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

Comparative study of population genomic approaches for mapping colony-level traits

Social insect colonies exhibit colony-level phenotypes such as social immunity and task coordination, which are produced by the individual phenotypes. Mapping the genetic basis of such phenotypes requires associating the colony-level phenotype with the genotypes in the colony. In this paper, we examine alternative approaches to DNA extraction, library construction, and sequencing for genome wide association studies (GWAS) of colony-level traits using a population sample of Cataglyphis niger ants. We evaluate the accuracy of allele frequency estimation from sequencing a pool of individuals (pool-seq) from each colony using either whole-genome sequencing or reduced representation genomic sequencing. Based on empirical measurement of the experimental noise in sequenced DNA pools, we show that reduced representation pool-seq is drastically less accurate than whole-genome pool-seq. Surprisingly, normalized pooling of samples did not result in greater accuracy than un-normalized pooling. Subsequently, we evaluate the power of the alternative approaches for detecting quantitative trait loci (QTL) of colony-level traits by using simulations that account for an environmental effect on the phenotype. Our results can inform experimental designs and enable optimizing the power of GWAS depending on budget, availability of samples and research goals. We conclude that for a given budget, sequencing un-normalized pools of individuals from each colony provides optimal QTL detection power.

Genomic mapping techniques are used to map phenotypes to genotypes. Mapping is of general interest in any biological system, including fundamental studies of biological traits, clinical studies of genetic predisposition to disease, and agro- and bio-technological studies of domesticated plants and animals. Typically, such studies associate phenotypic measurements of individuals with their genotypes. Here we evaluate methodological approaches for genomic mapping of phenotypes that are expressed at the level of a group rather than that of individuals. We demonstrate that genomic sequencing of a DNA pool from multiple samples provides increased statistical power within a limited budget. Our results facilitate more efficient use of resources in genomic mapping studies that investigate group-level phenotypes.

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.

Fine mapping of qGW1, a major QTL for grain weight in sorghum

We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.

Detection of agriculturally important QTLs in chickens and analysis of the factors affecting genotyping strategy

Three single cross populations were generated in order to analyze factors affecting the ability to detect true linkage with minimum false positive or false negative associations, and to detect associations between markers and quantitative traits. The three populations are: (1) a broiler x broiler cross of a single sire and 34 dams, resulting in 266 progeny; (2) a broiler x broiler cross of a single sire and 41 dams resulting in 360 progeny; and (3) a broiler x layer cross of a single sire with 56 dams resulting in 1180 progeny. Based on these three resource populations we show that: a) gradient selective genotyping was more effective than the random selective genotyping; b) selective genotyping was significant at a selected proportion less than 62% of the cumulative truncation point; c) as few as 10% of selected individuals (5% of each of the two tails) were sufficient to show significant association between markers and phenotypes; d) a gradient slices approach was more powerful than using replicates of the extreme groups; and e) in resource populations resulting from crosses between lines of different backgrounds, most of the microsatellite markers used are polymorphic. We also used simulation to test factors affecting power to detect true associations between markers and traits that are hard to detect in experimental resource populations. Using defined populations in the simulation, we concluded that the following guidelines provide reliable detection of linked QTLs: 1) the resource population size should be larger than 100; 2) a QTL effect larger than 0.4 SD is detectable with a reasonable number of markers (>100) and resource population size (>200 subjects); 3) the DNA pool from each tail of the trait distribution should contain at least 10% of the resource family; 4) each of the two DNA pools should include more than 35 individuals. Some of these guidelines that were deduced from the simulation analysis have been confirmed in the experimental part of this study.

Fractioned DNA pooling: a new cost-effective strategy for fine mapping of quantitative trait loci

Selective DNA pooling (SDP) is a cost-effective means for an initial scan for linkage between marker and quantitative trait loci (QTL) in suitable populations. The method is based on scoring marker allele frequencies in DNA pools from the tails of the population trait distribution. Various analytical approaches have been proposed for QTL detection using data on multiple families with SDP analysis. This article presents a new experimental procedure, fractioned-pool design (FPD), aimed to increase the reliability of SDP mapping results, by "fractioning" the tails of the population distribution into independent subpools. FPD is a conceptual and structural modification of SDP that allows for the first time the use of permutation tests for QTL detection rather than relying on presumed asymptotic distributions of the test statistics. For situations of family and cross mapping design we propose a spectrum of new tools for QTL mapping in FPD that were previously possible only with individual genotyping. These include: joint analysis of multiple families and multiple markers across a chromosome, even when the marker loci are only partly shared among families; detection of families segregating (heterozygous) for the QTL; estimation of confidence intervals for the QTL position; and analysis of multiple-linked QTL. These new advantages are of special importance for pooling analysis with SNP chips. Combining SNP microarray analysis with DNA pooling can dramatically reduce the cost of screening large numbers of SNPs on large samples, making chip technology readily applicable for genomewide association mapping in humans and farm animals. This extension, however, will require additional, nontrivial, development of FPD analytical tools.

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.

The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs

A large intercross between the domestic White Leghorn chicken and the wild ancestor, the red junglefowl, has been used in a Quantitative Trait Loci (QTL) study of growth and egg production. The linkage map based on 105 marker loci was in good agreement with the chicken consensus map. The growth of the 851 F2 individuals was lower than both parental lines prior to 46 days of age and intermediate to the two parental lines thereafter. The QTL analysis of growth traits revealed 13 loci that showed genome-wide significance. The four major growth QTLs explained 50 and 80% of the difference in adult body weight between the founder populations for females and males, respectively. A major QTL for growth, located on chromosome 1 appears to have pleiotropic effects on feed consumption, egg production and behaviour. There was a strong positive correlation between adult body weight and average egg weight. However, three QTLs affecting average egg weight but not body weight were identified. An interesting observation was that the estimated effects for the four major growth QTLs all indicated a codominant inheritance.

Mapping of quantitative trait loci for body weight at three, six, and nine weeks of age in a broiler layer cross

An F2 chicken population was established from a cross of a broiler sire-line and an egg laying (White Leghorn) line. There were two males and two females from both lines in the base population. The F1 progeny consisted of 8 males and 32 females. Over 500 F2 offspring from five hatches were reared to slaughter at a live weight of 2 kg at 9 wk of age. Body weights at 3, 6, and 9 wk were recorded. The DNA was extracted from blood samples, and genotypes for 101 microsatellite markers were determined. Data of 466 individuals from 30 families were available for analysis. Interval mapping QTL analyses were carried out. The QTL significant at the genome wide level that affected body weight at two ages were identified on chromosomes 1, 2, 4, 7, and 8 and a QTL on Chromosome 13 influenced body weight at all three ages. Genetic effects were generally additive, and the broiler allele increased body weight in all cases. The effects for significant individual QTL accounted for between 0.2 and 1.0 phenotypic standard deviations and the sum of the additive effects accounted for approximately 0.75 of the line difference in body weight at 6 wk of age. The largest single additive effect was on chromosome 4, and the effect of substituting one copy of the gene was an increase in weight of 249 g. Interactions of the QTL with sex or family were unimportant. There was no evidence for imprinting or of two or more QTL at the same location for any of the traits.

Comparison of sex-linked dwarf genes in chickens from two sources when introgressed into unrelated genetic backgrounds

1. Sex-linked dwarfing genes from 2 broiler stock origins (EU and US) were each introgressed into 2 White Leghorn populations that had been divergently selected for antibody response to sheep erythrocytes. 2. When the resulting backcrossed populations were 87.5% of their respective. White Leghorn line, non-dwarf pullets were assessed for body weights, shank lengths, immunoresponsiveness, age and body weight at sexual maturity, egg production, average egg weight, and duration of fertility. For measurements where there were no differences between non-dwarf pullets from the 2 origins of the dwarfing genes, then the dwarf pullets (which were full sisters to the non-dwarfs) were compared. 3. Shank length at 8 weeks of age and mature (24-week) body weights were higher for dwarf pullets from EU than US dwarf origin. Immune response and several egg production traits were higher for dwarf pullets from the high antibody backcross than from those of the low antibody backcross. 4. There were few differences in expression of the dwarfing genes from 2 origins in the unrelated backcross populations used in this study. Also each of the dwarfing genes, when introgressed into different genomic backgrounds, was not discernibly different in its expression in terms of antibody response or egg production characteristics.

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.

Commercial approaches to genetic selection for growth and feed conversion in domestic poultry

Tremendous genetic progress has been observed historically for growth and feed conversion through the efforts of the primary breeding companies. However, significant between-strain variation still exists due to differences in selection emphasis and selection techniques practiced by these organizations. This paper provides an overview of methods currently employed in commercial poultry breeding with reference to factors complicating program design and future challenges facing the industry. Mass selection for body weight has resulted in a significant reduction in the number of days required to grow bird to market weight with indirect improvements in feed conversion. Direct selection for feed conversion is accomplished through part record testing of males that have been preselected for body weight, conformation, and defect traits. Data are commonly subjected to complex statistical analysis both to correct feed conversion for variation in body weight and to improve the accuracy of breeding value estimates. Feed conversion breeding values of male sibs are sometimes used for the selection of female candidates as well. Selection for growth rate and efficiency has resulted in negative complications, such as ascites, reduced reproductive performance, skeletal abnormalities, and increased carcass fatness. Some of these factors may be partially ameliorated through modified selection practices. If not addressed by the breeding industry, the disruption of physiological homeostasis might ultimately represent economic and genetic barriers to further progress in improving growth and efficiency. Modern techniques in molecular genetics, utilized in conjunction with traditional quantitative genetic approaches, will provide additional opportunities to circumvent these physiological complications associated with genetic selection for growth and feed efficiency.

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.

Associations of individual genomic heterozygosity, estimated by molecular fingerprinting, and of dam major histocompatibility complex with growth and egg production traits in layer chickens

Growth and egg production data from F2 layer chickens produced from a mating of MHC-heterozygous B15B44 sires to B15B44 and B15B43 dams were analyzed for associations with the level of the individual's genomic heterozygosity and dam MHC. The F1 sires and dams were produced from mating of birds from two genetically distinct, highly inbred lines. Genomic heterozygosity (expressed as composite band frequency, CBF) was estimated based on the average proportion of shared bands of individual birds compared to a composite pool of Hinf I-digested DNA samples from the two inbred lines. Birds from dams of genotype B15B43 had significantly greater BW than progeny from B15B44 dams at 6 wk and thereafter. Dam MHC genotype differences were also significant for number of eggs laid from 20 to 28 wk of age, with B15B43 progeny being superior. Negative regression coefficients at hatch, 32 and 44 wk were observed for the effect of CBF on BW of progeny from B15B43 dams and at hatch and 32 wk from progeny of pooled dam genotypes. Similarly, negative regression coefficients were observed for the association of CBF with number of eggs within progeny from the B15B44 dam MHC genotypes at 20 to 28 wk and total period recorded, and at 28 to 36 wk for progeny from B15B43 dams. The CBF regression coefficients and the differences among progeny based on dam MHC genotypes suggest that individual heterozygosity and MHC genotype may be associated with BW and egg production in chickens.

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.

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.

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.

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.