AGB 691 (Seminar) By: Dr.

Kush Shrivastava PhD Scholar IVRI

INTRODUCTION
Most of the traits considered in animal genetic improvement programmes are quantitative, i.e. they are controlled by many genes together with environmental factors, and the underlying genes have small effects on the phenotype observed. Milk yield and growth rate in animals are typical examples of such quantitative traits (Kim and Park, 2001). In classical genetic improvement programmes, selection is carried out based on observable phenotypes of the individuals and/or their relatives. The potential benefits of using markers linked to genes of interest in breeding programmes, thus moving from phenotype based selection towards genotype-based selection, have been obvious for many decades (Beuzen et al., 2000). Molecular genetic markers are identifiable DNA sequences, found at specific locations of the genome and transmitted by the standard laws of inheritance from one generation to the next, they rely on a DNA assay, in contrast to morphological markers that are based on visible traits, and biochemical markers that are based on proteins produced by genes.

The information provided to the breeder by the markers varies depending on the type of marker system used. The molecular marker systems allow high-density DNA marker maps

(i.e. with many markers of known location, interspersed at relatively short intervals throughout the genome) to be constructed for a range of economically important livestock species, thus providing the framework needed for eventual applications of marker assisted selection (MAS). Using the marker map, putative genes affecting traits of interest can then be detected by testing for statistical associations between marker variants and any trait of interest. These traits might be genetically simple controlled by one or a few genes (Young, 1999), alternatively they could be genetically complex quantitative traits, involving many genes (i.e. quantitative trait loci [QTL]) and environmental effects.

What is a QTL?
A quantitative trait locus (QTL) is a region of DNA that is associated with a particular phenotypic trait. These QTLs are often found on different chromosomes. Knowing the number of QTLs that explains variation in the phenotypic trait tells us about the genetic architecture of a trait. It may tell us that milk yield for example is controlled by many genes of small effect, or by a few genes of large effect. QTL often interact in complex ways and their expression can also be influenced by nongenetic factors therefore phenotypes observed are thus the combined results of the action of large numbers of polygenes or quantitative trait loci (QTL) and environmental factors.

Figure 1: Arrangement of chromosomes (number 1 to 10), blue circles on the chromosomes show the QTLs for any quantitative trait.

Quantitative Trait Loci (QTL) provides a way to associate segments of genome locations with quantitative traits which represent the majority of economically important phenotypes measured in livestock animals. Over the past 15 years or so, thousands of QTL have been detected in pigs, cattle, chickens, and sheep. These data allow researchers to narrow down genomic regions and identify the genetic factors that contribute to trait variations (Hocking, 2005; Rothschild et al., 2007).

Types of genetic markers

As with genes, genetic markers are located on chromosomes, like the proverbial beads on a string. Genetic makers are of two types, indirect and direct genetic marker. Figure 2 shows a indirect genetic marker that is 'linked' to a gene.

Figure 2: Shows an indirect genetic marker (variants A and B) linked to a major gene (variants circle and triangle).

If we 'organize' this bulls semen we get

Figure 3: Bull semen after organization, showing non recombinants and recombinants.

Notice that the bull can make 4 types of sperm ,for example, marker A can end up with either the circle or the triangle variant of the major gene. This is because of 'recombination', or 'crossing-over'. The recombination fraction above is 4/17 or about 24%. The more loosely linked the marker and genes are - the more far apart they are - the higher the recombination fraction. The maximum recombination fraction is 50% (Figure: 3). Because of recombination we cannot be sure which marker variant is associated with each gene variant in an animal - hence they are termed as 'indirect' genetic marker. We have to record pedigree and make trait measurements in order to work with indirect markers. If a marker is located within a major gene, its called the direct genetic marker and then recombination is no longer the problem. In this case, knowledge of maker variants tells us directly about the variants of the gene carried by the animal, as in figure 4, we only need to measure the trait(s) involved for monitoring purposes.

A - Always circle, always good. B - Always triangle, always bad.

Figure 4: A direct genetic marker.

Significant association of marker alleles with the phenotype of interest suggests linkage of the marker to the gene of inetrest (QTL). Such a selection based on markers is called Marker Assisted Selection (MAS) (Mackinnon and Georges, 1998).

How can a marker genotype be helpful in selection?

Selection of animals could be based on genetic marker information only. However, in that case the effect of other genes not covered by the marker would be ignored. Optimal selection should aim for QTL as well as for polygenes. Therefore an optimum selection programme should be based on information from markers genotypes combined with information on animals phenotype.

Figure 5: The optimal method of selection programme incorporating the molecular information with the phenotypic observation.

The success of MAS is influenced by the relationship between the markers and the genes of interest. Dekkers (2004) distinguished three kinds of relationship: (i) The molecular marker is located within the gene of interest. (ii) The marker is in linkage disequilibrium (LD) with QTL throughout the whole population. (iii) The marker is not in linkage disequilibrium (i.e. it is in linkage equilibrium [LE]) with QTL throughout the whole population.

Linkage disequilibrium
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at two or more loci, not necessarily on the same chromosome. It is not the same as linkage, which describes the association of two or more loci on a chromosome with limited recombination between them. Linkage disequilibrium describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies. Linkage disequilibrium relates to dependence of alleles at different loci and is central to both QTL detection and MAS. Thus, a thorough understanding of LD and of the factors that affect the presence and extent of LD in populations is essential for a discussion of both QTL detection and MAS (Darvasi et al., 1993). The level of linkage disequilibrium is influenced by a number of factors including genetic linkage, selection, rate of recombination, rate of mutation, genetic drift, nonrandom mating and population structure. For example, some organisms (such as bacteria) may show linkage disequilibrium because they reproduce asexually and there is no recombination to break down the linkage disequilibrium.

- Indicates mutation
Figure 6: Shows linkage disequilibrium around an ancestral mutation. (Ardlie et al., 2002)

Chromosomal stretches derived from a common ancestor of all mutant chromosomes are shown in red, new stretches formed by recombination are shown in blue. Markers that are physically close (i.e., in red region of present day chromosome) tend to remain associated with the ancestral mutation even as the recombination limits the extent of the region of association over time.

Effect of recombination on the decay of Linkage Disequilibrium over generations

Figure 7: Effect of recombination (r) on the decay of LD over generations. The rate of decay depends on the rate of recombination between the loci. For tightly linked loci, any LD that has been created will persist over many generations but, for loosely linked loci (r > 0.1), LD will decline rapidly over generations.

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STATUS OF MAS IN LIVESTOCK & POULTRY

CATTLE
Olsen et al. (2002) carried out genome scan for QTL affecting milk production in Norwegian dairy cattle. Suggestive QTL for one or several of the five milk traits (milk yield, protein percentage, protein yield, fat percentage and fat yield) were detected on chromosomes 3, 5, 6, 11, 13, 18 and 20.
Table 1. The most likely positions of the putative QTL for milk production in the across-family genome scan and their corresponding significance levels. Trait1 Chromosome Position Marker - interval F- value P chromosome P genome2 MY 6 37 FBN12-BM143 3.74 0.019 NS 18 39 INRA121-BM7109 4.58 0.003 0.08 F% 5 120 UW48-ETH152 4.90 0.009 NS 6 41 FBN9-FBN13 11.76 <107 <105 FY 3 14 FCGR3-EAL 3.73 0.014 NS 5 115 BM1819-UW48 3.69 0.018 NS 11 83 HUJV174-ILSTS45 3.71 0.014 NS P% 6 41 FBN9-FBN13 16.38 <107 <105 13 32 BMC1222-BMS1352 4.62 0.005 NS PY 18 79 ILSTS2-EAC 3.47 0.018 NS 20 66 BMS2361-UWCA26 3.05 0.037 NS 1 MY = milk yield, F% = fat percentage, FY = fat yield, P% = protein percentage, PY = protein yield. 2 NS = not significant.

The results of the study are depicted in table 1. The genome scan for quantitative trait loci affecting milk production in Norwegian dairy cattle revealed putative QTL on chromosomes (BTA) 3, 5, 6, 11, 13, 18 and 20 (Table 1). A highly significant QTL for protein (Pgenome < 105) and fat (Pgenome < 105) percentages was found in the middle of chromosome 6, close to marker FBN9 (Figure 8). The analysis also suggested that a QTL affecting milk yield (Pchromosome = 0.02) could be positioned to the same region. For the other chromosomes, a putative QTL affecting milk yield on BTA18 was the most significant, with a genome-wise significance level of 8%.

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Figure 8: Across-family QTL results for milk production traits on bovine chromosome 6 in the Norwegian Dairy Cattle population. Markers are pointed out on the lower X-axis and map distances in cM from the centromere are shown on the upper X-axis. F-values are shown on the Y-axis.

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Guillaume et al. (2008) estimated the efficiency of French marker assisted selection by a simulation study. The data files of two different time periods were used: April 2004 and 2006. The simulation method used the structure of the existing French MAS: same pedigree, same marker genotypes and same animals with records, the details of the population used in the simulation study are given in the table 2.
Table 2. Population structure of French MAS program in April 2004 and 2006 April 2004 Animals in pedigree 34318 Animals with records 23137 Genotyped animals 16629 Male candidates 1180 1 Sires 72 Dams1 793 1 Genotyped dams 486 Maternal grand sires1 70 1 Sires with more than 20 genotyped progeny daughters 11 Progeny tested sire families with 30 sons or more 47
1

April 2006 55336 38859 27551 1689 79 1130 887 114 12 64

Of male candidates

The program simulated breeding values and new records based on this existing structure and knowledge on the QTL used in MAS (variance and frequency). Reliabilities of genetic values of young animals (less than one year old) obtained with and without marker information were compared to assess the efficiency of MAS for evaluation of milk, fat and protein yields and fat and protein contents (Table 3)
Table 3. Reliabilities (R2) of classical polygenic EBV* (POL) and MAS EBV (MAS) for male candidates from 2004 and 2006. Trait April 2004 April 2006 POL MAS Difference POL MAS Difference Milk yield 0.294 0.327 + 0.033 0.313 0.361 + 0.048 Fat yield 0.281 0.296 + 0.015 0.310 0.373 + 0.063 Protein yield 0.254 0.273 + 0.019 0.303 0.341 + 0.038 Fat content 0.313 0.407 + 0.094 0.342 0.453 + 0.111 Protein content 0.214 0.301 + 0.087 0.342 0.418 + 0.076 * EBV = Estimated Breeding Value

In 2004, the gain of reliability ranged from 0.015 for fat yield up to 0.094 for fat content. Gain was relatively limited for yield traits (0.033, 0.015 and 0.019 for milk, fat, and protein

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yields, respectively) and larger for content traits (0.094 and 0.087 for fat and protein contents, respectively). In 2006, the difference between MAS EBV and classical EBV was larger, especially for yield traits (0.048, 0.063 and 0.038 for milk, fat and protein yields, respectively).
Table 4. Reliabilities of classical polygenic EBV (POL) and marker assisted EBV (MAS) of candidates of 2004, depending on the status of their sires. Trait Sires of candidates without genotyped progeny daughters POL MAS Difference 0.266 0.302 +0.036 0.255 0.263 +0.008 0.243 0.265 +0.022 0.269 0.384 +0.115 0.200 0.301 +0.101 Sires of candidates with genotyped progeny daughters POL MAS Difference 0.291 0.353 +0.062 0.277 0.312 +0.035 0.267 0.307 +0.040 0.304 0.476 +0.172 0.210 0.372 +0.162

Milk yield Fat yield Protein yield Fat content Protein content

In 2004, MAS and classical EBV were also compared with respect to the amount of information available to estimate gametic effects of the sires (Table: 4). The improvement of accuracy due to MAS is larger for all traits when a group of progeny daughters is also genotyped.

In beef cattle
Abe et al. (2009) detected the QTLs affecting the muscle histochemical properties in F2 progeny of a cross between Japanese black and Limousin breed of beef cattle.
Table 5. Summary of chromosome wide significant QTL for muscle fiber traits Traits Muscle fiber Chromosome F- value1 Location type (cM) Diameter (m) Red 17 5.61 42 Composition Red 5 5.89 0 (%) Red 8 5.58 106 White 5 5.72 0 1 All F statistics are significant at 5% chromosome wide level.

Flanking markers MB008 IDVGA-40 BMS1095 BMS610 DIK1169 BMS2629 BMS1095 BMS610

The results provided evidence for a QTL affecting the diameter of the red muscle fiber (<5 % chromosome wide level) at 42 cM on BTA17; a QTL affecting the composition of the red & white muscle fibers (<5 % chromosome wide level) at 0 cM on BTA5 and a QTL affecting the composition of the red muscle fiber (<5 % chromosome wide level) at 106 cM on BTA8.

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SHEEP
Maddox et al. (2001) developed medium-density linkage map of the ovine genome. Marker data for 550 new loci were generated and merged with the previous sheep linkage map. The new map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome.

Wool traits in sheep

Purvis and Franklin (2004) published a review on major genes and QTL affecting wool production and wool quality traits in sheep. The QTLs for these traits where summarized as:
Table 6. Putative QTL for wool production and quality traits from linkage association studies. Trait Breeds Description Marker Reference (Chromosome no.) 1. Fiber diameter Peppin Merino Chro. 1 KRTAP6 and KRTAP8 Parsons et al. (1994) 2. Fiber diameter Merino x Linked but not named Henry et al. (1998) Romney 3. Fiber diameter INRA 401 Chro. 6 Segment OARE101 (20cM), Ponz et al. (2001) Chro. 25 Segment IDVGA8 to midpoint with IDVGA088 4. Staple length Romney Chro. 11 KRT1.2, B2A and B2c Rogers et al. (1994) 5. Staple length INRA 401 Chro. 3 Segment BMC1009 OARVH34, Ponz et al. (2001) Chro. 7 Segment ILST005 (20cM), Chro. 25 Segment IDGVA8 IDVGA088

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Bidinost et al. (2008) identified QTL affecting wool production and wool quality in Merino sheep. Greasy fleece weight and body weight were recorded at hogget and adult shearing. Individual mid-side fleece samples were collected to measure seven wool traits which are body weight at shearing (BW); greasy fleece weight (GFW); clean fleece weight (CFW); yield (YLD); fiber diameter (FD); staple strength (SS); staple length (SL) and coefficient of variation of fiber diameter (CV_FD). Specific regions of chromosomes 3, 4, 11 and 25 were analyzed in eight half-sib families. The study was successful in detecting QTL for wool traits in the analysis of the complete set of families, on three of the four chromosome regions studied (Table 7).
Table 7. QTL for wool traits in Merino sheeps. Chromosome Trait Position (cM) ,# 3 FD1 ** 201

Family no. 5 7 4 GFW2 * 28 2335 4 5 4 CFW2 * 43 41end 3 ,# 25 YLD1 * 39 Origin52 2 25 YLD2 * 50 4752 1 7 25 CV_FD2 * 53 51end 1 Greasy fleece weight, GFW; clean fleece weight, CFW; yield, YLD; fiber diameter, FD and coefficient of variation of fiber diameter, CV FD. Subscript 1: hogget 14 month of age; subscript 2: adult 23 month of age. CI: confidence interval of QTL position. * p < 0.05 chromosome-wide significance. ** p < 0.01 chromosome-wide. # p < 0.05 genome-wide significance.

CI (cM) 193 205

The F-statistics profile from interval mapping of sheep chromosomes 3, 4 & 25 is depicted in Figure 9.

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Figure 9: F-statistics profile from interval mapping of sheep chromosomes 3, 4 and 25. Bar on the left represent markers position on each chromosome. Fiber diameter ( ), greasy fleece weight ( ), clean fleece weight ( ), yield1 ( ), yield2 ( ) and coefficient of variation of fiber diameter ( ). Subscript 1 = hogget 14 month of age; subscript 2 = adult 23 month of age. Chromosome-wide significance p = 0.05 ( ). Experimental-wide significance p = 0.05 ( ) and information content ().

The QTL related to fiber diameter on chromosome 3 was near OARVH34 marker. Two QTL influencing adult fleece weight (clean and greasy) were detected on chromosome 4, near MCM218 and BMS1237 markers & because of the short distance between these two markers and the high genetic correlation between greasy fleece weight and clean fleece weight (rg = 0.8, Safari et al., 2005), these QTL could be a single QTL with effect on both traits, whereas a single QTL with an effect on CV_FD (coefficient of variation of fiber diameter) was detected on chromosome 25 near marker BM1714.

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Dairy traits in sheep

Barillet et al. (2004) mapped QTL for milk production in dairy sheep. The QTL results for production traits are reported in Table 8 which shows the significant QTL for production traits in the three QTL mapping programmes (BC, GDD and DD):
Table 8. 11-BC = Sarda x Lacaune backcross design; 2- DD= Churra daughter design; 3- GDD= Lacaune or Manech granddaughter design. 2 First lactation for BC, all lactations for DD and GDD resource populations. OAR 1 5 3 Programme 1 1 BC 3 GDD 1 - BC 1 - BC 1 - BC 2 DD 2 DD 3 - GDD 2-DD 3-GDD 1- BC 1- BC 1- BC 1- BC 1- BC 1- BC 1- BC Trait 2 Protein content Protein content Milk yield Fat yield Protein yield Milk yield Protein content Protein yield Fat content Fat content Milk yield Fat yield Protein yield Milk yield Fat yield Protein yield Fat content Closest marker MCM058 BMS2258 BMC1009 BMC1009 BMC1009 BM4311 BM4311 OARAE101 RHJI CSSM66 MAF214 MAF214 MAF214 BM1258 BM1258 BM1258 OARH56 Position (cM) 98 106 168 168 166 128 126 34 115 12 34 32 32 2 0 2 30 P- value % 0.5 4.3 0.12 2.3 0.05 3.5 3.2 3.9 5.0 0.15 0.37 0.59 0.34 0.68 1.04 0.05

9 16

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For the Sarda Lacaune backcross ewes, the most significant results related to production were on OAR 3, OAR 16 and OAR 20. These three QTL were found to segregate in the same families and to affect milk, fat and protein yields. The most significant QTL detected in this resource population was located on OAR 20 for fat content.

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In the Churra sheep, a QTL was suggested in the telomeric region of OAR6 in the neighbourhood of the casein region (marker BM4311) affecting both protein percentage and milk yield. For the Lacaune and Manech breeds, in agreement with dairy cattle results (Georges et al., 1995; Spelman et al., 1996; Coppieters et al., 1998; Zhang et al., 1998; Boichard et al., 2003) QTL for fat content, protein content and protein yield were found on OAR9, OAR 5 and OAR 6, respectively (Table 8). The most significant QTL was detected for fat content on OAR 9. This QTL was recently identified as a mutation in the DGAT1 gene on the homologous bovine chromosome (BTA 14) (Grisart et al., 2002).

Carcass traits in sheep

Margawati et al. (2009) detected QTL affecting carcass traits in backcross family of Indonesian Thin Tail Sheep. Four half-sib families were used to analyze QTL for carcass traits (carcass weight, body length, chest width, leg circumference). Population of 393 ITT x Merino x Merino backcross with carcass information (phenotype measurements) and their parents were genotyped for 136 micro-satellite markers covering the 26 autosomal ovine chromosomes. The results of significant chromosome wide threshold of permutation test on 3 phenotypes were presented on Table 9.
Table 9. Significance chromosome wide threshold of permutation test for carcass traits. Traits Chromosome F test statistics F test threshold 0.05 0.01 Carcass weight 2 3.7 3.67* 4.65 14 4.62 2.97 4.44** 23 3.32 3.05* 4.21 Carcass length 15 3.19 3.15* 3.15 17 4.73 4.42 4.56** 1 4.35 4.32* 5.76 Leg circumference 15 3.67 3.26* 4.75 17 3.63 3.39* 4.37 *Significant effect (p<0.05), **highly significant effect (p<0.01). There was not found significance for carcass chest circumference.

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Significant effect of QTL for carcass traits were identified for carcass weight located on 3 chromosomes (Table 9). Those significant effects were on chromosome 2 (p<0.05), highly significance on chromosome 14 (p<0.01) and chromosome 23 (p<0.05). The QTL locations for carcass length and leg circumference were identified on 2 and 3 chromosomes, respectively. The QTL for carcass length was highly significance (p<0.01) identified on chromosome 17. The QTL for carcass weight was detected on chromosome 2, it might be linked to meat production. QTL for carcass traits were detected in the 3 parameters, each of those QTLs were flanked by 2 markers. Details of flanking marker of each detected QTL are presented in Table 10.
Table 10. QTL location and flanking markers for carcass traits. Traits Chromosome QTL Location (cM) Flanking markers Carcass weight 2* 264 OARHH30 BMS1126 14** 8 BMS2213 LSCV30 23* 28 CSSM031 MCM136 Carcass length 15* 80 IDVGA10 BM0848 17** 104 BM7136 TGLA322 1* 256 BM6506 URB030 Leg circumference 15* 92 IDVGA10 BM0848 17* 104 BM7136 TGLA322 *Significant effect (p<0.05), **highly significant effect (p<0.01). There was no significance for carcass chest circumference.

PIGS
Pigs are reared for their meat (pork), from last decade breeders have tried to evaluate various genes encoding for carcass traits in pigs, genome scan based on linkage mapping DNA markers and candidate gene used in association tests are two main strategies to identify, to map and to characterize trait loci influencing meat quality (Andersson et al., 2004; Plastow et al., 2005; Van der Steen et al., 2005).

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Roberta Davoli and Silvia Braglia (2008) reviewed the advances in molecular genetics that have led to the identification of genes and markers associated with meat quality in pig and the main markers associated with meat & carcass quality in pigs applied in industry (Table 11).
Table 11. Main markers associated with meat and carcass quality in pigs applied in the industry. DNA Developer Trait First application Reference marker/ Gene MC4R ISU/PIC DG/FC/Lean 1998 Kim et al. (2000) RN-/rn+ INRA/Uppsala/Kiel; MQ 1997/1999/2000 Milan et al. (2000); Ciobanu (PRKAG3) ISU/PIC et al. (2001) IGF2 Liege/Uppsala Lean 2002 Jeon et al. (1999); Nezer et al. (1999); Van Laere et al. (2003) MQ (several PIC and ISU/PIC MQ 2001 Knap et al. (2002) genes) CAST ISU/PIC MQ 2003 Ciobanu et al. (2001); Meyers et al. (2007) RL, DA PIC RL, DA 2003 Plastow et al. (2003) MQ: meat quality; FC: feed conversion; DG: daily gain; RL: reproductive longevity; ISU: Iowa State University; INRA: Institut National de la Recherche Agronomique, France.

Ya-lan et al. (2007) evaluated the effect and profitability of gene-assisted selection in pig breeding system. The effect and profitability of using the quantitative trait loci (QTL)-linked direct marker (DR marker) in gene-assisted selection (GAS) was evaluated. Three populations (100, 200, or 300 sows plus 10 boars within each group) with segregating QTL were simulated stochastically. Five economic traits were investigated, including number of born alive (NBA), average daily gain to 100 kg body weight (ADG), feed conversion ratio (FCR), back fat at 100 kg body weight (BF) and intramuscular fat (IMF). Selection was based on the estimated breeding value (EBV) of each trait. The pigs selected for breeding were based on the EBV (estimated breeding value) estimated by three genetic models: SBLUP (standard BLUP) model, QBLUP (QTL-BLUP) model, and FBLUP (fixed-BLUP) model, the extra genetic gain was then calculated for the FBLUP & QBLUP models.

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Table 12. The extra returns for GAS in three populations

Extra economic returns (RMB yuan) 100 sow Model QBLUP P0= 0.1 3230647.3 P0= 0.3 559532.72 P0= 0.5 86018.29 P0= 0.1 5599108.49 200 sow P0= 0.3 2243969.4 P0= 0.5 2231599.7 P0= 0.1 6726772.5 300 sow P0= 0.3 3453732.4 P0= 0.5 4955329.35

FBLUP

3768478.9

2414493.2

614107.34

5354031.78

476440.35

3306397.2

6367686.5

4132929.7

5012847.05

P0: The initial frequency of the QTLs favorable allele

The extra economic returns for GAS schemes reduced dramatically when P0 increased, which was consistent with the pattern that the lower the P 0 was, the higher the genetic gain of the selected trait was, using GAS scheme (Table 12). Among the three populations, the 300-sow nucleus population had the highest extra profit, and the 100-sow population had the lowest one, because with the increase of the nucleus size, the total extra genetic gain for the population increased, and the pigs sent to slaughter per 6-month period increased too.

CHICKEN

During the last ten years, many QTL have been detected in poultry affecting production traits including growth rate, carcass traits and feed efficiency (Van Kaam et al., 1999a, 1999b; Tatsuda et al., 2001; Sewalem et al., 2002; Carlborg et al., 2003; de Koning et al., 2003; Hocking et al., 2003; Kerje et al., 2003), as well as disease resistance (Yonash et al., 2001; Yunis et al., 2002; Zhu et al., 2003; Heifetz et al., 2009; Van der Laan et al., 2009).

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Jennen et al. (2005) confirmed the quantitative trait locus (QTL) regions found for fatness traits in broilers. QTL analysis was performed on chromosomes 1, 3, 4, 15, 18, and 27. The advanced intercross line (AIL) was created by random intercrossing in each generation from generation 2 (G2) onwards until generation 9 (G9) was reached. QTL for abdominal fat weight (AFW) and/or percentage abdominal fat (AF %) on chromosomes 1, 3 and 27 were confirmed in the G9 population.
Table 13. QTL for abdominal fat weight (AFW), percentage abdominal fat (AF%), body weight at 5 (BW5) and 7 (BW7) weeks of age, and percentage intramuscular fat (IF%) in the G8/G9 population of chickens derived from a broiler broiler cross. Positions are given in cM on the Haldane scale. Position (cM) Marker bracket F- ratio P- value1 10 MCW0289 MCW0297 1.559 0.23 82 MCW0018 MCW0058 1.889 0.052c, 3 0 MCW0116 MCW0148 1.430 0.062c AF % 1 11 MCW0289 MCW0297 1.474 0.29 84 MCW0018 MCW0058 1.732 0.11c, 3 0 MCW0116 MCW0148 1.364 0.086c 27 11 MCW0076 ADL0376 1.848 0.016 c, BW5 1 68 ADL0359 MCW0018 2.135 0.018c,* 15 19 LEI0120 MCW0052 2.027 0.0093 c, 27 9 MCW0076 MCW0376 1.494 0.089 c, BW7 1 83 MCW0018 MCW0058 2.282 0.0061 c,* 3 0 MCW0116 MCW0148 1.397 0.080c IF % 1 114 MCW0018 MCW0101 1.464 0.30 27 23 MCW0328 ADL0376 1.750 0.036 c, 1 Chromosome-wise P-value; c chromosome-wise linkage; experiment-wise significant linkage; experiment-wise suggestive linkage. Trait AFW Chromosome 1

QTL were detected for at least one of the traits AFW, AF%, BW5, BW7, and/or IF% on chromosomes 1, 3, 15, and 27. For chromosomes 4 and 18, test statistics did not exceed the significance threshold for any of the traits measured in this experiment.

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Figure 10: Test statistic values from the full sib QTL analysis for abdominal fat weight (AFW), percentage abdominal fat (AF%), body weight at the age of 5 and 7 weeks (BW5 and BW7), and percentage intramuscular fat (IF%) on chicken chromosome 1. Average thresholds for significance linkage at the 5% level (______) and for suggestive linkage (- - - -) are included. Map positions are given in cM on the Haldane scale.

On chromosome 1 the QTL for AFW as well as AF% were confirmed (table 13). Moreover, for both traits the analysis revealed two distinct peaks on this chromosome at a distance of around 75 cM (Figure 10). Evidence for QTL for BW5 and/ or BW7 was found on chromosomes 1, 3, 15 and 27 (Table 13), suggestive evidence of QTL for IF% was also found on chromosome 1 and 27. The results of this study show the confirmation of QTL found in an earlier generation in an AIL. Moreover, it was able to identify two distinct regions for fat deposition on chromosome 1.

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Liu et al. (2007) carried out mapping quantitative trait loci affecting body weight and abdominal fat weight on chicken chromosome one. A total of 369 F2 individuals produced from 4 F1 families, their parents, and F0 birds were genotyped by 23 fluorescent microsatellite markers on chromosome 1. A linkage map was constructed, and interval mapping was conducted to identify putative QTL.

Figure 11: The linkage map of chromosome 1 of the Northeast Agricultural University (China) resource population.

Details of the markers flanking each QTL and the estimated location relative to the first marker of the NEAURP linkage map (Figure 11) are presented in table 14.

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Table 14. The QTL locations for BW and abdominal fat traits. Position (cM)1 Trait F- ratio Flanking markers 69 AFP 5.08 MCW0010-MCW0106 183 AFW 4.67 LEI0068-MCW0297 195 BW5# 11.54** MCW0297-LEI0146 219 BW0 3.92 LEI0146-MCW0018 231 BW3 4.01 LEI0146-MCW0018 271 BW2 4.51 MCW0018-MCW0058 339 BW4 11.43** ADL251-MCW0061 343 BW1 3.22 MCW0061-LEI0088 351 BW8 8.72* MCW0061-LEI0088 523 BW8 6.94 LEI0079-ADL328 528 BW9 14.29** LEI0079-ADL328 534 BW11 18.72** LEI0079-ADL328 534 BW12 28.12** LEI0079-ADL328 536 CW 28.06** LEI0079-ADL328 548 BW6 11.61** ADL0328-ROS0025 548 AFP 11.91** ADL0328-ROS0025 550 BW10 9.14** ADL0328-ROS0025 550 AFW 7.39* ADL0328-ROS0025 551 BW7 19.23** ADL0328-ROS0025 553 BW4 9.31** ADL0328-ROS0025 555 BW5 6.19* ADL0328-ROS0025 1 QTL positions relative to the genetic map of Northeast Agricultural University resource population in Figure 1. Suggestive linkage; *Chromosome wide significant, P < 0.05; **chromosome wide significant, P < 0.01. (BW Body Weight, # Numbers following body weight indicates age in weeks; CW Carcass weight; AFW Abdominal Fat Weight; AFP Abdominal Fat %, expressed as percentage of BW 12).

For BW, 10 QTL were identified at the 1% chromosome wide level, 2 QTL were identified at the 5% chromosome wide level, and 5 QTL were identified at the suggestive level. For abdominal fat traits, 1 QTL was identified at the 1% chromosome wide level, 1 QTL was identified at the 5% chromosome wide level, and 2 QTL were identified at the suggestive level. The test statistics for BW of 4 to 12 wk of age and CW peaked in the region 523 to 555 cM. The F-ratios of QTL mapping for BW11, BW12, and CW are shown in Figure 13. Test statistics for AFW peaked at 550 cM and AFP peaked at 548 cM. They were close to the QTL region associated with BW. Furthermore, test statistics for AFW and AFP also peaked at 183 and

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69 cM, respectively. However, the test statistics only reached suggestive linkage level. The Fratios of QTL mapping for AFW and AFP are shown in Figure 12.

Figure 12: The F-ratio of QTL mapping for abdominal fat weight (AFW) and abdominal fat percentage (AFP). Triangles above the X-axis indicate the marker positions.

Figure 13: The F-ratio of QTL mapping for BW at 11 (BW11), BW at 12 wk (BW12), and carcass weight (CW).Triangles above the X-axis indicate the marker positions.

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Incorporating MAS in selection programmes

Successful implementation of a MAS program requires a comprehensive integrated

approach that is closely aligned with business goals and markets. Components of such an approach are illustrated in Figure 14 (Dekkers, 2004).

Figure 14: Components of an integrated system for the use of molecular genetic information in breeding programs for marker-assisted selection (MAS).

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CURRENT STATUS & FUTURE PROSPECTS

Identification of new genes affecting quantitative traits are rapidly increasing and lot of theoretical and experimental results of QTL detection have accumulated (Zhi- Liang Hu et al., 2010). The current status of QTL-marker associations detected in livestock species is available on The Animal Quantitative Trait Locus (QTL) database (AnimalQTLdb) which is designed to house all publicly available QTL data on livestock animal species for easily locating and making comparisons within and between species. The database tools are also added to link the QTL data to other types of genome information, such as RH maps, physical maps, and human genome maps. The QTLdb is built on a RedHat Linux platform with MySQL (version 14.12) as the backend relational database and Apache (2.2.13) as the web server (Zhi Liang Hu et al., 2010). As per the 13th release of the database upto December 31, 2010, there were total 13825 QTL reported for 1354 different traits in four livestock species (Table :15 ).
Table 15. Summary of the Animal QTLdb content in terms of the number of QTL in the collection, number of published papers the data were taken from, and number of traits they represent. Species Pig Cattle Number of QTL Number of publication Number of traits 6344 4682 281 274 125 47 727 593 376 248 137 1354 (Source - Animal QTLdb)

Chicken 2451 Sheep Total 348 13825

Although there are a large number of scientific reports on detection of QTL for livestock (Bidanel and Rothschild, 2002; Bovenhuis and Schrooten, 2002; Hocking, 2003), most of these were identified in experimental populations using crosses between breeds or lines (Andersson, 2001). They can, however, provide an important stepping stone for identification of LD markers

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for QTL that segregate within breeds using positional candidate gene approaches (Rothschild and Soller, 1997; Zhao et al., 2003). In spite of success in QTL research for complex traits in livestock species in the last twenty years, location confidence intervals of many QTL are wide, possibly harbouring hundreds of genes. This is the major obstacle to finding causative mutations underlying any QTL identified. In addition, fine mapping techniques and positional cloning to reduce the location confidence interval of the initial QTL are time-consuming, especially for livestock species compared to plant and animal models. The level of expression of individual genes is dependent on both environmental circumstances & other genes within the genome. Several groups (Mootha et al., 2003; Hubner et al., 2005; Schadt et al., 2005; DeCook et al., 2006; Ghazalpour et al., 2006) have proposed combining QTL detection programs and high throughput transcriptome data to elucidate biological pathways associated with complex traits and their underlying genetic determinants. This new integrative approach, known as "Genetical Genomics (GG)" or "Integrative Genomics", treats the expression level of each gene present on a microarray as a quantitative trait and use genetic markers to identify genomic regions that regulate gene expression phenotypes. Such regions are named eQTL (expression Quantitative Trait Loci). Independently of the context of QTL identification for a complex trait, the eQTL identification approach was first applied by Brem et al. (2002) in order to understand the genetic architecture of natural variations in gene expression in yeast (Mignon et al., 2009). The transcription level of an individual gene has a heritable component (Gibson and Weir, 2005), which may be population &/or environment specific. If the relevant tissues of economic importance are profiled at appropriate stages of development, eQTL mapping can be used to identify candidate genes for production trait QTL & to elucidate the gene regulatory networks that lead to variation in the phenotypic traits (Sellner et al., 2007). eQTL studies in livestock have just been initiated on a limited scale, Mignon et al. (2009) using transcriptomic profile characterize the QTL regions on chicken chromosome 5, Ponsuksili et al. (2010) identified eQTL of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits in pigs. Collection of multiple tissues from significant number of individuals for

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gene expression profiling is cost intensive & it becomes a major impediment in eQTL studies of farm animals. However, high throughput techniques like microarray & RNA sequencing are just beginning to become widely available for transcription profiling in livestock. The traditional marker assisted selection (MAS) focuses only on those regions which are relatively certain to influence the trait of interest & leaves most of the genome & much of the unaccounted genetic variation. Meuwissen et al. (2001) predicted total genetic value using genome-wide dense marker maps, this put forward the concept of whole genome selection. Whole genome selection (WGS) approach uses DNA markers that are distributed throughout the entire genome. Genes affecting most economically important traits are distributed throughout the genome and there are relatively few that have large effects & many more genes with progressively smaller effects. It uses genotypes of thousands of single nucleotide polymorphisms (SNP) markers, to predict breeding values (Meuwissen, 2009). WGS allows SNPs with smaller effects on target traits to be used more effectively & to account for a greater proportion of genetic variation. Whole genome selection has been applied successfully to the selection of young bulls to enter AI in the dairy industry which uses limited number of high ranking sire (Moser et al., 2009). Theo Meuwissen and Mike Goddard (2010) suggested the use of whole genome resequencing for accurate prediction of genetic values for complex traits. Whole genome sequence analysis is traditionally done by shotgun approaches using automated Capillary Electrophoresis (CE) Systems. Once the initial sequence for a particular genome is available, it is then possible to perform comparative sequencing called resequencing. The entire genome sequence data can be used to predict the genetic value of an individual for complex traits, therefore in field of animal breeding it can be of great practical benefit because most important traits are complex, quantitative traits, i.e., traits that are affected by many genes and by the environment. Meuwissen and Goddard (2010) in a simulation study concluded that when using whole-genome sequence data, accuracies of prediction of genetic value were >40% increased relative to the use of dense ~ 30K SNP chips. At equal high density, the inclusion of the causative mutations yielded an extra increase of accuracy of 2.53.7%.

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CONCLUSION
Marker-assisted selection (MAS) is a complementary technology, for use in conjunction with more established conventional methods of genetic selection, for livestock and poultry improvement. Evaluation of MAS under simulation studies have shown promising results when it is used in combination with the existing conventional breeding system (Lande et al., 1990; Zhang et al., 1992; Dekkers, 2007). Marker assisted selection can be effectively applied for the traits with low heritability, are difficult or expensive to measure (disease resistance), cannot be measured until after selection has occurred (carcass data) and are currently not selected for due to lack of available phenotypic data (tenderness). However some constraints still remains by the direct application of MAS like cost of genotyping the animals, development of QTL linked markers & moreover farmers interest in using MAS over the conventional methods. Opportunities for the application of marker-assisted selection exist, in particular for gene-assisted selection and linkage disequilibrium markers-assisted selection and, to a lesser degree, for linkage equilibrium markers-assisted selection because of greater implementation requirements. Regardless of the strategy, successful application of marker-assisted selection requires a comprehensive integrated approach with continued emphasis on phenotypic recording programs to enable quantitative trait loci detection, estimation and confirmation of effects, and use of estimates in selection. Information on the genes that control commercially important traits is only just emerging from the numerous studies that are underway. For those genes that have been identified, the level of variation within the genes between individuals or populations is not known, nor is the effect of specific variations on phenotypes. It is therefore premature to start using DNA-based selection widely. However, some DNA tests for specific polymorphisms are being offered commercially, e.g. the GeneSTAR tests for tenderness (based on variations in the calpastatin gene) and marbling (based on variations in the thyroglobulin gene), and the Ingenity

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test for fat deposition (based on variations in the leptin gene). These tests can be used by breeders and evaluated in their populations (Williams, 2005). The opportunities to use marker assisted selection will grow as more associations between markers and traits are identified. However, the information from DNA alone will not replace traditional system of selection based on performance in near future. With recent advances in technology (transcriptomics and proteomics) and availability of whole genome sequence data, there would be paradigm shift from simple genotype- phenotype association studies to delineation of regulatory gene networks that underlie the expression of trait.

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References: Abe, T., H. Hasebe, T. Nakagawa, Y. Uemoto, K. Saito, T. Nade, T. Kawamura and E. Kobayashi (2009). Detection of Quantitative Trait Loci affecting muscle histochemical properties in the F2 progeny of a cross between Japanese Black and Limousin breed. J. Anim. Vet. Adv., 8(11): 2190- 2195. Andersson, L. (2001). Genetic dissection of phenotypic diversity in farm animals. Nat. Revs. Genet., 2: 130138. Andersson, L. and M. Georges (2004). Domestic-animal genomics: deciphering the genetics of complex traits. Nat. Rev. Genet., 5(3): 202-212. Animal QTLdb web site : http://www.animalgenome.org/cgi-bin/QTLdb/index. Ardlie, K.G., L. Kruglyak and M. Seielstad (2002). Patterns of linkage disequilibrium in the human genome. Nat. Revs. Genet., 3: 299 309. Barillet, F., J.J. Arranz and A. Carta (2004). Mapping quantitative trait loci for milk production and genetic polymorphisms of milk proteins in dairy sheep. Genet. Sel. Evol., 37 (1): 109123. Beuzen, N.D., M.J. Stear and K.C. Chang (2000). Molecular markers and their use in animal breeding. Vet. J., 160: 42-52. Bidanel, J.P. and M. Rothschild (2002). Current status of quantitative trait locus mapping in pigs. Pig News Info., 23: 3953. Bidinost, F., D.L. Roldan , A.M. Dodero , E.M. Canob, H.R. Taddeo, J.P. Mueller and M.A. Poli (2008). Wool quantitative trait loci in Merino sheep. Small Ruminant Res., 74 :113118 Boichard, D., C. Grohs, F. Bourgeois, F. Cerqueira, R. Faugeras, A. Neau, R. Rupp, Y. Amigues, M.Y. Boscher and H. Levziel (2003). Detection of genes influencing economic traits in three French dairy cattle breeds. Genet. Sel. Evol., 35: 77101.

34

Bovenhuis, H. and C. Schrooten (2002). Quantitative trait loci for milk production traits in dairy cattle. In: VII World Cong. Genet. Appl. Livest. Prod., Montpellier, Aug. 19- 23, France, Electronic communication 9:7. Brem, R.B., G. Yvert, R. Clinton and L. Kruglyak (2002). Genetic dissection of transcriptional regulation in budding yeast. Science, 296 (5568): 752-755. Carlborg, O., S. Kerje, K. Schutz, L. Jacobsson, P. Jensen and L. Andersson (2003). A global search reveals epistatic interaction between QTL for early growth in the chicken. Genome Res., 13: 413421. Ciobanu, D., J. Bastiaansen, M. Malek, J. Helm, G. Plastow, J. Woollard, and M. Rothschild (2001). Evidence for new alleles in the protein kinase adenosine monophosphate activated gamma3- subunit gene associated with low glycogen content in pig skeletal muscle and improved meat quality. Genetics, 158: 11511162. Coppieters, W., J. Riquet, J. J. Arranz, P. Berzi, N. Cambisano, B. Grisart, L. Karim, F. Marcq, L. Moreau, C. Nezer, P. Simon, P. Vanmanshoven, D. Wagenaar and M. Georges (1998). A QTL with major effect on milk yield and composition maps to bovine Chromosome 14. Mamm. Genome, 9: 540544. Darvasi, A., A. Vinreb, V. Minke, J.I. Weller and M. Soller (1993). Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics, 134: 943951. Davoli, R. and S. Braglia (2008). Molecular approaches in pig breeding to improve meat quality. Brief. Funct. Genomic. Proteomic., 6 (4): 313 321. de Koning, D.J., D. Windsor, P.M. Hocking, D.W. Burt, A. Law, C.S. Haley, A. Morris, J. Vincent and H. Griffin (2003). Quantitative trait locus detection in commercial broiler lines using candidate regions. J. Anim. Sci., 81: 11581165. DeCook, R., S. Lall, D. Nettleton and S.H. Howell (2006). Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics, 172 (2): 1155-1164.

35

Dekkers, J.C.M. (2004). Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci., 82: E313E328. Dekkers, J.C.M. (2007). Marker-assisted selection for commercial crossbred performance. J. Anim. Sci., 85: 2104-2114. Georges, M., D. Nielsen, M. Mackinnon, A. Mishra, R. Okimoto, A. T. Pasquino, L. S. Sargeant, A. Sorensen, M. R. Steele, X. Zhao, J. E. Womack and I. Hoeschele (1995). Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics, 139: 907920. Ghazalpour, A., X. Wang, A.J. Lusis and M. Mehrabian (2006). Complex inheritance of the 5lipoxygenase locus influencing atherosclerosis in mice. Genetics, 173(2): 943-951. Gibson, G. and B. Weir (2005). The quantitative genetics of transcription. Trends Genet., 21: 616-623. Grisart, B., W. Coppieters, F. Farnir, L. Karim, C. Ford, P. Berzi, N. Cambisano, M. Mni, S. Reid, P. Simon, R. Spelman, M. Georges and R. Snell (2002). Positional candidate cloning of a QTL in dairy cattle: identification of a mis-sense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res., 12: 222231. Guillaume, F., S. Fritz, D. Boichard and T. Druet (2008). Estimation by simulation of the efficiency of the French marker-assisted selection program in dairy cattle. Genet. Sel. Evol., 40: 91102. Guimares, E.P., J. Ruane, B.D. Scherf, A. Sonnino and J.D. Dargie (2007). Marker-assisted selection: Current status and future perspectives in crops, livestock, forestry and fish. FAO, Rome. Heifetz, E.M., J.E. Fulton, N.P. O'Sullivan, J.A. Arthur, H. Cheng, J. Wang, M. Soller and J.C.M. Dekkers (2009). Mapping QTL affecting resistance to Marek's disease in an F6 advanced intercross population of commercial layer chickens. BMC Genomics, 10 : 20 37.

36

Henry, H.M., K.G. Dodds, T. Wuliji, Z.A. Jenkins, A.E. Beattie and G.W. Montgomery (1998). A genome screen for QTL for wool traits in a Merino Romney backcross flock. Wool Tech. Sheep Bree., 46: 213217. Hocking, P.M. (2005). Review of QTL results in chicken. Wld. Poultry Sci. J., 61: 215226. Hocking, P.M., M. Bain, C.E. Channing, R. Fleming and S. Wilson (2003). Genetic variation for egg production, egg quality and bone strength in selected and traditional breeds of laying fowl. Br. Poult. Sci., 44: 365377. Hu, Z-L., C.A. Park, E.R. Fritz and J.M. Reecy (2010). QTLdb: A Comprehensive Database Tool Building Bridges between Genotypes and Phenotypes. In: IX World Congress on Genetics Applied to Livestock Production, Leipzig, Aug. 1- 6, Germany. Hubner, N., C.A. Wallace, H. Zimdahl, E. Petretto, H. Schulz, F. Maciver, M. Mueller, O. Hummel, J. Monti, V. Zidek, A. Musilova, V. Kren, H. Causton, L. Game, G. Born, S. Schmidt, A. Mller, S.A. Cook, T.W. Kurtz, J. Whittaker, M. Pravenec and T.J. Aitman (2005). Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat. Genet., 37 (3): 243-253. Jennen, D.G.J., A.L.J. Vereijken, H. Bovenhuis, R.M.P.A. Crooijmans, J.J. van der Poel and M.A.M. Groenen (2005). Confirmation of quantitative trait loci affecting fatness in chickens. Genet. Sel. Evol., 37: 215 228. Jeon, J., O. Carlborg, A. Tornsten, E. Giuffra, V. Amarger, P. Chardon, L. Andersson-Eklund, K. Andersson, I. Hansson, K. Lundstrom and L. Andersson (1999). A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus. Nat. Genet., 21: 157158. Kerje, S., O. Carlborg, L. Jacobsson, K. Schutz, C. Hartmann, P. Jensen and L. Andersson (2003). The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs. Anim. Genet., 34: 264274.

37

Kim, J.J. and Y.I. Park (2001). Current status of quantitative trait locus mapping in livestock species - review. Asian-Aust. J. Anim. Sci., 14: 587-596. Kim, K. S., N. Larsen, T. Short, G. Plastow and M. F. Rothschild (2000). A missense variant of the porcine melanocortin-4 receptor (MC4R) gene is associated with fatness, growth and feed intake traits. Mamm. Genome, 11: 131135. Knap, P.W., A.A. Sosnicki, R.E. Klont and A. Lacoste (2002). Simultaneous improvement of meat quality and growth and carcass traits in pigs. In: VII World Cong. Genet. Appl. Livest. Prod., Montpellier, Aug. 19- 23, France, 31: 339 346. Lande, R. and R. Thompson (1990). Efficiency of marker assisted selection in the improvement of quantitative traits. Genetics, 124: 743 756. Liu, X., H. Li, S. Wang, X. Hu, Y. Gao, Q. Wang, N. Li, Y. Wang and H. Zhang (2007). Mapping Quantitative Trait Loci Affecting Body Weight and Abdominal Fat Weight on Chicken Chromosome One. Poult. Sci., 86: 10841089. Mackinnon, M.J. and M.A.J. Georges (1998). Marker-assisted pre-selection of young dairy sires prior to progeny-testing. Livest. Prod. Sci., 54: 229250. Maddox, J.F., K.P. Davies, A.M. Crawford, D.J. Hulme, D. Vaiman, E.P. Cribiu, B.A. Freking, K.J. Beh, N.E. Cockett, N. Kang, C.D. Riffkin, R. Drinkwater, S.S. Moore, K.G. Dodds, J.M. Lumsden, T.C. van Stijn, S.H. Phua, D.L. Adelson, H.R. Burkin, J.E. Broom, J. Buitkamp, L. Cambridge, W.T. Cushwa, E. Gerard, S.M. Galloway, B. Harrison, R.J. Hawken, S.

Hiendleder, H.M. Henry, J.F. Medrano, K.A. Paterson, S.H. Phua, L. Schibler, R.T. Stone and B. van Hest (2001). An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res., 11: 12751289. Margawati, E.T., Indriawati, Subandriyo, K. Fullard and H. Raadsma (2009). Detection of Quantitative Trait Loci (QTL) Affecting Carcass Traits in Backcross Family of Indonesian Thin Tail Sheep. Journal of Biotechnology Research in Tropical Region, 2 (1): 1-4.

38

Meuwissen, T.H.E. (2009). Accuracy of breeding values of 'unrelated' individuals predicted by dense SNP genotyping. Genet. Sel. Evol., 41 :35 44. Meuwissen, T.H.E. and M. Goddard (2010). Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing. Genetics, 185: 623631. Meuwissen, T.H.E., B.J Hayes and M.E. Goddard (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157 :1819-1829. Meyers, S.N., S.L. Rodriguez-Zas and J.E. Beever (2007). Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2. BMC Genetics, 8: 69 - 83. Mignon, G.L., C. Dsert, F. Pitel, S. Leroux, O. Demeure, G. Guernec, B. Abasht, M. Douaire, P. Le Roy and S. Lagarrigue (2009). Using transcriptome profiling to characterize QTL regions on chicken chromosome 5. BMC Genomics, 10: 575 589. Milan, D., J. T. Jeon, C. Looft, V. Amarger, A. Robic, M. Thelander, C. Rogel-Gaillard, S. Paul, N. Iannuccelli, L. Rask, H. Ronne, K. Lundstrom, N. Reinsch, J. Gellin, E. Kalm, P. Le Roy, P. Chardon and L. Andersson (2000). A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science, 288: 12481251. Mootha, V.K., P. Lepage, K. Miller, J. Bunkenborg, M. Reich, M. Hjerrild, T. Delmonte, A. Villeneuve, R. Sladek, F. Xu, G.A. Mitchell, C. Morin, M. Mann, T.J. Hudson, B. Robinson, J.D. Rioux and E.S. Lander (2003). Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. In: Natl. Acad. Sci. USA, 100 (2): 605-610. Moser, G., B. Tier, R.E. Crump, M.S. Khatkar and H.W. Raadsma (2009). A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers. Genet. Sel. Evol., 41 :56 73. Nezer, C., L. Moreau, B. Brouwers, W. Coppieters, J. Detillieux, R. Hanset, L. Karim, A. Kvasz, P. Le-Roy and M. Georges (1999). An imprinted QTL with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs. Nat. Genet., 21: 155156.

39

Olsen, H.G., L. Gomez-Raya, D.I. Vage, I. Olsaker, H. Klungland, M. Svendsen, T. Adnoy, A. Sabry, G. Klemetsdal, N. Schulman, W. Kramer, G. Thaller, K. Ronningen and S. Lien (2002). A genome scan for quantitative trait loci affecting milk production in Norwegian dairy cattle. J. Dairy Sci., 85: 31243130. Parsons, Y.M., L.R. Piper and D.W. Cooper (1994). Linkage relationships between keratin associated protein (KRTAP) genes and growth hormone in sheep. Genomics, 20 : 500 502. Plastow, G. S. (2003). The changing world of genomics and its impact on the pork chain. Adv. Pork Prod., 14: 6771. Plastow, G.S., D.S. Carrion, M. Gil, J.A. Garca-Regueiro, M. Fonti Furnols, M. Gispert, M.A. Oliver, A. Velarde, M.D. Gua` rdia, M. Hortos, M.A. Ruis, C. Sarraga, I. Daz, A. Valero, A. Sosnicki, R. Klont, S. Dornan, J.M. Wilkinson, G. Evans, C. Sargent, G. Davey, D. Connolly, B. Houeix, C.M. Maltin, H.E. Hayes, V. Anandavijayan, A. Foury, N. Geverink, M. Cairns, R.E. Tilley, P. Morme`de and S.C. Blott (2005). Quality pork genes and meat production. Meat Sci., 70: 409421. Ponsuksili, S., E. Murani, M. Schwerin, K. Schellander and K. Wimmers (2010). Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits. BMC Genomics, 11: 572 586. Ponz, R., C. Moreno, D. Allain, J.M. Elsen, F. Lantier, I. Lantier, J.C. Brunel and M. Perez-Enciso (2001). Assessment of genetic variation explained by markers for wool traits in sheep via a segment mapping approach. Mamm. Genome, 12: 569572. Purvis, I.W. and I.R. Franklin (2005). Major genes and QTL influencing wool production and quality: a review. Genet. Sel. Evol., 37 (1): 97107. Rogers, G.R., J.G.H. Hickford and R. Bickerstaffe (1994). Polymorphism in two genes for B2 sulfur proteins of wool. Anim. Genet., 25 : 407415.

40

Rothschild, M. F. and M. Soller (1997). Candidate gene analysis to detect genes controlling traits of economic importance in domestic livestock. Probe, 8: 1320. Rothschild, M.F., Z-L Hu and Z. Jiang (2007). Advances in QTL Mapping in Pigs. Int. J. Biol. Sci., 3: 192-197. Safari, E., N.M. Fogarty and A.R. Gilmour (2005). A review of genetic parameter estimates for wool, growth, meat and reproduction traits in sheep. Livest. Prod. Sci., 92: 271289. Schadt, E.E., J. Lamb, X. Yang, J. Zhu, S. Edwards, D. GuhaThakurta, S.K. Sieberts, S. Monks, M. Reitman, C. Zhang, P.Y. Lum, A. Leonardson, R. Thieringer, J.M. Metzger, L. Yang, J. Castle, H. Zhu, S.F. Kash, T.A. Drake, A. Sachs and A.J. Lusis (2005). An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet., 37 (7): 710-717. Sellner, E.M., J.W. Kim, M.C. McClure, K.H. Taylor, R.D. Schnabel and J.F. Taylor (2007). Applications of genomic information in livestock. J. Anim Sci., 85 : 3148-3158. Sewalem, A., D.M. Morrice, A. Law, D. Windsor, C.S. Haley, C.O. Ikeobi, D.W. Burt and P.M. Hocking (2002). Mapping of quantitative trait loci for body weight at three, six and nine weeks of age in a broiler layer cross. Poult. Sci., 81: 17751781. Spelman, R.J., W. Coppieters, L. Karim, J.A.M. van Arendonk and H. Bovenhuis (1996). Quantitative trait loci analysis for five milk production traits on chromosome six in the Dutch Holstein- Friesian population. Genetics, 144: 17991808. Tatsuda, K. and K. Fujinaka (2001). Genetic mapping of the QTL affecting body weight in chickens using a F2 family. Br. Poult. Sci., 42: 333337. Van der Laan, M.H.P., B. Bed'hom, J.L. Coville, F. Pitel, K. Feve, S. Leroux, H. Legros, A. Thomas, D. Gourichon, J.M. Reprant and P. Rault (2009). Microsatellite mapping of QTLs affecting resistance to coccidiosis (Eimeria tenella) in a Fayoumi White Leghorn cross. BMC Genomics, 10 : 31 44.

41

Van der Steen, H.A.M., G.F.W. Prall and G.S. Plastow (2005). Application of genomics to the pork industry. J. Animal Sci., 83: 18. Van Kaam, J.B., M.A. Groenen, H. Bovenhuis, A. Veenendaal, A.L. Vereijken and J.A.M. van Arendonk (1999a). Whole genome scan in chickens for quantitative trait loci affecting carcass traits. Poult. Sci., 78: 10911099. Van Kaam, J.B., M.A. Groenen, H. Bovenhuis, A. Veenendaal, A.L. Vereijken and J.A. van Arendonk (1999b). Whole genome scan in chickens for quantitative trait loci affecting growth and feed efficiency. Poult. Sci., 78: 1523. Van Laere, A.S., M. Nguyen, M. Braunschweig, C. Nezer, C. Collette, L. Moreau, A.L. Archibald, C.S. Haley, N. Buys, M. Tally, G. Andersson, M. Georges and L. Andersson (2003). A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature, 425: 832836. Williams, J.L. (2005). The use of marker-assisted selection in animal breeding and biotechnology. Rev. sci. tech. Off. int. Epiz., 24 (1): 379-391. Ya-lan, L., Z. Qin and C. Yao-sheng (2007). Evaluation of the effect and profitability of geneassisted selection in pig breeding system. J. Zhejiang Univ. Sci. B., 8(11): 822-830. Yonash, N., H.H. Cheng, J. Hillel, D.E. Heller and A. Cahaner (2001). DNA microsatellites linked to quantitative trait loci affecting antibody response and survival rate in meat-type chickens. Poult. Sci., 80: 2228. Young, N.D. (1999). A cautiously optimistic vision for marker-assisted breeding. Mol. Breed., 5: 505510. Yunis, R., E.D. Heller, J. Hillel and A. Cahaner (2002). Microsatellite markers associated with quantitative trait loci controlling antibody response to Escherichia coli and Salmonella enteritidis in young broilers. Anim. Genet., 33: 407414.

42

Zhang, Q., D. Boichard, I. Hoeschele, C. Ernst, A. Eggen, B. Murkve, M.P. Genskow, L.E. Witte, F.E. Grignola, P. Uimari, G. Thaller and M. D. Bishop (1998). Mapping quantitative trait loci for milk production and health of dairy cattle in a large outbred pedigree. Genetics, 149: 19591973. Zhang, W. and C. Smith (1992). Computer simulation of marker assisted selection utilizing linkage disequilibrium. Theor. Appl. Genet., 83: 813820. Zhao, H., M.F. Rothschild, R.L. Fernando and J.C.M. Dekkers (2003). Tests of candidate genes in breed cross populations for QTL mapping in livestock. Mamm. Genome, 14 : 472482. Zhu, J.J., H.S. Lillehoj, P.C. Allen, C.P. van Tassell, T.S. Sonstegard, H.H. Cheng, D. Pollock, M. Sadjadi, W. Min and M.G. Emara (2003). Mapping quantitative trait loci associated with resistance to coccidiosis and growth. Poult. Sci., 82: 916.

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