Mapping economic trait loci for somatic cell score in Holstein cattle using microsatellite markers and selective genotyping

Marker-assisted selection (MAS) uses genetic marker genotypes to predict an animal's production potential and will provide additional selection information for progeny testing. With the discovery of highly polymorphic microsatellite markers, the tools now exist to begin the search for economic trait loci (ETL), which is the first step toward MAS. The objective of this study was to identify ETL for somatic cell score in an existing Holstein population. Using the granddaughter design, sons from seven grandsire families were genotyped with 20 autosomal microsatellites from five chromosomes (4, 8, 13, 17, 23), with an emphasis on chromosome 23, which is the location of the bovine major histocompatibility complex (BoLA). Selective genotyping was used to reduce the number of genotypes required, in which the 10 highest and 10 lowest sons from the phenotypic distribution curve were tested (140 sons in seven families). One marker (513), located near BoLA, showed evidence of an ETL in three of five polymorphic families. Additional sons were genotyped from the five families to estimate the effect and to compare selective and ‘complete’ genotyping. Both methods detected an ETL at marker 513, but in different families. This study provides evidence of the usefulness of microsatellite markers and the granddaughter design in the detection of ETL; however, additional markers need to be evaluated to determine the usefulness of selective genotyping. Based on the results from the 20 studied markers, the most likely position of a somatic cell score ETL lies near marker 513, located on chromosome 23.     

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

From an extensive review of public domain information on dairy cattle quantitative trait loci (QTL), we have prepared a draft online QTL map for dairy production traits. Most publications (45 out of 55 reviewed) reported QTL for the major milk production traits (milk, fat and protein yield, and fat and protein concentration (%)) and somatic cell score. Relatively few QTL studies have been reported for more complex traits such as mastitis, fertility and health. The collated QTL map shows some chromosomal regions with a high density of QTL, as well as a substantial number of QTL at single chromosomal locations. To extract the most information from these published records, a meta-analysis was conducted to obtain consensus on QTL location and allelic substitution effect of these QTL. This required modification and development of statistical methodologies. The meta-analysis indicated a number of consensus regions, the most striking being two distinct regions affecting milk yield on chromosome 6 at 49 cM and 87 cM explaining 4.2 and 3.6 percent of the genetic variance of milk yield, respectively. The first of these regions (near marker BM143) affects five separate milk production traits (protein yield, protein percent, fat yield, fat percent, as well as milk yield).     

Development of microsatellite markers and comparative mapping for bovine chromosome 19

Previous research has mapped an ovulation rate quantitative trait locus (QTL) to bovine chromosome 19. In an effort to enhance comparative mapping information and develop additional markers for refined QTL mapping, microsatellite markers were developed in a targeted approach. A bovine bacterial artificial chromosome (BAC) library was screened for loci with either known or predicted locations on bovine chromosome 19. An average of 6.4 positive BAC were identified per screened locus. A total of 10 microsatellite markers were developed for five targeted loci with heterozygosity of 7-83% in a sample of reference family parents. The newly developed markers were typed on reference families along with four previously mapped marker loci and used to create a linkage map. Comparison of locus order between human and cattle provides support for previously observed rearrangement. One of the mapped loci myotubularin related protein 4 (MTMR4) potentially extends the proximal boundary of a conserved linkage group.     

Mapping quantitative trait loci with DNA microsatellites in a commercial dairy cattle population

Individual loci affecting economically important traits can be located using genetic linkage between quantitative trait loci and genetic markers. In the ‘granddaughter’ experimental design, heterozygous grandsires and their sons are genotyped for the genetic marker, while the quantitative trait records of the granddaughters are used for statistical analysis. Ten DNA microsatellite markers were used to look for associations with quantitative trait loci affecting milk production traits in seven Israeli Holstein grandsire families. At least 60% more grandsires were heterozygous, and 40% fewer individuals were discarded because of unknown paternal allele origin, as compared with diallelic markers. The effects of paternal alleles for locus D21S4 on kg milk and protein were significant (P < 0.025). The allele substitution effects for sire 783 were 283 kg milk and 5.7 kg protein. For both traits, progeny of sire 783 that inherited allele ‘18’ had higher evaluations than progeny that inherited allele ‘21’. These results were verified by genotyping 151 of his daughters. Thus, the rate of genetic gain for protein production can be increased by selecting progeny of sire 783 carrying allele ‘18’ at this locus.     

A search for quantitative trait loci for ovulation rate in cattle

Seventy-seven polymorphic microsatellites were analysed in offspring of three elite sires that were part of the foundation of an experimental population selected for twinning rate at the US Meat Animal Research Center, Clay Center, Nebraska. All females were assessed for ovulation rate by rectal palpation of corpora lutea over 8–10 consecutive oestrous cycles from approximately 12 to 18 months of age, and associations between ovulation rate and sire allele were examined in each of the three sire groups. A preliminary analysis was performed using selectively genotyped daughters of each sire. Markers found significant or approaching significance were also genotyped in all daughters, sons and granddaughters of these sires. A test of marker associations limited to the granddaughter data provided an independent confirmation of marker effect and significance relative to the initial test with daughter data. Putative ovulation rate quantitative trait loci were detected on chromosomes 7 and 23. Marker UWCA20 on chromosome 7 was associated with an effect in excess of one phenotypic standard deviation and accounted for approximately 10% of phenotypic variation ovulation rate. Marker CYP21 (steroid 21-hydroxylase) on chromosome 23 was associated with an effect of slightly less than half a phenotypic standard deviation and accounted for approximately 4% of phenotypic variation.     

A search for quantitative trait loci for milk production traits on chromosome 6 in Finnish Ayrshire cattle

Cattle chromosome 6 was scanned with 11 markers, ten microsatellites and the casein haplotype, to identify quantitative trait loci (QTLs) affecting the following milk production traits: milk yield, fat percentage, fat yield, protein percentage and protein yield. Twelve Finnish Ayrshire half-sib families with a total of 480 sons were genotyped and used in a grand-daughter design. Interval mapping was performed with a multiple-marker regression approach with a one-QTL and a two-QTL model, and the significance threshold values were determined empirically using a permutation test. Across-family analysis with the one-QTL model revealed an effect on protein percentage (P < 0.05) and on milk yield (P < 0.05). The analysis with the two-QTL model identified significant effects (P < 0.05) on protein percentage, milk yield, and fat yield. Comparing these two cases, the results suggest the existence of two QTLs on chromosome 6 with an effect on milk production traits. One of the QTLs was located around the casein genes. As the other QTL was similar in location and effect to a QTL found previously in Holstein-Friesians, an identity-by-descent approach could be applied to fine map this region.     

Comparison of protein markers and microsatellites in differentiation of cattle populations

Five cattle populations, representing four breeds, were analysed for 14 protein markers and five microsatellite loci. The breeds studied were Brown Swiss and three autochthonous Spanish cattle: Avileña-Negra Ibérica (A-NI), two populations (A-NI 1 and A-NI 2) from different, reproductively isolated, locations; Sayaguesa; and Morucha. A total of 752 animals were examined for biochemical polymorphisms, of which 488 were also DNA typed. Genetic parameters and phylogenetic trees were obtained separately for each group of markers and results were compared. Estimates of heterozygosity and genetic distances from microsatellites were greater than those obtained using protein markers. The overall topology of the two dendrograms was similar. A-NI 1 and A-NI 2 populations were grouped together, related to Morucha, and the three of them related to Sayaguesa. Brown Swiss appeared in a separate branch from Spanish cattle. These results support the usefulness of microsatellites in the study of genetic relationships among closely related populations and breeds.     

Characterization of UMP synthase in dairy cattle heterozygous for a lethal recessive trait

UMP synthase was characterized biochemically in dairy cattle heterozygous for a deficiency of this enzyme. Both activities comprising this bifunctional enzyme are decreased, with OMP decarboxylase more affected than orotate phosphoribosyltransferase. Immunotitration of UMP synthase activity revealed the presence of the protein product of the mutant allele in the heterozygous animals. UMP synthases from normal and deficient cattle were not distinguished from one another by kinetic constants, responses to inhibitors, pH profiles, or thermal lability. It was concluded that the 50% reduction in enzyme activity in heterozygous cattle is the result of the presence of only half the normal level of catalytically active UMP synthase.     

Implementation of a parentage control system in Portuguese beef-cattle with a panel of microsatellite markers

A study was conducted to assess the feasibility of applying a panel of 10 microsatellite markers in parentage control of beef cattle in Portugal. In the first stage, DNA samples were collected from 475 randomly selected animals of the Charolais, Limousin and Preta breeds. Across breeds and genetic markers, means for average number of alleles, effective number of alleles, expected heterozygosity and polymorphic information content, were 8.20, 4.43, 0.733 and 0.70, respectively. Enlightenment from the various markers differed among breeds, but the set of 10 markers resulted in a combined probability above 0.9995 in the ability to exclude a random putative parent. The marker-set thus developed was later used for parentage control in a group of 140 calves from several breeds, where there was the suspicion of possible faulty parentage recording. Overall, 76.4% of the calves in this group were compatible with the recorded parents, with most incompatibilities due to misidentification of the dam. Efforts must be made to improve the quality of pedigree information, with particular emphasis on information recorded at the calf's birth.     

Isolation and characterization of microsatellite loci in Palinurus elephas

The European spiny lobster (Palinurus elephas) mean annual catches have decreased alarmingly during recent decades along its entire distribution area due to stock over‐exploitation, which makes it a primary target for conservation plans. A total of 164 microsatellite loci were isolated from a genomic library of P. elephas enriched for CA, GA, CAA and GATA repeats. A total of 15 polymorphic loci have been screened in 48 individuals. High numbers of alleles per locus (averaging 20 ± 10.5) and observed heterozygosity (averaging 0.789 ± 0.197) have been detected. None of the pairs of loci showed significant linkage disequilibrium. Two of the loci (Pael1 and Pael2) showed significant departure from Hardy–Weinberg equilibrium in Sagres, while Pael38 showed significant departure in Tunis. These highly polymorphic markers will be useful in determining the spatial patterns of genetic diversity between and within populations of Palinurus elephas.     

Evidence for quantitative trait loci affecting twinning rate in North American Holstein cattle

Twinning in dairy cattle has been associated with many negative health and reproductive events that cause economic loss to the producer. Reports have suggested that twinning rates are increasing and that there may be a positive relationship between milk production and twinning frequency. Putative quantitative trait loci (QTL) for twinning and ovulation rate on bovine chromosomes 5, 7, 19 and 23 have been previously identified in other populations. The objective of this study was to detect and possibly confirm the existence and effects of these QTL in the North American Holstein population. Half-sib families of 20 North American Holstein sires with above average twinning rate predicted transmitting abilities (PTA) comprised the sample population under investigation. Twinning rate PTA values had been estimated from calving data. DNA extracted from semen samples was analysed using 45-61 microsatellite markers across the four chromosomes. Marker heterozygosity of the patriarchs averaged 62%. Evidence of twinning QTL was found in multiple families on chromosomes 5, 7 and 23 and in one family on chromosome 19. Four of the sires formed one three-generation family: one sire and three half-sib sons with sons of their own. This extended family was analysed with additional markers confirming a twinning QTL of significant size on chromosome 5.     

Determination of the optimal tissue source and number of microsatellites for detection of zygotic origin of cattle twins

Abstract

Twenty pairs of cattle twins were genotyped for 3 to 12 microsatellites each using semen, blood, milk and hair roots. Chimaerism was recognized in 19 pairs by discrepancies in microsatellite analysis from milk and blood as opposed to semen and hair, or by detection of more than 2 alleles per genotype from milk and blood. Chimaerism of 2, 3 or 4 alleles was demonstrated in genotypes of twins from blood as compared to 1 or 2 alleles only from hair. The appearance of predominant bands in genotypes from blood or milk representing alleles of only one of the co‐twins was not consistent among the different microsatellites for the same twins. No evidence for germ cell chimaerism was found in semen of dizygotic male twins although our PCR system could detect cell mixes as small as a 1:100 ratio. Genotyping from either hair or semen for 4 microsatellites are sufficient to confirm zygotic origin of twins at .98 accuracy. Researchers should be aware of the possibility of erroneous genotyping when analyzing DNA from twins derived from blood or milk and the potential of chimaerism as an experimental model to study different immunological characteristics of cattle co‐twins.     

Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle

A whole‐genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4–5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome‐wise basis, in combined‐sire (seven QTL) or within‐sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome‐wise basis, in combined‐sire (five QTL) or within‐sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin‐derived and Jersey‐derived alleles on these two chromosomes, respectively.     

Optimum spacing of genetic markers for determining linkage between marker loci and quantitative trait loci

The cost of experiments aimed at determining linkage between marker loci and quantitative trait loci (QTL) was investigated as a function of marker spacing and number of individuals scored. It was found that for a variety of experimental designs, fairly wide marker spacings (ca. 50 cM) are optimum or close to optimum for initial studies of marker-QTL linkage, in the sense of minimizing overall cost of the experiment. Thus, even when large numbers of more or less evenly spaced markers are available, it will not always be cost effective to make full utilization of this capacity. This is particularly true when costs of rearing and trait evaluation per individual scored are low, as when marker data are obtained on individuals raised and evaluated for quantitative traits as part of existing programs. When costs of rearing and trait evaluation per individual scored are high, however, as in human family data collection carried out primarily for subsequent marker — QTL analyses, or when plants or animals are raised specifically for purposes of marker — QTL linkage experiments, optimum spacing may be rather narrow. It is noteworthy that when marginal costs of additional markers or individuals are constant, total resources allocated to a given experiment will determine total number of individuals sampled, but not the optimal marker spacing.     

An integrative approach for the identification of quantitative trait loci

The genetic dissection of complex traits is one of the most difficult and most important challenges facing science today. We discuss here an integrative approach to quantitative trait loci (QTL) mapping in mice. This approach makes use of the wealth of genetic tools available in mice, as well as the recent advances in genome sequence data already available for a number of inbred mouse strains. We have developed mapping strategies that allow a stepwise narrowing of a QTL mapping interval, prioritizing candidate genes for further analysis with the potential of identifying the most probable candidate gene for the given trait. This approach integrates traditional mapping tools, fine mapping tools, sequence-based analysis, bioinformatics and gene expression.     

Synteny mapping of human chromosome 8 loci in cattle

Four genes having homologous loci on the short arm of human chromosome 8 have been mapped to two different bovine syntenic groups. The gene coding for the tissue-type plasminogen activator mapped with GSR, a human chromosome 8 marker, of syntenic group U14 while lipoprotein lipase and the medium and light neurofilament polypeptide genes were shown to be syntenic with the human chromosome 9 marker GGTB2 of syntenic group U18.     

Detection of quantitative trait loci for growth and fatness in pigs

A quantitative trait locus (QTL) analysis of growth and fatness data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. Six boars and 23 F1 sows, the progeny of six LW boars and six MS sows, produced 530 F2 males and 573 F2 females. Nine growth traits, i.e. body weight at birth and at 3, 10, 13, 17 and 22 weeks of age, average daily gain from birth to 3 weeks, from 3 to 10 weeks and from 10 to 22 weeks of age, as well as backfat thickness at 13, 17 and 22 weeks of age and at 40 and 60 kg live weight were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using two interval mapping methods: a line-cross (LC) regression method where founder lines were assumed to be fixed for different QTL alleles and a half-/full-sib (HFS) maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Both methods revealed highly significant gene effects for growth on chromosomes 1, 4 and 7 and for backfat thickness on chromosomes 1, 4, 5, 7 and X, and significant gene effects on chromosome 6 for growth and backfat thickness. Suggestive QTLs were also revealed by both methods on chromosomes 2 and 3 for growth and 2 for backfat thickness. Significant gene effects were detected for growth on chromosomes 11, 13, 14, 16 and 18 and for backfat thickness on chromosome 8, 10, 13 and 14. LW alleles were associated with high growth rate and low backfat thickness, except for those of chromosome 7 and to a lesser extent early-growth alleles on chromosomes 1 and 2 and backfat thickness alleles on chromosome 6.     

Detection of genes influencing economic traits in three French dairy cattle breeds

A project of QTL detection was carried out in the French Holstein, Normande, and Montbéliarde dairy cattle breeds. This granddaughter design included 1 548 artificial insemination bulls distributed in 14 sire families and evaluated after a progeny-test for 24 traits (production, milk composition, persistency, type, fertility, mastitis resistance, and milking ease). These bulls were also genotyped for 169 genetic markers, mostly microsatellites. The QTL were analysed by within-sire linear regression of daughter yield deviations or deregressed proofs on the probability that the son receives one or the other paternal QTL allele, given the marker information. QTL were detected for all traits, including those with a low heritability. One hundred and twenty QTL with a chromosome-wise significance lower than 3% were tabulated. This threshold corresponded to a 15% false discovery rate. Amongst them, 32 were genome-wise significant. Estimates of their contribution to genetic variance ranged from 6 to 40%. Most substitution effects ranged from 0.6 to 1.0 genetic standard deviation. For a given QTL, only 1 to 5 families out of 14 were informative. The confidence intervals of the QTL locations were large and always greater than 20 cM. This experiment confirmed several already published QTL but most of them were original, particularly for non-production traits.     

Isolation and characterization of polymorphic nuclear microsatellite loci in Pinus cembra L

We developed eight polymorphic nuclear microsatellite markers for the Swiss stone pine (Pinus cembra L.), of which seven may be amplified in a multiplex polymerase chain reaction. Allelic polymorphism across all loci and 40 individuals representing two populations in the Swiss Alps was high (mean = 7.6 alleles). No significant linkage disequlibrium was displayed between pairs of loci. Significant deviation from Hardy–Weinberg equilibrium was revealed at three loci in one population. Cross–amplification was achieved in two related species within the genus (P. sibirica and P. pumila). Thus, the markers may be useful for population genetic studies in these three pine species. They will be applied in ongoing projects on genetic diversity and patterns of gene flow in P. cembra.     

Development of 52 new polymorphic microsatellite markers for the olive flounder, Paralichthys olivaceus

We characterized 52 new microsatellite markers isolated from (GT)(n) and (CT)(n) microsatellite-enriched genomic libraries of the olive flounder (Paralichthys olivaceus). All markers were polymorphic, with eight to 30 (mean 15.1) alleles detected in 30 individuals from a single natural population. Observed heterozygosity ranged from 0.20 to 1.0. Segregation analysis within a mapping family revealed non-amplifying null alleles at six loci. These results indicate that these new microsatellite markers will be useful for population genetic, parentage, and genome mapping studies.