Power of Daughter and Granddaughter Designs for Determining Linkage Between Marker Loci and Quantitative Trait Loci in Dairy Cattle

Abstract Using Cockerham's approach of orthogonal scales, we develop genetic models for the effect of an arbitrary number of multiallelic quantitative trait loci (QTLs) or neutral marker loci (NMLs) upon any number of quantitative traits. These models allow the unbiased estimation of the contributions of a set of marker loci to the additive and dominance variances and covariances among traits in a random mating population. The method has been applied to an analysis of allozyme and quantitative data from the European oyster. The contribution of a set marker loci may either be real, when the markers are actually QTLs, or apparent, when they are NMLs that are in linkage disequilibrium with hidden QTLs. Our results show that the additive and dominance variances contributed by a set of NMLs are always minimum estimates of the corresponding variances contributed by the associated QTLs. In contrast, the apparent contribution of the NMLs to the additive and dominance covariances between two traits may be larger than, equal to or lower than the actual contributions of the QTLs. We also derive an expression for the expected variance explained by the correlation between a quantitative trait and multilocus heterozygosity. This correlation explains only a part of the genetic variance contributed by the markers, i.e., in general, a combination of additive and dominance variances and, thus, provides only very limited information relative to the method supplied here.

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Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing.

Genetics ◽

10.1093/genetics/139.2.907 ◽

1995 ◽

Vol 139 (2) ◽

pp. 907-920 ◽

Cited By ~ 8

Author(s):

M Georges ◽

D Nielsen ◽

M Mackinnon ◽

A Mishra ◽

R Okimoto ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Dairy Cattle ◽

Milk Production ◽

Quantitative Trait ◽

Bovine Genome ◽

Progeny Testing ◽

Cattle Breeding ◽

Trait Loci ◽

Dairy Cattle Breeding ◽

Autosomal Microsatellites

Abstract We have exploited "progeny testing" to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of > 150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score > or = 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding.

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Molecular-Marker-Facilitated Investigations of Quantitative-Trait Loci in Maize. I. Numbers, Genomic Distribution and Types of Gene Action

Genetics ◽

10.1093/genetics/116.1.113 ◽

1987 ◽

Vol 116 (1) ◽

pp. 113-125

Author(s):

M D Edwards ◽

C W Stuber ◽

J F Wendel

Keyword(s):

Quantitative Trait Loci ◽

Phenotypic Variation ◽

Quantitative Trait ◽

Quantitative Traits ◽

Gene Action ◽

Individual Plant ◽

Gene Effects ◽

Individual Gene ◽

Trait Loci ◽

Marker Loci

ABSTRACT Individual genetic factors which underlie variation in quantitative traits of maize were investigated in each of two F2 populations by examining the mean trait expressions of genotypic classes at each of 17–20 segregating marker loci. It was demonstrated that the trait expression of marker locus classes could be interpreted in terms of genetic behavior at linked quantitative trait loci (QTLs). For each of 82 traits evaluated, QTLs were detected and located to genomic sites. The numbers of detected factors varied according to trait, with the average trait significantly influenced by almost two-thirds of the marked genomic sites. Most of the detected associations between marker loci and quantitative traits were highly significant, and could have been detected with fewer than the 1800–1900 plants evaluated in each population. The cumulative, simple effects of marker-linked regions of the genome explained between 8 and 40% of the phenotypic variation for a subset of 25 traits evaluated. Single marker loci accounted for between 0.3% and 16% of the phenotypic variation of traits. Individual plant heterozygosity, as measured by marker loci, was significantly associated with variation in many traits. The apparent types of gene action at the QTLs varied both among traits and between loci for given traits, although overdominance appeared frequently, especially for yield-related traits. The prevalence of apparent overdominance may reflect the effects of multiple QTLs within individual marker-linked regions, a situation which would tend to result in overestimation of dominance. Digenic epistasis did not appear to be important in determining the expression of the quantitative traits evaluated. Examination of the effects of marked regions on the expression of pairs of traits suggests that genomic regions vary in the direction and magnitudes of their effects on trait correlations, perhaps providing a means of selecting to dissociate some correlated traits. Marker-facilitated investigations appear to provide a powerful means of examining aspects of the genetic control of quantitative traits. Modifications of the methods employed herein will allow examination of the stability of individual gene effects in varying genetic backgrounds and environments.

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Effect of Quantitative Trait Loci for Milk Protein Percentage on Milk Protein Yield and Milk Yield in Israeli Holstein Dairy Cattle

Journal of Dairy Science ◽

10.3168/jds.2007-0655 ◽

2008 ◽

Vol 91 (4) ◽

pp. 1614-1627 ◽

Cited By ~ 11

Author(s):

E. Lipkin ◽

R. Tal-Stein ◽

A. Friedmann ◽

M. Soller

Keyword(s):

Quantitative Trait Loci ◽

Dairy Cattle ◽

Milk Yield ◽

Quantitative Trait ◽

Milk Protein ◽

Protein Yield ◽

Protein Percentage ◽

Trait Loci

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Linkage between Quantitative Trait Loci and Marker Loci: Resolution Power of Three Statistical Approaches in Single Marker Analysis

Biometrics ◽

10.2307/2532884 ◽

1996 ◽

Vol 52 (2) ◽

pp. 426 ◽

Cited By ~ 4

Author(s):

Abraham B. Korol ◽

Yefim I. Ronin ◽

Valery M. Kirzhner

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Single Marker Analysis ◽

Resolution Power ◽

Marker Analysis ◽

Trait Loci ◽

Marker Loci ◽

Single Marker ◽

Statistical Approaches

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Quantitative Trait Loci Mapping for Dairy Cattle Production Traits Using a Maximum Likelihood Method

Journal of Dairy Science ◽

10.3168/jds.s0022-0302(04)73188-4 ◽

2004 ◽

Vol 87 (2) ◽

pp. 491-500 ◽

Cited By ~ 12

Author(s):

Y. Liu ◽

G.B. Jansen ◽

C.Y. Lin

Keyword(s):

Quantitative Trait Loci ◽

Maximum Likelihood ◽

Dairy Cattle ◽

Quantitative Trait ◽

Maximum Likelihood Method ◽

Likelihood Method ◽

Quantitative Trait Loci Mapping ◽

Production Traits ◽

Cattle Production ◽

Trait Loci

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Genome-Wide Association Study in Mexican Holstein Cattle Reveals Novel Quantitative Trait Loci Regions and Confirms Mapped Loci for Resistance to Bovine Tuberculosis

Animals ◽

10.3390/ani9090636 ◽

2019 ◽

Vol 9 (9) ◽

pp. 636 ◽

Cited By ~ 2

Author(s):

Sara González-Ruiz ◽

Maria G. Strillacci ◽

Marina Durán-Aguilar ◽

Germinal J. Cantó-Alarcón ◽

Sara E. Herrera-Rodríguez ◽

...

Keyword(s):

Immune Response ◽

Quantitative Trait Loci ◽

Dairy Cattle ◽

Quantitative Trait ◽

Bovine Tuberculosis ◽

Genome Wide Association ◽

Economic Losses ◽

Genome Wide ◽

Trait Loci ◽

Mycobacterium Spp

Bovine tuberculosis (bTB) is a disease of cattle that represents a risk to public health and causes severe economic losses to the livestock industry. Recently, genetic studies, like genome-wide association studies (GWAS) have greatly improved the investigation of complex diseases identifying thousands of disease-associated genomic variants. Here, we present evidence of genetic variants associated with resistance to TB in Mexican dairy cattle using a case-control approach with a selective DNA pooling experimental design. A total of 154 QTLRs (quantitative trait loci regions) at 10% PFP (proportion of false positives), 42 at 5% PFP and 5 at 1% PFP have been identified, which harbored 172 annotated genes. On BTA13, five new QTLRs were identified in the MACROD2 and KIF16B genes, supporting their involvement in resistance to bTB. Six QTLRs harbor seven annotated genes that have been previously reported as involved in immune response against Mycobacterium spp: BTA (Bos taurus autosome) 1 (CD80), BTA3 (CTSS), BTA 3 (FCGR1A), BTA 23 (HFE), BTA 25 (IL21R), and BTA 29 (ANO9 and SIGIRR). We identified novel QTLRs harboring genes involved in Mycobacterium spp. immune response. This is a first screening for resistance to TB infection on Mexican dairy cattle based on a dense SNP (Single Nucleotide Polymorphism) chip.

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