Genetic components of grey cattle in Estonia as revealed by microsatellite analysis using two Bayesian clustering methods

SHORT REPORT Open Access Gene ic componen s o g ey ca le in Es onia as e ealed by mic osa elli e analysis using wo Bayesian clus e ing me hods Meng-Hua Li 1* , Juha Kan anen 1 , Annika Michelson 2 , U mas Saa ma 3 Abs ac Backg ound: I was ecen ly pos ula ed ha a ew indi idual g ey ca le s ill ound in Es onia migh be a elic o he old na i e ca le s ock. Geno ypes a 17 mic osa elli e loci om a o al o 243 ca le om No h Eu opean b eeds and 11 g ey ca le in Es onia we e used in an a emp o cla i y he gene ic composi ion o he g ey ca le. Findings: We cha ac e ize he gene ic componen s o 11 examples o he g ey ca le in Es onia a he popula ion and indi idual le els. Ou esul s show ha he g ey ca le in Es onia a e mos gene ically simila o he Hols ein- F iesian b eed and seconda ily o he Es onian Red ca le. Conclusions: Bo h Bayesian app oaches ga e simila esul s in e ms o he iden i ica ion o numbe s o clus e s and he es ima ion o p opo ions o gene ic componen s. This s udy sugges ed ha he Es onian g ey ca le included in he analysis a e a gene ic composi e esul ing om c oss-b eeding o Eu opean dai y b eeds. Backg ound Conse a ion o a m animal gene ic esou ces is o g ea alue o he ag icul u al, economic, social and cul- u al sec o s [1]. This is pa icula ly ue o na i e a m animals because he speci ic genes and gene combina- ions hey ca y may be use ul, o example o cope wi h he challenge o global clima e change (see [2]). Bal ic ca le popula ions ha e been g ea ly a ec ed by a ew p oduc i e b eeds such as Danish Red, Angeln, and Hols ein-F iesian [1]. As a esul , only e y ew popula ions, e.g. he Es onian Na i e, a e gene ically cha ac e is ic o he na i e ca le ha ha e su i ed in he Bal ic coun ies [3]. Mos o he o iginal ca le ha e de eloped in o new ed- o black-pied b eeds [1]. How- e e , a ecen su ey sugges ed ha he e could exis local g ey ca le in Es onia, wi h a o al popula ion size o ca. 60 animals, which we e pos ula ed o be a elic o he old na i e ca le s ock [4,5]. Today, hey a e main ained in small he ds owned by olde a me s, and as such, he e is limi ed pedig ee in o ma ion on hese indi iduals. Typically, hei hide is g ey, blue g ey, o g ey, ash g ey, black and whi e (see Figu e 1). So a he gene ic composi ion o g ey ca le ela i e o o he exis ing b eeds in Es onia is s ill unknown. In his s udy we use a panel o 17 mic osa elli e loci and Bayesian-based assignmen echniques o e alua e he ela ionship o Es onian g ey ca le o o he b eeds occu ing in No h Eu ope. Me hods Ca le samples and mic osa elli e da a Geno ypes o a o al o 254 animals om se en ca le popula ions (G ey ca le in Es onia, n= 11, see Table 1; Es onian Na i e, n= 40, Es onian Red, n=40,Finnish Hols ein-F iesian, n= 43, La ian Blue, n=40,La ian Danish Red, n= 40, La ian B own, n= 40) we e included in he analysis. Se en een (BM2113,HEL1,BM1824, BM1818,INRA032,INRA005,INRA035,ETH3,ILSTS006, HEL5,INRA023,INRA063,INRA037,ETH225,ILSTS005, CSSM66 and HEL13) o 30 mic osa elli e loci ecom- mended o gene ic di e si y s udies in ca le h p://www. p ojec s. oslin.ac.uk/cdi /ma ke s.h ml we e included in hisin es iga ion.Thegeno ypeda a o hesixpa en popula ions we e ob ained om an ea lie s udy [1]. * Co espondence: [email p o ec ed] 1 Bio echnology and Food Resea ch, MTT Ag i ood Resea ch Finland, FI-31600 Jokioinen, Finland Full lis o au ho in o ma ion is a ailable a he end o he a icle Li e al.BMC Resea ch No es 2011, 4:37 h p://www.biomedcen al.com/1756-0500/4/37 © 2011 Li e al; licensee BioMed Cen al L d. This is an Open Access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License (h p://c ea i ecommons.o g/licenses/by/2.0), which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal wo k is p ope ly ci ed. Ele en Es onian g ey ca le indi iduals om di e en s ocks we e blood-sampled. Pa icula e o s we e made in all cases, using bo h he limi ed pedig ee in o ma ion (e.g. mos ly only pa en -o sp ing and ull- sibling ela ionships) a ailable and he knowledge o local he dsmen (e.g. he a m o illage whe e he ca - le o igina e om and he p e ious owne s) ia he in e iew ques ionnai e, o ensu e ha he animals we e un ela ed and had cha ac e is ics ypical o he popula ion [4]. Genomic DNA was ex ac ed using a s anda d phenol/chlo o o m p o ocol [6]. PCRs we e ca ied ou ollowing he p o ocols a ailable a he Ca le Di e si y Da abase h p://www.p ojec s. oslin.ac. uk/cdi /ma ke s.h ml. The size cha ac e iza ion o PCR p oduc s was done on a MegaBACE™500 capil- la y sequence (GE Heal hca e Li e Sciences, Li le Chal on , UK) using he F agmen P o ile p og am e . 1.2 (GE Heal hca e Li e Sciences). In e na ional con ol samples we e also geno yped in o de o s an- da dize he size o allele agmen s. Blood sampling o he 11 G ey ca le in Es onia was aken by a e e ina - ian in a p ocedu e acco ding o he Es onian Ve e in- a y and Food Boa d and sa is ied all e hical conce ns. Da a analysis Tes s o geno ypic linkage disequilib ium (LD) o each locus pai and es s o de ia ion om Ha dy-Weinbe g equilib ium (HWE) we e analysed in GENEPOP e sion 3.4 [7]. The global and pai wise gene ic di e en ia ion we e de e mined as unbiased es ima es o F ST [8] using FSTAT e sion 2.9.3.2 [9]. Signi icance o he esul s was es ablished by applying sequen ial Bon e oni co - ec ions (see [10]). Figu e 1 A g ey cow om he Vah amäe a m in Es onia (Pho o c edi : Imbi Jäe ma). Table 1 Da a o he 11 g ey ca le analysed in Es onia Sample Coun y Village Gende Colou Le1 Läänemaa Silla ♀g ey Le2 Lääne-Vi umaa Kä sa ♀g ey Le3 Lääne-Vi umaa Kä sa ♀g ey Le4 Läänemaa Kinki ♀g ey Le5 Jõge amaa Maa dla ♀da k g ey (blackish) Le6 Jõge amaa Maa dla ♀g ey ( eddish) Le7 Jõge amaa Maa dla ♀da k g ey Le8 Jõge amaa Maa dla ♀da k g ey Le9 Ha jumaa Rooküla ♂g ey Le10 Ha jumaa Rooküla ♂g ey Le11 Raplamaa Laukna ♀da k g ey Li e al.BMC Resea ch No es 2011, 4:37 h p://www.biomedcen al.com/1756-0500/4/37 Page 2 o 6 A Bayesian clus e ing me hod was i s employed o assess popula ion s uc u e using he p og am STRUC- TURE e sion 2.2 [11]. We pe o med 10 uns o each K alue a 2 - 10 and an he p og am assuming a model o admix u e and co ela ed allele equencies. We did no use any p io in o ma ion abou he popula- ion o igin o he animals. A bu n-in pe iod o 200 000 gene a ions and MCMC simula ions o 500 000 i e a- ions we e used in all he abo e uns. The alues o LnP (D) ( he log p obabili y o da a) we e es ima ed assign- ing a p io om 2 o 10 and he op imal Kwas chosen based on he del a K(ΔK) alue. This c i e ion was o i- ginally desc ibed in E anno e al. [12] and was shown o be e ec i e in la e s udies [1,13]. We hen e alua ed he popula ion and indi idual membe ship coe icien s (Q) o he 11 g ey ca le in Es onia o he Kin e ed clus e s. BAPS e sion 5.4 [14] was un se ing he maximum numbe o clus e s a 20. Resul s we e based on 50 simula ions om he pos e io allele equencies. Since he mode o he pos e io dis ibu ion o Kalmos always p o ided an o e es ima e o K, we used he num- be o clus e s con aining mo e han 3 indi iduals as a poin es ima e o K, as ecommended by Tang e al. [14]. Fo uns in which Kwas co ec ly es ima ed, we calcula ed he a e age p obabili y (q) o assignmen o he ‘co ec ’clus e (’co ec ’de ined as q>0.9in he co ec clus e ). Indi iduals wi h a likelihood admix u e a io g ea e han 3.0 we e conside ed o be signi ican ly admixed. Resul s The F ST analysis ac oss b eeds showed ha 5.6% o he o al gene ic a ia ion could be explained by he di e - ence among popula ions. A low le el o gene ic di e en- ia ion was ound be ween he g ey ca le in Es onia and Finnish Hols ein-F iesian (F ST = 5.2%; esul s no shown) as well as be ween he g ey ca le in Es onia and he Es onia Red ca le (F ST = 5.6%; esul s no shown). Nei he o he alues was s a is ically signi ican a he 0.05 le el (P> 0.05). No speci ic locus pai s showed a consis en de ia ion om LE ha would ha e been in each, o e en in mos , o he popula ions. De ia ions om HWE ac oss he loci we e p esen in he popula- ion o g ey ca le in Es onia, which is mos p obably due o he small popula ion size. Howe e , no e idence o signi ican de ia ion om HWE was de ec ed when a es was pe o med ac oss all loci o all popula ions. Based on he popula ion Q- alues, he STRUCTURE p og am iden i ied six clus e s among he se en popula- ions, bu could no disce n all se en popula ions (Figu e 2A). Mo e exac ly, i ailed o di e en ia e be ween he g ey ca le in Es onia and Finnish Hols ein-F iesian. O e he en i e ca le popula ions, Ln P(D) inc eased om K=2 oK= 6, a e which i began o decline, indica ing he mos likely alue o be K= 6 ( esul s no shown). When we used ΔK o in e he numbe o clus e s, we ound ha K= 6 was clea ly a ou ed ( esul s no shown). A K= 6, all he g ey ca le in Es onia we e cha ac e ized, wi h he highes p opo ion o membe ship om he Fin- nish Hols ein-F iesian clus e (Q FiHF ). Fi e g ey ca le (Le1, Le4, Le9, Le10 and Le11) showed high alues o Q FiHF > 0.9 and he emaining g ey ca le a e sugges ed o ha e la ge membe ship ac ions in mul iple clus e s o he sampled popula ions. In pa icula , he g ey ca le Le8 ha e simila alues o Q o wo dis inc popula ions, Fin- nish Hols ein-F iesian (Q FiHF = 0.480) and he Es onian Red (Q EsR = 0.351; Table 1). Wi h espec o he o e all pa e n o popula ion clus- e ing, esul s wi h BAPS we e mos ly consis en wi h hose ob ained wi h STRUCTURE. The analysis o popu- la ion gene ic s uc u e ca ied ou wi h BAPS sugges ed K= 6 o be he bes clus e ing op ion (see Figu e 2B), wi h he six clus e s co esponding o he six sou ce popula ions. Figu e 2B shows he p opo ions o mem- be ship (q) o each g ey ca le indi idual in each o he six iden i ied clus e s, while he co esponding alues a e p esen ed in Table 2. Fi e samples (Le1, Le4, Le9, Le10 and Le11) exhibi ed q alues o 100% o he clus e o Hols ein-F iesian and one (Le8) o Es onian Red. The emaining samples ecei ed p opo ions o membe ship om mul iple clus e s, while he highe a e age p opo - ion o hei membe ship was om Finnish Hols ein- F iesian ollowed by Es onian Red (Table 1). Discussion On-a e age we ound highe p opo ions o membe ship o Finnish Hols ein-F iesian and Es onian Red ca le in he g ey ca le. The g ey ca le ep esen a composi e o No h Eu opean ca le. The composi e gene ic componen s may explain hei dis inc i eg eycolou ,whichisamix u eo colou s. This inding is also e idenced by he ac ha a g ey cow some imes has g ey and/o black-and-whi e cal es in he same bi h. Al hough he g ey ca le a e cha ac- e ized as ha ing mos o hei gene ic componen s om he black-and-whi e dai y ca le (i.e. Hols ein- F iesian) o Es onian Red, hey can be aluable in he in es iga ion o he gene ics o he colou genes. Bo h STRUCTURE and BAPS co ec ly in e ed he numbe o clus e s in a da ase when gene ic di e en ia- ion among popula ions was low. Howe e , i seems ha he p opo ions o indi idual membe ship in he clus e s es ima ed by he p og am STRUCTURE a e mo e con- sis en wi h he b eeding his o y o he popula ions. Fo example, La ian Danish Red, Es onian Red and La - ian B own a e he local de i ed popula ions om he Anglen and Danish Red ca le. This sha ed ances y is Li e al.BMC Resea ch No es 2011, 4:37 h p://www.biomedcen al.com/1756-0500/4/37 Page 3 o 6 e lec ed in he esul s o STRUCTURE, bu no o BAPS. Fo he 11 g ey ca le in Es onia, bo h p og ams ga e compa able esul s o p opo ions o indi idual membe ship. To secu e high con idence in esul s, we ad oca e using bo h p og ams o in e ing he numbe o clus e s and assignmen o indi iduals o clus e s, pa icula ly when he le el o gene ic di e en ia ion among popula ions is low. Finally, a g owing numbe o domes ic animal popula- ions a e geno yped o he same panel o mic osa elli es (see [15]), o example he ma ke s ecommended by he FAO (Food and Ag icul u e O ganiza ion o he Uni ed Na ions). This can help add ess simila kinds o ques ions ongene iccomponen sand hena u eo na i eanimal s ocks because mo e da a o po en ial e e ence and pa - en al popula ions a e a ailable. The li es ock popula ions Figu e 2 Popula ion s uc u e o 7 ca le popula ions using:(A) model-based STRUCTURE p og am (P i cha d e al. 2000) and (B) BAPS p og am (Tang e al. 2009). Each animal is ep esen ed by a single e ical line di ided in o Kcolou s, whe e Kis he numbe o clus e s assumed. The colou ed segmen shows he indi idual’s es ima ed p opo ion o membe ship (a e aged ac oss 10 uns a K= 6) in ha clus e o he STRUCTURE p og am and indica es he a e age p obabili y o assignmen o he “co ec ”clus e o he BAPS p og am. Black lines sepa a e he popula ions labelled abo e he igu e. The labels abo e he igu e indica e he numbe o animals analysed in each b eed and he names o he ca le popula ions analysed a e indica ed below he igu e. Li e al.BMC Resea ch No es 2011, 4:37 h p://www.biomedcen al.com/1756-0500/4/37 Page 4 o 6 o which he e is a high p io i y o conse a ion, in e ms o p opo ions o hei na i e gene ic componen s (e.g. [16-18]), can be iden i ied and, hus, need o be included in conse a ion p og ammes in he nea u u e. Conclusions In conclusion, gi en he low le els o gene ic di e en ia- ion among he popula ions in es iga ed, bo h Bayesian app oaches ga e simila esul s in e ms o iden i ica ion o he numbe s o clus e s and he es ima ion o p opo - ions o gene ic componen s. Ou s udy shows ha he Es onian g ey ca le analysed we e a gene ically admixed popula ion, mos in luenced by he Hols ein-F iesian and Es onian Red ca le. Acknowledgemen s We wish o hank Kaia Lepik om he Es onian Fund o Na u e o he gene ous help and p o esso Haldja Viinalass a he Es onian Uni e si y o Li e Sciences (Ta u, Es onia) o he commen s. This s udy was suppo ed by a g an om he Es onian Science Founda ion, a ge inancing p ojec SF0180122s08 om he Es onian Minis y o Educa ion and Sciences; and om he Eu opean Union h ough he Eu opean Regional De elopmen Fund (Cen e o Excellence FIBIR). Au ho de ails 1 Bio echnology and Food Resea ch, MTT Ag i ood Resea ch Finland, FI-31600 Jokioinen, Finland. 2 HAMK Uni e si y o Applied Sciences, FI-31310 Mus iala, Finland. 3 Depa men o Zoology, Ins i u e o Ecology and Ea h Sciences, Uni e si y o Ta u, 46 Vanemuise S ee , EE-51014 Ta u, Es onia. Au ho s’con ibu ions MHL designed he s udy, pe o med he da a analysis and w o e he manusc ip . JK planned and coo dina ed he whole s udy, and con ibu ed o he manusc ip w i ing. AM collec ed in o ma ion abou Es onian g ey ca le, con ac ed ca le owne s and in e iewed hem. US pa icipa ed in s udy design, sample collec ion o g ey ca le in Es onia and he p elimina y da a analysis. All he au ho s ead and app o ed he inal manusc ip . Compe ing in e es s The au ho s decla e ha hey ha e no compe ing in e es s. Recei ed: 6 July 2010 Accep ed: 11 Feb ua y 2011 Published: 11 Feb ua y 2011 Re e ences 1. Li MH, Kan anen J: Gene ic s uc u e o Eu asian ca le (Bos au us) based on mic osa elli es: cla i ica ion o hei b eed classi ica ion. Anim Gene 2010, 41:150-158. 2. Ho mann I: Clima e change and he cha ac e iza ion, b eeding and conse a ion o animal gene ic esou ces. Anim Gene 2010, 41(Suppl 1):32-46. 3. Dmi ie NG, E ns LK: Animal Gene ics Resou ces o he USSR. Rome (I aly): Food and Ag icul u e O ganiza ion o he Uni ed Na ions; 1989. 4. Michelson A: G ey ca le in Es onia. Mus iala (Finland): Depa men o Na u al Sciences and he En i onmen , HAMK Uni e si y o Applied Sciences; 2010. 5. Oska L: Endis-Ees i elu-olu. IV Lugemispalu Ka jakas a aja Elus . Ta u (Es onia): Ees i Ki jandusmuuseum; 2001. 6. Samb ook J, F i sch EF, Mania is T: Molecula Cloning: a Labo a o y Manual. 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Table 2 Membe ship p opo ions (Q) o he 11 g ey ca le in Es onia o he 6 gene ic clus e s Animals Clus e 1 (La ian B own) a Clus e 2 (La ian Blue) Clus e 3 (La ian Danish Red) Clus e 4 (Es onian Na i e) Clus e 5 (Es onian Red) Clus e 6 (Finnish Hols ein-F iesian) Le1 0.015(0.00) b 0.003(0.00) 0.006(0.00) 0.005(0.00) 0.008(0.00) 0.963(1.00) c Le2 0.015(0.01) 0.015(0.04) 0.081(0.40) 0.015(0.03) 0.145(0.05) 0.729(0.47) Le3 0.025(0.00) 0.017(0.06) 0.072(0.12) 0.008(0.00) 0.027(0.15) 0.852(0.67) Le4 0.009(0.00) 0.019(0.00) 0.008(0.00) 0.003(0.00) 0.008(0.00) 0.953(1.00) Le5 0.012(0.01) 0.023(0.15) 0.038(0.12) 0.016(0.02) 0.047(0.25) 0.864(0.45) Le6 0.013(0.02) 0.008(0.00) 0.032(0.08) 0.029(0.25) 0.169(0.34) 0.749(0.31) Le7 0.021(0.12) 0.036(0.10) 0.054(0.12) 0.009(0.10) 0.241(0.24) 0.639(0.32) Le8 0.006(0.00) 0.007(0.00) 0.351(0.00) 0.009(0.00) 0.147(1.00) 0.480(0.00) Le9 0.033(0.00) 0.009(0.00) 0.008(0.00) 0.012(0.00) 0.014(0.00) 0.925(1.00) Le10 0.009(0.00) 0.005(0.00) 0.007(0.00) 0.010(0.00) 0.014(0.00) 0.954(1.00) Le11 0.010(0.00) 0.035(0.00) 0.010(0.00) 0.014(0.00) 0.026(0.00) 0.905(1.00) a The gene ic clus e s in e ed using he STRUCTURE p og am. b The a e age p obabili y (q, in he pa en heses) o assignmen o he “co ec ”clus e ("co ec ”de ined as q> 0.9 in he co ec clus e ) by using he BAPS p og am. c Values o Q> 0.9 o q> 0.9 a e in bold. Li e al.BMC Resea ch No es 2011, 4:37 h p://www.biomedcen al.com/1756-0500/4/37 Page 5 o 6 17. Fan B, Wang ZG, Li YJ, Zhao XL, Liu B, Zhao SH, Yu M, Li MH, Chen SL, Xiong TA, Li K: Gene ic a ia ion analysis wi hin and among Chinese indigenous swine popula ions using mic osa elli e ma ke s. Anim Gene 2002, 33:422-427. 18. Li MH, Zhao SH, Bian C, Wang HS, Wei H, Liu B, Yu M, Fan B, Chen SL, Zhu MJ, Li SJ, Xiong TA, Li K: Gene ic ela ionships among wel e Chinese indigenous goa popula ions based on mic osa elli e analysis. Gene Sel E ol 2002, 34:729-744. doi:10.1186/1756-0500-4-37 Ci e his a icle as: Li e al.: Gene ic componen s o g ey ca le in Es onia as e ealed by mic osa elli e analysis using wo Bayesian clus e ing me hods. BMC Resea ch No es 2011 4:37. Submi you nex manusc ip o BioMed Cen al and ake ull ad an age o : • Con enien online submission • Tho ough pee e iew • No space cons ain s o colo igu e cha ges • Immedia e publica ion on accep ance • Inclusion in PubMed, CAS, Scopus and Google Schola • Resea ch which is eely a ailable o edis ibu ion Submi you manusc ip a www.biomedcen al.com/submi Li e al.BMC Resea ch No es 2011, 4:37 h p://www.biomedcen al.com/1756-0500/4/37 Page 6 o 6