DNA fingerprints of chickens selected for high and low body weight for 31 generations

Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds

Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.

Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Sixty years, constituting 60 generations, have passed since the founding of the Virginia body weight lines, an experimental population of White Plymouth Rock chickens. Using a stringent breeding scheme for divergent 8-week body weight, the lines, which originated from a common founder population, have responded to bidirectional selection with an approximate 15-fold difference in the selected trait. They provide a model system to study the genetics of complex traits in general and the influences of artificial selection on quantitative genetic architectures in particular. As we reflect on the 60th anniversary of the initiation of the Virginia body weight lines, there is opportunity to discuss the findings obtained using different analytical and experimental genetic and genomic strategies and integrate them with a recent pooled genome resequencing dataset. Hundreds of regions across the genome show differentiation between the 2 lines, reinforcing previous findings that response to selection relied on standing variation across many genes and giving insights into the haplotype complexity underlying regions associated with body weight.

Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens

Background

Scaleless (sc/sc) chickens carry a single recessive mutation that causes a lack of almost all body feathers, as well as foot scales and spurs, due to a failure of skin patterning during embryogenesis. This spontaneous mutant line, first described in the 1950s, has been used extensively to explore the tissue interactions involved in ectodermal appendage formation in embryonic skin. Moreover, the trait is potentially useful in tropical agriculture due to the ability of featherless chickens to tolerate heat, which is at present a major constraint to efficient poultry meat production in hot climates. In the interests of enhancing our understanding of feather placode development, and to provide the poultry industry with a strategy to breed heat-tolerant meat-type chickens (broilers), we mapped and identified the sc mutation.

Results

Through a cost-effective and labour-efficient SNP array mapping approach using DNA from sc/sc and sc/+ blood sample pools, we map the sc trait to chromosome 4 and show that a nonsense mutation in FGF20 is completely associated with the sc/sc phenotype. This mutation, common to all sc/sc individuals and absent from wild type, is predicted to lead to loss of a highly conserved region of the FGF20 protein important for FGF signalling. In situ hybridisation and quantitative RT-PCR studies reveal that FGF20 is epidermally expressed during the early stages of feather placode patterning. In addition, we describe a dCAPS genotyping assay based on the mutation, developed to facilitate discrimination between wild type and sc alleles.

Conclusions

This work represents the first loss of function genetic evidence supporting a role for FGF ligand signalling in feather development, and suggests FGF20 as a novel central player in the development of vertebrate skin appendages, including hair follicles and exocrine glands. In addition, this is to our knowledge the first report describing the use of the chicken SNP array to map genes based on genotyping of DNA samples from pooled whole blood. The identification of the sc mutation has important implications for the future breeding of this potentially useful trait for the poultry industry, and our genotyping assay can facilitate its rapid introgression into production lines.

Genetic distances estimated from DNA fingerprints in crosses of white Plymouth Rock chickens

Crosses were produced between two lines of White Plymouth Rock chickens, one of which had been selected for low 8-week body weight for 31 generations (L) and the other of which was a bantam population (B). The parental lines, reciprocal F1s, reciprocal F2s and all possible back-crosses to each parental line (total of 16 populations) were available for study. Blood was obtained from 10 females within each population. DNA was extracted from blood mixes (equal amounts of blood from each individual) for each population, and from blood samples of each individual in the two parental lines. Fourteen line-specific DNA fingerprint (DFP) bands (those bands present in one parental population, but not in the other parental population) were analysed (eight from line L and six from line B). Regression analyses were conducted to compare the known proportion of genomic contribution from each parental population with values based on relative band intensity obtained with a scanning densitometer. The resulting regression coefficient of 1.004 demonstrated that DFP analysis of relative band intensity is an effective method of estimating the relative proportion of genome contributed by parental populations.

DNA fingerprints of farm animals generated by microsatellite and minisatellite DNA probes

A multi-locus DNA probe, R18.1, derived from a bovine genomic library, detected DNA fingerprints of highly polymorphic loci in hybridization to genomic DNA from poultry and sheep, and of moderate polymorphic loci in cattle and human DNA. The average numbers of detected bands in chickens and sheep were 27.8 and 21.4, and the average band sharing levels were 0.25 and 0.33, respectively. In hybridization to cattle and human DNA, the results were less polymorphic; nevertheless, individual identification is feasible using probe R18.1. The results obtained by R18.1 were compared to results obtained by Jeffreys minisatellite probe 33.6 and two microsatellite oligonucleotides, (GT)12 and (GTG)5. The total number of detected loci using probes R18.1 and 33.6 were estimated in chickens through family analysis of broilers and the maximal number of detectable loci was calculated.

Genetic characteristics of the ostrich population using molecular methods

A genetic analysis was performed on Polish ostriches from the 3 principal ostrich breeds: red-, blue-, and black-necks. The analysis was based on 2 molecular methods: DNA fingerprinting and microsatellites. The DNA fingerprinting patterns were obtained using the restriction enzyme HinfI and Jeffrey's 33.15 probe. The second method consisted of a PCR procedure, for which 5 VIAS-OS primers specific to the ostrich were used. The PCR products were separated on polyacrylamide gel using ALFexpress (Authomated Laser Fluorescent DNA Sequencer). The study aimed at assessing the genetic variability within and among the 3 ostrich breeds as well as evaluating the genetic distance between them, and represents the first report on the genetic characteristics of the ostrich breeds. The results obtained by both methods showed considerable compatibility, especially with regard to the relationship among the breeds analyzed. The diversity within breeds, obtained on the basis of the DNA fingerprinting analysis, proved to be low. Among the ostrich populations analyzed, the highest variability potential was observed for black-necked ostriches (the mean diversity of patterns amounted to 29.04%, whereas the mean heterozygosity was 0.30) and the lowest was observed for the red-necks. The largest genetic similarity was recorded between red- and blue-necked ostriches, but the greatest genetic distance was between the red- and black-necks. This means that the use of birds of those breeds in crosses should result in the highest heterotic effect. Both of these methods measured the genetic distance between the analyzed ostrich breeds that was expected from the geographic origin of these birds. The results obtained in the present study showed that both analytic methods used can be successfully applied when elaborating on the genetic characteristics of the ostrich.

Analysis of Chicken TLR4, CD28, MIF, MD-2, and LITAF Genes in a Salmonella enteritidis Resource Population

Salmonella enteritidis is a foodborne pathogen that negatively affects both animal and human health. Genetic variations in response to pathogenic SE colonization or to SE vaccination were measured in a chicken resource population. Outbred broiler sires and 3 diverse, highly inbred dam lines produced 508 F1 progeny that were evaluated for either bacterial colonization after pathogenic SE inoculation or circulating antibody level after SE vaccination. Five candidate genes were selected for study, based on their biological function as possibly affecting response to SE: toll-like receptor 4 (TLR4), T-cell specific surface protein (CD28), macrophage migration inhibitory factor (MIF), MD-2, and lipopolysaccharide-induced tumor necrosis factor (TNF)-alpha factor (LITAF). Gene fragments were sequenced from the founder lines of the resource population. The LITAF and MIF genes were homozygous for all sires. Single nucleotide polymorphisms (SNP) were identified in 3 genes (TLR4, CD28, and MD-2) and were used to test for associations of sire SNP with SE response. Linear mixed models were used for statistical analyses. The CD28 broiler sire SNP was associated with both bacterial load in the cecum (P < 0.003) and vaccine antibody response (P < 0.05). The MD-2 SNP was associated (P < 0.04) with the bacterial load in the spleen. The use of these SNP in these genes in marker-assisted selection may result in enhancement of disease resistance.

Experimental population design for estimation of dominant molecular marker effect on egg-production traits

A potential limitation of the use of a dominant molecular marker system such as DNA fingerprinting (DFP) is the inability to distinguish homozygous from heterozygous allele state in an individual, and a resulting inaccuracy in estimating effects of the marker alleles. The objective of this study was to accurately estimate the effect of DFP markers on egg-production traits. A BC1 population was produced from two distinct layer lines. Four DFP bands, each originating predominantly in one of the two parental lines, were evaluated for linkage with egg-production quantitative trait loci in the BC1 population. The egg-production traits consisted of eight early period and seven late period measurements. Eight marker-trait linkages were identified out of 60 total statistical tests. By utilizing information on frequency of DFP bands in two parental lines, selecting F1 sires with DFP bands present, and backcrossing to the line lacking these bands, the population design allowed definitive identification of the DFP zygosity in the BC1 resource population hens. In this manner, accurate estimates of marker allele effects on egg-production traits were obtained from the dominant marker system of DNA fingerprinting.

Candidate gene approach: potentional association of caspase-1, inhibitor of apoptosis protein-1, and prosaposin gene polymorphisms with response to Salmonella enteritidis challenge or vaccination in young chicks

Salmonella enteritidis (SE) contamination of poultry products is a major cause of foodborne disease worldwide. Caspase-1 and inhibitor of apoptosis protein-1 (IAP-1) were selected as candidate genes for chicken response to SE because their proteins play critical roles in the apoptotic pathway when intracellular bacteria interact with host cells. Prosaposin (PSAP) was selected as a positional candidate gene based on a previous quantitative trait loci (QTL) linkage study using the same population. The F1 offspring of outbred sires crossed with three diverse, highly inbred dam lines (two major histocompatibility complex-congenic Leghorn lines named G-B1 and G-B2, and one Fayoumi line) were used to define the phenotypes. The F1 birds were involved in either pathogenic SE challenge, in which spleen and cecum content bacterial load were quantified, or SE vaccination, in which plasma antibody level to SE vaccine was evaluated. A polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) assay was developed to identify single-nucleotide polymorphism (SNP) in the three genes. The F1 offspring of heterozygous sires for each gene were genotyped. The sire caspase-1 gene was significantly associated with cecum content bacterial load (P = 0.04) in the three combined dam line crosses, and with spleen bacterial load in the G-B1 cross (P=0.02). The sire caspase-1 gene was also significantly associated with antibody level to SE vaccine (P=0.03) in F1 males in the three combined dam line crosses. The sire IAP-1 gene was significantly associated with spleen bacterial load (P=0.04) in the three combined dam-line crosses, and interacted with dam-line genetics (P = 0.01) for cecum content bacterial load. The sire PSAP gene significantly interacted with sex for spleen bacterial load (P = 0.004). This study is the first to demonstrate the association of SNPs for caspase-1, IAP-1, and PSAP genes with SE vaccine and with pathogen challenge response in chickens.

Natural resistance-associated macrophage protein 1 gene polymorphisms and response to vaccine against or challenge with Salmonella enteritidis in young chicks

Salmonella enteritidis (SE) contamination of poultry products is of global food-safety concern. The natural resistance-associated macrophage protein 1 (NRAMP1) affects host innate immunity to intracellular bacteria because of its ability to transport divalent cations in late endosome/lysosomes. Studying the association of the NRAMP1 gene and chicken innate immune response to SE can, therefore, aid understanding and enhancement of chicken genetic resistance to SE. The chicken NRAMP1 gene was investigated as a candidate gene for SE response in a unique resource population. Outbred broiler sires and three diverse, highly inbred dam lines (two major histocompatibility complex-congenic Leghorn and one Fayoumi line) produced F1 progeny that were evaluated as young chicks for either bacterial load in spleen and cecum after pathogenic SE inoculation or antibody level after SE vaccination. Thirty-seven single nucleotide polymorphisms (SNP) were identified in 3.1 kb of genomic DNA of the NRAMP1 gene. A PCR-RFLP assay was developed to identify a SNP in a conserved transport motif. The sire NRAMP1 gene SNP was associated (P < 0.02) with antibody level to SE vaccine for Sire 8170 offspring in the two Leghorn crosses. In Sire 8296 offspring, NRAMP1 was associated (P < 0.02) with spleen bacterial load in the combined dam-line crosses. This study demonstrated the association of a SNP polymorphism in a highly conserved region of NRAMP1 with SE vaccine and pathogen challenge response in young chicks, indicating that either NRAMP1 or a linked gene controls these SE-response traits.

Genetic diversity at the major histocompatibility complex (B) and microsatellite loci in three commercial broiler pure lines

Genetic diversity at the MHC and non-MHC loci was investigated in three commercial broiler chicken pure lines. The MHC class II and IV loci were evaluated in Southern hybridizations and molecular genotypes based on RFLP were interpreted from pedigreed families. Four MHC class II and eight class IV genotypes were identified in the broiler lines, and their frequencies differed among the lines. Line-specific MHC genotypes were identified. The observed heterozygosities (59 to 67%) suggest that the MHC loci are highly polymorphic in the broiler lines. At least 9% of the genetic variation at the MHC was due to line differences; the remainder reflected individual variations. To characterize non-MHC genes, 41 microsatellite loci located throughout the chicken genome were evaluated in the broiler lines. Genetic variation was also observed at the microsatellite loci for the broiler lines; the number of alleles at a single locus ranged from one to eight, and the average number of alleles per locus was 3.5, 2.8, and 3.1 for each of the lines, respectively. The observed heterozygosities for microsatellite loci ranged between 0 and 89% in the lines. Based on the fixation index (Fst), about 19% of the genetic variation at microsatellite loci was attributed to broiler line differences. Deviations from Hardy-Weinberg equilibrium were detected at both MHC and non-MHC loci. Possible explanations for these deviations include genetic selection by the primary broiler breeder or the presence of null alleles that were not identified by the typing procedures described in this report. This study contributes to our knowledge on the molecular characteristics and genetic structure of a commercial broiler chicken population. Analysis of MHC and non-MHC loci suggests that there is still sufficient genetic diversity in the broiler lines to continue the progress toward improved broiler chicken production.

Mapping of quantitative trait loci affecting quality and production traits in egg layers

A mapping population segregating for egg quality traits was created by a line cross between two egg layer lines and screened by a genome scan. The F2 generation consisted of 307 hens, which were scored for egg quality and production traits. The mapping population was genotyped for 99 microsatellite loci, spanning nine macrochromosomes and five small linkage groups. The linkage maps were used in mapping QTL affecting 14 traits, by using multiple markers and a least-squares approach. We detected 14 genomewide significant and six suggestive QTL that were located on chromosomes 2, 3, 4, 5, and, 8 and sex chromosome Z. A significant QTL affecting egg white thinning was found on chromosome 2. For eggshell strength, a significant QTL was found on chromosome Z. For production traits, the most interesting area was on chromosome 4, where highly significant QTL effects were detected for BW, egg weight, and feed intake in the same area. The most significant QTL explains 25.8% of the phenotypic variance in F2 of body weight. An area affecting the age at first egg, egg weight, and the number of eggs was located on chromosome Z.

Microsatellite markers linked to Salmonella enterica serovar enteritidis vaccine response in young F1 broiler-cross chicks

Reduction in Salmonella enteritidis (SE) contamination is of importance for poultry production as well as for food safety. The objectives of this study were to identify potential genetic markers of antibody response to SE vaccine in young broiler chicks and then to confirm this linkage in broiler-cross offspring, as well as to explore interactions of marker alleles with dam line and sex. The initial identification of suggestive quantitative trait loci (QTL) markers for antibody response to SE vaccine was conducted by using bulked segregant analysis (BSA) with 58 microsatellite markers in a broiler breeder male line. Four unlinked microsatellites that had allele frequency differences between the high and low antibody response DNA pools were selected for subsequent analysis in a linkage study. Antibody response was measured in an F1 population (n = 379) that was derived by crossing each of four males of the broiler line with several dams from four genetically distant, highly inbred lines (Spanish, Fayoumi, and MHC-congenic G-B1 and G-B2 Leghorn). These crosses enabled us to evaluate the broiler sire QTL-marker allele effects and to explore QTL interactions with the dam lines by individual genotyping. Each of the four microsatellites identified by BSA in the broiler population had a significant (P < 0.05) association with F1 population antibody response in one or more sire families. The effect of the interaction of microsatellite allele with dam line or sex on antibody response was frequently significant. Microsatellite markers linked to antibody response QTL were identified, and genetic interactions with dam line and sex were detected.

Molecular characterization of the Smyth chicken sublines and their parental controls by RFLP and DNA fingerprint analysis

The Smyth line (SL) chicken, a model for autoimmune human vitiligo, is characterized by a spontaneous posthatch epidermal pigment loss (vitiligo). Even though the immunological and morphological changes accompanying the vitiligo process have been well studied, the genetics of this phenomenon remains elusive. The SL lines have been maintained by nonpedigreed matings since their inception, and therefore, the inbreeding status is unknown. The present study was designed to provide an estimate of the inbreeding coefficients and the molecular genetic profiles of the SL sublines, each homozygous for a different MHC haplotype and their MHC-matched parental control (BL) sublines. The DNA fingerprint analysis revealed that there is a moderate level of inbreeding within the SL and BL parental sublines. Of the two SL sublines studied, SL101 had the highest level of inbreeding (0.948). Similarly, its parental control line (BL101) was more inbred than the parental subline of SL102 (BL102). The very high level of similarity between the SL sublines and their respective parental control lines is shown further by the similarity index (SI) estimates (SI between SL101 and BL101 was 0.949 and that between SL102 and BL102 was 0.932). Restriction fragment length polymorphism (RFLP) analysis of the endogenous viral genes (avian leukosis virus subgroup E, ALVE) showed that five ALVE-related BamH1 fragments were present in the SL101 and four in SL102 sublines, whereas the parental BL101 and BL102 sublines had five and six fragments, respectively. SL101 and SL102 shared two fragments, but the frequencies were different. Similarly, BL101 and BL102 shared two fragments. SL101 and BL101 shared three fragments, and SL102 and BL102 also shared three fragments.

Microsatellite polymorphism between and within broiler populations

Two independent broiler chicken populations were genotyped with microsatellite markers to determine genetic polymorphisms within and among broiler populations. Birds were genotyped with primers from the US Poultry Genome Mapping Kits 1 and 2. The 59 primer sets selected for this study provided wide genomic coverage. All 59 primer sets amplified a polymerase chain reaction product in Population L, whereas 57 primer sets produced a product in Population C. The average allele number per line per microsatellite was 2.8 and 2.9 for Populations L and C, respectively. Considering the 57 primer pairs generating product in both lines, 72.3% of the total alleles were unique to one or the other population. This study illustrates the high polymorphism level in broiler populations of microsatellites amplified from primers developed from Red Jungle Fowl or White Leghorn sequences.

Measurement of genetic variation within and between Japanese quail lines using DNA fingerprinting

The objective of the present experiment was to study genetic variation within and among well-defined Japanese quail lines by DNA fingerprinting. The Japanese quail lines included a randombred control line (R1) and lines developed from R1 by divergent selection over 30 generations for 4-wk BW (HW, LW) and total plasma phosphorus (TPP) (HP, LP), a measure of yolk precursor in the blood. In addition, two sublines (HW-HP, HW-LP) of HW, developed in the ninth generation, were included in the analysis. Males of the sublines were selected for increased 4-wk BW whereas females were selected for increased (HW-HP) or decreased (HW-LP) TPP. Sixteen individual DNA samples per line were digested with HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs designed to measure band sharing (BS). Within lines, BS ranged from 0.384 to 0.525. The BS within the R1 line was less than that of all selected lines, except for the HP and LP lines, indicating that, in general, selection had increased genetic homogeneity within the selected lines. Between lines, BS was less than within lines and the R1 line had the highest average level of BS (0.278) with the other lines. The BS between lines for the selected lines ranged from 0.230 to 0.308 with an average of 0.265. In the comparison of the R1 line with the selected lines, it appeared that selection for increased TPP or decreased BW may have influenced BS levels. The relationships of the HW line with its sublines (HW-HP and HW-LP) were not accurately predicted by the DNA fingerprinting technique used. All lines were separated, as indicated by the genetic distance between lines.

Research notes: Fresh and frozen pools of chicken red blood cells as substrates for direct polymerase chain reaction

A method is presented for reliable use of pooled chicken blood samples for estimation of microsatellite frequencies by direct polymerase chain reaction (PCR) amplification of DNA. This method overcomes the variability of hematocrit values in individual chickens and eliminates the step of DNA preparation. The estimated frequencies of polymorphic alleles in fresh and frozen pooled blood samples were similar to those obtained by calculating these frequencies from the individual genotyping. When frozen pooled blood samples are used, pools should be prepared prior to their freezing.

Genetic diversity of commercial turkey primary breeding lines as estimated by DNA fingerprinting

The genetic diversity of primary breeding sire and dam lines from the three largest turkey breeders was estimated by band sharing of DNA fingerprints and by genetic distance estimated from band sharing. For comparison, experimental lines selected for increased egg production (E line) or increased 16-wk body weight (F line) were also included in the analysis. Eighteen individual DNA samples per line were digested with HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs designed to measure band sharing. Within commercial lines, band sharing ranged from 0.370 to 0.508 and was greater in commercial sire lines (average = 0.475) than in commercial dam lines (average = 0.393), indicating that accumulated inbreeding was greater in the sire lines. Band sharing in the F and E lines was 0.479 and 0.522, respectively. The average band sharing among lines was higher for primary breeding sire lines (average = 0.267) than for primary breeding dam lines (0.207), suggesting more genetic diversity in the dam lines. Genetic distance estimated from band sharing was greater among commercial dam lines than commercial sire lines. Based on band sharing between lines and genetic distance estimates, it appears that the experimental E and F lines contain genetic variation not found in the commercial lines. The results of the present study, along with data published in the literature, suggest that commercial primary breeding turkey lines are as diverse, if not more diverse, than similar commercial chicken lines.

Evaluation of oligonucleotide probes for simple tandem repeats (STR) to produce informative DNA fingerprints of the chicken

1. DNA fingerprints of chickens from 2 commercial lines were used to identify oligonucleotide probes providing informative DNA fingerprints. 2. The oligonucleotides [CA]8, [CAC]5, [GGAT]4 and [GACA]4, producing a high number of bands of sufficient intensity and regular distribution, were chosen for further analysis out of 10 tested. 3. Analyses of banding patterns within families revealed Mendelian inheritance of the fragments detected. The DNA fingerprints obtained with the 4 chosen oligonucleotide probes showed about 40 scorable bands in total. 4. Comparison of banding patterns within and between the chicken lines for all 4 oligonucleotide probes revealed levels of bandsharing which did not differ significantly. The number of loci detected by these probes ranged from 25 to 30 each. 5. The probes [CA]8, [CAC]5, [GGAT]4 and [GACA]4 can be used to produce informative DNA fingerprints of chicken. These probes provide estimates of the genetic similarity/variability of individuals or of populations and provide a valid measure of the actual degree of genetic similarity/variability.

Major histocompatibility complex class II DNA polymorphisms in chicken strains selected for Marek's disease resistance and egg production or for egg production alone

The objective of this study was to investigate frequencies of major histocompatibility complex (MHC) class II restriction fragments in two groups of White Leghorn strains. Each group consisted of an unselected control, a strain selected for egg production traits, and a strain selected for egg production traits and Marek's disease (MD) resistance. PvuII-digested genomic DNA was hybridized with a chicken genomic MHC class II probe. The MHC class II DNA fragment frequencies in the selected strains differed from those in the related unselected control and in the strain selected using the same criteria from a different base population. Based on the sizes of the breeding populations, particularly those in the control strain and in the strain selected for egg production, it was considered unlikely that the observed changes of the MHC class II fragment frequencies were due to random genetic drift. The data suggested that some MHC class II bands are associated with production traits or with MD resistance, and that these associations tend to be unique to each genetic background. Hence, MHC class II genes are likely candidates for the investigation of quantitative trait loci in egg production and disease resistance traits such as those for which the studied strains were selected.

Assessment of parental genomic proportions in crossbred chickens by DNA fingerprints

SUMMARY

Starting with the second crossbred generation, parental genomic-proportion lines in individuals deviate considerably from expectation. These individual variations offer the potential to increase the efficiency of crossbreeding programmes. DNA fingerprinting was established as an approach, to quantify the genomic contribution of the parental lines in individuals of two crossbred generations. For this purpose, line-specific bands were identified in representative banding patterns of pooled DNA from purebreds. The representative banding patterns obtained with eight combinations of restriction enzymes HinfI and AluI, and oligonucleotide probes [CA]8, [CAC]5, [GGAT]4, and [GACA]4, contained between nine and 14 line-specific bands. The estimation of the proportion was based on the relative proportion of line-specific bands of one parental line in banding patterns of crossbreds. This was first done in F1 individuals with a definite 50% genomic proportion of each parental line, to determine the accuracy of the approach. The mean value, 51.0 ± 0.34%, observed in 45 F1s using all eight combinations of enzymes and probes, of genomic contribution of one parental line, was close to the theoretical value of 50%. In 24 animals of the BC1, considerable shifting of the parental genomic proportion was observed. ZUSAMMENFASSUNG: Schätzung der Genomanteile bei Hühnern verschiedener Kreuzungsstufen durch DNA-Fingerprinting Von der ersten Rückkreuzungsgeneration an treten erhebliche, individuelle Verscheibungen in der Verteilung der Genomanteile der parentalen Ausganslinien vom Durchschnitt auf. Diese individuelle Variation stellt ein Potential zur Steigerung der Effektivität von Kreuzungszuchtprogrammen dar. Mit der vorliegenden Arbeit wird eine Untersuchungsmethode zur direkten Quantifizierung der Genombeiträge der parentalen Ausganslinien bei Individuen verschiedener Kreuzungsstufen durch DNA fingerprints vor gestellt. Dazu wurden in für die Ausgangslinien repräsentativen Bandenmustern aus DNA-Gemischen linienspezifische Banden identifiziert. Die repräsentativen Bandenmuster wurden mit den Restriktionsenzymen HinfI and AluI sowie den Oligonukleotidsonen [CA](8) , [CAC](5) , [GGAT](4) , und [GACA](4) erzeugt und enthielten 9-14 linienspezifische Banden. Die Bestimmung der parentalen Genomanteile beruhte auf der Identifizierung linienspezifischer Banden in den Bandmustern von Kreuzungsindividuen und der anschließenden Berechnung des relativen Anteils an für eine parentale Linie spezifischen Banden. Um die Genauigkeit der Untersuchungsmethode zu evaluieren, wurde sie zunächst bei F(1) Tieren angewandt, die einen Anteil von jeweils 50% der elterlichen Linien aufweisen müssen. Der Durchschnittswert berechnet über alle 45 F(1) Individuen und alle acht Kombinationen von Enzymen und Sonden betrug 51,0 ± 0,34% Genomanteil der einen parentalen Linie und lag somit nahe dem theoretischen Wert von 50%. Bei 24 Tieren der R1 konnte eine beachtliche Verschiebung der Genombeiträge der parentalen Ausgangslinien gezeigt werden.

Long-term divergent selection for eight-week body weight in white Plymouth rock chickens

This paper provides an overview of results from a long-term (38 generations) selection experiment. Lines were developed from individual phenotypic selection for high or low body weight at 8 wk of age. Included are data for the selected lines, sublines in which selection was relaxed, crosses of the selected lines, and sublines in which the sex-linked dw gene was introduced. Periodically (and in some cases every generation) data were obtained for unselected traits. These unselected traits included feed consumption and intake behavior, reproduction, allomorphic relationships, and metabolic, immunological, endocrine, and molecular factors. These responses have been integrated into a resource allocation paradigm.

Molecular genetic research on IQ: can it be done? Should it be done?

An obvious requirement before embarking on molecular genetic investigation of a trait is prior evidence from ‘classic’ genetic studies that there is indeed a genetic component. Many behavioural traits are familial and these range from comparatively uncommon single gene disorders such as Huntington's disease which has a typical mendelian dominant pattern of transmission, to much commoner characteristics such as career choice or religious denomination which, it might be assumed, are heavily influenced by cultural factors. In between, there is a wide range of attributes including personality type, cognitive ability and liability to common disorders such as depression, that show a tendency to run in families, and which could conceivably be explained by shared genes, shared environment or a combination of the two.

Promoter and transcription of type X collagen gene in broiler chickens with tibial dyschondroplasia

Type X collagen is produced exclusively in hypertrophic chondrocytes of the growth plate of the proximal tibiotarsus and is believed to play an important role during normal development from chondrogenesis to osteogenesis. Chondrocytes of chickens with tibial dyschondroplasia (TD) fail to attain full hypertrophy and the amount of type X collagen, being a marker of hypertrophy, is likely to be reduced. It is not clear whether transcriptional regulation is functional for expression of the type X collagen gene in TD birds. Nucleotide sequence of the type X collagen gene promoter was determined by sequencing PCR-based DNA clones. Nucleotide identity of this fragment between the normal and TD carriers was 97.6%. Both normal and TD birds were similar in a putative transcription start site, the site of TATAA box, and neither had a CCAAT box. However, there were two gaps in TD carriers, four gaps in normals, and five nucleotide substitution sites. By rapid amplification of cDNA ends by PCR (RACE-PCR), transcription of the gene was assessed using total RNA and mRNA from both normal chondrocytes and TD lesions at 3 and 4 wk of age. The RACE-PCR product for type X collagen mRNA was detectable in both normal and TD birds at two stages. No difference was found between them. This result does not support the hypothesis that transcriptional regulation of type X collagen gene is important in TD development of chickens. Variations in the promoter region did not affect transcription of type X collagen gene in TD carrier chickens.

Measurement of genetic parameters within and between turkey lines using DNA fingerprinting

An experiment was conducted to estimate genetic parameters in six experimental and five commercial primary breeding turkey lines using DNA fingerprinting. Eighteen individual DNA samples per line were digested with an HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs to measure band sharing (BS) and band frequencies. Within lines, BS ranged from 0.39 to 0.62 and reflected the history of the experimental lines. Among lines, BS ranged from 0.21 to 0.33 with an average of 0.26. The BS among the experimental lines reflected known relationships. All lines were subdivided based on indices of population subdivision. About 26 hypervariable loci were estimated from band frequencies. Average heterozygosity and genetic variability estimated from band frequencies were significantly different among lines and displayed a result very similar to the BS among lines. Genetic distance indices among lines were also significantly different and reflected known relationships between the experimental lines. The experimental selected lines displayed lower genetic diversity than did the other lines. The parameters measuring genetic diversity within lines had higher correlation coefficients among them than did the parameters between lines. The computer program used in this study made DNA fingerprinting easier to use in population analysis.

Genetic markers linked to quantitative traits in poultry

This study utilized DNA fingerprints and crosses of two genetically distinct lines of layer-type chickens to identify genetic markers linked to quantitative trait loci (QTL). In phase I, backcross (BC1) hens were separately ranked for each of eight traits and then blood pools were produced in groups along each phenotypic distribution. The DNA was isolated from the blood pools and used in a gradient analysis to screen for DNA fingerprint bands that exhibited intensity gradients associated with the phenotypic traits. To identify linkage of bands with QTL and to estimate band effects, F2 progeny were produced in phase II from the phase I BC1 population. A single-trait animal model was used for analysis of associations of all individual DNA fingerprint bands of sires and their progeny phenotypic performance. Twenty fingerprint bands, only two of which had shown trait-associated gradients in phase I, were identified by the animal model analysis of the progeny test as QTL linked (P < or = 0.05) to specific traits of growth, reproduction and egg quality. These 20 bands warrant further study as potentially valuable molecular markers for QTL.

Single-parent segregant pools for allocation of markers to a specified chromosomal region in outcrossing species

Bulked co-segregant analysis is a method of rapidly allocating unmapped genetic markers to a specific chromosomal region. Although originally developed for utilization in populations derived from crosses between fully inbred lines, it has been proposed that co-segregant pools could also serve the same purpose in outbreeding populations, if individuals from only a single large family are pooled. Large, fully mapped, single-sire backcross and half-sib families are presently available as part of the international chicken and bovine reference family panels respectively. In this study, power and tests of significance for single-parent co-segregant analysis are derived for full-sib, single-parent back-cross and single-parent half-sib families, as a function of proportion of recombination between index marker and linked marker, pro-portion of single-parent alleles among the mates, number of individuals in each segregant pool and technical error variance. Power was found to be greater than 0.80 for many reasonable parameter combinations. The method is illustrated using microsatellite markers and a large single-sire bovine family, part of the international bovine reference family panel.

Random amplified polymorphic DNA comparisons among broiler lines selected for incidence of tibial dyschondroplasia

Lines selected for high (H) and low (L) incidence of tibial dyschondroplasia (TD) for eight generations and a randombred control (C) line of broiler chickens were fingerprinted by random amplification of genomic DNA mixed from 20 individuals of each line with 20 oligonucleotide primers. Among these 20 primers, 15 could distinguish the H from the L line, 14 the H from the C line, and 13 the L from the C line. Band sharing (BS), on the average over 20 primers, was .7 for the H vs L comparison and .8 for both H vs C and L vs C comparisons. The levels of BS calculated from individuals was .6 between the H and L line, .7 between the H and C line, and .7 between the L and C line. The ranking of BS values obtained from individual DNA samples was consistent with that obtained from the mixed DNA samples. Genomic distance between divergently selected lines (H vs L) was larger than that between the divergently selected lines and randombred line (H vs C and L vs C). Individual variation within lines was detected in spite of eight generations of selection. Results showed that eight generations of divergent selection for TD incidence in broiler chickens had resulted in genetic variation among lines. The procedure of random amplified polymorphic DNA assay using mixed DNA samples could be used to evaluate genetic distance among lines of chickens.

Genetic characterization of highly inbred chicken lines by two DNA methods: DNA fingerprinting and polymerase chain reaction using arbitrary primers

Thirteen highly inbred chicken lines were analysed at the DNA level by DNA fingerprinting (DEP) and by polymerase chain reaction (PCR) using random primers. In general, the DFP patterns of individuals within a line were identical. The DFP band-sharing (BS) values among lines from different breeds (Leghorn, Fayoumi, Spanish) ranged from 0.10 to 0.20. The DFP BS values among Leghorn lines from different genetic backgrounds ranged from 0.42 to 0.79. The DFP BS values among lines selected for different major histocompatibility complex serotypes from a common genetic background ranged from 0.70 to 0.95. Some randomly amplified polymorphic DNA (RAPD) PCR products were specific to a single line, some to all lines from the same genetic base, and some to all lines from the same breed. The RAPD-PCR band-sharing values ranged from 0.66 to 0.99 for all between-line comparisons. Thus, the ability to detect biodiversity at the DNA level was greater in this study for DFP than for RAPD-PCR. The possible origin of line-specific bands, relative advantages of detecting biodiversity by using different molecular screening techniques and uses of highly inbred chicken lines in molecular analysis are discussed.

Genetic diversity among commercial chicken populations estimated from DNA fingerprints

Blood samples were obtained from parental pure lines representing a large majority of commercial meat-type (broiler) and white egg layer lines presently available in the USA. From blood mixes of each line, DNA was extracted and a DNA fingerprint pattern characteristic of that line was produced. Additionally, DNA fingerprints representing wild jungle fowl and two randombred control populations were produced. Three analyses were conducted: 1) among broiler sire lines, jungle fowl, and one control line; 2) among broiler dam lines, jungle fowl, and one control line; and 3) among parental lines of white egg layers, jungle fowl, and the second control line. Bandsharing levels were calculated, providing an estimate of genetic diversity among lines. Conclusions were that, at present, broiler sire lines, broiler dam lines, and parental lines of white egg layers that make up the majority of commercial breeding populations available in the USA contain a considerable reservoir of genetic diversity.

Estimates of relatedness and inbreeding in goose strains from DNA fingerprints

The purpose of this study was to determine if DNA fingerprints (DFPs) could be used to estimate relatedness and inbreeding of strains of geese and to compare three methods of calculating relatedness indices. Strains included a control and selected strain from each of the Chinese and Synthetic (Chinese, Hungarian and Pilgrim) breeds. DFP patterns for each strain were based on individual DNA samples from six females, or on pooled DNA from 15 females different from those used for individual samples. Three relatedness indices were used, namely, genetic distance, modified Rogers distance and band sharing. All relatedness indices showed a closer relationship of strains within than between breeds. Correlation coefficients among relatedness indices were higher based on pooled DNA (r > or = magnitude of 0.97) than those based on individual DNA (r > or = magnitude of 0.741). Inbreeding estimates were higher for selected compared with control strains. It appears that the use of DFPs to estimate relatedness, regardless of index used, and inbreeding can be valuable for studying geese where there is a limited breeding history.

A novel molecular fingerprint probe based on the endogenous avian retroviral element (EAV) of chickens

We have developed a novel molecular probe that is useful for DNA fingerprint analysis in chickens. The probe is based on the middle-repetitive, chicken endogenous retroviral (EAV) element. It consists of 1503 bp of the 3' portion of the EAV element, extending from the down-stream end of the envelope gene to the beginning of the downstream long terminal repeat (LTR). Unlike other probes that are currently in use for fingerprint analysis with chicken DNA, the EAV-based probe works well at normal levels of stringency, and with standard hybridization buffers. Digestion of chicken genomic DNA with a variety of restriction enzymes routinely yields up to 30 resolvable bands per bird in the 500 bp to 20 kbp range. In order to test the efficacy of the EAV-based fingerprint probe, we have used it to estimate the degree of inbreeding in the inbred WG strain of White Leghorns. We find that the estimates derived with the EAV probe are very similar to those reported previously for the WG strain. These results suggest that molecular probes based on endogenous retroviruses and other middle-repetitive DNA elements should be useful for fingerprint analysis in chickens, and in vertebrates in general.

Evaluating linkage between DNA fingerprint bands and quantitative traits in chickens: interactions

This study assessed the influence of background genome on expression of genes linked to DNA fingerprint (DFP) bands in chickens. Two experimental lines of White Plymouth Rocks previously selected for high or low 8-wk body weight were crossed to produce two F1 males that served as heads of two sire families. Each of these sires was mated to three hens from an unrelated White Leghorn population to produce progeny in which quantitative traits of 4-, 8-, and 12-wk body weight and shank length at 12 wk were measured. The DFP patterns were produced for all individuals in the study. For the 12 sire-specific DFP bands (common to both F1 sires but not found in the dams), each offspring was classified as having or not having each band. Then, an analysis of variance was conducted for each DFP sire band with sex, hatch, dam family, and presence or absence of the sire band as main effects. Interactions between dam family and presence or absence of sire band were also tested. Of 48 possible analyses of variance (12 sire bands by 4 quantitative traits), 3 resulted in significant effects due to sire band, and 2 indicated significant interactions. Thus, associations of a DFP band and a gene coding for a quantitative trait were present, but, in some cases, the expression of the trait differed, depending on the dam family in which it occurred. These data suggest that associations between DFP bands and quantitative traits may not be consistent in different genetic backgrounds.

DNA fingerprint bands applied to linkage analysis with quantitative trait loci in chickens

An efficient approach to detect association between quantitative traits and bands of DNA fingerprint patterns uses intra-family tail analysis, which compares fingerprints of DNA mixes from individuals at the two tails of a phenotypic distribution. In analysis of 67 paternal half-sibs of a meat-type chicken family, of 57 sire bands generated by two probes, one sire-specific band (S6.6) was associated with abdominal fat deposition. The band effect was estimated by a linear model analysis to be 0.88 standard deviations, or about 30% of the family mean. The association between band S6.6 and abdominal fat was further examined by testing progeny of paternal half-sibs of the chickens which were used in the tail analysis, establishing genetic linkage between the DNA marker and a genetic locus affecting abdominal fat deposition.

Deoxyribonucleic acid fingerprint bands linked to loci coding for quantitative traits in chickens

Efficacy of DNA fingerprint (DFP) bands in marker-assisted selection programs for quantitative traits in chickens was evaluated. A cross between two populations of White Plymouth Rock chickens that had been selected for 31 generations for high (HW) or low (LW) 8-wk body weight served as the base population for the experiment. Full- and half-sib families were produced over four generations and 400 offspring were measured for body weight at 8 wk (BW8) and shank length at 12 wk of age (SL12). Distributions were constructed for each quantitative trait in offspring of one F1 sire. The DFP produced from mixed blood of the individuals within each tail of the distribution were compared. From a total of 13 DFP bands that were disparate in intensity between the tails, four bands were chosen for analysis. Matings were made between males and females based on the presence or absence of these bands, but were limited to individuals that were within .5 standard deviation of the mean for the distribution of a particular trait. Quantitative traits of the resulting progeny were analyzed to determine whether parental type (presence or absence of the DFP band) influenced expression of the trait in the offspring. One band out of the four tested was associated with SL12, was an effective predictor of phenotype for both SL12 and BW8, and appeared to be inherited in a dominant fashion.

Deoxyribonucleic acid fingerprint comparisons between selected populations of chickens

A pair of lines of White Plymouth Rock chickens selected for high or low juvenile body weight, a pair of White Leghorn chickens selected for high or low antibody response to sheep erythrocytes, and an F1 cross between each pair of lines, were used to produce DNA fingerprints (DFP). These DFP were prepared by mixing equal amounts of DNA from several individuals of a particular population, resulting in a DFP characteristic of the population. The populations provided individuals of known genetic relationships and inbreeding levels to evaluate the sensitivity of the DFP technique with DNA mixing. Levels of band sharing between breeds were lowest, those between selected lines within a breed were intermediate, and those between the selected lines and their F1 crosses were highest. These results show that DFP analysis is sensitive to several levels of genetic relationship.

Identification of markers associated with quantitative trait loci in chickens by DNA fingerprinting

Three approaches for identifying VNTR alleles associated with quantitative traits in chickens are described. One approach is based on the comparison of well-defined selected and non-selected control strains. The second approach is based on analyzing chickens within a breeding population ranked according to specific traits and the third approach involves segregation analysis. In this latter approach a large number of offspring of a single male segregating for a quantitative trait are produced and tested for trait association of the male DNA fingerprinting bands. In all cases pooled DNA samples of birds, rather than individual samples, are analyzed and band intensity is assumed to reflect the relative frequency of an allele. Examples from the literature and from our laboratory indicate that these methods permit the identification of DNA fingerprinting bands associated with quantitative traits. After developing locus-specific probes for these bands it should ultimately be possible to detect and map quantitative trait loci.

Genetic factors accountable for line-specific DNA fingerprint bands in quail

DNA fingerprints, prepared from mixes of DNA of individuals sampled from lines of Japanese quail selected for high or low 4-week body weight, were used to evaluate the relative contribution of several evolutionary forces to genetic diversity among populations. Comparisons between lines--two replicates of each selection direction and a control unselected line--were used to determine the frequency of line-specific DNA fingerprint bands produced by each of three major evolutionary forces: 1) mutation; 2) genetic drift; 3) selection. The latter force is expected to generate line-specific bands only if there is linkage disequilibrium between DNA fingerprint loci and quantitative loci (QTLs) controlling body weight. Using probes 33.6 and R18.1, an average of 48.4 DNA fingerprint bands in each line were analyzed. On average, 27.8 bands were found to be line-specific among the 96.8 (2 x 48.4) bands analyzed in an average comparison between pairs of lines. Based on the frequencies of line-specific bands in each particular comparison, it was calculated that 21% of the line-specific bands were due to mutation, 11% due to a single genetic drift event, 11% due to selection, 21% due to the combined effects of genetic drift and selection, 22% due to double independent events of genetic drift, and 14% due to undefined factors. Although evidence was found for a high frequency of genetic changes attributable to genetic drift, and a higher than expected frequency of linkage disequilibrium, the emphasis of this report is on the methodology suggested rather than on the particular results.