Genetic mapping of quantitative trait loci for growth and fatness in pigs

Expansion of the pig comparative map by expressed sequence tags (EST) mapping

We have used a PCR-based approach for the genetical and physical mapping of 34 transcripts isolated from a porcine small intestine cDNA library. All but one gene were regionally localized by using a somatic pig-rodent cell hybrid panel, and 12 genes were mapped by linkage analysis of single-stranded conformational polymorphisms developed in 3' untranslated regions of transcripts. For 20 of the transcripts, the human homolog has already been mapped. This study thus represents a significant contribution to the pig comparative map. Some important findings were that we could clarify the extent of a previously identified inversion event in a region of conserved synteny between SSC6q and HSA1p, that SSC14q does contain a region homologous to HSA1, a situation not clear from earlier ZOO-FISH studies, and that the homology between SSC17 and HSA20 includes the p-arm of HSA20.

Mapping of 22 expressed sequence tags isolated from a porcine small intestine cDNA library

Complementary DNA sequences were selected from a resource of tentatively identified clones from a porcine small intestine cDNA library. Forty PCR primer pairs were designed to amplify 101-309 base pairs of the 3' untranslated region of the genes. The PCR conditions were optimized by altering both formamide and magnesium concentrations on samples of pig, mouse, and hamster DNA. Twenty primer pairs that, under stringent conditions, were pig-specific and amplified the expected fragments were chosen for regional assignment in a pig/rodent hybrid cell panel. Furthermore, 22 primer pairs were chosen to amplify DNA from the parental animals of the PiGMaP shared reference families in order to detect possible polymorphisms. Primer pairs that generated polymorphisms were used for genetic mapping. A total of 22 porcine expressed sequence tags (ESTs) were cytogenetically or genetically mapped by this approach. Twelve of the mapped ESTs could be added to the human-porcine comparative map.

Genetical and physical assignments of equine microsatellites--first integration of anchored markers in horse genome mapping

Twenty equine microsatellites were isolated from a genomic phage library, and their genetical and physical localization was sought by linkage mapping and fluorescent in situ hybridization (FISH). Nineteen of the markers were found to be polymorphic with, in most cases, heterozygosities exceeding 50%. The markers were mapped in a Swedish reference family for gene mapping, comprising eight half-sib families from Standardbred and Icelandic horse sires. Segregation was analyzed against a set of 35 other markers typed in the pedigree. Thirteen of the microsatellites showed linkage to at least one other marker, with a total of 21 markers being involved in these linkages. In parallel, 18 of the microsatellites could be assigned to their chromosomal region by FISH. These assignments involved eight equine autosomes: ECA1, 2, 4, 6, 9, 10, 15, and 16. The genetical and physical mappings revealed by this study represent a significant extension of the current knowledge of the equine genome map.

Mapping of microsatellite markers developed from a flow-sorted swine chromosome 6 library

Swine Chromosome (Chr) 6-enriched libraries, generated with size-fractionated DNA isolated from chromosomes sorted by flow cytometry, have been used to develop new Chr 6 microsatellite markers. Chromosome isolation procedures were established to reproducibly prepare high quality chromosomes from phytohemagglutinin (PHA)-stimulated swine peripheral blood lymphocytes and to sort individual chromosomes after staining with Hoechst 33258 and chromomycin A3. Chromosome purity was verified by specific staining of swine Chr 6 with fluorescence in situ hybridization (FISH) by use of painting probes generated by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) amplification of as few as 300 sorted Chr 6. For library construction, DNA was extracted from flow-sorted pools representing Chr 6, amplified, size selected for fragments from 300 to 700 bp, and ligated into pBluescript SK II+ or Lambda ZAP Express. The libraries were then screened with a radiolabeled poly-(dCA) DNA probe. Of 107 (CA)n repeat-containing clones verified by sequencing, 21 were polymorphic and used to genotype the University of Illinois swine reference families. Linkage analysis was then performed with CRIMAP 2.4 (LOD > 3.0), and the results showed that 15 of the microsatellites mapped to swine Chr 6. At least three of these new markers map to locations where there were gaps in the consensus Chr 6 map. Another four markers, because of their PIC values, should provide more informative markers in other areas of the map. Most of the new markers can also be used for automated genotyping with fluorescent labeling. This set of 15 new Chr 6 markers will, therefore, be useful in helping to define QTL associated with swine Chr 6.

A second-generation linkage map of the bovine genome

We report a bovine linkage map constructed with 1236 polymorphic DNA markers and 14 erythrocyte antigens and serum proteins. The 2990-cM map consists of a sex-specific, X chromosome linkage group and 29 sex-averaged, autosomal linkage groups with an average interval size of 2.5 cM. The map contains 627 new markers and 623 previously linked markers, providing a basis for integrating the four published bovine maps. Orientation and chromosomal assignment of all the linkage groups, except BTA20 and BTA22, was provided by 88 markers that were assigned previously to chromosomes. This map provides sufficient marker density for genomic scans of populations segregating quantitative trait loci (QTL) and subsequent implementation of marker-assisted selection (MAS) mating schemes.

The human obesity gene map: the 1996 update

An update of the human obesity gene map up to October 1996 is presented. Evidence from Mendelian disorders exhibiting obesity as a clinical feature, single-gene mutation rodent models, quantitative trait loci uncovered in crossbreeding experiments with mouse, rat, and pig models, association and case-control studies with candidate genes, and linkage studies with genes and other markers is reviewed. All chromosomal locations of the animal loci are converted into human genome locations based on syntenic relationships between the genomes. A complete listing of all these loci reveals that only 4 of the 24 human chromosomes are not yet represented, i.e., 9, 18, 21, and Y. Several chromosome arms are characterized by the presence of several putative loci. The following arms include at least three such loci: 1p, 1q, 3p, 4q, 6p, 7q, 8p, 8q, 11p, 11q, 15q, 20q, and Xq. Studies with negative association and linkage results are also reviewed.

Toward genetic dissection of high and low antibody responsiveness in Biozzi mice

Several distinct chromosomal segments were recently identified by cosegregation analysis of polymorphic markers with antibody responsiveness in an F2 cross between high (H) and low (L) antibody responder lines of Biozzi mice. The effect associated with the relevant markers has now been investigated in backcross populations (toward the L line) bred from H and L mice made coisogenic at the H-2 locus. The antibody titers, measured on days 5 and 14 of the primary response to sheep red blood cells, were considered to be two distinct quantitative phenotypes. The results of single or multilocus analyses demonstrated the significant involvement, at one or the two titration times, of Im gene(s) on four distinct chromosomes: 4, 8, 12, and 18. The regions on chromosomes 6 and 10 have a lesser but still suggestive effect. The contribution of each locus ranged from 3% to 13%, and together these loci accounted for about 40% of the phenotypic variance at each titration time. The data are compatible with an additive effect of the relevant loci and suggestive of some interaction effects. In a second backcross toward L line, the H line alleles of the putative Im genes on chromosomes 6, 8, and 12 were isolated from each other and their effects were still detected.

Genetics of obesity in humans and animal models

Human obesity has a significant genetic component which contributes to the risk for this disorder. The application of molecular genetic techniques to identify these genes using a variety of approaches, including information from animal models, will help clarify the role of specific genes in the etiology of human obesity. Identification of these genetic mechanisms is likely to lead to new approaches, both pharmacologic and nonpharmacologic, for the prevention and treatment of this disease.

Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor

Comparative mapping data suggested that the dominant white coat color in pigs may be due to a mutation in KIT which encodes the mast/stem cell growth factor receptor. We report here that dominant white pigs lack melanocytes in the skin, as would be anticipated for a KIT mutation. We found a complete association between the dominant white mutation and a duplication of the KIT gene, or part of it, in samples of unrelated pigs representing six different breeds. The duplication was revealed by single strand conformation polymorphism (SSCP) analysis and subsequent sequence analysis showing that white pigs transmitted two nonallelic KIT sequences. Quantitative Southern blot and quantitative PCR analysis, as well as fluorescence in situ hybridization (FISH) analysis, confirmed the presence of a gene duplication in white pigs. FISH analyses showed that KIT and the very closely linked gene encoding the platelet-derived growth factor receptor (PDGFRA) are both located on the short arm of Chromosome (Chr) 8 at band 8p12. The result revealed an extremely low rate of recombination in the centromeric region of this chromosome, since the closely linked (0.5 cM) serum albumin (ALB) locus has previously been in situ mapped to the long arm (8q12). Pig Chr 8 shares extensive conserved synteny with human Chr 4, but the gene order is rearranged.

Characterization of 42 highly polymorphic bovine microsatellite markers

We have isolated 42 highly polymorphic microsatellite (GT/CA)n markers from Japanese black cattle Wagyu (Bos taurus). Forty-one of the markers were assigned to bovine autosomes with lod scores > 6, through linkage analyses performed on the International Bovine Reference Family Panel (IBRP). The remaining marker showed X-linked inheritance. These markers exhibited an average heterozygosity value of 0.67 with between four and 17 alleles on the IBRP.

Livestock genomics comes of age

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DNA polymorphisms of lipogenesis genes and analysis of linkage with fatness in turkeys

DNA variability of lipogenesis genes was evaluated by Restriction Fragment Length Polymorphism (RFLP) on four selected lines of turkeys. Thirteen polymorphisms were obtained, four on the acetyl-coenzyme A carboxylase gene, one on the apoprotein AI gene, two on the malic enzyme gene, four on the fatty acid synthase gene, and two on the stearoyl-coenzyme A mesaturase gene. Six of these RFLP were studied in more detail on 64 female turkeys sampled in two lines. Large differences in terms of number of DNA profiles and haplotype frequencies were observed between the two genes, in accordance with the variability of recorded fatness performances. An additive model including the effects of RFLP profiles was used to assess linkage between polymorphisms on lipogenesis genes and fatness measured either in vivo by an ultrasonic instrument or, after slaughter, by the ratio of skin plus subcutaneous fat weight to the whole leg weight. In each line, two polymorphisms suggested a statistical association with fat deposit, one on the malic enzyme gene detected by DNA digestion with HindIII and one on the fatty acid synthase gene detected by MspI. A multiple comparison of means associated with each RFLP profile enabled the identification of two lean profiles in one strain, and a fat profile in the other.

Prospects for development of genetic markers for resistance to gastrointestinal parasite infection in sheep

Selection of sheep for resistance to internal parasites represents a viable option for future parasite control. Many phenotypic measures are available for determining the level of infection in individual sheep, although no phenotypic markers are available which allow prediction of an individual's resistance status. Genetic markers are therefore the best way to incorporate parasite resistance into selection programmes. With the recent development of genetic maps, several experiments are underway to search for markers linked to parasite-resistance genes in sheep. It can be predicted confidently that markers associated with resistance will be discovered within 12 months. Markers useful as selection criteria will be available within 5 years, although considerable quantitative genetic analysis needs to be done to find the best way to utilise marker information in selection programmes. In future, methods for differential DNA analysis or mRNA expression will lead to isolation of the genes involved.

A comprehensive linkage map of the pig based on a wild pig-Large White intercross

A comprehensive linkage map, including 236 linked markers with a total sex-average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to approximately all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK-HPX) to chromosome 9. The linkage map includes 77 types I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1.4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.

Evaluation and characterization of a porcine small intestine cDNA library: analysis of 839 clones

A porcine small intestine directionally cloned cDNA library was constructed in the vector lambda Zap II. Clones were hybridized with total labeled cDNA such that putative high-copy number transcripts could be differentiated from middle- and low-copy number transcripts prior to selection and characterization by DNA sequencing. More than 2000 non-hybridizing and 242 hybridizing clones were collected. In total, 839 clones were sequenced from the 3' end of the cDNA, and after inter-clone comparison, the unique clones were sequenced from the 5' end of the cDNA. The 5' data were used to query the sequence in databases and resulted in the identification of 630 different gene transcripts, of which 604 are new porcine genes. The identity of 361 transcripts could be identified from sequence comparison studies. The validity of this semi-random selection approach was verified by the identification of a large number of unique transcripts.

Porcine linkage and cytogenetic maps integrated by regional mapping of 100 microsatellites on somatic cell hybrid panel

Recently two main genetic maps [Rohrer et al. Genetics 136, 231 (1994); Archibald et al. Mamm. Genome 6, 157 (1995)] and a cytogenetic map [Yerle et al. Mamm. Genome 6, 175 (1995)] for the porcine genome were reported. As only a very few micro-satellites are located on the cytogenetic map, it appears to be important to increase the relationships between the genetic and cytogenetic maps. This document describes the regional mapping of 100 genetic markers with a somatic cell hybrid panel. Among the markers, 91 correspond to new localizations. Our study enabled the localization of 14 new markers found on both maps, of 54 found on the USDA map, and of 23 found on the PiGMaP map. Now 21% and 43% of the markers on the USDA and PiGMaP linkage maps respectively are physically mapped. This new cytogenetic information was then integrated within the framework of each genetic map. The cytogenetic orientation of the USDA linkage maps for Chromosomes (Chrs) 3, 8, 9, and 16 and of PiGMaP for Chr 8 was determined. USDA and PiGMaP linkage maps are now oriented for all chromosomes, except for Chrs 17 and 18. Moreover, the linkage group "R" from the USDA linkage map was assigned to Chr 6.

Integration of the PiGMaP and USDA maps for porcine chromosome 14

In order to align two previously published genetic linkage maps, a set of four of the United States Department of Agriculture (USDA) microsatellite linkage markers was mapped in the International Pig Gene Mapping Project (PiGMaP) reference families. Two-point linkage analysis was used between these USDA markers and the set of genes and markers previously mapped on the PiGMaP chromosome 14 map. Markers with threshold lod scores of three or greater were used for multipoint map construction. The USDA and PigGMaP linkage maps of chromosome 14 were aligned using the four USDA microsatellite markers along with three markers that are common to both maps. The PiGMaP genetic linkage map order for chromosome 14 was confirmed and the map was expanded to 193 cM with addition of the new markers.

Cloning and characterization of 414 polymorphic porcine microsatellites

We report the sequences, sizes, and number of alleles of 414 new porcine microsatellites that were cloned in our laboratory and 21 microsatellites derived from GenBank DNA sequences. We also confirm the usefulness of porcine microsatellite primer pairs derived from short interdispersed elements.

A comprehensive map of the porcine genome

We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups (18 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization (FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on 11q1.7-qter and 14 cen-q1.2. Recombination rates (cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci (QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

A comparative map of the porcine and human genomes demonstrates ZOO-FISH and gene mapping-based chromosomal homologies

ZOO-FISH with chromosome-specific DNA libraries (CSLs) from individual flow-sorted human chromosomes was applied on porcine metaphase chromosomes to establish segment homology between the pig and human karyotypes. Forty-seven porcine chromosomal segments corresponding to all human chromosomes except the Y were delineated, resulting in a nearly complete coverage of the porcine karyotype. The syntenic segments detected were further confirmed by the gene mapping information available in the two species. A map demarcating physical boundaries of human homologies on individual pig chromosomes is complemented with a detail survey of the physical and genetic linkage mapping data in the two species. The resultant map, thus, provides a comprehensive and updated comparative status of the human and porcine genomes.

Zoo-FISH delineates conserved chromosomal segments in horse and man

Human chromosome specific libraries (CSLs) were individually applied to equine metaphase chromosomes using the fluorescence in situ hybridization (FISH) technique. All CSLs, except Y, showed painting signals on one or several horse chromosomes. In total 43 conserved chromosomal segments were painted. Homoeology could not, however, be detected for some segments of the equine genome. This is most likely related to the very weak signals displayed by some libraries, rather than to the absence of similarity with the human genome. In spite of divergence from the human genome, dated 70-80 million years ago, a fairly high degree of synteny conservation was observed. In seven cases, whole chromosome synteny was detected between the two species. The comparative painting results agreed completely with the limited gene mapping data available in horses, and also enabled us provisionally to assign one linkage group (U2) and one syntenic group (NP, MPI, IDH2) to specific equine chromosomes. Chromosomal assignments of three other syntenic groups are also proposed. The findings of this study will be of significant use in the expansion of the hitherto poorly developed equine gene map.

Assignment of 19 porcine type I loci by somatic cell hybrid analysis detects new regions of conserved synteny between human and pig

Nineteen so-called type I-loci, including ACO2, ADRA2, CAST, CCK, CHAT, IGKC, IGLV, IL4, IL6, INHA, LIF, MX1, PTH, RBP2, TCRA, TCRB, TGFB2, TGFB3, and UOX have been mapped in the pig with an informative somatic cell hybrid panel. By analyzing these new assignments in the knowledge of heterologous chromosome painting (Zoo-FISH) data for the porcine genome, it is possible to predict subchromosomal locations for most of these loci. Previously defined regions of conserved synteny were confirmed, and the extent of six of these regions was refined. These improvements in the porcine gene map facilitate the transfer of gene mapping data from "map-rich" species such as humans and mice.

Genes and obesity

Several twin and adoption studies as well as animal models have confirmed that obesity has a strong genetic component. It is apparent that obesity in humans has a complex polygenic background; that is, the phenotype is determined by an unknown number of genes together with environmental factors. However, there may well be single genes playing a major role within certain families, but the gene may vary from family to family. Two interesting gene candidates have been found in mouse experiments, the ob and the db gene, the products of which are probably a satiety hormone and its receptor, respectively, which regulate food intake. The recent cloning of the ob gene and its human homologue constitute a major breakthrough in this field. The 16-kD protein encoded by the ob gene is called leptin, and is well conserved among vertebrate species. The pig could be a valuable large animal model for human obesity. A fatness locus has been mapped to pig chromosome 4 and most probably a similar locus resides on human chromosome 1q. A more precise definition of the pig-human homology as regards this region is currently being investigated.

The estrogen receptor locus is associated with a major gene influencing litter size in pigs

Identification of individual major genes affecting quantitative traits in livestock species has been limited to date. By using a candidate gene approach and a divergent breed cross involving the Chinese Meishan pig, we have shown that a specific allele of the estrogen receptor (ER) locus is associated with increased litter size. Female pigs from synthetic lines with a 50% Meishan background that were homozygous for this beneficial allele produced 2.3 more pigs in first parities and 1.5 more pigs averaged over all parities than females from the same synthetic lines and homozygous for the undesirable allele. This beneficial ER allele was also found in pigs with Large White breed ancestory. Analysis of females with Large White breed background showed an advantage for females homozygous for the beneficial allele as compared to females homozygous for the other allele of more than 1 total pig born. Analyses of growth performance test records detected no significant unfavorable associations of the beneficial allele with growth and developmental traits. Mapping of the ER gene demonstrated that the closest known genes or markers were 3 centimorgans from ER. To our knowledge, one of these, superoxide dismutase gene (SOD2), was mapped for the first time in the pig. Analysis of ER and these linked markers indicated that ER is the best predictor of litter size differences. Introgression of the beneficial allele into commercial pig breeding lines, in which the allele was not present, and marker-assisted selection for the beneficial allele in lines with Meishan and Large White background have begun.

Chromosomal mapping of genetic loci associated with non-insulin dependent diabetes in the GK rat

Goto-Kakizaki (GK) rats are a well characterized model for non-insulin dependent diabetes mellitus (NIDDM). We have used a combination of physiological and genetic studies to identify quantitative trait loci (QTLs) responsible for the control of glucose homeostasis and insulin secretion in a F2 cohort bred from spontaneously diabetic GK rats. The genetic dissection of NIDDM allowed us to map up to six independently segregating loci predisposing to hyperglycaemia, glucose intolerance or altered insulin secretion, and a seventh locus implicated in body weight. QTLs implicated in glucose tolerance and adiposity map to the same region of rat chromosome 1, and may indicate the influence of a single locus. Our study demonstrates that distinct combinations of genetic loci are responsible for different physiological characteristics associated with the diabetic phenotype in the GK rat, and it constitutes an important step for directing the search for the genetic factors involved in human NIDDM.

First international workshop on porcine chromosome 6. Report and abstracts

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.

Evaluating genetic models of cognitive evolution and behaviour

Cognitive evolution can be studied at several different levels, ranging from complex societies of interdependent persons to the DNA molecules coding for enzymes that synthesize neurotransmitter molecules. Genetic models of cognitive evolution can be fairly evaluated only if they involve one or two genetic loci, maybe three loci if a massive investment of resources is made. If a simple genetic model is seriously proposed, it ought to be tested by genetic linkage analysis so that future theorizing can be guided and constrained by facts. For more complex behavioural characteristics based on large numbers of genes and intricate interrelations with the environment, genetic analysis and genetic theories are not likely to yield conclusive results. Instead, studying individual differences in the brain and neural correlates of cognitive processes will likely provide more rapid progress toward a deeper understanding of evolution.

Livestock QTLs--bringing home the bacon?

Markers have been used for some time to study the genetic control of economically important traits in livestock. The early work was based on single loci and detected some significant effects, but results were often inconsistent across studies. Now that complete microsatellite-based maps of the major species are becoming available, more complete and rigorous scans of the genome are possible. The first of these have detected some surprisingly large effects, both within breeds and in breed crosses. As research workers digest these results and their implications for livestock breeding programmes and ponder further research, commercial breeding companies have already started applying the first fruits of marker research to breed a better animal.

Genetic variation at the growth hormone locus in a wild pig intercross; test of association to phenotypic traits and linkage to the blood group D locus

A polymorphism in the TATA-box of the porcine growth hormone (GH) gene was analysed in a wild pig/Large White intercross, in which 129 markers had been scored previously. Linkage analyses demonstrated that the GH locus belonged to a linkage group on chromosome 12 together with a previously unassigned marker, the erythrocyte antigen D (EAD) locus. The linear order of this linkage group is EAD-GH-S0096-S0090-S0106-arachidonate 12-lipoxygenase (ALOX12)-inhibin beta A (INHBA). The length of the linkage group was estimated at 93 cM (sex average). The effects of the GH genotype on growth and fat deposition traits were investigated using phenotypic data from the 191 F2 animals. No significant effect of GH was detected, and we therefore conclude that this locus does not play a major role in defining the genetic differences between the wild and Large White pigs for these traits.

Molecular dissection of quantitative traits: progress and prospects

QTL mapping is an increasingly useful approach to the study and manipulation of complex traits important in agriculture, evolution, and medicine. The molecular dissection of quantitative phenotypes, supplementing the principles of classical quantitative genetics, is accelerating progress in the manipulation of plant and animal genomes. A growing appreciation of the similarities among different organisms and the usefulness of comparative genetic information is making genome analysis more efficient, and providing new opportunities for using model systems to overcome the limitations of less-favorable systems. The expanding repertoire of techniques and information available for studying heredity is removing obstacles to the cloning of QTLs. Although QTL mapping alone is limited to a resolution of 0.1%-1.0% of a genome, use of QTL mapping in conjunction with a search for mapped candidate genes, with emerging technologies for isolation of genes expressed under conditions likely to account for the quantitative phenotype, and with ever more efficient megabase DNA manipulation and characterization bodes well for the prospect of isolating the genetic determinants of QTLs in the foreseeable future. In the words of Thoday (1961), "An extensive attack on quantitative genetics made from this point of view as well as the biometric approach should be a great help in answering questions concerning the nature of polygenes...."

Osteochondrosis in wild boar-Swedish Yorkshire crossbred pigs (F2 generation)

Osteochondrotic lesions occur in very high frequency in growing pigs of all commercial breeds and are claimed to be associated with high growth rate, and not to occur, or to be milder, in slow-growing pigs. The present study monitored the magnitude and distribution of osteochondrotic lesions in a crossbred pig population of wild boar and Swedish Yorkshire ancestry. In this population, having a low growth rate, the distribution and extent of osteochondrotic lesions was similar to that of purebred Swedish Yorkshire pigs, and only weak relationships between the studied growth parameters and osteochondrosis could be found.

A small-insert bovine genomic library highly enriched for microsatellite repeat sequences

A bovine genomic phagemid library was constructed with randomly sheared DNA. Enrichment of this single-stranded DNA library with CA or GT primers resulted in 45% positive clones. The 14% of positive clones with (CA.GT) > 12, and not containing flanking repetitive elements, were sequenced, and the efficiency of marker production was compared with random M13 bacteriophage libraries. Primer sequences and genotyping information are presented for 390 informative bovine microsatellite markers. The genomic frequency for 11 tri- and tetranucleotide repeats was estimated by hybridization to a lambda genomic library. Only GCT, GGT, and GGAT were estimated to have a frequency of > 100 per genome. Enrichment of the phagemid library for these repeats failed to provide a viable source of microsatellite markers in the bovine. Comparison of map interval lengths between 100 markers from the enriched library prepared from randomly sheared DNA and M13 bacteriophage libraries prepared from Mbo1 restriction digests suggested no bias in skeletal genomic coverage based on source of small insert DNA. In conclusion, enrichment of the bovine phagemid library provides a sufficient source of microsatellites so that small repeat lengths and flanking repetitive sequences common in the bovine can be eliminated, resulting in a high percentage of informative markers.

Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci

Independent domestication of sorghum, rice, and maize involved convergent selection for large seeds, reduced disarticulation of the mature inflorescence, and daylength-insensitive flowering. These similar phenotypes are largely determined by a small number of quantitative trait loci (QTLs) that correspond closely in the three taxa. The correspondence of these QTLs transcends 65 million years of reproductive isolation. This finding supports models of quantitative inheritance that invoke relatively few genes, obviates difficulties in map-based cloning of QTLs, and impels the comparative mapping of complex pheno-types across large evolutionary distances, such as those that separate humans from rodents and domesticated mammals.

A biometrical genome search in rats reveals the multigenic basis of blood pressure variation

A genome-wide search for multiple loci influencing salt-loaded systolic blood pressure (NaSBP) variation among 188 F2 progeny from a cross between the Brown-Norway and spontaneously hypertensive rat strains was pursued in an effort to gain insight into the polygenic basis of blood pressure regulation. The results suggest that loci within five to six genomic regions collectively explain approximately 43% of the total NaSBP variation exhibited among the 188 F2 progeny. Many of these loci are in regions that previous studies have not implicated in blood pressure regulation. Ultimately, however, this study not only sheds light on the multigenic basis of blood pressure but provides further evidence that the identification of the genetic determinants of polygenic traits in mammals is possible with modern biometrical and molecular genetic tools in controlled settings (i.e., breeding paradigm and model organism).

Genetic variation on chromosome 1 associated with variation in body fat distribution in men

BACKGROUND

Interindividual variation in fat deposition in swine is determined by loci on porcine chromosome 4, which are contained in a region that is syntenic with part of the long arm of human chromosome 1. We hypothesized that genomic variation of chromosome 1q would be associated with variation in the ratio of waist-to-hip circumference in male North American Hutterites, a genetic isolate characterized by significant relatedness and sharing of environmental factors.

METHODS AND RESULTS

In 316 male Hutterites, we tested for phenotype-genotype association of two DNA polymorphisms on chromosome 1q and the ratio of waist-to-hip circumference. We included control loci on 10 other chromosomes in the multivariate model. We observed that DNA variation on chromosome 1q was significantly associated with variation in the ratio of waist-to-hip circumference in men (P = .0029).

CONCLUSIONS

The association of DNA variation chromosome 1q with the ratio of waist-to-hip circumference in male Hutterites suggests that there are important structural elements in this genomic region that have a functional impact on body fat distribution.

Marker assisted selection for genetic improvement of animal populations when a single QTL is marked

A Monte Carlo simulation study to evaluate the benefits of marker assisted selection (MAS) in small populations with one marked bi-allelic quantitative trait locus (QTL) is described. In the base generation, linkage phase equilibrium between the markers, QTL and polygenes was assumed and frequencies of 0.5 for the two QTL alleles were used. Six discrete generations of selection for a single character measured on both sexes followed. An additive genetic model was used with the QTL positioned midway between two highly polymorphic markers. Schemes were simulated with a distance of 10 cM between the QTL and either of the two markers and with the QTL explaining 1/8 of the total genetic variance in the base generation. Values of 0.5, 0.25 or 0.1 were assumed for the heritability. Eight males and 16, 32 or 64 females were selected each generation with each dam producing four sons and four daughters as candidates for the next generation. Animals were evaluated with a conventional BLUP animal model or with a model using marker information. MAS resulted in substantially higher QTL responses (4-54%), especially with low heritabilities, than conventional BLUP but lower polygenic responses (up to 4%) so that the overall effect on the total genetic response, although in the majority of cases favourable, was relatively small. With QTLs of larger size (explaining 25% of the genetic variance) comparable results were found. When the distance between the QTL and the markers was reduced to 2 cM, genetic responses were increased very slightly with a heritability of 0.5 whereas with a heritability of 0.1 responses were increased by up to 10%, compared with conventional BLUP. Results emphasize that MAS should be most useful for lowly heritable traits and that once QTLs for such traits have been identified the search for closely linked polymorphic markers should be intensified.

Sheep linkage mapping: RFLP markers for comparative mapping studies

Restriction fragment length polymorphisms (RFLPs) detected using cDNA probes for conserved genes provide an important set of markers that anchor or link syntenic groups in a range of divergent mammalian species. DNA probes from sheep, cattle, pig, human and mouse were screened against sheep DNA samples and 24 new RFLP markers for sheep were identified. Among the loci tested, 22 had a homologue that has been mapped in humans. An RFLP for fibronectin (FN1) was linked to alpha-inhibin (INHA) at a distance of 5cM. The FN1 locus has been assigned to sheep chromosome 2q41-q44 and linkage between FN1 and INHA assigns INHA to the same chromosome in sheep. In addition to the new loci reported here, 28 RFLPs have been published previously by this group and these are collated together with RFLPs published from other laboratories. RFLPs have been reported for 86 loci in sheep. Fifty-four loci have been mapped to 16 different chromosomes.

Chromosomal assignment of seventeen porcine microsatellites and genes by use of a somatic cell hybrid mapping panel

Swine-specific sequence tagged (microsatellite) sites, STS and STMS, were assigned chromosomally by polymerase chain reaction analysis of a somatic cell hybrid panel. This study confirms the localization from genetic mapping of seven anonymous microsatellites and the genes ANPEP, ATP2, CGA, DAGK, FSHB, IFNG, IGF1, IL1B and SPP1. New assignment for the gene BNP1 to chromosome 6 is reported. The confirmed and the new assignments extend the information of the previously established linkage maps and provide framework loci on which to order additional informative markers.

The porcine intestinal receptor for Escherichia coli K88ab, K88ac: regional localization on chromosome 13 and influence of IgG response to the K88 antigen

The loci encoding the porcine intestinal receptors for Escherichia coli K88ab and K88ac (K88abR and K88acR) were firmly assigned to chromosome 13 by linkage analysis using a three-generation pedigree. The linear order of these loci and seven other markers on chromosome 13 was determined by multipoint analyses. The K88abR and K88acR loci were tightly linked (theta = 0.01, zeta = 41.06) with the K88abR locus localized 7.4 cM (sex average) proximal to the transferrin locus. The results, together with previous reports from two other groups, provide an unequivocal assignment of the K88 receptor loci to chromosome 13, and reject a previous assignment to chromosome 4. Pigs possessing the receptor had a slightly higher specific IgG response to the K88 antigen after an intramuscular immunization with an E. coli vaccine.

Structure of the gene for porcine peptide antibiotic PR-39, a cathelin gene family member: comparative mapping of the locus for the human peptide antibiotic FALL-39

PR-39 is a porcine 39-aa peptide antibiotic composed of 49% proline and 24% arginine, with an activity against Gram-negative bacteria comparable to that of tetracycline. In Escherichia coli, it inhibits DNA and protein synthesis. PR-39 was originally isolated from pig small intestine, but subsequent cDNA cloning showed that the gene is expressed in the bone marrow. The open reading frame of the clone showed that PR-39 is made as 173-aa precursor whose proregion belongs to the cathelin family. The PR39 gene, which is rather compact and spans only 1784 bp has now been sequenced. The coding information is split into four exons. The first exon contains the signal sequence of 29 residues and the first 37 residues of the cathelin propart. Exons 2 and 3 contain only cathelin information, while exon 4 codes for the four C-terminal cathelin residues and the mature PR-39 peptide extended by three residues. The sequenced upstream region (1183 bp) contains four potential recognition sites for NF-IL6 and three for APRF, transcription factors known to regulate genes for both cytokines and acute phase response factors. Genomic hybridizations revealed a fairly high level of restriction fragment length polymorphism and indicated that there are at least two copies of the PR39 gene in the pig genome. PR39 was mapped to pig chromosome 13 by linkage and in situ hybridization mapping. The gene for the human peptide antibiotic FALL-39 (also a member of the cathelin family) was mapped to human chromosome 3, which is homologous to pig chromosome 13.

Combined genetic and physiological analysis of a locus contributing to quantitative variation

The natural variation of many traits is controlled by multiple genes, individually referred to as quantitative trait loci (QTL), that interact with the environment to determine the ultimate phenotype of any individual. A QTL has yet to be described molecularly, in part because strategies to systematically identify them are underdeveloped and because the subtle nature of QTLs prevents the application of standard methods of gene identification. Therefore, it will be necessary to develop a systematic approach(es) for the identification of QTLs based upon the numerous positional data now being accumulated through molecular marker analyses. We have characterized a QTL by the following three-step approach: (1) identification of a QTL in complex populations, (2) isolation and genetic mapping of this QTL in near-isogenic lines, and (3) identification of a candidate gene using map position and physiological criteria. Using this approach we have characterized a plant height QTL in maize that maps to chromosome 9 near the centromere. Both map position and physiological criteria suggest the gibberillin biosynthesis gene dwarf3 as a candidate gene for this QTL.