Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

Xiaoting Xia, Kaixing Qu, Yan Wang, Mikkel-Holger S. Sinding, Fuwen Wang, Quratulain Hanif, Zulfiqar Ahmed, Johannes A. Lenstra, Jianlin Han, Chuzhao Lei, Ningbo Chen

Stress Biology ›› 2023, Vol. 3 ›› Issue (1) : 8. DOI: 10.1007/s44154-023-00085-2
Review

Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

Author information +
History +

Abstract

Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.

Keywords

Cattle / Origin / Domestication / Migration route / Environmental adaptation / Selective pressure

Cite this article

Download citation ▾
Xiaoting Xia, Kaixing Qu, Yan Wang, Mikkel-Holger S. Sinding, Fuwen Wang, Quratulain Hanif, Zulfiqar Ahmed, Johannes A. Lenstra, Jianlin Han, Chuzhao Lei, Ningbo Chen. Global dispersal and adaptive evolution of domestic cattle: a genomic perspective. Stress Biology, 2023, 3(1): 8 https://doi.org/10.1007/s44154-023-00085-2

References

[1]
AchilliA, OlivieriA, PellecchiaM, UboldiC, ColliL, Al-ZaheryN, AccetturoM, PalaM, Hooshiar KashaniB, PeregoUA, BattagliaV, FornarinoS, KalamatiJ, HoushmandM, NegriniR, SeminoO, RichardsM, MacaulayV, FerrettiL, BandeltHJ, Ajmone-MarsanP, TorroniA. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Curr Biol, 2008, 18(4):R157-158
CrossRef Google scholar
[2]
AguiarTS, TorrecilhaRBP, MilanesiM, UtsunomiyaATH, TrigoBB, TijjaniA, MusaHH, LopesFL, Ajmone-MarsanP, CarvalheiroR, NevesHHR, do Carmo AS, Hanotte O, Sonstegard TS, Garcia JF, Utsunomiya YT. Association of copy number variation at intron 3 of HMGA2 with navel length in Bos indicus. Front Genet, 2018, 9: 627
CrossRef Google scholar
[3]
Ajmone-MarsanP, GarciaJF, LenstraJ. On the origin of cattle: how aurochs became domestic and colonized the world. Evol Anthropol, 2010, 19: 148-157
CrossRef Google scholar
[4]
BahbahaniH, TijjaniA, MukasaC, WraggD, AlmathenF, NashO, AkpaGN, Mbole-KariukiM, MallaS, WoolhouseM, SonstegardT, Van TassellC, BlytheM, HusonH, HanotteO. Signatures of selection for environmental adaptation and zebu × taurine hybrid fitness in East African Shorthorn zebu. Front Genet, 2017, 8: 68
CrossRef Google scholar
[5]
BarshG, GunnT, HeL, SchlossmanS, Duke-CohanJ. Biochemical and genetic studies of pigment-type switching. Pigment Cell Res, 2000, 13: 48-53
CrossRef Google scholar
[6]
BeallCM, CavalleriGL, DengL, ElstonRC, GaoY, KnightJ, LiC, LiJC, LiangY, McCormackM, MontgomeryHE, PanH, RobbinsPA, ShiannaKV, TamSC, TseringN, VeeramahKR, WangW, WangduiP, WealeME, XuY, XuZ, YangL, ZamanMJ, ZengC, ZhangL, ZhangX, ZhaxiP, ZhengYT. Natural selection on EPAS1 (HIF2alpha) associated with low hemoglobin concentration in Tibetan highlanders. Proc Natl Acad Sci U S A, 2010, 107(25):11459-11464
CrossRef Google scholar
[7]
BermanA. Invited review: Are adaptations present to support dairy cattle productivity in warm climates?. J Dairy Sci, 2011, 94(5):2147-2158
CrossRef Google scholar
[8]
BernabucciU, BiffaniS, BuggiottiL, VitaliA, LaceteraN, NardoneA. The effects of heat stress in Italian Holstein dairy cattle. J Dairy Sci, 2014, 97(1):471-486
CrossRef Google scholar
[9]
BooneM, DeenPM. Physiology and pathophysiology of the vasopressin-regulated renal water reabsorption. Pflugers Arch, 2008, 456(6):1005-1024
CrossRef Google scholar
[10]
BoykoAR, QuignonP, LiL, SchoenebeckJJ, DegenhardtJD, LohmuellerKE, ZhaoK, BrisbinA, ParkerHG, vonHoldtBM, CargillM, AutonA, ReynoldsA, ElkahlounAG, CastelhanoM, MosherDS, SutterNB, JohnsonGS, NovembreJ, HubiszMJ, SiepelA, WayneRK, BustamanteCD, OstranderEA. A simple genetic architecture underlies morphological variation in dogs. PLoS Biol, 2010, 8(8):e1000451
CrossRef Google scholar
[11]
BrunsonK, ZhaoX, HeN, DaiX, RodriguesA, YangD. New insights into the origins of oracle bone divination: Ancient DNA from Late Neolithic Chinese bovines. J Archaeol Sci, 2016, 74: 35-44
CrossRef Google scholar
[12]
BuggiottiL, YurchenkoAA, YudinNS, Vander JagtCJ, VorobievaNV, KusliyMA, VasilievSK, RodionovAN, BoronetskayaOI, ZinovievaNA, GraphodatskyAS, DaetwylerHD, LarkinDM. Demographic history, adaptation, and NRAP convergent evolution at amino acid residue 100 in the world northernmost cattle from Siberia. Mol Biol Evol, 2021, 38(8):3093-3110
CrossRef Google scholar
[13]
CaiD, ZhangN, ZhuS, ChenQ, WangL, ZhaoX, MaX, RoyleTCA, ZhouH, YangDY. Ancient DNA reveals evidence of abundant aurochs (Bos primigenius) in Neolithic Northeast China. J Archaeol Sci, 2018, 98: 72-80
CrossRef Google scholar
[14]
CaoY, XiaX, HouJ, ChenN, ZhaoX, ChenS, DangR, HuangY, ChenH, LeiC. Y-chromosomal haplogroup distributions in Chinese cattle. Anim Genet, 2019, 50(4):412-413
CrossRef Google scholar
[15]
ChenN, LeiC. The origins and utilization history of Chinese cattle as revealed by DNA analysis (in Chinese). Quaternary Sciences, 2021, 41: 92-100
CrossRef Google scholar
[16]
ChenS, LinBZ, BaigM, MitraB, LopesRJ, SantosAM, MageeDA, AzevedoM, TarrosoP, SasazakiS, OstrowskiS, MahgoubO, ChaudhuriTK, ZhangYP, CostaV, RoyoLJ, GoyacheF, LuikartG, BoivinN, FullerDQ, MannenH, BradleyDG, Beja-PereiraA. Zebu cattle are an exclusive legacy of the South Asia neolithic. Mol Biol Evol, 2010, 27(1):1-6
CrossRef Google scholar
[17]
ChenFH, DongGH, ZhangDJ, LiuXY, JiaX, AnCB, MaMM, XieYW, BartonL, RenXY, ZhaoZJ, WuXH, JonesMK. Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P. Science, 2015, 347(6219):248-250
CrossRef Google scholar
[18]
ChenN, CaiY, ChenQ, LiR, WangK, HuangY, HuS, HuangS, ZhangH, ZhengZ, SongW, MaZ, MaY, DangR, ZhangZ, XuL, JiaY, LiuS, YueX, DengW, ZhangX, SunZ, LanX, HanJ, ChenH, BradleyDG, JiangY, LeiC. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun, 2018, 9(1):2337
CrossRef Google scholar
[19]
ChenN, HuangJ, ZulfiqarA, LiR, XiY, ZhangM, DangR, LanX, ChenH, MaY, LeiC. Population structure and ancestry of Qinchuan cattle. Anim Genet, 2018, 49(3):246-248
CrossRef Google scholar
[20]
ChenN, FuW, ZhaoJ, ShenJ, ChenQ, ZhengZ, ChenH, SonstegardTS, LeiC, JiangY. BGVD: An integrated database for bovine sequencing variations and selective signatures. Genom Proteom Bioinf, 2020, 18(2):186-193
CrossRef Google scholar
[21]
ChenQ, ShenJ, HanifQ, ChenN, HuangY, DangR, LanX, ChenH, LeiC. Whole genome analyses revealed genomic difference between European taurine and East Asian taurine. J Anim Breed Genet, 2021, 138(1):56-68
CrossRef Google scholar
[22]
ChiangC, ScottAJ, DavisJR, TsangEK, LiX, KimY, HadzicT, DamaniFN, GanelL, MontgomerySB, BattleA, ConradDF, HallIM. The impact of structural variation on human gene expression. Nat Genet, 2017, 49(5):692-699
CrossRef Google scholar
[23]
CieslakM, ReissmannM, HofreiterM, LudwigA. Colours of domestication. Biol Rev, 2011, 86(4):885-899
CrossRef Google scholar
[24]
CrysnantoD, LeonardAS, FangZH, PauschH. Novel functional sequences uncovered through a bovine multiassembly graph. Proc Natl Acad Sci U S A, 2021, 118(20):e2101056118
CrossRef Google scholar
[25]
Cubric-CurikV, NovoselD, BrajkovicV, Rota StabelliO, KrebsS, SölknerJ, ŠalamonD, RistovS, BergerB, TrivizakiS, BizelisI, FerenčakovićM, RothammerS, KunzE, SimčičM, DovčP, BunevskiG, BytyqiH, MarkovićB, BrkaM, KumeK, StojanovićS, NikolovV, ZinovievaN, SchönherzAA, GuldbrandtsenB, ČačićM, RadovićS, MiracleP, VernesiC, CurikI, MedugoracI. Large-scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol Appl, 2022, 15(4):663-678
CrossRef Google scholar
[26]
DaetwylerHD, CapitanA, PauschH, StothardP, van BinsbergenR, BrøndumRF, LiaoX, DjariA, RodriguezSC, GrohsC, EsquerréD, BouchezO, RossignolMN, KloppC, RochaD, FritzS, EggenA, BowmanPJ, CooteD, ChamberlainAJ, AndersonC, VanTassellCP, HulseggeI, GoddardME, GuldbrandtsenB, LundMS, VeerkampRF, BoichardDA, FriesR, HayesBJ. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet, 2014, 46(8):858-865
CrossRef Google scholar
[27]
DikmenS, KhanFA, HusonHJ, SonstegardTS, MossJI, DahlGE, HansenPJ. The SLICK hair locus derived from Senepol cattle confers thermotolerance to intensively managed lactating Holstein cows. J Dairy Sci, 2014, 97(9):5508-5520
CrossRef Google scholar
[28]
EdwardsCJ, GinjaC, KantanenJ, Pérez-PardalL, TressetA, StockF, GamaLT, PenedoMC, BradleyDG, LenstraJA, NijmanIJ. Dual origins of dairy cattle farming–evidence from a comprehensive survey of European Y-chromosomal variation. PLoS ONE, 2011, 6(1):e15922
CrossRef Google scholar
[29]
FeliusM, BeerlingM-L, BuchananDS, TheunissenB, KoolmeesPA, LenstraJA. On the history of cattle genetic resources. Diversity, 2014, 6(4):705-750
CrossRef Google scholar
[30]
Felius M, Koolmees PA, Theunissen B, Consortium ECGD, Lenstra JA. On the breeds of cattle—historic and current classifications. Diversity, 2011, 3(4):660-692
CrossRef Google scholar
[31]
Flórez MurilloJM, Landaeta-HernándezAJ, KimES, BostromJR, LarsonSA, Pérez O'BrienAM, Montero-UrdanetaMA, GarciaJF, SonstegardTS. Three novel nonsense mutations of prolactin receptor found in heat-tolerant Bos taurus breeds of the Caribbean Basin. Anim Genet, 2021, 52(1):132-134
CrossRef Google scholar
[32]
FloriL, ThevenonS, DayoGK, SenouM, SyllaS, BerthierD, Moazami-GoudarziK, GautierM. Adaptive admixture in the West African bovine hybrid zone: insight from the Borgou population. Mol Ecol, 2014, 23(13):3241-3257
CrossRef Google scholar
[33]
GaoY, GautierM, DingX, ZhangH, WangY, WangX, FaruqueMO, LiJ, YeS, GouX, HanJ, LenstraJA, ZhangY. Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep, 2017, 7(1):16196
CrossRef Google scholar
[34]
GautierM, FloriL, RieblerA, JaffrézicF, LaloéD, GutI, Moazami-GoudarziK, FoulleyJL. A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics, 2009, 10: 550
CrossRef Google scholar
[35]
GhoreishifarSM, ErikssonS, JohanssonAM, KhansefidM, Moghaddaszadeh-AhrabiS, ParnaN, DavoudiP, JavanmardA. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol, 2020, 52(1):52
CrossRef Google scholar
[36]
Gong M, Yang P, Fang W, Li R, Jiang Y (2022) Building a cattle pan-genome using more de novo assemblies. J Genet Genomics 49(9):906-8. https://doi.org/10.1016/j.jgg.2022.01.003
[37]
Gutiérrez-GilB, Esteban-BlancoC, WienerP, ChitneediPK, Suarez-VegaA, ArranzJJ. High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds. Genet Sel Evol, 2017, 49(1):81
CrossRef Google scholar
[38]
HansenPJ. Physiological and cellular adaptations of zebu cattle to thermal stress. Anim Reprod Sci, 2004, 82–83: 349-360
CrossRef Google scholar
[39]
HaraH, WadaT, BakalC, KozieradzkiI, SuzukiS, SuzukiN, NghiemM, GriffithsEK, KrawczykC, BauerB, D’AcquistoF, GhoshS, YehWC, BaierG, RottapelR, PenningerJM. The MAGUK family protein CARD11 is essential for lymphocyte activation. Immunity, 2003, 18(6):763-775
CrossRef Google scholar
[40]
HoSS, UrbanAE, MillsRE. Structural variation in the sequencing era. Nat Rev Genet, 2020, 21(3):171-189
CrossRef Google scholar
[41]
IgoshinAV, YurchenkoAA, BelonogovaNM, PetrovskyDV, AitnazarovRB, SoloshenkoVA, YudinNS, LarkinDM. 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. BMC Genet, 2019, 20(Suppl 1):26
CrossRef Google scholar
[42]
IshikawaH, MaZ, BarberGN. STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity. Nature, 2009, 461(7265):788-792
CrossRef Google scholar
[43]
JianW, DuangjindaM, VajrabukkaC, KatawatinS. Differences of skin morphology in Bos indicus, Bos taurus, and their crossbreds. Int J Biometeorol, 2014, 58(6):1087-1094
CrossRef Google scholar
[44]
JiangL, KonT, ChenC, IchikawaR, ZhengQ, PeiL, TakemuraI, NsobiLH, TabataH, PanH, OmoriY, OguraA. Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour. Sci Rep, 2021, 11(1):17359
CrossRef Google scholar
[45]
KaderA, LiY, DongK, IrwinDM, ZhaoQ, HeX, LiuJ, PuY, GorkhaliNA, LiuX, JiangL, LiX, GuanW, ZhangY, WuDD, MaY. Population variation reveals independent selection toward small body size in Chinese Debao pony. Genome Biol Evol, 2015, 8(1):42-50
CrossRef Google scholar
[46]
KantanenJ, EdwardsCJ, BradleyDG, ViinalassH, ThesslerS, IvanovaZ, KiselyovaT, CinkulovM, PopovR, StojanovićS, AmmosovI, VilkkiJ. Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus). Heredity, 2009, 103(5):404-415
CrossRef Google scholar
[47]
KimJ, HanotteO, MwaiOA, DessieT, BashirS, DialloB, AgabaM, KimK, KwakW, SungS, SeoM, JeongH, KwonT, TayeM, SongKD, LimD, ChoS, LeeHJ, YoonD, OhSJ, KempS, LeeHK, KimH. The genome landscape of indigenous African cattle. Genome Biol, 2017, 18(1):34
CrossRef Google scholar
[48]
KimK, KwonT, DessieT, YooD, MwaiOA, JangJ, SungS, LeeS, SalimB, JungJ, JeongH, TarekegnGM, TijjaniA, LimD, ChoS, OhSJ, LeeHK, KimJ, JeongC, KempS, HanotteO, KimH. The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism. Nat Genet, 2020, 52(10):1099-1110
CrossRef Google scholar
[49]
KochF, ThomU, AlbrechtE, WeikardR, NolteW, KuhlaB, KuehnC. Heat stress directly impairs gut integrity and recruits distinct immune cell populations into the bovine intestine. Proc Natl Acad Sci U S A, 2019, 116(21):10333-10338
CrossRef Google scholar
[50]
KühnC, WeikardR. An investigation into the genetic background of coat colour dilution in a Charolais x German Holstein F2 resource population. Anim Genet, 2007, 38(2):109-113
CrossRef Google scholar
[51]
KurthI, PammingerT, HenningsJC, SoehendraD, HuebnerAK, RotthierA, BaetsJ, SenderekJ, TopalogluH, FarrellSA, NürnbergG, NürnbergP, De JongheP, GalA, KaetherC, TimmermanV, HübnerCA. Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy. Nat Genet, 2009, 41(11):1179-1181
CrossRef Google scholar
[52]
Lango AllenH, EstradaK, LettreG, BerndtSI, WeedonMN, RivadeneiraF, WillerCJ, JacksonAU, VedantamS, RaychaudhuriS, FerreiraT, WoodAR, WeyantRJ, SegrèAV, SpeliotesEK, WheelerE, SoranzoN, ParkJH, YangJ, GudbjartssonD, Heard-CostaNL, RandallJC, QiL, Vernon SmithA, MägiR, PastinenT, LiangL, HeidIM, LuanJ, ThorleifssonG, WinklerTW, GoddardME, Sin LoK, PalmerC, WorkalemahuT, AulchenkoYS, JohanssonA, ZillikensMC, FeitosaMF, EskoT, JohnsonT, KetkarS, KraftP, ManginoM, ProkopenkoI, AbsherD, AlbrechtE, ErnstF, GlazerNL, HaywardC, HottengaJJ, JacobsKB, KnowlesJW, KutalikZ, MondaKL, PolasekO, PreussM, RaynerNW, RobertsonNR, SteinthorsdottirV, TyrerJP, VoightBF, WiklundF, XuJ, ZhaoJH, NyholtDR, PellikkaN, PerolaM, PerryJR, SurakkaI, TammesooML, AltmaierEL, AminN, AspelundT, BhangaleT, BoucherG, ChasmanDI, ChenC, CoinL, CooperMN, DixonAL, GibsonQ, GrundbergE, HaoK, Juhani JunttilaM, KaplanLM, KettunenJ, KönigIR, KwanT, LawrenceRW, LevinsonDF, LorentzonM, McKnightB, MorrisAP, MüllerM, Suh NgwaJ, PurcellS, RafeltS, SalemRM, SalviE, SannaS, ShiJ, SovioU, ThompsonJR, TurchinMC, VandenputL, VerlaanDJ, VitartV, WhiteCC, ZieglerA, AlmgrenP, BalmforthAJ, CampbellH, CitterioL, De GrandiA, DominiczakA, DuanJ, ElliottP, ElosuaR, ErikssonJG, FreimerNB, GeusEJ, GloriosoN, HaiqingS, HartikainenAL, HavulinnaAS, HicksAA, HuiJ, IglW, IlligT, JulaA, KajantieE, KilpeläinenTO, KoiranenM, KolcicI, KoskinenS, KovacsP, LaitinenJ, LiuJ, LokkiML, MarusicA, MaschioA, MeitingerT, MulasA, ParéG, ParkerAN, PedenJF, PetersmannA, PichlerI, PietiläinenKH, PoutaA, RidderstråleM, RotterJI, SambrookJG, SandersAR, SchmidtCO, SinisaloJ, SmitJH, StringhamHM, Bragi WaltersG, WidenE, WildSH, WillemsenG, ZagatoL, ZgagaL, ZittingP, AlavereH, FarrallM, McArdleWL, NelisM, PetersMJ, RipattiS, van MeursJB, AbenKK, ArdlieKG, BeckmannJS, BeilbyJP, BergmanRN, BergmannS, CollinsFS, CusiD, den HeijerM, EiriksdottirG, GejmanPV, HallAS, HamstenA, HuikuriHV, IribarrenC, KähönenM, KaprioJ, KathiresanS, KiemeneyL, KocherT, LaunerLJ, LehtimäkiT, MelanderO, MosleyTH Jr, MuskAW, NieminenMS, O'DonnellCJ, OhlssonC, OostraB, PalmerLJ, RaitakariO, RidkerPM, RiouxJD, RissanenA, RivoltaC, SchunkertH, ShuldinerAR, SiscovickDS, StumvollM, TönjesA, TuomilehtoJ, van OmmenGJ, ViikariJ, HeathAC, MartinNG, MontgomeryGW, ProvinceMA, KayserM, ArnoldAM, AtwoodLD, BoerwinkleE, ChanockSJ, DeloukasP, GiegerC, GrönbergH, HallP, HattersleyAT, HengstenbergC, HoffmanW, LathropGM, SalomaaV, SchreiberS, UdaM, WaterworthD, WrightAF, AssimesTL, BarrosoI, HofmanA, MohlkeKL, BoomsmaDI, CaulfieldMJ, CupplesLA, ErdmannJ, FoxCS, GudnasonV, GyllenstenU, HarrisTB, HayesRB, JarvelinMR, MooserV, MunroePB, OuwehandWH, PenninxBW, PramstallerPP, QuertermousT, RudanI, SamaniNJ, SpectorTD, VölzkeH, WatkinsH, WilsonJF, GroopLC, HarituniansT, HuFB, KaplanRC, MetspaluA, NorthKE, SchlessingerD, WarehamNJ, HunterDJ, O'ConnellJR, StrachanDP, WichmannHE, BoreckiIB, van DuijnCM, SchadtEE, ThorsteinsdottirU, PeltonenL, UitterlindenAG, VisscherPM, ChatterjeeN, LoosRJ, BoehnkeM, McCarthyMI, IngelssonE, LindgrenCM, AbecasisGR, StefanssonK, FraylingTM, HirschhornJN. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature, 2010, 467(7317):832-838
CrossRef Google scholar
[53]
LarsonG, PipernoDR, AllabyRG, PuruggananMD, AnderssonL, Arroyo-KalinM, BartonL, Climer VigueiraC, DenhamT, DobneyK, DoustAN, GeptsP, GilbertMT, GremillionKJ, LucasL, LukensL, MarshallFB, OlsenKM, PiresJC, RichersonPJ, Rubio de CasasR, SanjurOI, ThomasMG, FullerDQ. Current perspectives and the future of domestication studies. Proc Natl Acad Sci U S A, 2014, 111(17):6139-6146
CrossRef Google scholar
[54]
LenstraJA, Ajmone-MarsanP, Beja-PereiraA, BollonginoR, BradleyDG, ColliL, De GaetanoA, EdwardsCJ, FeliusM, FerrettiL, GinjaC, HristovP, KantanenJ, LirónJP, MageeDA, NegriniR, RadoslavovGA. Meta-analysis of mitochondrial DNA reveals several population bottlenecks during worldwide migrations of cattle. Diversity, 2014, 6(1):178-187
CrossRef Google scholar
[55]
LeonardAS, CrysnantoD, FangZH, HeatonMP, Vander LeyBL, HerreraC, BollweinH, BickhartDM, KuhnKL, SmithTPL, RosenBD, PauschH. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nat Commun, 2022, 3(1):3012
CrossRef Google scholar
[56]
LiP, XiaoS, WeiN, ZhangZ, HuangR, GuY, GuoY, RenJ, HuangL, ChenC. Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene. Genet Sel Evol, 2012, 44(1):6
CrossRef Google scholar
[57]
LiangM, MiaoJ, WangX, ChangT, AnB, DuanX, XuL, GaoX, ZhangL, LiJ, GaoH. Application of ensemble learning to genomic selection in Chinese Simmental beef cattle. J Anim Breed Genet, 2021, 138(3):291-299
CrossRef Google scholar
[58]
LittlejohnMD, HentyKM, TipladyK, JohnsonT, HarlandC, LopdellT, SherlockRG, LiW, LukefahrSD, ShanksBC, GarrickDJ, SnellRG, SpelmanRJ, DavisSR. Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle. Nat Commun, 2014, 5(1):5861
CrossRef Google scholar
[59]
LowWY, TearleR, LiuR, KorenS, RhieA, BickhartDM, RosenBD, KronenbergZN, KinganSB, TsengE, Thibaud-NissenF, MartinFJ, BillisK, GhuryeJ, HastieAR, LeeJ, PangAWC, HeatonMP, PhillippyAM, HiendlederS, SmithTPL, WilliamsJL. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nat Commun, 2020, 11(1):2071
CrossRef Google scholar
[60]
MaX, ChengH, LiuY, SunL, ChenN, JiangF, YouW, YangZ, ZhangB, SongE, LeiC. Assessing genomic diversity and selective pressures in Bohai Black cattle using whole-genome sequencing data. Animals (basel), 2022, 12(5):665
CrossRef Google scholar
[61]
MeiC, WangH, LiaoQ, WangL, ChengG, WangH, ZhaoC, ZhaoS, SongJ, GuangX, LiuGE, LiA, WuX, WangC, FangX, ZhaoX, SmithSB, YangW, TianW, GuiL, ZhangY, HillRA, JiangZ, XinY, JiaC, SunX, WangS, YangH, WangJ, ZhuW, ZanL. Genetic architecture and selection of Chinese cattle revealed by whole genome resequencing. Mol Biol Evol, 2018, 35(3):688-699
CrossRef Google scholar
[62]
MeiC, GuiL, HongJ, RazaSHA, AorigeleC, TianW, GarciaM, XinY, YangW, ZhangS, ZanL. Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China. Mol Ther Nucleic Acids, 2021, 23: 959-967
CrossRef Google scholar
[63]
MeyerhofW, BatramC, KuhnC, BrockhoffA, ChudobaE, BufeB, AppendinoG, BehrensM. The molecular receptive ranges of human TAS2R bitter taste receptors. Chem Senses, 2010, 35(2):157-170
CrossRef Google scholar
[64]
MohamadK, OlssonM, van TolHT, MikkoS, VlamingsBH, AnderssonG, Rodríguez-MartínezH, PurwantaraB, PalingRW, ColenbranderB, LenstraJA. On the origin of Indonesian cattle. PLoS ONE, 2009, 4(5):e5490
CrossRef Google scholar
[65]
NewmanJH, HoltTN, CoganJD, WomackB, PhillipsJA, LiC, KendallZ, StenmarkKR, ThomasMG, BrownRD, RiddleSR, WestJD, HamidR. Increased prevalence of EPAS1 variant in cattle with high-altitude pulmonary hypertension. Nat Commun, 2015, 6(1):6863
CrossRef Google scholar
[66]
NoyesH, BrassA, ObaraI, AndersonS, ArchibaldAL, BradleyDG, FisherP, FreemanA, GibsonJ, GicheruM, HallL, HanotteO, HulmeH, McKeeverD, MurrayC, OhSJ, TateC, SmithK, TapioM, WambuguJ, WilliamsDJ, AgabaM, KempSJ. Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection. Proc Natl Acad Sci U S A, 2011, 108(22):9304-9309
CrossRef Google scholar
[67]
OlsonTA, LucenaC, ChaseCC Jr, HammondAC. Evidence of a major gene influencing hair length and heat tolerance in Bos taurus cattle. J Anim Sci, 2003, 81(1):80-90
CrossRef Google scholar
[68]
ParkSD, MageeDA, McGettiganPA, TeasdaleMD, EdwardsCJ, LohanAJ, MurphyA, BraudM, DonoghueMT, LiuY, ChamberlainAT, Rue-AlbrechtK, SchroederS, SpillaneC, TaiS, BradleyDG, SonstegardTS, LoftusBJ, MacHughDE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol, 2015, 16: 234
CrossRef Google scholar
[69]
PengH, WangK, ChenZ, CaoY, GaoQ, LiY, LiX, LuH, DuH, LuM, YangX, LiangC. MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. Nucleic Acids Res, 2020, 48(D1):D1085-D1092
CrossRef Google scholar
[70]
Pérez-PardalL, Sánchez-GraciaA, ÁlvarezI, TraoréA, FerrazJBS, FernándezI, CostaV, ChenS, TapioM, CantetRJC, PatelA, MeadowRH, MarshallFB, Beja-PereiraA, GoyacheF. Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa. Sci Rep, 2018, 8(1):18027
CrossRef Google scholar
[71]
PittD, SevaneN, NicolazziEL, MacHughDE, ParkSDE, ColliL, MartinezR, BrufordMW, Orozco-terWengelP. Domestication of cattle: Two or three events?. Evol Appl, 2019, 12(1):123-136
CrossRef Google scholar
[72]
PomerantzJL, DennyEM, BaltimoreD. CARD11 mediates factor-specific activation of NF-kappaB by the T cell receptor complex. EMBO J, 2002, 21(19):5184-5194
CrossRef Google scholar
[73]
Porto-NetoLR, BickhartDM, Landaeta-HernandezAJ, UtsunomiyaYT, PaganM, JimenezE, HansenPJ, DikmenS, SchroederSG, KimES, SunJ, CrespoE, AmatiN, ColeJB, NullDJ, GarciaJF, ReverterA, BarendseW, SonstegardTS. Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor. Front Genet, 2018, 9: 57
CrossRef Google scholar
[74]
RandhawaIA, KhatkarMS, ThomsonPC, RaadsmaHW. A meta-assembly of selection signatures in cattle. PLoS ONE, 2016, 11(4):e0153013
CrossRef Google scholar
[75]
RowellLB. Hyperthermia: a hyperadrenergic state. Hypertension (dallas, Tex: 1979), 1990, 15(5):505-507
CrossRef Google scholar
[76]
SchmutzSM, DregerDL. Interaction of MC1R and PMEL alleles on solid coat colors in Highland cattle. Anim Genet, 2013, 44(1):9-13
CrossRef Google scholar
[77]
SilvaPS, HooperHB, ManicaE, MerigheGKF, OliveiraSA, TraldiAS, NegrãoJA. Heat stress affects the expression of key genes in the placenta, placental characteristics, and efficiency of Saanen goats and the survival and growth of their kids. J Dairy Sci, 2021, 104(4):4970-4979
CrossRef Google scholar
[78]
SimonsonTS, YangY, HuffCD, YunH, QinG, WitherspoonDJ, BaiZ, LorenzoFR, XingJ, JordeLB, PrchalJT, GeR. Genetic evidence for high-altitude adaptation in Tibet. Science, 2010, 329(5987):72-75
CrossRef Google scholar
[79]
SindingMS, CiucaniMM, Ramos-MadrigalJ, CarmagniniA, RasmussenJA, FengS, ChenG, VieiraFG, MattiangeliV, GanjooRK, LarsonG, Sicheritz-PonténT, PetersenB, FrantzL, GilbertMTP, BradleyDG. Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience, 2021, 24(11):103226
CrossRef Google scholar
[80]
SudrajadP, SubihartaS, AdinataY, LathifahA, LeeJH, LenstraJA, LeeSH. An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis. PLoS ONE, 2020, 15(11):e0241038
CrossRef Google scholar
[81]
SunL, QuK, LiuY, MaX, ChenN, ZhangJ, HuangB, LeiC. Assessing genomic diversity and selective pressures in Bashan cattle by whole-genome sequencing data. Anim Biotechnol, 2021, 11: 1-12
CrossRef Google scholar
[82]
TalentiA, PowellJ, HemminkJD, CookEAJ, WraggD, JayaramanS, PaxtonE, EzeasorC, ObishakinET, AgusiER, TijjaniA, MarshallK, FischA, FerreiraBR, QasimA, ChaudhryU, WienerP, ToyeP, MorrisonLJ, ConnelleyT, PrendergastJGD. A cattle graph genome incorporating global breed diversity. Nat Commun, 2022, 13(1):910
CrossRef Google scholar
[83]
TrigoBB, UtsunomiyaATH, FortunatoA, MilanesiM, TorrecilhaRBP, LambH, NguyenL, RossEM, HayesB, PadulaRCM, SussaiTS, ZavarezLB, CiprianoRS, CaminhasMMT, LopesFL, PelleC, LeebT, BannaschD, BickhartD, SmithTPL, SonstegardTS, GarciaJF, UtsunomiyaYT. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genet Sel Evol, 2021, 53(1):40
CrossRef Google scholar
[84]
TruszkowskaGT, BilińskaZT, MuchowiczA, PollakA, BiernackaA, Kozar-KamińskaK, StawińskiP, GasperowiczP, KosińskaJ, ZielińskiT, PłoskiR. Homozygous truncating mutation in NRAP gene identified by whole exome sequencing in a patient with dilated cardiomyopathy. Sci Rep, 2017, 7(1):3362
CrossRef Google scholar
[85]
UtsunomiyaYT, MilanesiM, FortesMRS, Porto-NetoLR, UtsunomiyaATH, SilvaM, GarciaJF, Ajmone-MarsanP. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet, 2019, 50(6):557-568
CrossRef Google scholar
[86]
VerdugoMP, MullinVE, ScheuA, MattiangeliV, DalyKG, Maisano DelserP, HareAJ, BurgerJ, CollinsMJ, KehatiR, HesseP, FultonD, SauerEW, MohasebFA, DavoudiH, KhazaeliR, LhuillierJ, RapinC, EbrahimiS, KhasanovM, VahidiSMF, MacHughDE, ErtuğrulO, Koukouli-ChrysanthakiC, SampsonA, KazantzisG, KontopoulosI, BulatovicJ, StojanovićI, MikdadA, BeneckeN, LinstädterJ, SablinM, BendreyR, GourichonL, ArbuckleBS, MashkourM, OrtonD, HorwitzLK, TeasdaleMD, BradleyDG. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science, 2019, 365(6449):173-176
CrossRef Google scholar
[87]
WangX, JuZ, JiangQ, ZhongJ, LiuC, WangJ, HoffJL, SchnabelRD, ZhaoH, GaoY, LiuW, WangL, GaoY, YangC, HouM, HuangN, RegitanoLCA, Porto-NetoLR, DeckerJE, TaylorJF, HuangJ. Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle. Genomics, 2021, 113(3):1491-1503
CrossRef Google scholar
[88]
WeedonMN, LettreG, FreathyRM, LindgrenCM, VoightBF, PerryJR, ElliottKS, HackettR, GuiducciC, ShieldsB, ZegginiE, LangoH, LyssenkoV, TimpsonNJ, BurttNP, RaynerNW, SaxenaR, ArdlieK, TobiasJH, NessAR, RingSM, PalmerCN, MorrisAD, PeltonenL, SalomaaV, Davey SmithG, GroopLC, HattersleyAT, McCarthyMI, HirschhornJN, FraylingTM. A common variant of HMGA2 is associated with adult and childhood height in the general population. Nat Genet, 2007, 39(10):1245-1250
CrossRef Google scholar
[89]
WeedonMN, LangoH, LindgrenCM, WallaceC, EvansDM, ManginoM, FreathyRM, PerryJR, StevensS, HallAS, SamaniNJ, ShieldsB, ProkopenkoI, FarrallM, DominiczakA, JohnsonT, BergmannS, BeckmannJS, VollenweiderP, WaterworthDM, MooserV, PalmerCN, MorrisAD, OuwehandWH, ZhaoJH, LiS, LoosRJ, BarrosoI, DeloukasP, SandhuMS, WheelerE, SoranzoN, InouyeM, WarehamNJ, CaulfieldM, MunroePB, HattersleyAT, McCarthyMI, FraylingTM. Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet, 2008, 40(5):575-583
CrossRef Google scholar
[90]
WeldenegodguadM, PopovR, PokharelK, AmmosovI, MingY, IvanovaZ, KantanenJ. Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions. Front Genet, 2018, 9: 728
CrossRef Google scholar
[91]
WillDH, HicksJL, CardCS, AlexanderAF. Inherited susceptibility of cattle to high-altitude pulmonary hypertension. J Appl Physiol, 1975, 38(3):491-494
CrossRef Google scholar
[92]
Wollenberg Valero KC, Pathak R, Prajapati I, Bankston S, Thompson A, Usher J, Isokpehi RD (2014) A candidate multimodal functional genetic network for thermal adaptation. PeerJ 2: e578. doi: https://doi.org/10.7717/peerj.578
[93]
WuDD, DingXD, WangS, WójcikJM, ZhangY, TokarskaM, LiY, WangMS, FaruqueO, NielsenR, ZhangQ, ZhangYP. Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nat Ecol Evol, 2018, 2(7):1139-1145
CrossRef Google scholar
[94]
WuDD, YangCP, WangMS, DongKZ, YanDW, HaoZQ, FanSQ, ChuSZ, ShenQS, JiangLP, LiY, ZengL, LiuHQ, XieHB, MaYF, KongXY, YangSL, DongXX, EsmailizadehA, IrwinDM, XiaoX, LiM, DongY, WangW, ShiP, LiHP, MaYH, GouX, ChenYB, ZhangYP. Convergent genomic signatures of high-altitude adaptation among domestic mammals. Natl Sci Rev, 2020, 7(6):952-963
CrossRef Google scholar
[95]
XiaX, QuK, ZhangG, JiaY, MaZ, ZhaoX, HuangY, ChenH, HuangB, LeiC. Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle. Anim Genet, 2019, 50(1):70-73
CrossRef Google scholar
[96]
XiaX, YaoY, LiC, ZhangF, QuK, ChenH, HuangB, LeiC. Genetic diversity of Chinese cattle revealed by Y-SNP and Y-STR markers. Anim Genet, 2019, 50(1):64-69
CrossRef Google scholar
[97]
XiaX, ZhangS, ZhangH, ZhangZ, ChenN, LiZ, SunH, LiuX, LyuS, WangX, LiZ, YangP, XuJ, DingX, ShiQ, WangE, RuB, XuZ, LeiC, ChenH, HuangY. Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data. BMC Genomics, 2021, 22(1):43
CrossRef Google scholar
[98]
XuL, BickhartDM, ColeJB, SchroederSG, SongJ, TassellCP, SonstegardTS, LiuGE. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. Mol Biol Evol, 2015, 32(3):711-725
CrossRef Google scholar
[99]
XuL, YangL, ZhuB, ZhangW, WangZ, ChenY, ZhangL, GaoX, GaoH, LiuGE, LiJ. Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle. BMC Genomics, 2019, 20(1):494
CrossRef Google scholar
[100]
YanCL, LinJ, HuangYY, GaoQS, PiaoZY, YuanSL, ChenL, RenX, YeRC, DongM, ZhangHL, ZhouHQ, JiangXX, JinWZ, ZhouXM, YanCG. Population genomics reveals that natural variation in PRDM16 contributes to cold tolerance in domestic cattle. Zool Res, 2022, 43(2):275-284
CrossRef Google scholar
[101]
YiX, LiangY, Huerta-SanchezE, JinX, CuoZX, PoolJE, XuX, JiangH, VinckenboschN, KorneliussenTS, ZhengH, LiuT, HeW, LiK, LuoR, NieX, WuH, ZhaoM, CaoH, ZouJ, ShanY, LiS, YangQ, AsanNP, TianG, XuJ, LiuX, JiangT, WuR, ZhouG, TangM, QinJ, WangT, FengS, LiG, HuasangLJ, WangW, ChenF, WangY, ZhengX, LiZ, BianbaZ, YangG, WangX, TangS, GaoG, ChenY, LuoZ, GusangL, CaoZ, ZhangQ, OuyangW, RenX, LiangH, ZhengH, HuangY, LiJ, BolundL, KristiansenK, LiY, ZhangY, ZhangX, LiR, LiS, YangH, NielsenR, WangJ, WangJ. Sequencing of 50 human exomes reveals adaptation to high altitude. Science, 2010, 329(5987):75-78
CrossRef Google scholar
[102]
YurchenkoAA, DaetwylerHD, YudinN, SchnabelRD, Vander JagtCJ, SoloshenkoV, LhasaranovB, PopovR, TaylorJF, LarkinDM. Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation. Sci Rep, 2018, 8(1):12984
CrossRef Google scholar
[103]
ZhangH, PaijmansJL, ChangF, WuX, ChenG, LeiC, YangX, WeiZ, BradleyDG, OrlandoL, O'ConnorT, HofreiterM. Morphological and genetic evidence for early Holocene cattle management in northeastern China. Nat Commun, 2013, 4: 2755
CrossRef Google scholar
[104]
ZhangK, LenstraJA, ZhangS, LiuW, LiuJ. Evolution and domestication of the Bovini species. Anim Genet, 2020, 51(5):637-657
CrossRef Google scholar
[105]
ZhaoS, ZhengP, DongS, ZhanX, WuQ, GuoX, HuY, HeW, ZhangS, FanW, ZhuL, LiD, ZhangX, ChenQ, ZhangH, ZhangZ, JinX, ZhangJ, YangH, WangJ, WangJ, WeiF. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat Genet, 2013, 45(1):67-71
CrossRef Google scholar
[106]
ZhouY, YangL, HanX, HanJ, HuY, LiF, XiaH, PengL, BoschieroC, RosenBD, BickhartDM, ZhangS, GuoA, Van TassellCP, SmithTPL, YangL, LiuGE. Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Res, 2022
CrossRef Google scholar
Funding
China Agriculture Research System-the National Beef Cattle and Yak Industrial Technology System(CARS-37); National Natural Science Foundation of China(32102523); Fellowship of China Postdoctoral Science Foundation(2020M683587); Shaanxi Youth Science and Technology New Star(2022KJXX-77); Natural Science Basic Research Program of Shaanxi Province(2021JQ-137); Fundamental Research Funds for the Central Universities; Scientific Research Fund of Department of Education of Yunnan(2022J0830)

Accesses

Citations

Detail

Sections
Recommended

/