Mapping, Fine Mapping, and Molecular Dissection of Quantitative Trait Loci in Domestic Animals

Georges, Michel

doi:10.1146/annurev.genom.8.080706.092408

Cited by 120 publications

(115 citation statements)

References 112 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, recent genome-wide studies involving dogs and cattle have illustrated the possibility of mapping Mendelian traits within and across breeds without creating experimental crosses. This approach, in the absence of pedigree information, takes full advantage of the phenotypic diversity found within and across different livestock breeds (Georges, 2007). By exploiting the greater number of recombination events that have occurred since breed divergence, as compared with a mapping resource pedigree, it is possible to map a phenotype to a smaller region than might be possible using a mapping pedigree.…”

Section: Introductionmentioning

confidence: 99%

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

et al. 2012

View full text Add to dashboard Cite

Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide singlenucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r 2 X0.3) in both traditional and village chickens at pairwise marker distances of B10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling B75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.

show abstract

Section: Introductionmentioning

confidence: 99%

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

et al. 2012

View full text Add to dashboard Cite

show abstract

“…In QTL detection studies, we can locate one QTL in a chromosome as a region of about 20 to 40 cM (probably harbouring 200 to 400 genes), which makes it difficult to identify the underlying gene responsible, as has been recently emphasized by Georges (2007). To refine the position several actions can be taken.…”

Section: Qtl Detection In Domestic Speciesmentioning

confidence: 99%

“…This has led to some well established and replicated associations as, for example, that between the porcine melanocortin-4 receptor (MC4R) and fatness, growth, and feed intake (Kim et al, 2000). Unfortunately, the candidate gene literature has too many non-reproducible results that made the field a bit problematic and it has been suggested that the standard used in these type of studies should be raised (Georges, 2007). At present, we have tools (microarrays) that allow us to quantify the level of expression of virtually all genes in a large number of livestock species.…”

Section: Qtl Detection In Domestic Speciesmentioning

confidence: 99%

“…Georges (2007) describes three successful stories: DGAT1 and ABCG2 that affect milk composition in cattle and IGF2 and MSTN influencing muscle mass in pigs and sheep respectively. The DGAT1 gene, which is located on the BTA14 chromosomal site and encodes Acyl-coenzyme A : diacylglycerol acyltransferase, is known to catalyse the last step in triglyceride synthesis and influences milk yield and composition.…”

Section: Future Trends In Animal Breedingmentioning

confidence: 99%

See 1 more Smart Citation

Future trends in Animal Breeding due to new genetic technologies

Toro

2010

Advances in Animal Biosciences

View full text Add to dashboard Cite

“…The pig, for instance, was domesticated across wide different geographic areas from Europe to Asia starting from the local wild boar populations; the Asian and European wild boar lineages diverged since at least 600 KYA (Larson et al, 2005). Thus, extreme breeds are important resources to investigate the genetic control underlying phenotypic variation (Georges, 2007).…”

Section: Introductionmentioning

confidence: 99%

Large-scale SNP genotyping in crosses between outbred lines: how useful is it?

Ledur¹,

Navarro²,

Pérez‐Enciso³

2009

Heredity

View full text Add to dashboard Cite

Although genome-wide association (GWA) studies are not worth the effort in crosses between inbred lines, many crosses are actually made up of divergent yet outbred populations. Despite its relevance, however, this experimental setting has not been studied at a time when SNP microarrays are available in many species. To assess whether GWA can be useful in this setting, we performed combined coalescence-gene dropping simulations. We studied the influence of marker density, QTL effect and QTL allele frequency on power, false discovery rate (FDR) and accuracy. Our results suggest that GWA in outbred F 2 crosses is useful, especially in large populations. Under these circumstances, accuracy increased and FDR decreased as compared with classical linkage analysis. However, current SNP densities (in the order of 30-60 K SNPs/genome or equivalent to 10-20 SNPs per cM) may not be much better than linkage analysis and higher SNP densities may be required. SNP ascertainment had an important effect; the best option was to select SNPs as uniformly as possible without setting any restriction on allele frequency. Using only SNPs with fixed alternative alleles in each breed controlled false positive rate but was not useful to detect variability within lines. Finally, the most significant SNP was not necessarily the closest to the causal SNP, although the closest SNPs were usually above the significance threshold; thus, it is prudent to follow-up significant signals located in regions of interest even if they do not correspond to absolute maxima.

show abstract

Mapping, Fine Mapping, and Molecular Dissection of Quantitative Trait Loci in Domestic Animals

Cited by 120 publications

References 112 publications

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Future trends in Animal Breeding due to new genetic technologies

Large-scale SNP genotyping in crosses between outbred lines: how useful is it?

Contact Info

Product

Resources

About