Evaluation of genetic diversity and selection signals in gayal populations across four countries through whole-genome resequencing

Abstract

Gayal (Bos frontalis) an endangered bovine species inhabitingChina, India, Bangladesh, Myanmar and Bhutan, has a mysterious evolutionary origin. Shaped by natural selection, its unique traits make it a valuable genetic resource; however, its populations are rapidly declining. In this study, comprehensive whole-genome resequencing of fifty-eight samples of Gayal from China, India, Myanmar and Bangladesh was performed. We identified over 44 million SNPs across four Gayal populations. Nucleotide diversity analysis revealed variations in genetic diversity, with the lowest occurring in India and the highest occurring in China. Phylogenetic tree analysis revealed three distinct clades representing China, India and Bangladesh-Myanmar, which were further confirmed by principal component and admixture analyses. The genetic exchanges between Gayal and other bovine species indicate limited influence from domestic cattle in both the Chinese and Bangladeshi Gayal populations. Mitochondrial DNA sequences and a phylogenetic tree highlighted the unique mitochondrial genome of Gayal. Genome-wide selection signals pinpointed candidate genes linked to mitochondrial function, immunity, musculoskeletal development, reproduction and growth performance. Distinct haplotype patterns emerged for the CCDC157, KIAA0753 and MTFP1 genes in the Chinese and Bangladesh-Myanmar Gayal populations, indicating artificial selection in the Chinese population. KEGG pathway and gene ontology enrichment analyses provided insights into processes related to neurodevelopment, cardiac function, tissue growth, immunity and metabolism. In summary, our study enhances our understanding of Gayal genetics, population structure and selection signals across four countries. This knowledge is crucial for conserving this endangered species amid its rapid decline.

Keywords

Gayal / Genetic diversity / Mitochondrial genome / Selection signal / Whole-genome resequencing

References

[1] Alexander DH, Novembre J, Lange KJGR. Fast model-based estimation of ancestry in unrelated individuals. Genome Res, 2009, 19(9): 1655-1664.

[2] Baig M, Mitra B, Qu K, Peng MS, Ahmed I, Miao YW, Zan LS, Zhang YP. Mitochondrial DNA diversity and origin of Bos frontalis. Curr Sci, 2013, 10: 115-120

[3] Belenguer G, Mastrogiovanni G, Pacini C, Hall Z, Dowbaj AM, Arnes-Benito R, Sljukic A, Prior N, Kakava S, Bradshaw CR. RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state. Nat Commun, 2022, 13(1): 334.

[4] Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 2014, 30(15): 2114-2120.

[5] Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 17:325(5938):318–321. https://doi.org/10.1126/science.1174462

[6] Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet, 2007, 81(5): 1084-1097.

[7] Bu D, Luo H, Huo P, Wang Z, Zhang S, He Z, Wu Y, Zhao L, Liu J, Guo J. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res, 2021, 49(W1): W317-W325.

[8] Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res, 2010, 20(3): 393-402.

[9] Chi J, Fu B, Nie W, Wang J, Graphodatsky A, Yang F. New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis). Cytogenet Genome Res, 2004, 108(4): 310-316.

[10] Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry STJB. The variant call format and VCFtools. Bioinformatics, 2011, 27(15): 2156-2158.

[11] Deng W, Wang L, Ma S, Jin B, He T, Yang Z, Mao H, Wanapat M. Comparison of Gayal (Bos frontalis) and Yunnan Yellow cattle (Bos taurus): rumen function, digestibilities and nitrogen balance during feeding of pelleted lucerne (Medicago sativum). Asian Australas J Anim Sci, 2007, 20(6): 900-907.

[12] Dorji T, Wangdi J, Shaoliang Y, Chettri N, Wangchuk K (2021) Mithun (Bos frontalis): the neglected cattle species and their significance to ethnic communities in the Eastern Himalaya - A review. Anim Biosci 34(11):1727–1738. https://doi.org/10.5713/ab.21.0020

[13] Gallagher DJ, Womack JE. Chromosome conservation in the Bovidae. J Hered, 1992, 83(4): 287-298.

[14] Ganapathi M, Friocourt G, Gueguen N, Friederich MW, Le Gac G, Okur V et al (2022) A homozygous splice variant in ATP5PO, disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families. J Inherit Metab Dis 45(5):996–1012. https://doi.org/10.1002/jimd.12526

[15] Gautier M, Klassmann A, Vitalis R (2017) rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Mol Ecol Resour 17(1):78–90. https://doi.org/10.1111/1755-0998.12634

[16] Ge C, Tian Y, Chen T, Wu Y. Studies on the meat feature of gayal (Bos Frontalis). Sci Agric Sin, 1996, 29: 75-78

[17] Giasuddin M, Huque K, Alam J. Reproductive potentials of gayal (Bos frontalis) under semi-intensive management. Asian Australas J Anim Sci, 2003, 16(3): 331-334.

[18] Gou X, Wang Y, Yang S, Deng W, Mao H. Genetic diversity and origin of Gayal and cattle in Yunnan revealed by mtDNA control region and SRY gene sequence variation. J Anim Breed Genet, 2010, 127(2): 154-160.

[19] Hammarsjo A, Wang Z, Vaz R, Taylan F, Sedghi M, Girisha KM, Chitayat D, Neethukrishna K, Shannon P, Godoy R, Gowrishankar K, Lindstrand A, Nasiri J, Baktashian M, Newton PT, Guo L, Hofmeister W, Pettersson M, Chagin AS, Nishimura G, Yan L, Matsumoto N, Nordgren A, Miyake N, Grigelioniene G, Ikegawa S. Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies. Sci Rep, 2017, 7(1): 15585.

[20] He Z, Qu K, Yuan X, San Y, Ma W, Zhang J, Li Z. Appearance characteristics and major behavior of gayal (Bos frontalis) on the conservation ex situ in Pheonix mountains. J Yunnan Agric Univ (Nat. Sci. Ed.), 2009, 24(2): 25-30

[21] Hudson RR, Slatkin M, Maddison WP (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132(2):583–589. https://doi.org/10.1093/genetics/132.2.583

[22] Huque K, Rahman M, Jalil M (2001) Study on the growth pattern of gayals (Bos frontalis) and their crossbred calves. Asian Australas J Anim Sci 14(9):1245–1249. https://doi.org/10.5713/ajas.2001.1245

[23] Kory N, Wyant GA, Prakash G, uit de Bos J, Bottanelli F, Pacold ME, Chan SH, Lewis CA, Wang T, Keys HR, Guo YE, Sabatini DM (2018) SFXN1 is a mitochondrial serine transporter required for one-carbon metabolism. Science 362(6416):eaat9528. https://doi.org/10.1126/science.aat9528

[24] Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol, 2016, 33(7): 1870-1874.

[25] Lan H, Xiong X, Lin S, Liu A, Shi L (1993) Mitochondrial DNA polymorphism of cattle (Bos taurus) and mithun (Bos frontalis) in Yunnan Province. Acta Genet Sini 20(5):419–425

[26] Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44(W1):W242-W245. https://doi.org/10.1093/nar/gkw290

[27] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics, 2009, 25(16): 2078-2079.

[28] Ma G, Chang H, Li S, Chen H, Ji D, Geng R, Chang C, Li Y. Phylogenetic relationships and status quo of colonies for gayal based on analysis of cytochrome b gene partial sequences. J Genet Genomics, 2007, 34(5): 413-419.

[29] Mannen H, Kohno M, Nagata Y, Tsuji S, Bradley DG, Yeo JS, Nyamsamba D, Zagdsuren Y, Yokohama M, Nomura K, Amano T. Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle. Mol Phylogenet Evol, 2004, 32(2): 539-544.

[30] McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res, 2010, 20(9): 1297-1303.

[31] Mei C, Wang H, Zhu W, Wang H, Cheng G, Qu K, Guang X, Li A, Zhao C, Yang W. Whole-genome sequencing of the endangered bovine species Gayal (Bos frontalis) provides new insights into its genetic features. Sci Rep, 2016, 6(1): 19787.

[32] Mondal M, Dhali A, Rajkhowa C, Prakash BS. Secretion patterns of growth hormone in growing captive mithuns (Bos frontalis). Zoolog Sci, 2004, 21(11): 1125-1129.

[33] Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol, 2015, 32(1): 268-274.

[34] Nyunt M, Win N (2004) Mithan (Bos frontalis) in Myanmar. Rep Soc Res Nativ Livest 21:19–22

[35] Patitucci C, Hernandez-Camacho JD, Vimont E, Yde S, Cokelaer T, Chaze T, Giai GQ, Matondo M, Gazi A, Nemazanyy I, Stroud DA, Hock DH, Donnarumma E, Wai T. Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis. Nat Commun, 2023, 14(1): 8474.

[36] Patrick GJ, Liu H, Alphonse MP, Dikeman DA, Youn C, Otterson JC et al (2021) Epicutaneous Staphylococcus aureus induces IL-36 to enhance IgE production and ensuing allergic disease. J Clin Invest 131(5):e143334. https://doi.org/10.1172/jci143334

[37] Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet, 2006, 2(12): e190.

[38] Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 2007, 81(3): 559-575.

[39] Qian X, Li X, Shi Z, Bai X, Xia Y, Zheng Y, Xu D, Chen F, You Y, Fang J (2019) KDM3A senses oxygen availability to regulate PGC-1α-mediated mitochondrial biogenesis. Mol Cell 76(6):885–895. https://doi.org/10.1016/j.molcel.2019.09.019

[40] Qu K, He Z, Nie W, Zhang J, Jin X, Yang G, Yuan X, Huang B, Zhang Y, Zan L. Karyotype analysis of mithun (Bos frontalis) and mithun bull x Brahman cow hybrids. Genet Mol Res, 2012, 11: 131-140.

[41] Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF et al (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419(6909):832–837. https://doi.org/10.1038/nature01140

[42] Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York

[43] Shan XN, Chen YF, Luo LH, Cao XM, Song JZ, Zeng YZ. The karyotype analysis of Gayal. Hereditas (Beijing), 1980, 2(5): 25-27

[44] Stephen J, Vilboux T, Mian L, Kuptanon C, Sinclair CM, Yildirimli D, Maynard DM, Bryant J, Fischer R, Vemulapalli M, Mullikin JC, Huizing M, Gahl WA, Malicdan M, Gunay-Aygun M. Mutations in KIAA0753 cause Joubert syndrome associated with growth hormone deficiency. Hum Genet, 2017, 136(4): 399-408.

[45] Szpiech ZA, Hernandez RD. selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol, 2014, 31(10): 2824-2827.

[46] Tanaka K, Takizawa T, Murakoshi H, Dorji T, Nyunt MM, Maeda Y, Yamamoto Y, Namikawa T. Molecular phylogeny and diversity of Myanmar and Bhutan mithun based on mtDNA sequences. Anim Sci J, 2011, 82(1): 52-56.

[47] Uzzaman MR, Bhuiyan MSA, Edea Z, Kim K-S. Semi-domesticated and Irreplaceable genetic resource gayal (Bos frontalis) needs effective genetic conservation in Bangladesh: a review. Asian Australas J Anim Sci, 2014, 27(9): 1368-1372.

[48] Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res, 2010, 38(16): e164-e164.

[49] Wu DD, Ding XD, Wang S, Wojcik JM, Zhang Y, Tokarska M, Li Y, Wang MS, Faruque O, Nielsen R, Zhang Q, Zhang YP (2018) Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nat Ecol Evol 2(7):1139–1145. https://doi.org/10.1038/s41559-018-0562-y

[50] Wu Z, Zhang Z, Lei Z, Lei P. CD14: Biology and role in the pathogenesis of disease. Cytokine Growth Factor Rev, 2019, 48: 24-31.

[51] Xi D, Wu M, Fan Y, Liu Q, Leng J, Gou X, Mao H, Deng W. Polymorphisms of the insulin-like growth factor-binding protein 3 gene (IGFBP3) in gayal (Bos frontalis). Gene, 2012, 497(1): 98-102.

[52] Yamaji M, Jishage M, Meyer C, Suryawanshi H, Der E, Yamaji M, Garzia A, Morozov P, Manickavel S, McFarland HL, Roeder RG, Hafner M, Tuschl T. DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs. Nature, 2017, 543(7646): 568-572.

[53] Yuan X, Zheng H, Su Y, Guo P, Zhang X, Zhao Q, Ge W, Li C, Xi Y, Yang X. Drosophila Pif1A is essential for spermatogenesis and is the homolog of human CCDC157, a gene associated with idiopathic NOA. Cell Death Dis, 2019, 10(2): 125.

[54] Zhang Z, Shen X, Gude DR, Wilkinson BM, Justice MJ, Flickinger CJ, Herr JC, Eddy EM, Strauss JR. MEIG1 is essential for spermiogenesis in mice. Proc Natl Acad Sci USA, 2009, 106(40): 17055-17060.

[55] Zhang C, Dong SS, Xu JY, He WM, Yang TL. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 2019, 35(10): 1786-1788.

Funding

the Yunnan Expert Workstation(202305AF150156)

the China Agriculture Research System of MOF and MARA(CARS-37)

the Yunling cattle special program of the Yunnan Joint Laboratory of the Seeds and Seeding Industry(202205AR070001)

the Construction of the Yunling Cattle Technology Innovation Center and Industrialization of Achievements(2019ZG007)

RIGHTS & PERMISSIONS

The Author(s)