marker-assisted selection in wheat - ictsd

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Chapter 17 – Marker-assisted selection in fish and shellfish breeding schemes 3351999). Although it is possible to use basequality values to discern true allelic variationsfrom sequencing errors, validationis a key step for true positive detection ofSNPs (Marth et al., 1999). This is generallycarried out using a proportion of the SNPsdetected in a sample of individuals from thetarget population. This strategy has beenused recently for SNP detection using ESTsequences from Atlantic salmon (Panitz etal., 2002; Hayes et al., 2004).Linkage mapsA linkage map is an ordered collection ofthe genes and genetic markers occurringalong the lengths of the chromosomes ofa species, with distances between themestimated on the basis of the number ofrecombination events observed in the data.Genetic linkage maps have been publishedfor rainbow trout (Young et al., 1998;Sakamoto et al., 2000; Nichols et al., 2003),channel catfish (Waldbieser et al., 2001),tilapias (Kocher et al., 1998; Lee et al., 2005)and Japanese flounder (Coimbra et al.,2003). References to updated linkage mapsof the major aquaculture species are givenin Table 1. Dense linkage maps includinga relatively large number of markers areunder development.Different patterns of recombinationappear among regions of linkage groups incertain male maps, with markers clusteredin centromeric regions, an extremeexample being Atlantic salmon whererecombination in males is greatly reduced(Moen et al., 2004b). The molecularmechanisms responsible for the differencesin recombination rates between sexes arenot well understood, although studies onmodel organisms such as zebrafish, wheregenomic sequencing is currently underway, may help to clarify this (Singer etal., 2002).Using markers to aidconventional fish and shellfishbreeding programmesMolecular markers may be used in a numberof ways to aid conventional breeding of fishand shellfish species, and some of these aredescribed and exemplified below.Parentage analysisOne of the main constraints facing effectivebreeding programmes for fish and shellfishis that newborn individuals are too small tobe tagged individually. Application of theanimal model approach (i.e. using a statisticalgenetic model to predict individualbreeding values) requires tagging a constantnumber of individuals from each familywith passive integrated transponders (PITtags) when they become sufficiently largeafter a period of individual family rearing.However, this system of early managementcreates common environmental (i.e.tank) effects for full-sib families (Martinez,Neira and Gall, 1999). To address thisissue, mixtures of equal-aged progeny fromdifferent families can be reared communallyto preclude the development of suchfamily-specific environmental effects, andgenetic markers can be used subsequentlyto assign individuals to families after evaluationof individual performance (Doyleand Herbinger, 1994). Thus, the impactof early common environmental effectsis considerably reduced if markers areused for parentage analysis when selectingindividuals for early growth rate traits(Herbinger et al., 1999; Norris, Bradley andCunningham, 2000).The amount of marker data needed toachieve acceptable levels of correct parentageassignment depends on the numberof loci, the number of alleles and the numberof parent-pairs (sires and dams) availablefor reconstructing the pedigree (Jamieson
336Marker-assisted selection – Current status and future perspectives in crops, livestock, forestry and fishFigure 1Predicted probability of assigning the correct sire-dam (parent-pair) for a given number ofparent-pairs (x axis) using different combinations of three microsatellites (L1, L2 and L3)amplified in Oncorhynchus kisutch1L1 (0.985) L2 (0.644) L3 (0.646)L1+L2 (0.995) L1+L3 (0.995) L2+L3 (0.874)L1+L2+L3 (0.998)0.9P (correctly assigning the true parent-pair)0.80.70.60.50.40.30.20.100 50 100 150 200 250 300 350 400Number of parent-pairsProbabilities of exclusion included between parentheses in the legend are obtained using the deterministic methodof Villanueva, Verspoor and Visscher, 2002.Data obtained from Diagnotec SA.and Taylor, 1997; Villanueva, Verspoor andVisscher, 2002). The information from themarker data available for each species canbe studied using exclusion probabilities,which are then used to calculate the probability(PC) of correctly assigning the trueparent-pair (sire and dam) to offspring thatare genotyped (Villanueva, Verspoor andVisscher, 2002).Figure 1 presents the results for threemicrosatellites and combinations of microsatellitesto predict the probabilities ofexclusion and PC. The allelic frequenciesof the three microsatellites were calculatedwith a sample (n=100) from a coho salmon(O. kisutch) farm in southern Chile managedunder commercial conditions. The analysisshowed that the probability of assigningthe true parent-pair depended greatly onthe number of parent pairs available forparentage. Only for an unrealistically smallnumber of ten sires and dams is there ahigh probability of assigning the correctparent-pair to offspring. For a breedingprogramme of 200 or 300 parent-pairs,PC decreased considerably. Therefore, inthis example, more markers are needed foraccurate pedigree reconstruction. Successfulparentage assignment experiments typicallyhave used six to eight microsatellite markers(Herbinger et al., 1995; Garcia de Leon etal., 1998; Norris, Bradley and Cunningham,2000; Castro et al., 2004). In practice, thepresence of genotyping errors, null alleles,realized mutations and non-Mendeliansegregation can seriously affect the efficiencyof parentage assignment (Castro etal., 2004). Parentage assignment in the con-
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iiiContentsAcknowledgementsForeword
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Section v - marker-assisted selecti
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viiForewordSince almost the beginni
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ixAbbreviations and acronymsAATFAB-
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xiFIVIMSFNPFSCFSILGABIGASGCAGCPGDPG
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xiiiOBMOECDOIEOPVPAGEPBRsPCRPGRFAPI
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xvContributorsAmalia BaroneProfesso
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xviiElcio Perpétuo GuimarãesSenio
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xixAndrea SonninoSenior Agricultura
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Chapter 1Marker-assisted selection
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Chapter 1 - An overview of the issu
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Chapter 3Molecular markers for use
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Chapter 3 - Molecular markers for u
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Chapter 6Targeted introgression of
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Chapter 10Strategies, limitations a
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Chapter 10 - Strategies, limitation
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Chapter 20Impacts of intellectual p
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Chapter 20 - Impacts of intellectua
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This book provides a comprehensive
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