Quantitative trait loci mapping in dairy cattle: review and meta-analysis

Joint analysis of the influence of CYP11B1 and DGAT1 genetic variation on milk production, somatic cell score, conformation, reproduction, and productive lifespan in German Holstein cattle1

Recent publications indicate genetic variation in milk production traits on proximal BTA14, which cannot be explained solely with genetic variation in the DGAT1 gene. To elucidate these QTL effects, animals from a German Holstein granddaughter design (18 families, 1,291 sons) were genotyped for CYP11B1 (V30A) and DGAT1 (K232A) polymorphisms. Frequencies of alleles of maternal descent were estimated for CYP11B1(V) (0.776) and DGAT1(K) (0.549). Allele substitution effects (alpha/2) were first calculated for both alleles in separate models and then in a joint model. From the joint analysis, CYP11B1(V) effects on fat content (+0.04%) and protein content (+0.01%) were positive. Effects on milk yield (-82 kg), fat yield (-0.5 kg), and protein yield (-1.9 kg) were negative. Compared with the individual analysis, DGAT1(K) effects on fat content (+0.28%), protein content (+0.06%), and milk yield (-258 kg) were reduced; fat yield (+10.8 kg) was enhanced; and protein yield (-3.8 kg) was reduced. In the joint analysis, allele substitution effects of CYP11B1(V) and DGAT1(K) together explained more of the variation in milk production traits than DGAT1(K) alone. Further significant effects were found for CYP11B1(V) and DGAT1(K) among 6 reproduction traits and 14 conformational traits. These observations indicate a possible negative influence of DGAT1(K) on maternal nonreturn rate, and thus, on length of productive life.

Further studies on using multiple-cross mapping (MCM) to map quantitative trait loci

We have completed whole-genome scans for quantitative trait loci (QTLs) associated with acute ethanol-induced activation in the six F(2) intercrosses that can be formed from the C57BL/6J (B6), DBA/2J (D2) , BALB/cJ (C), and LP/J (LP) inbred strains. The goal was to test the hypothesis that given the relatively simple structure of the laboratory mouse genome, the same QTLs will be detected in multiple crosses which in turn will provide support for the strategy of multiple-cross mapping (MCM). QTLs with LOD scores greater than 4 were detected on Chrs 1, 2, 3, 8, 9, 13, 14, and 16. Only for the QTL on distal Chr 1 was there convincing evidence that the same or at least a very similar QTL was detected in multiple crosses. We also mapped the Chr 2 QTL directly in heterogeneous stock (HS) animals derived from the four inbred strains. At G(19) the QTL was mapped to an approximately 3-Mbp interval and this interval was associated with a haplotype block with a largely biallelic structure: B6-L:C-D2. We conclude that mapping in HS animals not only provides significantly greater QTL resolution, at least in some cases it provides significantly more information about the QTL haplotype structure.

DGAT1 and ABCG2 polymorphism in Indian cattle (Bos indicus) and buffalo (Bubalus bubalis) breeds

BACKGROUND

Indian cattle (Bos indicus) and riverine buffalo (Bubalus bubalis) give a poor yield of milk but it has a high fat and protein percentage compared to taurine cattle. The identification of QTLs (Quantitative Trait Loci) on BTA14 and BTA6 and its subsequent fine mapping has led to identification of two non conservative mutations affecting milk production and composition. Our objective was to estimate the frequency of K232A (DGAT1--diacylglycerol-acyltransferase 1) and Y581S (ABCG2--ATP binding cassette sub family G member 2) polymorphisms in diverse cattle and buffalo breeds of India having large variation in terms of milk production.

RESULTS

We screened the reported missense mutations in six cattle and five buffalo breeds. The DGAT1K and ABCG2Y alleles were found to be fixed in Indian cattle and buffalo breeds studied.

CONCLUSION

This study provides an indirect evidence that all the Indian cattle and buffalo breeds have fixed alleles with respect to DGAT1 and ABCG2 genes reported to be responsible for higher milk fat yield, higher fat and protein percent.

QTL and candidate genes for fecundity in sows

Fecundity in pigs is a trait of major economic interest but low heritability. For the improvement of fecundity, genetic markers for selection are desirable and therefore, several searches for genetic variation influencing fecundity have been performed. The aim of this review is to compare and to evaluate all published QTL analyses and candidate gene approaches concerning reproductive traits in sows. For this purpose, we present a comprehensive cytogenetic map comprising 54 QTL and 11 candidate genes with influence on reproductive traits. The evaluation and comparison of the results showed similarities, but also marked differences among studies. Reasons for different results are multicausal and are due to differences between resource populations, number of evaluated animals, mating systems, measured phenotypical traits and environmental influences. We could show that chromosome 8 and to a lower extend chromosome 7 are the most important chromosomes with regard to reproductive traits in pigs. For further research, fine mapping of the identified QTL regions is necessary in order to confirm and to narrow the most likely chromosomal intervals. Although difficult to perform, an advance would be a standardization of the experimental setup in particular, in respect to the collection of phenotypic data. Furthermore, we suggest to publish the information on further identified QTL and candidate genes as comprehensive and accurate as possible in order to allow a more transparent comparison and collation of the results.

Characterization of the DGAT1 Mutations and the CSN1S1 Promoter in the German Angeln Dairy Cattle Population

The identification of quantitative trait loci (QTL) and genes with influence on milk production traits has been the objective of various mapping studies in the last decade. In the centromeric region of Bos taurus autosome (BTA) 14, the acyl-CoA:diacylglycerol acyltransferase1 gene (DGAT1) has been identified as the most likely causative gene underlying a QTL for milk fat yield and content. Recently, a second polymorphism in the promoter of DGAT1 emerged as an additional source of variation. In this study, the frequencies and the effects of alleles at the DGAT1 K232A and at the DGAT1 promoter variable number of tandem repeat (VNTR) locus on BTA14, and of alleles at the CSN1S1 (alpha(S1)-casein-encoding gene) promoter on BTA6 in the German Angeln dairy cattle population were investigated. Analyzed traits were milk, fat, protein, lactose, and milk energy yield, fat, protein, lactose, and milk energy content and somatic cell score. The lysine variant of the DGAT1 K232A mutation showed significant effects for most of the milk production traits. A specific allele of the DGAT1 promoter VNTR showed significant effects on the traits lactose yield and content, milk energy content, and SCS compared with the other alleles. Additionally, a regulation mechanism between the DGAT1 K232A mutation and the DGAT1 promoter VNTR was found for fat yield and content, which could be caused by an upper physiological bound for the effects of the DGAT1 gene. At the CSN1S1 promoter, 2 of 4 alleles showed significant allele substitution effects on the milk yield traits.

A first-generation metric linkage disequilibrium map of bovine chromosome 6

We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein-Friesian dairy cattle, which makes such populations ideal for whole-genome association studies.

The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

Background

Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface.

Description

The QTL (Quantitative Trait Locus) data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL) populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position.

Conclusion

We present a web accessible, integrated database of bovine (dairy and beef cattle) QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at .

The role of the bovine growth hormone receptor and prolactin receptor genes in milk, fat and protein production in Finnish Ayrshire dairy cattle

We herein report new evidence that the QTL effect on chromosome 20 in Finnish Ayrshire can be explained by variation in two distinct genes, growth hormone receptor (GHR) and prolactin receptor (PRLR). In a previous study in Holstein-Friesian dairy cattle an F279Y polymorphism in the transmembrane domain of GHR was found to be associated with an effect on milk yield and composition. The result of our multimarker regression analysis suggests that in Finnish Ayrshire two QTL segregate on the chromosomal region including GHR and PRLR. By sequencing the coding sequences of GHR and PRLR and the sequence of three GHR promoters from the pooled samples of individuals of known QTL genotype, we identified two substitutions that were associated with milk production traits: the previously reported F-to-Y substitution in the transmembrane domain of GHR and an S-to-N substitution in the signal peptide of PRLR. The results provide strong evidence that the effect of PRLR S18N polymorphism is distinct from the GHR F279Y effect. In particular, the GHR F279Y has the highest influence on protein percentage and fat percentage while PRLR S18N markedly influences protein and fat yield. Furthermore, an interaction between the two loci is suggested.

Multitrait Quantitative Trait Loci Mapping for Milk Production Traits in Danish Holstein Cattle

The aims of this study were (1) to confirm previously identified quantitative trait loci (QTL) on bovine chromosomes 6, 11, 14, and 23 in the Danish Holstein cattle population, (2) to assess the pleiotropic nature of each QTL on milk production traits by building multitrait and multi-QTL models, and (3) to include pedigree information on nongenotyped individuals to improve the estimation of genetic parameters underlying the random QTL model. Nineteen grandsire families were analyzed by single-trait (ST) and multitrait (MT) QTL mapping methods. The variance component-based QTL mapping model was implemented via restricted maximum likelihood (REML) to estimate QTL position and parameters. Segregation of the previously identified QTL was confirmed on bovine chromosomes 6, 11, and 14, but not on 23. A highly significant (1% chromosome-wise level) QTL was found on chromosome 6, between 37 and 73 cM. This QTL had a strong effect on protein percentage (PP) and fat percentage (FP) according to ST analyses, and effects on PP, FP, milk yield (MY), fat yield (FY), and protein yield (PY) in MT analyses. A QTL affecting PP was detected on chromosome 11 (at 70 cM) using ST analysis. The MT analysis revealed a second QTL (at 67 cM) approaching significance with an effect on MY. The ST analysis identified a QTL for MY and FP on chromosome 14, between 10 and 24 cM. The extended pedigree (nongenotyped animals) was included to estimate genetic parameters underlying the random QTL model; that is, additive polygenic and QTL variances. In general, the estimates of the QTL variance components were smaller but more precise when the extended pedigree was considered in the analysis.

Major advances in determining appropriate selection goals

Substantial increases of 3,500 kg of milk, 130 kg of fat, and 100 kg of protein per cow per lactation have resulted from improvements in genetics, nutrition, and management during the past 20 yr. At the same time, the interval from calving to conception increased (unfavorable) by 24 d. Genetics has accounted for about 55% of gains in the yield traits and about one-third of the change in interval to conception. Genetic gains in the yield traits and productive life have accumulated to around 1.7 and 1.2 genetic standard deviations since 1980. Unfavorable genetic changes in conception interval since 1980 and somatic cell score since 1990 have accumulated to 1.0 and 0.12 genetic standard deviations. The most important advance in selection indexes has been the introduction of nonyield traits. Advances in selection indexes have gone hand in hand with advances in data collection and genetic evaluation. As new traits were recorded in dairy management databases and as genetic evaluations were developed for these traits, they were incorporated into selection indexes. Until 1994, when somatic cell score and productive life were introduced, selection indexes provided by USDA included only yield traits. In 2000, composite type indexes for udder, feet and legs, and body size were added. Daughter pregnancy rate and service sire- and daughter-calving ease were included in 2003. The lifetime merit indexes introduced in 2003 have, for the first time, resulted in theoretical selection responses in the desired direction for all traits. During this time, the percentage relative economic weights in selection indexes increased from 0 to 45% for the nonyield traits. Selection emphasis on nonyield traits should continue to increase as additional traits (e.g., calf survival, metabolic disease, and male fertility) are introduced in the future. Wide variation exists among countries in traits included in selection indexes and in relative economic weights. Molecular genetic studies have identified many chromosome regions with potentially important major genes for economic traits. Use of DNA markers for genetic improvement is currently limited by lack of precision in marker location. Discovery of major genes will be accelerated by the availability of the bovine genome sequence, comparative genome maps and genome sequences across species, and increased use of breed crosses in molecular studies. As major genes are identified, their effects will be incorporated into genetic evaluations and selection indexes.

Association of the OLR1 Gene with Milk Composition in Holstein Dairy Cattle

Oxidized low-density lipoprotein receptor (OLR1) is the major protein that binds, internalizes, and degrades oxidized low-density lipoprotein. The role of OLR1 in lipid metabolism and the results of previous whole-genome scan studies prompted the investigation of OLR1 as a candidate gene affecting milk composition traits. Direct cDNA and genomic sequencing of OLR1 revealed 2 single nucleotide polymorphisms (SNP) in exon 4, 5 SNP in intron 4, and 1 in the 3' untranslated region (UTR). Four intragenic haplotypes comprising SNP positions 7,160, 7,161, 7,278, 7,381, 7,409, 7,438, 7,512, and 8,232 were inferred. Haplotype analysis showed that one of the haplotypes was associated with a significant increase in fat yield and fat percentage. Single SNP analysis showed that allele C of SNP 8,232 (in the 3'-UTR) had significant effects on fat yield and fat percentage, whereas SNP 7,160 and 7,161 (in exon 4) had no significant effects. Both single SNP and haplotype analyses indicate that SNP 8,232 in the 3'-UTR is associated with milk fat yield and percentage and it may be in linkage disequilibrium with the functional polymorphism. To provide support for the hypothesis that SNP 8,232 is responsible for OLR1 expression, OLR1 expression levels in individuals bearing different genotypes were assessed. It was found that OLR1 expression was reduced in genotype AA individuals compared with CC and AC individuals, suggesting that A at position 8,232 may be the nucleotide causing decreased OLR1 expression. The 3'-UTR polymorphism found in this study might control translation or stability of OLR1 mRNA.

Using mating designs to uncover QTL and the genetic architecture of complex traits

Analysis of quantitative trait loci (QTL) affecting complex traits is often pursued in single-cross experiments. For most purposes, including breeding, some assessment is desired of the generalizability of the QTL findings and of the overall genetic architecture of the trait. Single-cross experiments provide a poor basis for these purposes, as comparison across experiments is hampered by segregation of different allelic combinations among different parents and by context-dependent effects of QTL. To overcome this problem, we combined the benefits of QTL analysis (to identify genomic regions affecting trait variation) and classic diallel analysis (to obtain insight into the general inheritance of the trait) by analyzing multiple mapping families that are connected via shared parents. We first provide a theoretical derivation of main (general combining ability (GCA)) and interaction (specific combining ability (SCA)) effects on F(2) family means relative to variance components in a randomly mating reference population. Then, using computer simulations to generate F(2) families derived from 10 inbred parents in different partial-diallel designs, we show that QTL can be detected and that the residual among-family variance can be analyzed. Standard diallel analysis methods are applied in order to reveal the presence and mode of action (in terms of GCA and SCA) of undetected polygenes. Given a fixed experiment size (total number of individuals), we demonstrate that QTL detection and estimation of the genetic architecture of polygenic effects are competing goals, which should be explicitly accounted for in the experimental design. Our approach provides a general strategy for exploring the genetic architecture, as well as the QTL underlying variation in quantitative traits.

Lactational traits of importance in dairy cows and applications for emerging biotechnologies

New molecular and quantitative genetic technologies are the latest in a long list of technologies that have been introduced to dairy industries over many decades to improve the performance of cows. The catalysts for future advances will be sequencing of the bovine genome and development of high-throughput technologies to identify and exploit relevant variation in DNA sequences. The new technologies will allow the selection of animals based on specific genotypes that suit specific applications such as once-daily (OAD) milking or extended lactation. These technologies will also allow exploitation of between-cow variation in milk composition, which is currently hidden by bulking of milk on and between farms. Thus, there are opportunities to produce milk from herds of cows selected for specific milk composition that might be, for example, more suitable for cheese-making or have milkfat with specific properties to enhance human health. Identification of genes and gene polymorphisms associated with improved resistance to specific diseases in cows and other farm species also represents a real opportunity to improve animal health over the coming decade. New levels of genetic regulation have been identified, e.g. microRNA and epigenetics, the impacts of which on the performance of cows and humans are only just beginning to be understood. There is a potential role for veterinarians to provide or be the interface for provision of genetic advice to farmers in much the same way that nutritional advice is currently given.

Farm animal genomics and informatics: an update

Farm animal genomics is of interest to a wide audience of researchers because of the utility derived from understanding how genomics and proteomics function in various organisms. Applications such as xenotransplantation, increased livestock productivity, bioengineering new materials, products and even fabrics are several reasons for thriving farm animal genome activity. Currently mined in rapidly growing data warehouses, completed genomes of chicken, fish and cows are available but are largely stored in decentralized data repositories. In this paper, we provide an informatics primer on farm animal bioinformatics and genome project resources which drive attention to the most recent advances in the field. We hope to provide individuals in biotechnology and in the farming industry with information on resources and updates concerning farm animal genome projects.

Fine mapping and physical characterization of two linked quantitative trait loci affecting milk fat yield in dairy cattle on BTA26

Previously, a highly significant QTL affecting fat yield and protein yield and mapped to the bovine BTA26 chromosome has been reported to segregate in the French Holstein cattle population. To confirm and refine the location of this QTL, the original detection experiment was extended by adding 12 new families and genotyping 25 additional microsatellite markers (including 11 newly developed markers). Data were then analyzed by an approach combining both linkage and linkage disequilibrium information, making it possible to identify two linked QTL separated by 20 cM corresponding to approximately 29 Mb. The presence of a QTL affecting protein yield was confirmed but its position was found to be more telomeric than the two QTLunderlying fat yield. Each identified QTL affecting milk fat yield was physically mapped within a segment estimated to be <500 kb. Two strong functional candidate genes involved, respectively, in fatty acid metabolism and membrane permeability were found to be localized within this segment while other functional candidate genes were discarded. A haplotype comprising the favorable allele at each QTL position appears to be overrepresented in the artificial insemination bull population.

Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations

Recent studies report a surprisingly high degree of marker-to-marker linkage disequilibrium (LD) in ruminant livestock populations. This has important implications for QTL mapping and marker-assisted selection. This study evaluated LD between microsatellite markers in a number of breeding populations of layer chickens using the standardized chi-square (chi(2')) measure. The results show appreciable LD among markers separated by up to 5 cM, decreasing rapidly with increased separation between markers. The LD within 5 cM was strongly conserved across generations and differed among chromosomal regions. Using marker-to-marker LD as an indication for marker-QTL LD, a genome scan of markers spaced 2 cM apart at moderate power would have good chances of uncovering most QTL segregating in these populations. However, of markers showing significant trait associations, only 57% are expected to be within 5 cM of the responsible QTL, and the remainder will be up to 20 cM away. Thus, high-resolution LD mapping of QTL will require dense marker genotyping across the region of interest to allow for interval mapping of the QTL.

The genetic dissection of immune response using gene-expression studies and genome mapping

Functional genomics has been applied to the genetic dissection of immune response in different ways: (1) experimental crosses between lines that differ in their (non-) specific immune response have been used to detect quantitative trait loci (QTL) underlying these differences. (2) The measurement of gene expression levels for thousands of genes using microarrays or oligonucleotide chips to identify differential expression with regard to antigen challenge: (a) before and after infection, (b) resistant versus susceptible lines, or (c) combinations of both. Interpretation of QTL results is hampered by the fact that confidence regions of the QTL are large and can contain hundreds of potential candidate genes for the QTL. At the same time, the microarray experiments tend to show large numbers of differentially expressed genes without identifying the relationships between these genes. In the recently proposed 'genetical genomics' framework, members of a segregating population are characterised for genome-wide molecular markers and for gene expression levels. This facilitates the mapping of expression-QTL (eQTL): loci in the genome that control the expression of genes. Initial applications of this approach are critically reviewed and potential applications of this approach with regard to immune response are presented.

Fine-mapping milk production quantitative trait loci on BTA6: analysis of the bovine osteopontin gene

Bovine chromosome six (BTA6) harbors up to six quantitative trait loci (QTL) influencing the milk production of dairy cattle. In stark contrast to human, there is long-range linkage disequilibrium in dairy cattle, which has previously made it difficult to identify the mutations underlying these QTL. Using 38 microsatellite markers in a pedigree of 3,147 Holstein bulls, we fine mapped regions of BTA6 that had previously been shown to harbor QTL. Next, we sequenced a 12.3-kb region harboring Osteopontin, a positional candidate for the statistically most significant of the identified QTL. Nine mutations were identified, and only genotypes for the OPN3907 indel were concordant with the QTL genotypes of eight bulls that were established by segregation analysis. Four of these mutations were genotyped, and a joint linkage/linkage disequilibrium mapping analysis was used to demonstrate the existence of only two functionally distinct clusters of haplotypes within the QTL region, which were uniquely defined by OPN3907 alleles. We estimate a probability of 0.40 that no other mutation within this region is concordant with the QTL genotypes of these eight bulls. Finally, we demonstrate that the motif harboring OPN3907, which is upstream of the promoter and within a region known to harbor tissue-specific osteopontin regulatory elements, is moderately conserved among mammals. The motif was not retrieved from database queries and may be a novel regulatory element.

Association of the Protease Inhibitor Gene with Production Traits in Holstein Dairy Cattle

Positional, comparative candidate gene analysis and previous quantitative trait loci linkage mapping results were used to search for candidate genes affecting milk production and reproduction traits in dairy cattle. The protease inhibitor (PI) gene was chosen for examination, and 5 single nucleotide polymorphisms were detected in coding regions of the gene by direct sequencing of reverse transcription-polymerase chain reaction products from a wide range of cattle tissues. A total of 6 different intragenic haplotypes were identified in North American Holstein population, and these were examined for associations with milk production traits in 24 half-sib families comprising 1007 sons utilizing a granddaughter design. One common haplotype was associated with increased milk and fat yields, increased productive life, and decreased somatic cell score. Another common haplotype was associated with decreased productive life and increased somatic cell score. One rare haplotype was associated with decreased milk, fat, and protein yields and increased milk protein percentage; another rare haplotype was associated with decreased milk yield, increased protein percentage, and decreased productive life. The observation that the PI gene is associated with analogous traits in humans demonstrates the effectiveness of the positional comparative candidate gene analysis that utilizes information about genes present in chromosomal regions with conserved synteny in other species.

Estimation of Quantitative Trait Loci Parameters for Milk Production Traits in German Holstein Dairy Cattle Population

The main objective of this study was to estimate the proportion of total genetic variance attributed to a quantitative trait locus (QTL) on Bos taurus autosome 6 (BTA6) for milk production traits in the German Holstein dairy cattle population. The analyzed chromosomal region on BTA6 spanned approximately 70 cM, and contained 6 microsatellite markers. Milk production data were obtained from routine genetic evaluation for 4500 genotyped German Holstein bulls. Technical aspects related to the estimation of model parameters for a large data set from routine genotype recording were outlined. A fixed QTL model and a random QTL model were introduced to incorporate marker information into parameter estimation and genetic evaluation. Estimated QTL variances, expressed as the ratio of QTL to polygenic variances, were 0.04, 0.03, and 0.07 for milk yield; 0.06, 0.08, and 0.14 for fat yield; and 0.04, 0.04, and 0.11 for protein yield, in the first 3 parities, respectively. The estimated QTL positions, expressed as distances from the leftmost marker DIK82, were 18, 31, and 17 cM for milk yield; 25, 17, and 9 cM for fat yield; and 16, 30, and 17 cM for protein yield in the 3 respective parities. Because the data for the parameter estimation well represented the current population of active German Holstein bulls, the QTL parameter estimates have been used in routine marker-assisted genetic evaluation for German Holsteins.

Mapping of a milk production quantitative trait locus to a 420-kb region on bovine chromosome 6

A QTL affecting milk production traits was previously mapped to an interval of 7.5 cM on chromosome 6 in Norwegian dairy cattle. This article aimed to refine this position by increasing the map density in the region by a set of single-nucleotide polymorphisms and analyzing the data with a combined linkage and linkage disequilibrium approach. Through a series of single- and multitrait and single- and multipoint analyses, the QTL was positioned to an interval surrounded by the genes ABCG2 and LAP3. As no recombinations were detected in this interval, physical mapping was required for further refining. By using radiation hybrid mapping as well as BAC clones, the bovine and human comparative maps in the region are resolved, and the QTL is mapped within a distance of 420 kb.