Quantitative genetics in apple

147 Pages·2011·2.21 MB·English

by  Currie, Alastair John

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Quantitgaetnievtieina c psp l(eM alus
domest(iBcoar kbhr.e)e)d ing:
X
Fruisth apter aigtesn,e tpiacr ameteesrt imatainodn
breedisntgr atdeegvye lopment
A thesipsr esenitnep da rtfiuallf ilomfet nhter equirements
fotrh ed egroefe
DoctoorfP hilosoipnhA yn imaSlc ien(cBer eedainndg Genetics)
at
MasseUyn iversity
PalmersNtoornth
NewZ ealand
AlastJaoihrnC urrie
2000
Abstarct
Thea iomf t htihse wsaitsso i vnestisgoamatese p eocfbt rsde ienfgoq ru antittraatiitvse
ina ppleF.i rst,s tutedhxyip srl eotdh mee asuremeinntrh tieaanndc ea coofm plex
quantita(tfiirvtsue h atprFeao)iu.tr a inaelry wsaissu setdom atheimcaatdlelsyc ribe
appflreiu sth paei n oabjne ctmiavnen aenrpd r incciopmaplo naenanlty gsriosu ptehde
Fourideers criipnttomore sai nnfugls haptert asiH.e rbiitilaeiwste rees mtaitetdo
detmeirngee neltliyce ariinsthheadt prea aintgdse ,n otbyyep nev ironimneetrnaotcn tsi
werees ttiemtdao d etmeirnteh set bailoiftt yht er aeixtep srsiaocnr oesnisvr onments.
Friuats pecta crcaotuifnoot orev de 7r6 %o ft hpeh enotvyapriicai tnsi hoan,p f eriut
conyi cif6to%ra ndfr iuts quarefnooerns ls2 y% .Th ester ahiatdms o dertaoht ei gh
narro-wsenhseerb iiitltai(e0s. 709.,3a 8n d0 .3r8e spievyce)tlw,h icihn dtiectdah at
inidvidsuealle cwtouilobdnee fifceinHti.hg b etwne-eesg ietnectoierclrt aio(nr> A0 .8),
incdaitleodgw e noty-peen-vbiyrointnmeeronantca t nisdu ggebesretndsgi b asaetdo ne
siwtoeu lbdee fifcifeonartl tesrhianapgtoe t hseir.t essAh acphea rtc owsnatsr utcot ed
enabtlheet sher aepep le tsrhaatipobte ese vatleuqdau kilcayn adc ctuerilaynt hfei eld,
avoiditnhngee efdoi rm gaec patuarneFd o urainaelsryi s.
Seconhde,r itaabnigdle inteicteoiserc lrt aiownesre es ttiemfdao arr angea poptflr ea its
froamg eneltiybc raolad-abpapsbleredde ienpgo pUlaotf7i 1fo mani liNearsr.o- wsense
herilttiaywb aise smtaiteadte acohft wos itaensda corsssi tesfr iuftaoc ri d(i01t.-7y
0.2f2r)iu,ts u ga(r0s. 25-a0n.td2r 6eg)er, o whtahb (i01t9. -01.)H4.ig hehre ritabilities
werees mtaitefdo frr iuts quare(n.0e30s2.s- 43fru)i,ct o nic(i.0t3-y20 .4p6o)w,d ery
mildeiwcn iednc(e0 .4v0io)gu,(r 0.28-f0ur.if6tri2 m)en,s (s04 .40-.5h3a)rv,e tsitm e
(06.6-.208)l,ef naig( 06.00-.8f3r)iua,ts percatt( i0o.0 7.48-f9l)o,w e(r0i.)na9 gn2 fdr iut
siz(e00 .-190.1.)T raiwtista h h ihg narrow-hseernilsttieayc b oiubldes eelctfeord
efifciewnittilhny d iidvusaell oen.cH tiihgg enectoierclr atbieotnw eseienst( r�A 0 6.4)
inidcatleodwg enotbyyep neiv ronmietnnetr acatnitdoh nab etre ndgib asaetdo ne site
woulbde e fcfiiefnotir m pvriontgh etsrea aitto st hseir.t H eisgpho sie tgievnetic
coerlrtaiobnest weena tst irta1we ie trsee s taitmefdo lre ianfwgi ht floweri(n09g.5 ),
harvteismte fwriiufttim hrn es(s0 .9l2e)a,fw iihnth ga rvteism(te0 .69)fur,i atac nidd ity
witfhru it fi(r0m1.n.)6He ishgs n egatgievneec toierclrt aiownesr ree ptoerfdo vri gour
witfhru istq uare(0n-.e8sa2sn) td r ee ghraobwitthl ewiainft(gh- 5 03.R)a.p giadni sc an
bem adwei tpho sitcioverealrltyet drt asbi,u hti gnhe gatciovrerleytl raatwieitdmls al k e
smiultangeaoiiunnsb otthr adiiftifsc uClatu.t miuosnt apbpel wiheedin n etrepitrng
genectoircr elbaettiwotenresnad iutteso h ihgs tandearrradon rds ptohsbesl iien fluence
ofe nivronmeinnettraalc tiont rbae(itdtwesep eenn daennldnci kea)dg ies ieblqriumi.u
Thidr,t hter atdiionaaplpb lrede einsgta rte(gmya ssse lecwtaisoc no)ma pretdoa n
opotnib aseodnr ecursreelnetc ftoigro enn ecroamlnb iinagbl iyi t(RSG-CA)T.h e
excseisvlenolgyg e nerianttieoornftv hatelr atdiiobnradelie nsgt ramteeagnnyte ggliible
gainwser em adHeo.w evtehrte,rd aitiborndeaielns gt ragteeengrya tgerde agtaienrps e r
generatthiatonhnR e S -GCsAt rabtueatgt y g rae actoesirtnt eromfse rodgiennge tic
divseirttyh,e rreebdyu ctihpneog t enftoira gll- otmne grainT.h eso lwerra toefg aiinn
thReS -GCAw as tdoute hs el owreartof eg aiinnt hber enegdp ioplutaoinH.o wever,
thReS G-CAs tratmeagdyeg reagtaienris n t hceu lrtsir vealattoit vhebe r enegdi
poplutaiodne spsiitmeris lealecitnitoenn dsuitet obi eetsut teirtl iioosnfat hbee tween­
faimlgye nevtaiarcni caesw elalst hwei hti-nfmailgye nevtairci ance.
Brenedgi strabtaesgoeindqe usa nttiivgteea nethiacvbsee eanp plwiietdsh u ccteos s
animcarloa,pn fdo srtter berede ei,nb guotn lrye ceinnta lpypb lree negdI.it is clear that
ftuurber eedpirnogg rawmomueslb dee nffirto tmh aep plicoafqt uiaotnnat tigievenet ic
theory.
if
Acknoweldgemnets
Thitseh sicsou lndo t havmea dbpeeo esns iwbilteht ohupeta tieansscitesa,n acned
encouragfremom ewani tdr ea nogfpe e ople.
Ia mg ratteofPu rlo Dfo.r iGaanr r(iMcaks sey Univcehrisseiuftp ye)r,vf iomsryo r,
takionngy eta nothsetru deinnh ti she avy worIk hlaovaaedp .p rechiiatse d
encoguermaeanntdg uidatnhcreo tuhgtehh eoorfby r eiendga,n dh icsl re,ca oncise
cirticfioesram cp hrj oect.
Ia mg reaitneldbyt teoDd r D.o minuieNq oit(oHno rtReswehaowr acsfhi )rm sybt o ss,
themny s upervwirsiotrti,un tgao nrda lwaay fsre indD.o mniiuqed evelotpheed
quantigteanteiptvrieoc gsr aamnmsdee tt husepc hroslhatioep n abmlete o p ursfuluel ­
timset udTyh.r ougthhoeul ta sftwe yearssh e bheaesan cosntasnotu rocfe
encouraggeumiednaatnn,cmd eo tvitai.o naIl saop prectihmaeot rere e ceenftf oorft s
DrN.n daozOirea gu(zHioer tRcehs)we,ha osr upplied avdavlioucnate bh wlere i gt in
ansdrt uctouftr hete h easswi es lalso fefringu lsh ueglgpefsftorei aocnchsh apter.
Ia mt haunlfk ofDrr T.o nSyhe lboeus'rn( ForReesste airnclvhua)ba liepn uittn o every
aspeocftt hs ti ehsiHsei. nr todumceet dot hfeo rtersebter enegdt iheotrhyat th is thesis
isfo nudeodn I.h ave baelnseoff iortmte hdie n poufot t hberre edaetFr osr eRsetsr ecah
(DrM.i kCea rsDorn.R, o wlaBnurdod nD,r L. uis DGre.Pa a,u Jlef efrsoSnio,mn
WeaveDrr,.K eitJha yawriacmkaa nd DSrue. C arsoTnhe)i.ir n puhta sb een
eduicoantmaolt,i vaatngidrn ega atplpyir eacted.
Thisteh siwosu lndoh ta vbee epno sbslwiei thaocuctet sofsn i naclis aupoprftca,ii iltes
andt haep pblree negdp irograomfemfree bdyT heH orticualntdFu oroaRdle saerch
Insutti(etH ortRcehs)Ne,ea wrZ ealaInnpd a.r tiIct uhlaanrk P aDurGl l uciDnra.,
DominiNqouieta onnd NDnra.d oOzriaeg u(zmiaen ageamnedMn tad)e leHionf stee
anJda niFcrea s(etre chansiscaianslct e).
Freaec cetsoAs r thGuimrlo u'rsA SREML proagnrdha me luplsf uggeswteiroen s
appraetcefido r etshteti imooafng eneptraiacm e.tT ehrems aps wgeernete erwdai tthh e
iii
map-makpirnogg raavma ilaobnl teh eC harlSetsu rUtn iverwseibts yi te
ht:t//pilef.c.seu.duauc/g-ibin/gis/Map.
Througmhyot uitma etM assIeh yav eb eelnu ctkohy a vgeo ofdre indasn cdo lglueeas
thhaatv per oviqdueeidsno tsa,ns werfsee,d baancddki verTshiaonynko! eu s pieacltloy
SatisKhu maLru,i Asp izoalL,ai sWaa tsoNni,c< oiVlsi llloabaonsd t hree sotft he
posatdguraitne sr 2o.o0m2 .
AlhtougaPh h Ds tudheasnl tti lter ets ipmaIet ,h amnekm beorfSs tA lbaPnrse sbyterian
Churfcohsr t crheitmnygh orizboenyso tnhdhe e raen dn o.wT hey hparvoev ided
balainnmc yel eia fnhde lpmeed ftocou osn wihrsae tla yil mportant.
Lasyt lwIo udl likteog ivaes pecaicakln owledtgome ymf emanit,l e yscpieamlyl y
wifeD,e borfaorlh o, vaens du prtp tohroughout.
Twoa re btehtaotnne ebr,e catuhseheya vaeg oorde tfuorrnt ehiwro kr:
Ifo nfeal ldso wnh,if sri encda hne plh iump .
Buptiy tt hmea n wfahlola sn d nhoao sn teo h eplh imu p!
Eec 94-:1 0
iv
Contents
ABSTRACT 1
................................................................................................................................................
ACKNOWLEDGEMEN..T...S... ..........................................................................................................I.. II
CONTENT..S... ..........................................................................................................................................V
LISOTF T ABLEASN DF IGURES VI
.......................................................................................................
CHAPTE1R: I NTRODUCTION
SUMMARYO FC HAPTERS 2
....................................................................................................................
CHAPTE2R .RE VIEWO FL ITERATUARpEP:L EB REEDINSGT RATEGAYN DO BJECTIVES . 2
.......... ...................
CHAPTE3R .Ap PLES HAPTER AITS ..... . .. 3
............. .... .............. ............ . ............................ .............................
CHAPTER E4S.T IMATIGNEGN ETIPCA RAMETERS .. . . 4
........... ............. ............. ....... .................. ...................
CHAPTE5R. Ap PLBER EEDINGS TRATEGY . 5
..................... ...................................... .....................................
REFERENCES 6
...........................................................................................................................................
CHAPTE2R: L ITERATURREEV IEWO FA PPLEB REEIDNG
INTRODUCTION 8
................................................................................................................................. .....
GENETIOCR IGIONF T HEA PPLE 8
......................................................................................................
TAXONOMYO FA PPLE .. . . . 8
............................... .. ........................ ..... .... ....................... .................................
SPECIEWSI THITNH EM ALUSG ENUS. .. . . . . . . 9
. . .. ...... ........ ...... ..... .................. ... ......................... .....................
GEOGRAPHIDCI STRIBUTOIFOM N. X DOMESTlC.A.... ..........................................................1...1
BREEDINSGT RATEGIFEOSR A PPLE 12
.............................................................................................
INITIBARLE EDINSGT RATEGIES . 12
................. ......................... ... .................................................................
CONTROLLEPDO LLINATION .. . . 14
............................... . ........ .................................................... ....................
CURRENT BREESDTIRNAGT EGIES. . . .. . .1 4
..... ............. ........... ............ ........... ........................ ........................
Recurrmeanstss e lecti.o.n . ... . . . 15
........ ...... .... . ... ......................... .............. ........................ .....................
Recurrseenlte cftoiGroC nA ( RS-GC..A) . . . . 15
.. ......................... ..... ............................ ................. .........
Inbreeding . . 17
............... .... ................................................................................. ...................................
Modifbiaecdk cross . .. . 18
.............................. ................................. ...... . ................................... ..............
Markeasrs issteelde cti.on ... . 19
..... .......... ................... ... . ............................................... ........................
Genter ansform.a.tion . . .. . . . .2 1
.... ................... ..... ............. .. ..... ....... ........... ................ . ............................
Mutation breedin.g . . 21
.................... .............. ...................... ...... ............................................... .............
BREEDINOGB JECTIVAENSD S ELECTICORNI TERFIOAR A PPLE 23
.......................................
WHATA REB REEDINGO BJECTIVAENSDS ELECTIOCNR ITERI.A.? . . ... 23
... ............ ......... ...... . ........................
MULTIPLE TSREALIETC TIIONNA PPLIEM PROVEMENT . . 23
....................... ....................... ....................... .....
DEVELOPMEONFTB REEDINOGB JECTIVAENSDS ELECTICORNI TERIINAA PPLE 24
.............. ........................
CURRENDTE SSERATP PLBER EEDINGO BJECTIVES .. . .25
.................................. . ............ .............................. ..
Fruqiuta l.ity . . ... . . . 25
........................... .... ....... .. ... ........ ............. .................................................... .........
Producctoisso tn . . 30
....................... ............................................ ........................... ................................
Productivi.ty. . . . .. . 34
........... . .................. ...... ..... ..................... .. ...................... .......... ...............................
SELECTIIONND EX . . 37
...... ................ ..................................... ........... ......................... ..................................
SUMMARy 38
...............................................................................................................................................
v
REFERENC.E...S.... .................................................................................................................................3 8
CHAPTER 3: QUANTITATIVEE VALUATIONO F APPLE (MALUS
XDOMESTICAB ORKH.)F RUITS HAPE BY PRINCAILP COMPONENT
ANALYSIOSF F OURIEDRE SCRIPTORS
ABSTRAC...T... ........................................................................................................................................5 6
ABBREVITAI ON..S... ..............................................................................................................................5 7
INTRODUCTI...O...N... ...........................................................................................................................5 7
MATERIALASN DM ETHOD.S... ......................................................................................................... 58
VISUALISATOIFOP NR INCIPCAOLM PONEN(TP CS)H APE TR.A.I..T.S... ..........................................5..8.. .
. . . . . .
GENETIACN ALyS.I.S. ...................................................................................6...0... ...... ...............................
SHAPE CHART D..E.S.I.G...N.. .................................................................................................6..1
.. . .. .. ... . . . . . .
RESULTS 62
..................................................................................................................................................
VISUALISATOIFOP NC S HAPET RAIT.S. ............................................................................6..2... .......
. . . . . . . . . . .
GENETIC ANAL.y.S.I.S. .....................................................................................................6...2 .. ...
. . . .. . . . . . . . . . .
INTERPRETATOIFPO NC T RAIT.S. .........................................................6...3... ....... .....................................
SHAPEC HART. ..........................................................................................................................6. 4. ....
. . . . . . . .
DISCUSSI...O....N... ..................................................................................................................................6 4
ACKNOWLEDGEMENTS . . . .67
.................................................................................................................
REFERENCES . .. 67
......................................................................................................................................
CHAPTER 4: ESTIMATESO F HERITAIBLITIESA ND GENETIC
CORRELATIOFNOSR A PPLE( MX.D OMESTIBCAO RKH.T)R AITS
ABSTRAC.T. .........................................................8..0.. ...............................................................................
INTRODUCTION. . .. . 80
...............................................................................................................................
MAT ERIALASN DM ETHODS . . . . . 84
........................................................................................................
EXPERIMENTADLE SIG.N... .........................................................................................................8..4. ....
. . . .. .
MODELE QUATIO.N. ...............................................................................................8.4. ..............
. .. .. . . .. . . . . .. . .
HERITABIL.I.T..Y.. ..............................................................................................................8.6. .......
. . . .. . . . . . . .
GENETICCO RRELATI..O.N. .....................................................................................,.... ... .......8.8. .......
. . . . . . . ..
RESULTS . . 88
................................................................................................................................................
ESTIMATIVNAGR IANCCEO MPONEN.T.S. .................................................................................8..8.. .....
. . . . . . .
HERITABILI..T..y.. ........................................................................................................8 ..9.. ......
.. . . . .. . . . . . . . . . .
GENETICCO RRELATIBOENT WEESNI TE.S. ........................................................................8.9. .................
. . . .
GENETICCO RRELATIBOENT WEETNR AIT.S. ..............................................................................8...9 . ....
. . . . . .
DISCUSSION . . 90
..........................................................................................................................................
REFERENC.E.S. ................................................................................9...5.. .................................................
Vl
CHAPTER5 :C OMPARISOONF T WO BREEDINSGT RATEGIIENS APPL(EM .
XDOMESTICBAO RKH.)
ABSTRACT 104
............................................................................................................................................
INTRODUCTION 104
..................................................................................................................................
TRADITIONAAPLP LBER EEDINSGT RATEGY I07
...........................................................................
TRADITIONBARLE EDING POPULSATTRIUOCNT URE 107
............. .......................... .......................................
TRADITIONMAALT INDGE SIGN 108
........................................ .....................................................................
TRADITIONSAELL ECTION 108
.............................................. ..................................... ..................................
RS-GCSAT RATEGY 109
............................................................................................................................
RS-GCBAR EEDINPGO PULATION 110
.........................................................................................................
RS-GCbA reedpionpgu lasttirounc ture 110
.......................... ................................................................
RS-GCbA reedpionpgu lation mating design 111
........... .......................................................................
RS-GCBA reedpionpgu lasteiloenc tion 113
................... ................................... ....................................
RS-GCCAU LTIVAPRR ODUCTIPOONP ULATION 114
.............. ............................ ..........................................
RS-GCAc ultipvraord ucptoipounl asttirounc ture 115
..........................................................................
RS-GCAc ultipvraord ucptoipounl amtaitoindn egs ign 115
...... ........................ ....................................
RS-GCcA ultipvraord ucptoipounl asteiloenc tion 115
..........................................................................
SIMULATION 116
........................................................................................................................................
SIMULATIMOENT HOD 116
........................... ............................... .................................................................
Traditbiroeneadlsi tnrga tmeogdye l 117
................................... .................................. ..........................
RS-GCbA reedsitnrga tneTgoyd el 118
.................................... ...............................................................
SIMULATIROENS ULTS 118
......................... ................................. ..................... ............. ...............................
SIMULATIODN! SCUSSION 119
.................... ........................... .......................................................................
CONCLUSIONS . 120
....................................................................................... ............. ................................
REFERENCES 120
...................................................................... .................................................................
CHAPTER6 :G ENERADLI SCUSSION
REFERENCES 136
.......................................................................................................................................
vii
Lisotf f iguraensd t ables
Chapte2r: L itetruaroef a pplber eeding
Figu1r.De ia graomft hpeo sseei vbolluotfti hoReno sacseuabef laeimsbi asoend
moroplhogiccyatlo,l oagncidhc eamli dcaat(laC hiacl1el9, 7) 4 50
. ...........................
Figu2r.We o rld omfta hpoe ir gionfas p pslpee cies. . . 51
............ ........ ........................ .......
Figeu3 r.Wo rld omfta hpoe ir gionfs aspppelcei inoevvlse idn t haen ceosft rtyh e
domesatplipec .. . . 52
.................... ....................... ........................ ......................... .... ....
Figu4r.Me ap o ft hdei striabnudt idoonm esotfai pcpa(ltMeiX. o d no mesti.ca5)3
...... ....
Tab1le.O r giiann bdo tandiecsaclr ipatpipsolnpe ee ocsifi vn olvientdh d eo mestication
ofa ppl.e . . . . . .54
.. ............ ................ ..... ............ ...................................... ............... ...... ..
Chapter3 :Q uantittaiveev aluatioofna ppl(eM aluxs d omestica
Borkhf.r)u it shbaypp rei ncipcaolmp onenatn aylsiso fF ouirer
descirptors
Tab1le.P r optoiroofnt hteo tpahle notvyapriicaa nccceo ufnotre tdbh fyei r6Ps Ct.s 7 1
Tab2l.eV isulaitsiaoofnt hferi sstiP xC s hatprea (imtimsnu imt o miamuxmv ael)u.
Appslhea paerdser awwni tthhs et eemn adtt h teo apn tdh ceay lxa tt hbeo tt7o2m .
Tab3l.eH erbiiityltae sttiemsa s(atannddae rrdr ofroPsrC) a pple tsrhaaaitptt ehs e
HavelNooctrkha nNde lssoint es . . 73
............................ ......................................... ....
Tab4l.eG enectoiercalrt io(rnbg e)t wseietnae nssd t arndde rarfoorar p ple tsrhaaiptes
74
............................................................................ ....................................................
Tab5l.eR egersscioofenif ciebnettsw eenP Cas phppaelt er aaintcdsla leirp
measurements .. .. 75
.......................... ....... ... .................... ........................................ ......
Tab6l.Ae p pslhea cphaer bta soenda speccotn,i acnisdtq yu arePnCt ersta.ssAi pple
shapaerdser awwni tthhs et eemn adtt he atnotdph c eay lxa tt hbeo ttom 76
...........
Figeu1 r.Ap pclreo ss-ssehcontwgiti ohcnea lelrmi epasuernetBms =. s teGm =, c alyx,
BG= stem-caaxi,lsC yHx= lnegt(hL D)E, = width El(= Wm)a,x imwuimtd h
dsitan(cMeW D)A,C= stecma vwiitdytF Hh= , c aylxb aisnw id.t..h. .......79.. .........
Chapter4 :E stiamteso fh eritlaiybt iandg eneitcc orreltaiofno r
appl(eM aluxs d omesticBao rk.h)t riats
Tab1le.N a mea ndde scrifpoetrai coahnp ptlre.a .i.t. ................9.9. .................................
Tab2l.Be asisct atiforsa tpipctlsre a aitHt asv elNoocrk(t ihst 1e,)N eslo(ns ei2 t)a nd
combisnietodef ts hb er eiendpgo pulation. . 100
................. ................................... .....
Tab3l.eU nirvaiatnera ro-wsehnesrebi ityla( itstandearrrdio nbr r ackfeoatrsp )pt lrea its
esttiemsdae rpaaltyfeo r HaveloacnNkde loNsnoa,rnt adhc robsosts hi .t.e.s1. 0.1. .
viii