Map-based quantitative trait locus identification

Mapping quantitative trait loci for egg production traits in an F2 intercross of Oh-Shamo and White Leghorn chickens

We performed quantitative trait locus (QTL) analyses for egg production traits, including age at first egg (AFE) and egg production rates (EPR) measured every 4 weeks from 22 to 62 weeks of hen age, in a population of 421 F(2) hens derived from an intercross between the Oh-Shamo (Japanese Large Game) and White Leghorn breeds of chickens. Simple interval mapping revealed a main-effect QTL for AFE on chromosome 1 and four main-effect QTL for EPR on chromosomes 1 and 11 (three on chromosome 1 and one on chromosome 11) at the genome-wide 5% levels. Among the three EPR QTL on chromosome 1, two were identified at the early stage of egg laying (26-34 weeks of hen age) and the remaining one was discovered at the late stage (54-58 weeks). The alleles at the two EPR QTL derived from the Oh-Shamo breed unexpectedly increased the trait values, irrespective of the Oh-Shamo being inferior to the White Leghorn in the trait. This suggests that the Oh-Shamo, one of the indigenous Japanese breeds, is an untapped resource that is important for further improvement of current elite commercial laying chickens. In addition, six epistatic QTL were identified on chromosomes 2, 4, 7, 8, 17 and 19, where none of the above main-effect QTL were located. This is the first example of detection of epistatic QTL affecting egg production traits. The main and epistatic QTL identified accounted for 4-8% of the phenotypic variance. The total contribution of all QTL detected for each trait to the phenotypic and genetic variances ranged from 4.1% to 16.9% and from 11.5% to 58.5%, respectively.

An optimal DNA pooling strategy for progressive fine mapping

We present a cost-effective DNA pooling strategy for fine mapping of a single Mendelian gene in controlled crosses. The theoretical argument suggests that it is potentially possible for a single-stage pooling approach to reduce the overall experimental expense considerably by balancing costs for genotyping and sample collection. Further, the genotyping burden can be reduced through multi-stage pooling. Numerical results are provided for practical guidelines. For example, the genotyping effort can be reduced to only a small fraction of that needed for individual genotyping at a small loss of estimation accuracy or at a cost of increasing sample sizes slightly when recombination rates are 0.5% or less. An optimal two-stage pooling scheme can reduce the amount of genotyping to 19.5%, 14.5% and 6.4% of individual genotyping efforts for identifying a gene within 1, 0.5, and 0.1 cM, respectively. Finally, we use a genetic data set for mapping the rice xl(t) gene to demonstrate the feasibility and efficiency of the DNA pooling strategy. Taken together, the results demonstrate that this DNA pooling strategy can greatly reduce the genotyping burden and the overall cost in fine mapping experiments.

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.

Use of a novel outbred by inbred F1 cross to detect genetic markers for growth

A unique outbred by inbred F1 resource population was established. The population structure facilitated the unique opportunity of examining gene by genetic background interaction through crossing two modern broiler sires with dams from two unrelated inbred lines, with no selection for growth rate, to produce about 600 F1 chicks. Pools of DNA were generated from the phenotypic extremes (20% high and low) for 8-week body weight for each of the four combinations of sire and dam line. For one sire family, pools were also separately generated for each sex. The pools were genoyped with 25 informative (segregating) microsatellites. This unique F1 cross between outbred and inbred populations allowed use of the inbred alleles as an 'internal control' for polymerase chain reaction amplification quality in DNA pools. Ten microsatellites showed marked differences (P < 0.05) in allele frequencies between high and low pools, suggesting an association between marker and quantitative trait loci (QTL). These differences were verified using selective genotyping. For many markers, differences in allele frequencies between the high and the low pools, or marker effect, varied between the two dam lines and the two sexes, suggesting an interaction between some genes and the genetic background as represented by different dam lines or sexes. The suggestive marker-QTL associations identified in this F1 population demonstrate the efficiency of this population design while different QTL effects in different genetic line crosses and sexes highlight the importance of gene by genetic background interaction in QTL detection.

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.

DNA microsatellites linked to quantitative trait loci affecting antibody response and survival rate in meat-type chickens

Selection for immune response parameters may lead to improved general disease resistance. Because disease resistance and immune response are hard-to-measure quantitative traits with low to moderate heritability, they may respond more efficiently to marker-assisted selection (MAS) than to phenotypic selection. To detect DNA markers linked to quantitative trait loci (QTL) associated with immune response, a resource half-sib family of 160 backcross (BC1) and intercross (F2) birds was derived from a cross between two meat-type lines divergently selected for high or low antibody (Ab) response to Escherichia coli. By using 25 microsatellite DNA markers covering approximately 25% of the chicken genome, initial genotyping of 40% of the resource family was followed by complete genotyping of the entire family with four suggestive markers. Three of these markers exhibited significant association with immune response: (1) ADL0146 on Chromosome 2 associated with Ab to SRBC and Newcastle disease virus (NDV), (2) ADL0290 on linkage group 31 affecting Ab to NDV, and (3) ADL0298 on linkage group 34 associated with Ab to E. coli and survival. The family was also genotyped with five linked markers from two of the suggested regions, and interval mapping was applied. The results confirmed the significant effects, suggested the location of the QTL, and confirmed the genetic association between immune responses and disease resistance. These findings support the idea of improving poultry immunocompetence by MAS.

Screening for highly heterozygous chickens in outbred commercial broiler lines to increase detection power for mapping quantitative trait loci

Two commercial broiler lines were used in an experiment to map quantitative trait loci (QTL) affecting disease resistance. Chickens from these lines were genotyped with 27 microsatellite markers to estimate heterozygosity and polymorphism information content (PIC), the probability that one parent is heterozygous at a marker locus and the other has a different genotype. Heterozygosity estimated from allelic frequencies was 0.52 for the two lines; however, heterozygosity calculated from actual counts of heterozygous loci was much lower (0.36) than the estimated heterozygosity. The PIC was 0.45 in these lines, and average allele number per marker locus was about 3.5. Twenty-five males produced from a cross between these two lines were screened with the DNA markers to select birds with high heterozygosity at marker loci. Mating simulation showed that uninformative matings could be reduced by about 5% if 12 pairs of males and females with the highest heterozygosity at marker loci were selected, which was about a 25% reduction in total uninformative matings. This experiment demonstrated that the heterozygosity and PIC in commercial broiler lines were low and selection for the birds with high heterozygosity at marker loci could increase informative content in chickens used in the experiments of QTL mapping, thus increasing detection power for QTL mapping.