Rosen, B. D., et al. (2022) · Genome Research · doi:10.1101/gr.276550.122 · Cited by 89 · see citing works
Self-citationDavenport, K. M., Bickhart, D. M., Worley, K. C., Murali, S. C., Salavati, M., Clark, E. L., Cockett, N. E., Heaton, M. P., Smith, T. P. L., Murdoch, B. M., et al. (2022) · GigaScience · doi:10.1093/gigascience/giab096 · Cited by 88 · see citing works
Self-citationDe novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations
Wong, K. H. Y., Levy-Sakin, M., & Kwok, P.-Y. (2018) · Nature Communications · doi:10.1038/s41467-018-05513-w · Cited by 84 · see citing works
Exploring evidence of positive selection signatures in cattle breeds selected for different traits
Taye, M., Lee, W., Jeon, S., Yoon, J. H., Dessie, T., Hanotte, O., Mwai, O. A., Kemp, S. J., Cho, S., Oh, S. J., et al. (2017) · Mammalian Genome · doi:10.1007/s00335-017-9715-6 · Cited by 77 · see citing works
HUPAN: a pan-genome analysis pipeline for human genomes
Duan, Z., Qiao, Y., Lu, J., Lu, H., Zhang, W., Yan, F., Sun, C., Hu, Z., Zhang, Z., Li, G., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1751-y · Cited by 77 · see citing works
Leonard, A. S., Crysnanto, D., Fang, Z., Heaton, M. P., Ley, B. L. V., Herrera, C., Bollwein, H., Bickhart, D. M., Kuhn, K. L., Smith, T. P. L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30680-2 · Cited by 76 · see citing works
Self-citationBolormaa, S., Pryce, J. E., Kemper, K. E., Hayes, B. J., Zhang, Y., Tier, B., Barendse, W., Reverter, A., & Goddard, M. E. (2013) · Genetics Selection Evolution · doi:10.1186/1297-9686-45-43 · Cited by 75 · see citing works
Fast characterization of segmental duplication structure in multiple genome assemblies
Išerić, H., Alkan, C., Hach, F., & Numanagić, I. (2022) · Algorithms for Molecular Biology · doi:10.1186/s13015-022-00210-2 · Cited by 74 · see citing works
Gao, X., Wang, S., Wang, Y., Li, S., Wu, S., Yan, R., Zhang, Y., Wan, R.-D., He, Z., Song, R., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32164-9 · Cited by 69 · see citing works
Long-read sequencing data analysis for yeasts
Yue, J., & Liti, G. (2018) · Nature Protocols · doi:10.1038/nprot.2018.025 · Cited by 58 · see citing works
Smith, T. P. L., Bickhart, D. M., Boichard, D., Chamberlain, A. J., Djikeng, A., Jiang, Y., Low, W. Y., Pausch, H., Demyda-Peyrás, S., Prendergast, J., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02975-0 · Cited by 57 · see citing works
Li, R., Fu, W., Su, R., Tian, X., Du, D., Zhao, Y., Zheng, Z., Chen, Q., Gao, S., Cai, Y., et al. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.01169 · Cited by 51 · see citing works
Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., et al. (2023) · Genome Research · doi:10.1101/gr.277481.122 · Cited by 43 · see citing works
Self-citationGenomic diversity and population structure of the indigenous Greek and Cypriot cattle populations
Papachristou, D., Koutsouli, P., Laliotis, G. P., Kunz, E., Upadhyay, M. R., Seichter, D., Ruß, I., Bunevski, G., Kostaras, N., Bizelis, I., et al. (2020) · Genetics Selection Evolution · doi:10.1186/s12711-020-00560-8 · Cited by 32 · see citing works
Guangxin, E., Basang, W., & Zhu, Y. (2019) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12403 · Cited by 31 · see citing works
Mukherjee, S., Cai, Z., Mukherjee, A., Longkumer, I., Mech, M., Vüpru, K., Khate, K., Rajkhowa, C., Mitra, A., Guldbrandtsen, B., et al. (2019) · BMC Genomics · doi:10.1186/s12864-019-5980-y · Cited by 24 · see citing works
Masharing, N., Sodhi, M., Chanda, D., Singh, I., Vivek, P., Tiwari, M., Kumari, P., & Mukesh, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-32418-6 · Cited by 22 · see citing works
Animal Genetic Resources of India - An Overview
Ahmad, S. F., Kour, G., Singh, A., & Gulzar, M. (2019) · International Journal of Livestock Research · doi:10.5455/ijlr.20181025013931 · Cited by 15 · see citing works
Sajjanar, B., Aalam, M. T., Khan, O., Tanuj, G. N., Sahoo, A. P., Manjunathareddy, G. B., Gandham, R. K., Dhara, S. K., Gupta, P. K., Mishra, B. P., et al. (2023) · Genes and Environment · doi:10.1186/s41021-023-00271-8 · Cited by 14 · see citing works
Self-citationRistanić, M., Zorc, M., Glavinić, U., et al. (2024) · Animals · doi:10.3390/ani14050669 · Cited by 13 · see citing works
Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle
Low, W. Y., Rosen, B. D., Ren, Y. X., Bickhart, D. M., To, T., Martin, F. J., Billis, K., Sonstegard, T. S., Sullivan, S. T., Hiendleder, S., et al. (2022) · BMC Genomics · doi:10.1186/s12864-022-08561-1 · Cited by 10 · see citing works
Self-citationOoi, E. C., Xiang, R., Chamberlain, A. J., & Goddard, M. E. (2024) · Journal of Dairy Science · doi:10.3168/jds.2023-23699 · Cited by 9 · see citing works
Mediator dynamics during heat shock in budding yeastPreprint
Sarkar, D., Zhu, Z., Knoll, E. R., Paul, E., Landsman, D., & Morse, R. H. (2021) · Genome Research · doi:10.1101/gr.275750.121 · Cited by 7 · see citing works
Assessing Bos taurus introgression in the UOA Bos indicus assembly
Naji, M. M., Utsunomiya, Y. T., Sölkner, J., Rosen, B. D., & Mészáros, G. (2021) · Genetics Selection Evolution · doi:10.1186/s12711-021-00688-1 · Cited by 7 · see citing works
Self-citationPHLDA1 Does Not Contribute Directly to Heat Shock-Induced Apoptosis of Spermatocytes
Janus, P., Mrowiec, K., Vydra, N., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms21010267 · Cited by 5 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- [44]Ripley BD. The R project in statistical computing. MSOR connect. Educational development unit. Univ Greenwich. 2001;1:23–5.
- [69]Bison bison bison genome assembly Bison_UMD1. https://www.ncbi.nlm.nih.gov/data-hub/assembly/gcf_000754665.1/. Accessed 13 Mar 2024.
Cited by
Sorted by citations
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
- Authors
- Azam, S., Sahu, A., Pandey, N. K., Neupane, M., Van Tassell, C. P., Rosen, B. D., Gandham, R. K., Rath, S. N., & Majumdar, S. S.
- Affiliations
- National Institute of Animal Biotechnology (IN)
- Agricultural Research Service (US)
- Indian Council of Agricultural Research (IN)
- Indian Institute of Technology Hyderabad (IN)
- Corresponding author
- Rosen, Benjamin D
- Gandham, Ravi Kumar
- ORCID
- Venue
- Journal of Animal Science and Biotechnology
- Published
- 2025-02-07
- Volume
- 16
- Issue
- 1
- Pages
- 21-21
- ISSN
- 1674-9782 (ISSN-L)
- 2049-1891
- PMC
- PMC11804092
- OpenAlex
- W4407204082
- Cited by
- 5
- References
- 88
- Citations by year
- 2026: 3 · 2025: 2
- FWCI
- 2.92
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Department of Biotechnology (DBT), India (BT/PR26466/AAQ/1/704/2017, BT/PR32758/AAQ/1/760/2019)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- Bos indicus, Indian cattle, pan-genome, non-reference sequences, dairy cattle breeds, Gir, Tharparkar, Sahiwal, Red Sindhi, long interspersed nuclear elements, interspersed repeats, quantitative trait loci, milk production traits, comparative genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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