RESEARCH ARTICLE Open Access
De ec ion o g ow h- ela ed QTL in u bo
(Scoph halmus maximus)
En ique Sánchez-Molano
1
, Alex Ce na
2
, Miguel A To o
2
, Ca men Bouza
3
, Miguel He mida
3
, Belén G Pa do
3
,
San iago Cabalei o
4
, Jesús Fe nández
1*
and Paulino Ma ínez
3
Abs ac
Backg ound: The u bo (Scoph halmus maximus) is a highly app ecia ed Eu opean aquacul u e species. G ow h
ela ed ai s cons i u e he main goal o he ongoing gene ic b eeding p og ams o his species. The ecen
cons uc ion o a consensus linkage map in his species has allowed he selec ion o a panel o 100
homogeneously dis ibu ed ma ke s co e ing he 26 linkage g oups (LG) sui able o QTL sea ch. In his s udy we
add essed he de ec ion o QTL wi h e ec on body weigh , leng h and Ful on’s condi ion ac o .
Resul s: Eigh amilies om wo gene ic b eeding p og ams comp ising 814 indi iduals we e used o sea ch o
g ow h ela ed QTL using he panel o mic osa elli es a ailable o QTL sc eening. Two di e en app oaches,
maximum likelihood and eg ession in e al mapping, we e used in o de o sea ch o QTL. Up o ele en
signi ican QTL we e de ec ed wi h bo h me hods in a leas one amily: ou o weigh on LGs 5, 14, 15 and 16;
i e o leng h on LGs 5, 6, 12, 14 and 15; and wo o Ful on’s condi ion ac o on LGs 3 and 16. In hese LGs an
associa ion analysis was pe o med o asce ain he mic osa elli e ma ke wi h he highes appa en e ec on he
ai , in o de o es he possibili y o using hem o ma ke assis ed selec ion.
Conclusions: The use o eg ession in e al mapping and maximum likelihood me hods o QTL de ec ion
p o ided consis en esul s in many cases, al hough he high a ia ion obse ed o ai s mean among amilies
made i di icul o e alua e QTL e ec s. Fine mapping o de ec ed QTL, looking o igh ly linked ma ke s o he
causa i e mu a ion, and compa a i e genomics a e sugges ed o deepen in he analysis o QTL in u bo so hey
can be applied in ma ke assis ed selec ion p og ams.
Backg ound
G ow h ela ed ai s (e.g. body weigh o leng h) cons i-
u e he main goal o gene ic b eeding p og ams in
aquacul u e. An inc ease in g ow h a e educes p oduc-
ion cos s because i dec eases he ea ing ime a a m
acili ies, hus inc easing bene i s o aquacul u e com-
panies [1]. The pheno ype o hese ai s is gene ally
associa ed o many genes o small e ec acco ding o
he in ini esimal model [2], bu also o ew genes o
high e ec . The e a e wo main app oaches o add ess
his ac : a) The iden i ica ion o QTL o b) he iden i i-
ca ion o associa ed ma ke s. QTL can be de ined as
DNA egions con aining a gene o genes wi h ela i e
high e ec on a ai o in e es [3]. The de elopmen o
QTL s udies h ough ine linkage maps may e en ually
lead o he iden i ica ion o he pa icula gene/s unde -
lying he ai , which p omo es hei use o b eeding
p og ams (GAS: Gene Assis ed Selec ion). On he o he
hand, a ai associa ed ma ke is a neu al genome posi-
ion in linkage disequilib ium wi h a gene/s unde lying
he ai . Thus, a ia ion in he associa ed ma ke pa -
ially explains he pheno ypic a ia ion o he ai
h ough a co ela ion wi h a ia ion in he ac ual ai
de e mining gene. Hence, associa ed ma ke s can be
also used in b eeding p og ams (MAS: Ma ke Assis ed
Selec ion).
The e ec s o allele seg ega ion a molecula ma ke s
h oughou he genome can be used o de e mine he
numbe , posi ion and magni ude o QTL ela ed o a
pa icula ai [4]. Fo his pu pose, he de elopmen o
* Co espondence: [email p o ec ed]
1
Depa amen o de Mejo a Gené ica Animal, Ins i u o Nacional de
In es igación y Tecnología Ag a ia y Alimen a ia, C a. Co uña Km. 7.5. 28040
Mad id, Spain
Full lis o au ho in o ma ion is a ailable a he end o he a icle
Sánchez-Molano e al.BMC Genomics 2011, 12:473
h p://www.biomedcen al.com/1471-2164/12/473
© 2011 Sánchez-Molano 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.
linkage gene ic maps is essen ial [5]. Such maps ha e
been de eloped o se e al comme cial ish species [6].
To da e, he e a e ew s udies on QTL a ec ing
g ow h ela ed ai s in ish. Mos o hem we e ca ied
ou in salmonids [7-9], and a numbe o signi ican QTL
in he ange om 2 o 4 was iden i ied o each ai
accoun ing o 20-25% o hei pheno ypic a ia ion.
Simila esul s we e ob ained in ilapia [10,11] and in
sea bass [12-14]; in he la e case, QTL explained a
highe p opo ion o he pheno ypic a iance ( om 28%
o 60%).
Tu bo (Scoph halmus maximus) is a la ish ha has
been in ensi ely cul u ed du ing he las decade due o
i s g ea comme cial alue. Wi h 22 haploid ch omo-
somes (2 o hem subme acen ic, 11 sub elocen ic and
9 elocen ic) [15] and one o he smalles genomes
among cul u ed ishes (< 800 Mb) [16], i s p oduc ion
in Eu ope has inc eased om 3000 Tm in 1996 o 9246
Tm in 2009 [17]. As in many o he cul u ed species,
weigh and leng h a e ai s o special in e es . Size dis-
pe sion(bo hweigh andleng h)in u bo cul u e,
mainly due o sexual dimo phism since emales la gely
ou g ow males, is ano he key issue o i s a ming [18].
Only wo s udies abou QTL de ec ion ha e been ca -
ied ou in his species. In he i s one, a highly signi i-
can QTL o sex de e mina ion was iden i ied [19], and
in hesecondoneasingleQTL o bodyleng hwas
de ec ed [20].
I has been sugges ed ha la ish (o de Pleu onec i-
o mes) g ow h is allome ic [21]. These au ho s p o-
ided da a in se en la ish species om h ee di e en
amilies: Soleidae, Bo hidae and Ci ha idae, and clea
depa u es om isome ic g ow h we e obse ed in ou
o hem ( wo om Bo hidae, one om Ci ha idae and
one om Soleidae), whe eas in h ee species (one om
Bo hidae and wo om Soleidae) isome ic g ow h
appea ed plausible. The e o e, g ow h model is expec ed
o a y among di e en species, e en conside ing species
o he same o de . As indica ed, no da a on species o
Scoph halmidae, amily o which u bo pe ains, ha e
been p o ided by hese au ho s. A ecen s udy in his
species has shown ha a ia ion was no s a is ically di -
e en om isome ic g ow h [22]. Howe e , o he s u-
dies in u bo ha e shown posi i e allome y associa ed
wi h empe a u e [23], nega i e allome ic g ow h being
hus obse ed in la e summe and au umn ( empe a u e
a ound 22°C), while posi i e allome ic g ow h holds up
in win e and sp ing ( empe a u e a ound 7-10°C).
Ma ínez e al. de eloped a panel o homogeneously
dis ibu ed ma ke s ideal o QTL iden i ica ion in u -
bo based on p e ious gene ic mapping in o ma ion
[15,24,25]. The a e age dis ance be ween hese ma ke s
in he consensus map is 14.43 cM, he e o e mee ing
he minimum equi emen s o QTL analysis [26]. The
ecombina ion equency a io be ween males and
emales was de e mined o be 1.6:1 ( emale:male) in u -
bo [15], and consequen ly, he same linkage map can
be used o bo h sexes wi hou la ge e o s.
Conside ing he comme cial alue o u bo and he
a ailabili y o a sui able se o ma ke s o QTL sc een-
ing, i is possible o conduc a s udy on he de ec ion o
g ow h ela ed QTL. The main objec i es o his s udy
a e wo old: a) o de ec and loca e QTL a ec ing h ee
g ow h- ela ed ai s in u bo : body weigh , leng h and
Ful on’s condi ion ac o , and b) o de e mine he asso-
cia ion be ween mic osa elli e ma ke s and g ow h
ela ed ai s and compu e hei appa en e ec s.
Me hods
Tu bo Families
Eigh amilies coming om wo gene ic b eeding p o-
g ams o u bo companies loca ed in NW Spain we e
used in his s udy. Se en o hem we e ob ained om
S ol Sea Fa m SA (FamPA-1, FamPA-3, FamPA-4,
FamPA-6,FamAS-1,FamAS-2 and FamAS-3)andone
om Insuiña SA (FamAP).
Families we e ob ained ollowing a h ee gene a ion
scheme s a ing om un ela ed g andpa en s om na -
u al popula ions o he A lan ic Ocean u bo ishe ies
a ea which led o ull sibling pai analysis. Families we e
main ained unde he same condi ions a cons an wa e
empe a u e o 18°C in sepa a ed b eeding anks and
using he s anda d cul u e p ocedu e o his species
[27]. Family size anged om 85 o 113 indi iduals
(Table 1).
All expe imen s in his wo k ha e been e iewed and
app o ed by he CETGA (Clus e de Acuicul u a de
Galicia) Commi ee on Bioe hics.
T ai measu emen s
Th ee g ow h ela ed ai s we e e alua ed: body weigh
(We), leng h (Le) and Ful on’s condi ion ac o (FK).
Ful on’s condi ion ac o , de eloped by Ful on [28], is a
Table 1 Desc ip i es o amily mapping
Family N NM LG ML D NMG
FamPA-1 93 100 26 1113.46 15.45 4.22
FamPA-3 85 193 26 1074.90 6.79 7.64
FamPA-4 91 90 23 1002.90 15.77 3.91
FamPA-6 90 98 26 1106.84 16.09 3.63
FamAS-1 100 104 22 1147.80 15.62 4.73
FamAS-2 100 98 22 1105.10 15.53 4.46
FamAS-3 100 99 22 1132.30 15.90 4.50
FamAP 113 101 23 1149.40 16.06 4.39
Nis he numbe o e alua ed indi iduals, NM is he numbe o mic osa elli es
analysed, LG is he numbe o linkage g oups, ML is he map leng h in cM, D
is he a e age dis ance be ween ma ke s in cM and NMG is he a e age
numbe o ma ke s pe linkage g oup.
Sánchez-Molano e al.BMC Genomics 2011, 12:473
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measu e o a ish a ness and can be compu ed as 100 *
We/Le
3
,whe eWe is he body weigh o he ish in
g ams and Le is he leng h o he ish in cen ime e s. In
ou s udy, wa e empe a u e was main ained cons an
a 18°C. Then isome ic g ow h in he s udied amilies
would be expec ed, and Ful on’s ac o should be a good
app oxima ion o ish condi ion, hus making i unne-
cessa y o apply an allome ic coe icien .
Pea son co ela ion coe icien ( ) was used o de e -
mine he linea co ela ion be ween all pai s o analysed
ai s. Since di e ences in g ow h a e be ween sexes a e
signi ican only a e 9 mon hs pos -ha ching [18] and
he age o e alua ion was i e mon hs pos -ha ching o
amilies FamAS-1,FamAS-2,FamAS-3 and FamAP and
eigh mon hs pos -ha ching o amilies FamPA-1,
FamPA-3,FamPA-4 and FamPA-6, hesexo e alua ed
indi iduals is no expec ed o in luence he measu ed
ai s.
Mic osa elli es and gene ic map
Table 1 shows he numbe o mic osa elli es analysed
o each amily, he numbe o LGs hey co e ed in he
gene ic map, he map leng h, he a e age dis ance
be ween mic osa elli es and he a e age numbe o
mic osa elli es pe linkage g oup. No all LGs we e
ep esen ed in all amilies because some ma ke s we e
non-in o ma i e a speci ic amilies (e.g. bo h pa en s
being homozygous) o he e was only one ma ke
a ailable.
The panel o ma ke s used o QTL iden i ica ion was
epo ed by Ma inez e al. [19] and i is based on he
consensus map by Bouza e al.[15], hemappingo
ESTs by Bouza e al. [24] and he cen ome e mapping
by Ma inez e al. [25].
S a is ical p ocedu es
QTL analyses
Two me hodologies we e used o de ec QTL: Linea
eg ession (LR) in e al mapping using he G idQTL
p og am [29,30] and maximum likelihood (ML) using
he QTLMap p og am [31,32]. Each amily was analysed
sepa a ely, as di e ences in he age o e alua ion and/o
he main enance o each amily in sepa a ed anks could
dis o he es ima ion o QTL e ec s i hey we e ana-
lysed oge he . The analysis o QTL in di e en amilies
unde di e en me hods is expec ed o p o ide mo e
con iden es ima ions o he QTL exis ence (i.e. i i
appea s in di e en amilies o i i is de ec ed wi h bo h
me hods). Also, a join analysis o he 5- and he 8-
mon h-old amilies, espec i ely, was done. All geno yp-
ing in o ma ion (including g andpa en s) was used o
ob ain phase pe o mance alues.
G idQTL conside s he linkage phase be ween ma ke s
in acco dance wi h pedig ee in o ma ion. No ixed ac o
o co a ia e was included in he model excep in
FamPA-3, whe e sex in o ma ion was a ailable and i
was conside ed o be a ixed ac o . A single QTL was
assumed a each LG and he de aul eg ession me hod
(Haseman-Els on) was applied [33]. Ch omosome-wide
and genome wide signi icance h esholds we e es ima ed
by implemen ing a boo s apping me hod a p=0.05
and 0.01 [34], wi h a pe mu a ion es se o 10,000
i e a ions [35].
QTLMap de ec s QTL h ough in e al mapping using
ML es ima es along he LG and he QTL posi ion is
es ima ed h ough he likelihood a io [36,37]. Fo he
compu a ion o signi ican h esholds, 10,000 simula-
ions we e used unde he null hypo hesis (no QTL) o
each ai and LG.
As p e iously sugges ed [7], ch omosome-wide signi i-
cance o QTL be ween 5% and 1% en ailed i s classi ica-
ion as sugges i e, and signi icance below 1% en ailed i s
classi ica ion as signi ican o bo h s a is ical me hodol-
ogies applied. Genome-wide signi icances we e also
es ed bu no signi ican esul s we e ob ained.
Associa ion analysis
In o de o in es iga e associa ions be ween pheno ypic
ai s and molecula geno ypes, a one-way ANOVA was
pe o med o he p ogeny o each amily, using he di -
e en geno ypes o ma ke s in he same LG whe e he
QTL was de ec ed. Each ANOVA p o ided also a co -
ec ed R
2
alue ha measu ed he educ ion o he o e -
all pheno ypic a iance o he ai due o he model
i ing, hus p o iding he p opo ion o he a iance o
he ai ha can be p edic able om he gi en ma ke
geno ypes.
Be o e he ANOVA analysis, es s o check o no -
mali y (Shapi o-Wilk es ) and homogenei y o a iances
(Le ene es ) we e pe o med. Also a Bon e oni co ec-
ion pe LG was applied o he signi icance h eshold
o ANOVAs in o de o cope wi h he p oblem o alse
posi i es in mul iple compa isons.
Resul s and discussion
This s udy ep esen s he i s wide QTL analysis o
g ow h- ela ed ai s in u bo . A ew s udies ha e been
add essed o de ec g ow h- ela ed QTL in ish and
mos o hem ha e been ca ied ou in salmonids [7-9],
ilapia [10,11] and sea bass [12-14].
The powe o de ec QTL depends on he he i abili y
o he ai , he ecombina ion dis ance be ween he
QTL and associa ed ma ke s, he p opo ion o pheno y-
pic a iance explained by he QTL, he QTL allele e-
quencies and he sample size [38]. In his s udy,
he i abili ies assumed o weigh , leng h and Ful on’s
ac o we e, espec i ely, 0.45, 0.3 and 0.2 [39], and he
numbe o mic osa elli es and ma ke densi y is shown
Sánchez-Molano e al.BMC Genomics 2011, 12:473
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in Table 1. The numbe o mic osa elli es analysed in
amily FamPA-3 is highe han in o he amilies because
i was he e e ence amily used o cons uc ing he
mic osa elli e gene ic map o u bo [15]. The powe o
QTL analysis is limi ed, since only seg ega ing QTL in
one o bo h pa en s can be de ec ed. In his s udy, he
analysed amilies came om un ela ed g andpa en s
om di e en na u al popula ions o he A lan ic a ea,
whe e no signi ican gene ic di e ences be ween popula-
ions we e de ec ed, excluding Bal ic Sea popula ions
[40,41]. In consequence, al hough he de ec ed QTL
migh be ep esen a i eo hegene ica chi ec u eo
g ow h ela ed ai s in u bo , hey should be e i ied in
mo e u bo amilies p e iously o hei use in b eeding
p og ams.
Pheno ypic alues and co ela ions among g ow h- ela ed
ai s
Fo each amily, means (wi h s anda d e o ) o weigh ,
leng h and Ful on’s condi ion ac o a e shown in Table
2. The high dispe sal o means ac oss amilies is due o
he amily e ec , o he di e en age o ishes and o
some uncon olled ac o s. This ac hinde s he join
analysis o amilies.
The ewasahighlysigni ican posi i eco ela ion
be ween weigh and leng h wi h an a e age alue o
0.890 (p< 0.001) (Addi ional ile 1 Table S1). Also, a
signi ican posi i e co ela ion, bu lowe , was obse ed
be ween weigh and condi ion ac o (a e age alue o
0.279 wi h p< 0.01). Howe e , no signi ican co ela ion
was de ec ed be ween leng h and condi ion ac o . Simi-
la esul s we e ob ained in ilapia (O eoch omis sp.)
wi h 0.91 o weigh -leng h [10] and A lan ic salmon (S.
sala ) wi h 0.8 o body weigh -condi ion ac o [7].
Conce ning condi ion ac o and leng h, he non-signi i-
can co ela ion could sugges ha loci in luencing hese
ai s may be seg ega ing independen ly, al hough i
should also be conside ed ha linea co ela ions could
be meaningless due o he cubic na u e o he condi ion
ac o .
De ec ion o QTL using G idQTL and QTLmap
Table 3 shows he QTL de ec ed wi h each me hod o
each ai . Al hough an impo an conco dance was
obse ed wi h bo h me hods in he de ec ed QTL, di -
e ences do exis , and he LR me hod (G idQTL) iden i-
ied some QTL ha we e no de ec ed using he ML
one (QTLMap). Also ML p o ided, in gene al, highe
signi icance o conco dan QTL. Simila esul s we e
ob ained by Kao [42], who de ec ed ha ML me hods
end o be mo e powe ul and di e ences be ween bo h
me hods end o be la ge as he ma ke in e al
becomes wide and he QTL posi ion mo es om
bounda y o he middle o an in e al. He sugges ed he
applica ion o eg ession me hods as he ini ial p oce-
du e o ob ain p elimina y esul s and hen using he
ML me hod in o de o p oduce conclusi e esul s. Also
acco ding o Imsland e al. [18], ou esul s showed ha
sex does no ha e a signi ican e ec a e he analysis
o FamPA-3.
QTL a ec ing all ai s we e de ec ed in LG16 by bo h
me hods, and in some cases in mo e han one amily,
which e idences i s high consis ency. Likewise, bo h
me hods de ec ed QTL o weigh and leng h in LG5,
LG6, LG14 and LG15 in only one amily (excluding
LG15 de ec ed by ML o weigh , in wo amilies). In
he case o LG1 in FamPA-3 and LG12 in FamAP,a
QTL was de ec ed o weigh and leng h in one amily
by using he ML me hod (QTLMap), bu only an e ec
on leng h was de ec ed using he LR me hod (G idQTL).
Rega ding Ful on’s condi ion ac o (FK), bo h me h-
ods de ec ed a signi ican QTL in LG3. Sugges i e QTL
we e de ec ed in LG2 by ML in wo amilies and in LG4
by LR in o he wo amilies. LR me hod de ec ed a QTL
in LG11 a ec ing weigh and FK, bu his QTL was no
de ec ed using he ML me hod.
The numbe o LGs wi h a signi ican QTL in he p e-
sen s udy ( om wo o i e depending on he ai and
me hodology used) is o he same o de as epo ed in
A c ic cha [8] o Asian seabass [12], using he expe i-
men al design o amilies o sibling pai s o QTL de ec-
ion. Some QTL we e ound o a ec wo o mo e
ai s. This could be due o a gene/s being pa o an
ea ly s ep in a me abolic ou e o ac ing in ea ly s ages
o de elopmen a ec ing bo h ai s, bu also o linked
genes a ec ing di e en ai s. Simila posi ions o he
QTL o weigh -leng h and weigh -condi ion ac o we e
consis en wi h he posi i e co ela ions obse ed
be ween hese ai s (0.890 and 0.279 espec i ely).
Join analyses o he 5- o 8-mon h-old ishes, espec-
i ely, p o ided no signi ican o sugges i e QTL, p ob-
ably due o di e ences in s ain gene ic backg ound ha
in luences he deg ee o QTL exp ession as epo ed by
W inge e al. [43] o he exis ence o ano he uncon-
olled ac o in each amily.
Table 2 Desc ip i es o each amily and analised ai
Family Weigh (g) Leng h (cm) Ful on’s ac o
Mean SEM Mean SEM Mean SEM
FamPA-1 39.79 1.19 12.64 0.13 1.93 0.02
FamPA-3 97.05 3.12 16.61 0.33 1.93 0.02
FamPA-4 119.28 3.89 17.66 0.20 2.09 0.02
FamPA-6 51.69 1.45 13.47 0.12 2.07 0.02
FamAS-1 46.31 0.90 12.81 0.08 2.18 0.02
FamAS-2 26.69 0.60 10.70 0.08 2.15 0.02
FamAS-3 31.62 0.72 11.33 0.09 2.14 0.02
FamAP 32.13 0.49 11.43 0.06 2.13 0.01
SEM is he s anda d e o o he mean.
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Associa ion analysis be ween mic osa elli e ma ke s and
g ow h- ela ed ai s
Fo each LG wi h a de ec ed QTL (sugges i e o signi -
ican ), an associa ion analysis was pe o med be ween
he ai and all mic osa elli es in ha LG (Tables 4, 5
and 6). The pe cen age o pheno ypic a iance
explained by he ma ke (R
2
) was only calcula ed when
he associa ion was ound signi ican . I could be
expec ed ha only he closes ma ke o he es ima ed
posi ion o QTL showed a signi ican associa ion bu
in se e al cases, he associa ed ma ke was no always
he closes one. This ac could be explained by se e al
easons: a) a low in o ma i e con en o he eal closes
ma ke ( his occu ed o example in he case o
ScmM1 a LG5, whe e he closes ma ke was Sma-
USC56, bu i had only wo alleles and one o he pa -
en s was homozygous); b) a la ge ex ension a ea in
linkage disequilib ium wi h he de ec ed QTL could
also co e se e al ma ke s, esul ing in posi i e asso-
cia ions be ween he ai and he geno ypes a se e al
ma ke s ( his occu ed in he QTL de ec ed o leng h
in LG15 in FamPA-1 which, al hough showing a maxi-
mum LR alue a 15.8 cM wi h QTLMap,co e eda
dis ance o many cM, including h ee ma ke s) and c)
he exis ence o a seconda y seg ega ing QTL, since
ma ke s could be in linkage disequilib ium wi h one o
o he QTL. Al hough no seconda y QTL we e de ec ed
in ou s udy, his possibili y should be aken in o
accoun o u u e s udies. Also, i should be consid-
e ed ha he map posi ions in his s udy a e no de i-
ni i e, and he inclusion o new ma ke s may p oduce
some eo ganiza ions.
Rega ding weigh (Table 4), he highes R
2
(17.90%)
was associa ed o Sma-USC220 in LG14, whe e a signi i-
can QTL was de ec ed by bo h QTLMap and G idQTL
in amily FamPA-1. Sma-USC15 and Sma-USC32 p o-
ided also a high R
2
(13.70% and 13.60%), being loca ed
espec i ely in LG1 in FamPA-3 (whe eaQTLwas
de ec ed only wi h QTLMap) and in LG15 in FamPA-1
(whe e a QTL was de ec ed by bo h me hods).
Table 3 QTL de ec ed wi h QTLMap (maximum likelihood) and G idQTL ( eg ession in e al mapping)
Me hod Weigh Leng h Ful on’s ac o
Family LG QTL posi ion (cM) Family LG QTL posi ion (cM) Family LG QTL posi ion (cM)
QTLMap FamPA-1 1 18.00 FamPA-1 15* 16.36 FamPA-1 2 45.00
15* 18.36 16 38.37 FamPA-3 16* 0.00
16 40.37 FamPA-3 1* 5.00 FamPA-4 3* 15.10
FamPA-3 1 5.00 5* 20.31 FamPA-6 7 17.00
5* 21.31 16 53.00 FamAS-1 4 60.00
16* 52.00 17 13.00 7* 0.00
17 15.00 FamPA-4 14* 30.92 FamAP 2 80.00
20 24.00 FamPA-6 2 15.00
FamPA-4 14* 30.92 FamAS-2 6* 91.85
15 44.36 12* 49.57
FamPA-6 2 14.00 FamAP 12* 1.00
FamAS-2 6 91.85
FamAP 12 2.00
G idQTL FamPA-1 15 9.36 FamPA-1 15 12.36 FamPA-1 4* 0.00
17 63.03 16 3.54 8 2.75
FamPA-3 5* 26.18 17 63.03 FamPA-3 16* 0.00
12* 52.90 FamPA-3 1 8.00 24 3.00
16* 55.00 5 24.31 FamPA-4 3* 12.10
17 20.00 12* 52.90 FamPA-6 11 23.05
20 24.00 FamPA-4 14* 25.92 FamAS-1 4 70.00
FamPA-4 14* 25.92 FamAS-1 13 30.00 FamAP 10 9.21
FamPA-6 11 22.10 FamAS-2 1 0.00 16* 8.00
FamAS-1 13 10.00 6 91.85 21 13.43
FamAS-2 1 0.00 12 45.57
6 91.85 FamAS-3 3 36.10
FamAS-3 18 0.00 FamAP 12 1.00
FamAP 3 60.10
A QTL can be signi ican (*) o sugges i e.
Sánchez-Molano e al.BMC Genomics 2011, 12:473
h p://www.biomedcen al.com/1471-2164/12/473
Page 5 o 9
Conside ing leng h (Table 5), he highes R
2
(16.20%)
was explained again by Sma-USC220, wi h a signi ican
QTL de ec ed by bo h me hods. Ma ke SmaUSC32
p o ided also a high R
2
(12.90%) wi h a QTL again
de ec ed wi h bo h me hods.
Fo Ful on’s ac o (Table 6), he highes R
2
(25.8%)
was associa ed o ma ke SmaUSC-E11, when analysing
LG16 in amily FamPA-3. I was associa ed o a signi i-
can QTL bo h de ec ed by QTLMap and G idQTL.
Ma ke Sma-USC144 in LG3 in amily FamPA-4 also
showed a high R
2
(12.20%) in associa ion o a signi ican
QTL de ec ed by QTLMap.
In gene al, he p opo ion o pheno ypic a iance
explained by igh es linked ma ke s o he signi ican
QTL o weigh a ied om 8 o 13.6%, om 8.2 o
12.9% o leng h and om 3.3 o 25.8% o Ful on’scon-
di ion ac o . Simila esul s we e ob ained in salmon by
Reid e al. [7]. In ou s udy, i was ema kable he case o
Sma-USC32 ma ke , associa ed o a QTL in LG15, which
showed he maximum R
2
o bo h weigh and leng h,
hus indica ing a high associa ion wi h he ai and he
possibili y o using i o MAS. Also, as bo h QTLmap
and G idQTL ag eed on he de ec ion and posi ioning o
11 QTL, hese a e expec ed no o be alse posi i es.
Mo eo e , associa ion analyses wi h mic osa elli e ma -
ke s in hese LGs we e signi ican , gi ing addi ional sup-
po o ou indings. No associa ion was ound in se e al
LGs wi h de ec ed QTL, p obably due o he low in o -
ma i eness o in ol ed ma ke s. These we e some cases
o weigh in LGs 2, 3, 11, 12, 13, 17, 18 and 20; o
leng h in LGs 1, 2, 3, 13 and 17; and o Ful on’s ac o in
LGs 8, 10 and 24.
Mos signi ican associa ed ma ke s wi h he QTL
de ec ed on g ow h ai s we e anonymous mic osa elli es
Table 4 Signi ican ly associa ed ma ke s wi h weigh
Family LG Associa ed ma ke s Ma ke posi ion QTL
In e al
(QTLMap)
QTL
In e al
(G idQTL)
R
2
NG
FamPA-1 15 Sma-USC214 8.36 8-36 0.4-11.4 8.00% 3
15 Sma-USC32 23.32 13.60% 4
15 Sma-USC211 24.22 6.80% 2
16 Sma-USC256 35.36 35-46 - 7.00% 3
FamPA-3 1 Sma-USC15 0.00 3-7/9-11 - 13.70% 4
5 ScmM1 24.71 10-30 16.3-30.3 11.20% 2
16 Sma-USC223 53.01 45-56 49-55 12.90% 4
16 Sma-USC50 55.84 12.90% 4
FamPA-4 14 Sma-USC220 8.60 20-38 5-28 17.90% 4
14 Sma-USC82 25.40 10.60% 4
14 Sma-USC63 30.50 10.60% 4
15 Sma-USC149 45.20 40-46 - 12.90% 4
FamAS-2 6 SmaUSC-E7 92.40 90-93 - 8.00% 4
All posi ions and in e als a e gi en in cM. R
2
is he co ec ed coe icien o de e mina ion om he ANOVA. NG is he numbe o geno ypes obse ed o he
ma ke in he ull-sib amily. Func ionally anno a ed ma ke s (BLAST; E- alue < 10
-5
): Sma-USC223 (4SNc-Tudo Domain P o ein; E- alue: 7 × 10
-15
); Sma-USCE7
(simila o Fib oblas G ow h Fac o Recep o Subs a e 2; E- alue < 2 × 10
-14
).
Table 5 Signi ican associa ed ma ke s de ec ed on leng h
Family LG Associa ed ma ke s Ma ke posi ion QTL
In e al
(QTLMap)
QTL
In e al
(G idQTL)
R
2
NG
FamPA-1 15 Sma-USC214 8.36 8-36 8.3-30.4 8.50% 3
15 Sma-USC32 23.32 12.90% 4
15 Sma-USC211 24.22 7.70% 2
16 Sma-USC256 35.36 35-49 3.54-7.07 8.20% 3
FamPA-3 5 ScmM1 24.71 10-30 17.3-28.3 10.30% 2
FamPA-4 14 Sma-USC220 8.60 20-38 8.9-31.9 16.20% 4
FamAS-2 6 SMA-USC-E7 92.40 90-93 90.9-93 10.90% 4
FamAP 12 3/9CA15 0.57 0-13 0-7 9.60% 4
12 SmaUSC-E14 1.50 12.80% 4
All posi ions and in e als a e gi en in cM. R
2
is he co ec ed coe icien o de e mina ion om he ANOVA. NG is he numbe o geno ypes obse ed o he
ma ke in he ull-sib amily. Func ionally anno a ed ma ke s (BLAST; E- alue < 10
-5
): Sma-USCE7 (simila o Fib oblas G ow h Fac o Recep o Subs a e 2; E- alue
<2×10
-14
).
Sánchez-Molano e al.BMC Genomics 2011, 12:473
h p://www.biomedcen al.com/1471-2164/12/473
Page 6 o 9
isola ed om pa ial genomic lib a ies [15], since only a
small numbe o gene-linked ma ke s ha e been mapped
in he u bo o da e [24]. In e es ingly, ou o hem we e
unc ionally anno a ed as g ow h- ela ed genes, he e o e
ep esen ing pu a i e candida e genes o he ai s unde
s udy o be u he e alua ed in o he u bo amilies.
Thus, he anonymous locus SmaUSC223 (LG16: 53.01
cM; Table 4), which explained almos 13% o pheno ypic
a iance o a weigh QTL, could be anno a ed as 4SNc-
Tudo domain p o ein. This gene belongs o an e olu io-
na ily conse ed amily o key egula o s o gene exp es-
sion in euka yo es, wi h ele an ole in bo h ansc ip ion
and p e-mRNA splicing, bu also in RNA-induced gene
silencing and cell p oli e a ion ia ac i a ing ansc ip ion
ac o s [44]. Also, we de ec ed o he h ee ma ke s asso-
cia ed o unc ionally anno a ed g ow h- ela ed genes: i)
SmaUSC-E11 (LG16: 0.00 cM; Table 6), which explained
close o 26% o pheno ypic a iance o a Ful on’s ac o
QTL, was anno a ed as Chlo ide Channel-3. This gene
may be indi ec ly ela ed o g ow h, as poin ed ou in se -
e al s udies ha e ealed an in luence o wa e salini y on
ish de elopmen and g ow h, om ea ly emb yogenesis o
adul s ages [45,46]; ii) SmaUSC7 (LG4: 54.9 cM; Table 6),
which explained close o 10% o pheno ypic a iance o a
Ful on’s ac o QTL, was anno a ed as Insulin-like G ow h
Fac o 1 Recep o , a highly ele an g ow h- ela ed gene
ac oss animal species, including ish [47,48]; and iii)
SmaUSC-E7 (LG6: 92.4 cM; Tables 4 and 5), signi ican ly
associa ed wi h weigh and leng h QTL, was anno a ed as
Fib oblas G ow h Fac o Recep o Subs a e 2, a gene
igh ly associa ed wi h muscle mass g ow h in eleos s
[48]. All hese u bo candida e sequence ags should be
checked ac oss new amilies o con i m he de ec ed asso-
cia ion and analysed o gene exp ession using Q-PCR in
indi iduals o amilies showing ma ked di e ences in
g ow h a e. Sea ching o new ma ke s a ound he
de ec ed QTL, especially o hose gene-linked ones, will
be essen ial o e ine ma ke -associa ions wi hin each
amily and o p o ide new pu a i e candida es o a unc-
ional explana ion.
Ano he way o check QTL associa ions and look o
candida e genes is compa a i e mapping [49,50]. In a
s udybyBouzae al. [15], syn enic ela ionships we e
obse ed be ween sequences o u bo and he model
ish Te aodon nig o i idis, sugges ing ue homology o
hose associa ed egions. Thus, a collinea syn enic
block was iden i ied be ween u bo LG16 and he ch o-
mosome 19 o T. nig o i idis (Tni19) based on h ee
loci (Sma-USC136, Sma-USC285 and Sma-USC223; ~10
cM in e al). In he p esen wo k, a QTL o weigh was
de ec ed in LG16 associa ed o he closely linked ma -
ke s (~2 cM) Sma-USC223 and Sma-USC50 (Table 4),
al hough his la e one did no show sequence simila -
i y agains T. nig o i idis genome. The s udy o his syn-
enic block in T. nig o i idis could p o ide in o ma ion
abou candida e genes o he de ec ed QTL, gi en he
high syn eny conse a ion among phylogene ically
di e se ish genomes [50]. The e o e, we decided o
examine he mic osyn enic egion om 1,000 kbp o
5,000 kbp in Tni19 in mo e de ail, ying o co e he
small gene ic dis ance be ween he wo weigh -QTL
associa ed ma ke s, SmaUSC223 and Sma-USC50,
assuming a physical-gene ic a io o abou 0,5 kbp/cM
[15]. A gene lis om his egion o Tni19 was ob ained
using he BioMa ool om Ensembl. Se e al o hese
genes appea ed associa ed o GO e ms ela ed o
g ow h egula ion and cell p oli e a ion (GO:0030308;
GO:0001558; GO:0040008; GO:0042127), some o hem
e y close o he syn enic posi ion o he QTL asso-
cia ed ma ke SmaUSC223 (e.g. CD9 molecule; CCND2-
Cyclin D2; HCLS1-B-cell ansloca ion gene 1, an i-p o-
li e a i e; BTG1-Hema opoie ic cell-speci ic Lyn sub-
s a e 1; FOXM1- o khead box M1; PTN-Pleio ophin;
PAWR-Apop osis WT1 egula o ; LAMB1-Laminin,
be a 1; NRCAM-Neu onal cell adhesion molecule; ADI-
POR2-Adiponec in ecep o 2; SEMA3A-Semapho in
Table 6 Signi ican associa ed ma ke s de ec ed on Ful on’s ac o
Family LG Associa ed ma ke s Ma ke posi ion (cM) QTL
In e al
(QTLMap)
QTL
In e al
(G idQTL)
R
2
NG
FamPA-3 16 SmaUSC-E11 0.00 0-19 0-14 25.80% 4
FamPA-4 3 Sma-USC30 4.10 4-39 4-31 10.90% 2
3 Sma-USC144 23.94 12.20% 4
FamPA-6 7 Sma-USC135 53.49 10-30 - 6.20% 2
11 Sma-USC158 23.39 - 20-24 10.00% 4
FamAS-1 4 Sma-USC7 54.90 50-79 54-78 9.40% 2
7 Sma4-14INRA 0.00 0-10 - 9.90% 4
FamAP 21 Sma-USC41 0.40 - 4-20 3.30% 2
All posi ions and in e als a e gi en in cM. R
2
is he co ec ed coe icien o de e mina ion om he ANOVA. NG is he numbe o geno ypes obse ed o he
ma ke in he ull-sib amily. Func ionally anno a ed ma ke s (BLAST; E- alue < 10
-5
): SmaUSC-E11 (Chlo ide Channel 3; 2 × 10
-19
); Sma-USC7 (Insulin-like G ow h
Fac o 1 Recep o ; E- alue: 0).
Sánchez-Molano e al.BMC Genomics 2011, 12:473
h p://www.biomedcen al.com/1471-2164/12/473
Page 7 o 9
3A; CHPT1-Choline phospho ans e ase 1). The lis also
included some ele an g ow h- ela ed candida e genes
p e iously epo ed in ish (e.g. HGF-Hepa ocy e
G ow h Fac o ; FGF6-Fib oblas G ow h Fac o 6; IGF1-
Insuline G ow h Fac o 1) [48,50]. Pu ing o wa d new
gene ic ma ke s o hese candida e genes and es ing
hem in u bo amilies will be essen ial o go u he in
he unc ional explana ion o he de ec ed associa ions,
as in he p e ious ma ke -associa ed app oach.
Conclusions
The use o di e en s a is ical me hods (LR in e al map-
ping and ML) o QTL de ec ion p o ided consis en
esul s, he use o se e al amilies o look o he epea -
abili y o de ec ed QTL also being o g ea ad an age.
Al hough he age o e alua ion and he cul u e condi ions
ha e been con olled, a high a ia ion o mean ai s was
obse ed e en be ween amilies o simila age, hus mak-
ing i di icul o e alua e QTL e ec s and he es ima ion
o he i abili y (da a no shown). This high a ia ion can be
due o uncon olled ac o s. Fine mapping o de ec ed
QTL could lead o he iden i ica ion o candida e genes
use ul o GAS. Fa ou ed by an inc ease o ma ke densi y,
ano he app oach could be looking o igh ly linked ma -
ke s ha canbeusedinMAS.Inaddi ion, heuseo
gene ically di e gen g andpa en s in new s udies would
p o ide highe accu acy o es ima ion o QTL e ec s, also
allowing he es ima ion o QTL gene equencies. Finally,
compa a i e genomics in homologous egions wi h model
ish eme ges as a use ul s a egy o e i ica ion o he
iden i ied QTL and o look o candida e genes.
Addi ional ma e ial
Addi ional ile 1: Pai wise co ela ion be ween ai s.
Acknowledgemen s
This s udy was suppo ed by he Consolide Ingenio Aquagenomics
(CSD200700002), he Xun a de Galicia local Go e nmen
(PGIDIT06RMA26101PR) and he Spanish Minis e io de Ciencia e Inno ación
(AGL2009-13273) p ojec s. Belén G.Pa do is suppo ed by Isid o Pa ga Pondal
ellowship (Xun a de Galicia). We hank Lucía Insua and Sonia Gómez o
echnical assis ance.
Au ho de ails
1
Depa amen o de Mejo a Gené ica Animal, Ins i u o Nacional de
In es igación y Tecnología Ag a ia y Alimen a ia, C a. Co uña Km. 7.5. 28040
Mad id, Spain.
2
Depa amen o de P oducción Animal, ETS Ingenie os
Ag ónomos, Uni e sidad Poli écnica de Mad id, Ciudad Uni e si a ia, 28040
Mad id, Spain.
3
Depa amen o de Xené ica, Uni e sidade de San iago de
Compos ela, Facul ade de Ve e ina ia, 27002, Lugo, Spain.
4
Clus e de la
Acuicul u a de Galicia (CETGA), Pun a de Couso s/n, 15965, Aguiño, Ribei a,
Spain.
Au ho s’con ibu ions
ES was esponsible o he inal e sion o QTL and ma ke analysis and he
w i ing o he a icle. AC was esponsible o a i s e sion o he QTL
analysis. MAT and JF we e esponsible o o e seeing QTL and ma ke
analysis, as well as pape supe ision. SC was esponsible o ish ea ing and
pheno ypic ai measu ing. BP, CB and MH pe o med geno yping on all
amilies and compa a i e mapping analysis. PM was esponsible o he
whole wo k and managed all asks. All au ho s ha e ead and app o ed he
inal manusc ip .
Recei ed: 22 Ma ch 2011 Accep ed: 29 Sep embe 2011
Published: 29 Sep embe 2011
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