BioMed Cen al
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BMC Genomics
Open Access
Resea ch a icle
A i s -gene a ion mic osa elli e-based gene ic linkage map o he
Sibe ian jay (Pe iso eus in aus us): insigh s in o a ian genome
e olu ion
Sonja Jaa i, Meng-Hua Li* and Juha Me ilä
Add ess: Ecological Gene ics Resea ch Uni , Depa men o Biological and En i onmen al Sciences, PO Box 65, FIN-00014 Uni e si y o Helsinki,
Finland
Email: Sonja Jaa i - sonja.jaa i@helsinki. i; Meng-Hua Li* - menghua.li@helsinki. i; Juha Me ilä - juha.me il[email p o ec ed]
* Co esponding au ho
Abs ac
Backg ound: Genomic esou ces o he majo i y o ee-li ing e eb a es o ecological and e olu iona y
impo ance a e sca ce. The e o e, linkage maps wi h high-densi y genome co e age a e needed o p og ess in
genomics o wild species. The Sibe ian jay (Pe iso eus in aus us; Co idae) is a passe ine bi d which has been subjec
o lo s o esea ch in he a eas o ecology and e olu iona y biology. Knowledge o i s genome s uc u e and
o ganiza ion is equi ed o ad ance ou unde s anding o he gene ic basis o ecologically impo an ai s in his
species, as well as o p o ide insigh s in o a ian genome e olu ion.
Resul s: We desc ibe he i s gene ic linkage map o Sibe ian jay cons uc ed using 117 mic osa elli es and a
mapping pedig ee o 349 animals ep esen ing i e amilies om a na u al popula ion b eeding in wes e n Finland
om he yea s 1975 o 2006. Ma ke s we e esol ed in o nine au osomal and a Z-ch omosome-speci ic linkage
g oup, 10 ma ke s emaining unlinked. The bes -posi ion map wi h he mos likely posi ions o all signi ican ly
linked loci had a o al sex-a e age size o 862.8 cM, wi h an a e age in e al dis ance o 9.69 cM. The emale map
co e ed 988.4 cM, whe eas he male map co e ed only 774 cM. The Z-ch omosome linkage g oup comp ised six
ma ke s, h ee pseudoau osomal and h ee sex-speci ic loci, and spanned 10.6 cM in emales and 48.9 cM in males.
Eigh y-one o he mapped loci could be o de ed on a amewo k map wi h odds o >1000:1 co e ing a o al size
o 809.6 cM in emales and 694.2 cM in males. Signi ican sex speci ic dis o ions owa ds educed male
ecombina ion a es we e e ealed in he en i e bes -posi ion map as well as wi hin wo au osomal linkage g oups.
Compa a i e mapping be ween Sibe ian jay and chicken ancho ed 22 homologous loci on 6 di e en linkage
g oups co esponding o chicken ch omosomes Gga1, 2, 3, 4, 5, and Z. Qui e a ew cases o in a-ch omosomal
ea angemen s wi hin he au osomes and h ee cases o in e -ch omosomal ea angemen be ween he
Sibe ian jay au osomal linkage g oups (LG1, LG2 and LG3) and he chicken sex ch omosome GgaZ we e
obse ed, sugges ing a conse ed syn eny, bu changes in ma ke o de , wi hin au osomes du ing abou 100
million yea s o a ian e olu ion.
Conclusion: The cons uc ed linkage map ep esen s a aluable esou ce o in aspeci ic genomics o Sibe ian
jay, as well as o a ian compa a i e genomic s udies. Apa om p o iding no el insigh s in o sex-speci ic
ecombina ion a es and pa e ns, he desc ibed maps – om a p e iously genomically uncha ac e ized
supe amily (Co idae) o passe ine bi ds – p o ide new insigh s in o a ian genome e olu ion. In combina ion wi h
high- esolu ion da a on quan i a i e ai a iabili y om he s udy popula ion, hey also p o ide a ounda ion o
QTL-mapping s udies.
Published: 3 Janua y 2009
BMC Genomics 2009, 10:1 doi:10.1186/1471-2164-10-1
Recei ed: 16 July 2008
Accep ed: 3 Janua y 2009
This a icle is a ailable om: h p://www.biomedcen al.com/1471-2164/10/1
© 2009 Jaa i 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.
BMC Genomics 2009, 10:1 h p://www.biomedcen al.com/1471-2164/10/1
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Backg ound
Unde a ious comple ed o ongoing p ojec s, apid
p og ess has been a ained in he gene a ion o genomic
esou ces o model o ganisms and domes ic animals o
medical, economic, o ag icul u al impo ance (e.g. [1-
3]). Howe e , genomic esou ces o he majo i y o ee-
li ing e eb a es o ecological and e olu iona y impo -
ance a e s ill sca ce. Fo ins ance, in wild bi ds, de elop-
men o genomic esou ces a e s ill in hei in ancy, and
only ew ini ial e o s in linkage mapping [4-8], es ima-
ion o he ex en o linkage disequilib ium [9,10], and
syn enic compa ison be ween ela ed species [7,8,11-14] ]
ha e been conduc ed. Hence, e y limi ed in o ma ion on
he genome s uc u e o wild bi d species is a ailable o
u he syn hesis, as well as o s udy and cha ac e ize
molecula unde pinnings o pheno ypic ai s. Since wild
passe ine bi ds a e impo an 'model' o ganisms in ecol-
ogy and e olu iona y biology, and in s udies o li e his o y
e olu ion (e.g. [15]), beha iou (e.g. [16,17]) and e olu-
iona y quan i a i e gene ics in pa icula (e.g. [18-20]),
knowledge o hei genome s uc u e and o ganiza ion is
i al o ad ance ou unde s anding o he gene ic basis o
ecologically impo an ai s [21].
Gene ic maps cons i u e essen ial and powe ul o ganiza-
ional ools o genomic esea ch [22]. Among he mos
impo an applica ions o gene ic maps in genomic anal-
yses is in ha hey p o ide a pla o m o suppo s udies
u ilizing o aiming o apply candida e gene app oaches
[21,23], QTL mapping [24], compa a i e genomics [25],
and genome anno a ion [26]. Howe e , cons uc ion o
gene ic linkage maps o non-model o ganisms is compli-
ca ed by se e al ac o s [27,28]. One o he majo obs a-
cles o he cons uc ion o linkage maps in passe ine
bi ds (bu see [4]) is he sca ci y o in o ma i e gene ic
ma ke s. Among a a ie y o molecula make s p e iously
employed in linkage mapping in di e en o ganisms,
mic osa elli e ma ke s ha e o en p o en mos use ul due
o hei hype a iabili y, as e olu iona y a es, codomi-
nance, wide dis ibu ion h oughou he genomes, and
he ela i e ease wi h which hey can be de eloped and
geno yped using he polyme ase chain eac ion (PCR; e.g.
[29]). While gene ic maps exis in one o m o ano he o
a ious species, i is wo h no icing ha he s udies a e so
a gene ally limi ed o domes ic animals o na u al pop-
ula ions o wild species ha can easily be b ed in cap i i y,
o whe e su icien ly la ge li e sizes a e being p oduced
in na u al se ings and a e accessible o sampling o allow
he es ablishmen o he pedig ee necessa y o linkage
analysis [9]. Un o una ely, he cha ac e is ics ha make
popula ions p ac ical o linkage mapping [9] a e ound
only among a small ac ion o species s udied by ecolo-
gis and e olu iona y biologis s. Linkage maps ha e now
been cons uc ed in ou popula ions o non-model ani-
mals o which long- e m indi idual-based da ase s a e
a ailable (see also: [8]), and whe e na u al long- e m ped-
ig ees ( a he han expe imen al b eeding p og ammes)
ha e been used o ollow he co-seg ega ion o ma ke
alleles [28]. Two o hese mapping popula ions a e in
ungula e species (soay sheep, O is a ies [24]; ed dee , Ce -
us elaphus [27]) and wo a e in passe ine bi ds (g ea eed
wa ble , Ac ocephalus a undinaceus [4,6,13]; colla ed ly-
ca che , Ficedula albicollis [5,9,11]).
The Sibe ian jay (Pe iso eus in aus us) is a passe ine bi d
which has been subjec o conside able ecological and
e olu iona y esea ch du ing he pas decades. S udies in
i s b eeding biology [30-33], ma ing sys em [34,35], o -
aging beha iou [36], ep oduc i e success [37], pa en al
ca e and dispe sal pa e n [38,39], amily s uc u e [40],
pheno ypic plas ici y [41] and le els o inb eeding [42]
ha e been conduc ed. Thus, hese p e ious s udies o m
an app op ia e se ing in an ini ia i e o explo e he in e-
g a ion o genomics wi h he domain o ecology and e o-
lu iona y biology [43], p o ided ha a leas some basic
knowledge o he species' genome can be ob ained. Wi h
an access o de ailed pedig ees o a Sibe ian jay popula-
ion moni o ed o e 30 yea s [40,42], as well as access o
a no el se o polymo phic mic osa elli es de eloped o
his species [44], cons uc ion o a linkage map is now
ealis ic. In an e olu iona y con ex , he chicken genome
sequence [45] eleased ecen ly acili a es genomic s udies
in o he bi d species by compa a i e genomic app oaches
[13,25]. Mo eo e , gi en he ea ly di e gence o a ian lin-
eages be ween passe i o ms and galli o ms (≈ 100 million
yea s ago; [46]) and he high le el o phylogene ic di e -
gence be ween jays belonging o he Co idae amily and
he o he passe ines o which linkage maps ha e been
published (e.g. [47,48]), a linkage map o he Sibe ian jay
may p o ide new insigh s in o a ian genome e olu ion,
and he eby also o he ex ensi e mo phological, li e his-
o ical and beha iou al di e si ica ion wi hin he o de
Passe i o mes (see [47]).
The aim o his s udy was o de elop a i s -gene a ion
gene ic linkage map o a wild popula ion o Sibe ian jays
on he basis o 117 mic osa elli es, including a no el se
o 108 ma ke s. To his end, a amewo k map was con-
s uc ed o iden i y ma ke s whose local ela i e o de s
we e s a is ically well suppo ed wi h an unambiguous
loca ion in he map. Since he e ochiasmy has been
obse ed in p e ious s udies o many species (e.g.
zeb a ish [49]; and g ea eed wa ble [4]), sex-speci ic
a ia ion in he ecombina ion a e and he gene ic map
dis ance we e also in es iga ed. Fu he mo e, o p o ide a
compa a i e pe spec i e o add ess he e olu ion o
genome o ganisa ion he ex en o syn eny and locus
o de conse a ion be ween Sibe ian jay and chicken was
e alua ed by a BLAST analysis agains he chicken genome
sequence.
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Resul s
Cha ac e is ics o polymo phic mic osa elli es
O he 117 mic osa elli es sco ed, six loci (SJ009, SJ046,
SJ048, SJ069, SJ083 and SJ108) we e assigned o he Z-
ch omosome by obse a ion o comple e coseg ega ion
wi h sex and he obse a ion o he e ozygosi y in some
males bu none o he emales in he pedig ees. None o
he ma ke s examined appea ed o be si ua ed in W-ch o-
mosome since all he ma ke s had alleles in he males. The
numbe o in o ma i e meioses a ied om 33 (SJ047) o
474 (CKL5) wi h an a e age o 284.63 in o ma i e mei-
oses pe locus. Mo e de ails abou le els o gene ic a ia-
bili y (HO, HE and PIC) a e shown in Addi ional File 1.
Gene ic linkage maps
An o e iew o he linkage da a is gi en in Figu es 1, 2 and
Table 1 depic ing he bes -posi ion and amewo k link-
age maps and hei cha ac e is ics. O he 117 mic osa el-
li es, 107 loci (91%) we e assembled in o 9 au osomal
linkage g oups (LG1 – LG9) and one Z-ch omosome link-
age g oup (LGZ), and he o he 10 polymo phic mic osa -
elli es (SJ002, SJ003, SJ005, SJ020, SJ030, SJ034, SJ118,
MJG1, PER1 and LTML8) appea ed o be unlinked o any
o he ma ke by wo-poin analysis wi h LOD sco es < 3.0.
O he en unmapped ma ke s, six had less han 60
in o ma i e meioses while ou had mo e han 200
in o ma i e meioses. O he nine au osomal LGs, se en
comp ised o six o mo e loci and he emaining h ee LGs
each con ained wo o h ee loci, wi h an a e age o ca. 11
mic osa elli es pe LG. Fo he sex-a e age au osomal LGs
in he bes -posi ion map (Figu e 1), he meio ic leng hs,
e alua ed as he dis ance be ween he ou e mos ma ke s
on each LG, anged om 10.6 cM (LG09) o 185.6 cM
(LG01) spanning in o al 862.8 cM o he Sibe ian jay
genome. The a e age ma ke in e al was 9.69 cM calcu-
la ed as he a i hme ic mean o he map dis ances be ween
adjacen ma ke s (Table 1). On he maps, 35.9% (33/92)
o he in e als be ween ma ke s a ied om 0 o 5 cM,
31.5% (29/92) anged om 5 o 10 cM, and 20.7% (19/
92) om 10 o 20 cM, and 12% (11/92) we e > 20 cM.
Sex-speci ic au osomal maps we e also cons uc ed (Fig-
u e 1). The sum o he leng h o all au osomal LGs was
774.0 cM in males and 988.4 cM in emales, wi h an a e -
age in e ma ke spacing o 8.6 cM and 12.1 cM, espec-
i ely. The male map comp ises LGs anging in leng h
om 7.7 cM o 171.1 cM while he emale map con ains
LGs wi h a leng h om 9.2 cM o 229.2 cM (Table 1). Ou
o he nine pai s o male and emale LGs, se en we e la ge
in he emale map and wo we e la ge in he male map.
In o al, he au osomal LGs we e smalle in males as com-
pa ed o emales wi h a emale- o-male map a io o 1.28.
The sex-a e age map was in e media e in leng h be ween
sex-speci ic maps, and 1.12 imes longe han he male
map.
F amewo k ma ke s, which could be o de ed wi h LOD
sco e o 3.0 o g ea e (indica ing odds o 1000:1), a e
indica ed in bold on s in he bes -posi ion map (Figu e
1). O he o al 107 mapped ma ke s, 81 loci we e signi -
ican ly o de ed in he amewo k map and mos (16/24)
o he emaining loci could be placed wi h signi ican sup-
po in ei he o wo al e na i e in e als. When only he
amewo k ma ke s we e conside ed, he o al size o
au osomal linkage g oups was 692.1 cM in he sex-a e age
map, 649.4 cM in he male map, and 799 cM in he emale
Table 1: Cha ac e is ics o he bes -posi ion and amewo k maps o Sibe ian jay
LG Bes -posi ion map (cM) F amewo k map (cM)
No. o loci Sex
a e age
씸씹A e age
in e -
ma ke
dis ancea
Ra io o 씸/
씹 maps
No. o loci Sex
a e age
씸씹A e age
in e -
ma ke
dis ancea
Ra io o 씸/
씹 maps
LG1 29 185.6 213.6 168.3 6.87 1.27 20 167.0 182.8 156.7 8.35 1.17
LG2 27 181.5 229.2 141.3 6.72 1.62 21 141.3 212.1 116.8 6.73 1.82
LG3 13 182.6 197.9 171.1 16.6 1.16 10 170.2 175.5 171.3 17.02 1.02
LG4 11 98.2 110 86.7 9.82 1.27 9 76.0 88.3 63.8 8.44 1.38
LG5 8 85.2 92.9 82.1 12.17 1.13 7 83.9 93.4 78.4 11.99 1.19
LG6 6 78.2 98.9 65.4 15.64 1.51 3 14.4 15.5 13.2 4.80 1.17
LG7 3 26.4 24.3 32.3 13.2 0.75 2 14.2 9.8 22.4 7.10 0.44
LG8 2 14.5 9.2 19.1 15.5 0.48 2 14.5 9.2 19.1 7.25 0.48
LG9 2 10.6 12.4 7.7 10.6 1.61 2 10.6 12.4 7.7 5.30 1.61
LGAb101 862.8 988.4 774 9.69 1.28 76 692.1 799 649.4 9.11 1.23
LGZ 6 23.8 10.6 48.9 4.76 0.22 5 22.1 10.6 44.8 4.42 0.24
씸 Female-speci ic linkage g oups
씹 Male-speci ic linkage g oups
a The a e age in e -ma ke dis ance is based on he sex-a e age map
b o al au osomal linkage g oups
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The bes -posi ion linkage g oups (male-speci ic, M; sex-a e age, A; and emale-speci ic; F) in Kosambi cen imo gans o he Sibe ian jayFigu e 1
The bes -posi ion linkage g oups (male-speci ic, M; sex-a e age, A; and emale-speci ic; F) in Kosambi cen i-
mo gans o he Sibe ian jay. The ma ke s in bold ace on a e amewo k loci wi h unambiguous ela i e posi ion be ween
each o he .
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The amewo k linkage g oups (male-speci ic, M; sex-a e age, A; and emale-speci ic; F) in Kosambi cen imo gans o he Sibe- ian jayFigu e 2
The amewo k linkage g oups (male-speci ic, M; sex-a e age, A; and emale-speci ic; F) in Kosambi cen imo -
gans o he Sibe ian jay.

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map (Figu e 2 and Table 1). We compa ed ecombina ion
dis ances be ween adjacen amewo k ma ke s ha we e
mapped on bo h he bes -posi ion map and he ame-
wo k map and o e all he emale- o-male a io o he
amewo k map was 1.23, sligh ly lowe han he a io o
1.28 obse ed abo e in he bes -posi ion map.
Among he Z-linked mic osa elli es, all six ma ke s
showed highly signi ican linkage be ween each o he
wi h LODs > 37.0. This linkage g oup spanned 23.8 cM in
he sex-a e age map, 48.9 cM in he male map and 10.6
cM in emale map, which co esponds o a emale- o-male
a io o 0.22. The emale linkage map indica es he posi-
ion and app oxima e ex en o a pseudoau osomal egion
(PAR) om SJ069 o beyond SJ048. In emales, no ecom-
bina ion was obse ed be ween SJ083 and SJ046 and no
he e ozygosi y was obse ed o hese ma ke s; he e o e
hey mus lie ou side he pseudoau osomal egion, sug-
ges ing ha he pseudoau osomal bounda y lies be ween
SJ048 and SJ046. As expec ed, he e is conside able di e -
ence in male and emale ecombina ion a es o he pseu-
doau osomal egion o he Z-ch omosome, wi h he male
dis ance be ween SJ108 and SJ069 being 41.7 cM as com-
pa ed o he emale dis ance o 5.1 cM. This inc eased sex-
speci ic ecombina ion a e be ween he h ee pseudoau-
osomal loci was simila o he obse a ions in he pseu-
doau osomal egions o he mammalian sex
ch omosomes, o example in humans [50], o ines [51]
and bo ines [52]. In he sex-a e age map, he map densi y
was 4.0 cM/ma ke among all Z-linked ma ke s and 3.3
cM/ma ke among he i e amewo k loci.
Di e ences in ecombina ion a e be ween sexes
In addi ion o a much sho e o al leng h o au osomal
linkage maps in males han in emales, he maps allowed
compa ison o meio ic ecombina ion a e be ween sexes.
The sexes show signi ican di e ences in ecombina ion
a es, bo h in gene al and o speci ic pai s o linked ma k-
e s (Wilcoxon's signed- ank es , P = 0.037; Figu e 3 and
Table 2). In he bes -posi ion map (Figu e 1), he p opo -
ion o in e als in he au osomal linkage g oups ha
demons a ed a highe ecombina ion ac ion in emales
was 54.3%. Among all adjacen au osomal ma ke s he
ecombina ion ac ion was 1.28 imes highe in emales
han in he males. Howe e , he e we e excep ions o his
in some LGs, and in some speci ic in e als wi hin LGs.
Fo ins ance, LG7 and LG8 exhibi ed highe ecombina-
ion ac ions in males han in emales (Table 2). The
numbe o in e als ha show highe ecombina ion ac-
ions in he male map ela i e o he emale map was less,
bu no negligible (Figu e 3). When in es iga ing he dis-
o ions o e he au osomal linkage g oups, wo o he
nine linkage g oups showed signi ican (P < 0.05) di e -
ence in ecombina ion a e be ween he sex-speci ic maps
(Table 2). This was also obse ed when he o e all map
leng h was in es iga ed o sex-speci ic di e ence. All in
all, hese esul s sugges ha o e all ecombina ion is sig-
ni ican ly supp essed in male meiosis as compa ed o
emale meiosis.
Compa a i e mapping
The BLAST sea ches unde bo h se ings gene a ed he
same se o signi ican hi s a 1e-10. We ound 25 homolo-
gous (21.4%, 25/117) zeb a inch sequences using a
c oss-species MEGABLAST sea ch in NCBI's zeb a inch
genome da abase (Table 3). By BLAST sea ching using wo
me hods, in o al 22 mapped (20.5%, 22/107) and h ee
unlinked loci o which a homologous sequence could be
iden i ied in chicken we e assigned o a ch omosomal
loca ion in he chicken genome (Table 3). The 10 Sibe ian
jay LGs co esponded o i e di e en au osomal and one
Z ch omosome in chicken. Loci om he same Sibe ian
jay LG ma ched sequences on a single chicken ch omo-
some in he BLAST analysis (Figu e 4 and Table 3), wi h
he excep ion o loci SJ039, SJ101 and SJ076 on he au o-
somal LGs (LG1, LG2, and LG3, espec i ely) ha
mapped o chicken ch omosome Z (GgaZ), whe eas he
o he loci on hese LGs mapped o he chicken au osomes.
Table 2: The Wilcoxon's signed- ank es esul s o ecombina ion ac ion (
θ
) be ween sexes wi h linkage g oups
Linkage g oups NaA e age
θ
FbA e age
θ
Mc
θ
F/
θ
MWilcoxon's signed- ank es (P)d
LG1 28 0.071 0.055 1.29 0.174
LG2 26 0.085 0.054 1.57 0.046 *
LG3 12 0.152 0.133 1.14 0.323
LG4 10 0.101 0.077 1.31 0.038 *
LG5 7 0.127 0.110 1.15 0.687
LG6 5 0.178 0.126 1.41 0.192
LG7 2 0.115 0.145 0.79 0.5
LG8 1 0.09 0.18 0.5 -
LG9 1 0.12 0.08 1.5 -
To al au osomal 92 0.101 0.079 1.28 0.037 *
LGZ 5 0.02 0.094 0.21 0.025*
a numbe o in e als; b a e age ecombina ion ac ion in emales; c a e age ecombina ion ac ions in males; d *, signi ican , P < 0.05.
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Likewise, mos loci on he same chicken ch omosome
ma ched sequences on a single Sibe ian jay LG, wi h he
excep ions o h ee unlinked loci (SJ005, SJ020 and
SJ034) and loci SJ009, SJ039, SJ101 and SJ076 on GgaZ
ha mapped o ou di e en LGs, LGZ and LG1, LG2,
and LG3, espec i ely.
The ela i e o de o he ma ke s mapped o he Sibe ian
jay LGs was compa ed wi h he same loci on chicken ch o-
mosomes in Figu e 4. The chicken-Sibe ian jay compa i-
son indica ed ha he o de o loci was s ikingly di e en
be ween he chicken mac och omosomes Gga1, Gga2 and
Sibe ian jay LG1, LG2 in he bes -posi ion map, espec-
i ely. Al hough some loci sha ed he same ela i e o de
in he wo species, la ge ea angemen s o he ch omo-
some would ha e been necessa y o gi e ise o he di e -
en o de s ound he e. The cases o in e - and in a-
ch omosomal ea angemen s we e in ol ed mos ly in
he amewo k loci and ep esen ed a la ge p opo ion o
Gga-LG1 ha spanned a ound a 120-cM Sibe ian jay/20-
Mb chicken in e al. The h ee unlinked loci, SJ005,
SJ020, and SJ034, we e loca ed a he dis al ends o wo
chicken mac och omosomes, Gga1 and Gga2.
Discussion
This s udy cons i u es he i s mapping e o o he Sibe-
ian jay genome, and is among he i s ones o p esen a
p elimina y linkage map o any en i ely na u al e e-
b a e species om he wild ( e iewed in [28]). The linkage
map was composed using 107 polymo phic mic osa elli e
loci yped on ca. 350 animals, making i one o he mos
de ailed linkage maps a ailable o na u al animal popu-
Female s. male ecombina ion ac ion o 97 pai s o adjacen ma ke s om he 10 linkage g oups in he Sibe ian jayFigu e 3
Female s. male ecombina ion ac ion o 97 pai s o adjacen ma ke s om he 10 linkage g oups in he
Sibe ian jay.
BMC Genomics 2009, 10:1 h p://www.biomedcen al.com/1471-2164/10/1
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(page numbe no o ci a ion pu poses)
la ions [28]. In ac , i is one o only a ew gene ic linkage
maps o wild bi d species o da e. Apa om he e ealing
e idence o sex di e ences in ecombina ion a es, he
cons uc ed maps ep esen an excellen esou ce om
which he ma ke s may be selec ed o u u e mapping
p ojec s in his and ela ed species, as well as o compa -
a i e genomic s udies o genome o ganisa ion. In wha
ollows, we will discuss he salien ea u es o he con-
s uc ed linkage maps in compa ison o simila maps and
esul s om ea lie s udies. In pa icula , we will pay
a en ion o sex-speci ic di e ences in ecombina ion
a es, map co e age and some o he issues dese ing
u u e a en ion.
Geno yping in he mapping popula ion
The cons uc ed map con ains 107 mic osa elli es, o
which 101 a e au osomal, h ee Z-ch omosome-speci ic
and h ee pseudoau osomal loci (see below). The ideal se
o molecula ma ke da a o linkage mapping has no
missing alues, no geno yping e o s and he ma ke s seg-
ega e in he expec ed a io o he speci ic ype o popula-
ion [53]. In p ac ice, howe e , mapping da a is
comp omised in all o hese espec s. Howe e , as simu-
la ed and concluded in p e ious esea ch [53], he e ec
o missing geno ypes depends g ea ly on he sample size:
he smalle he sample, he mo e se e e he e ec s a e
likely o be. In compa ison o published simula ions, in
Table 3: The homologous loci o mic osa elli es mapped in Sibe ian jay on he chicken and zeb a inch genome assigned using BLAST
analyses o he clone sequences o he mic osa elli es and he homologous zeb a inch WGS sequences.
Locus Linkage g oup Zeb a inch Ensemble ID Chicken Ensemble ID Gga aChicken genome s a posi ion (bp)
SJ010 LG1 gb|AC188472.1 NW_001471554.1 Gga1_WGA51_2b1 9,129,918
SJ016 LG1 - NW_001471545.1 Gga1_WGA43_2b1 9,256,107
SJ022 LG1 - NW_001471526.1 Gga1_WGA26_2b1 2,462,620
SJ025 LG1 gb|AC188472.1 NW_001471534.1 Gga1_WGA33_2b1 20,407,077
SJ057 LG1 - NW_001471554.1 Gga1_WGA51_2b1 7,801,901
SJ094 LG1 - NW_001471554.1 Gga1_WGA51_2b1 22,042,793
SJ113 LG1 - NW_001471545.1 Gga1_WGA43_2b1 8,757,200
SJ020 unlinked - NW_001471529.1 Gga1_WGA29_2b1 1,098,266
SJ005 unlinked gb|AC188184.3 NW_001471513.1 Gga1_WGA14_2c1 2,080,202
SJ036 LG2 - NW_001471639.1 Gga2_WGA66_2b2 20,469,429
SJ072 LG2 - NW_001471633.1 Gga2_WGA60_2b2 32,273,874
CK.1B5D LG2 gb|AC225878.2 NW_001471639.1 Gga2_WGA66_2b2 23,539,833
SJ026 LG2 gb|AC206427.2 NW_001471639.1 Gga2_WGA66_2c2 21,465,630
SJ054 LG2 gb|AC188186.2 NW_001471633.1 Gga2_WGA60_2c2 6,229,425
SJ116 LG2 gb|AC148379.2 NW_001471633.1 Gga2_WGA60_2c2 22,279,892
SJ034 unlinked - NW_001471654.1 Gga2_WGA81_2b2 2,075,856
SJ015 LG3 gb|AC188188.2 NW_001471673.1 Gga3_WGA106_2c3 3,458,567
SJ032 LG7 - NW_001471681.1 Gga4_WGA107_2b4 8,679,773
SJ087 LG7 gb|AC155211.2 NW_001471681.1 Gga4_WGA107_2c4 4,015,500
SJ117 LG7 - NW_001471681.1 Gga4_WGA107_2b4 8,679,607
SJ049 LG4 - NW_001471710.1 Gga5_WGA136_2b5 9,314,084
SJ009 LGZ - NW_001488876.1 GgaZ_WGA457_2bZ 1,412,682
SJ101 LG2 gb|AC213969.2 NW_001488849.1 GgaZ_WGA430_2bZ 1,097,987
SJ039 LG1 gb|AC231254.2 NW_001488882.1 GgaZ_WGA463_2cZ 1,315,022
SJ076 LG3 gb|AC188376.1 NW_001488862.1 GgaZ_WGA443_2cZ825,441
SJ050 LG1 gb|AC189030.1 - - -
SJ051 LG1 gb|AC189030.1 - - -
SJ055 LG1 gb|AC189030.1 - - -
SJ064 LG1 gb|AC206426.2 - - -
SJ112 LG1 gb|AC192320.2 - - -
CK.2A5A LG1 gb|AC188469.1 - - -
SJ029 LG4 gb|AC188184.3 - - -
SJ033 LG4 gb|AC188469.1 - - -
SJ106 LG4 gb|AC188184.3 - - -
SJ017 LG5 gb|AC192320.2 - - -
SJ041 LG9 gb|AC210531.1 - - -
SJ069 LGZ gb|AC188466.2 - - -
SJ083 LGZ gb|AC229626.2 - - -
a Chicken ch omosome numbe ; b Via he clone sequences o he Sibe ian jay mic osa elli es; c Via he homologous zeb a inch WGS sequences
BMC Genomics 2009, 10:1 h p://www.biomedcen al.com/1471-2164/10/1
Page 9 o 17
(page numbe no o ci a ion pu poses)
Compa ison o he whole o all sex-a e age linkage g oups in he Sibe ian jay and he whole o chicken ch omosomesFigu e 4
Compa ison o he whole o all sex-a e age linkage g oups in he Sibe ian jay and he whole o chicken ch o-
mosomes. The homologous loci on linkage g oups and ch omosomes a e p esen ed wi h hei gene ic posi ions (cM) on he
bes -posi ion map o hei genomic loca ions (Mb) in he chicken genome. Sibe ian Jay ma ke names in bold on indica e
amewo k loci.
BMC Genomics 2009, 10:1 h p://www.biomedcen al.com/1471-2164/10/1
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(page numbe no o ci a ion pu poses)
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