Multiple marker mapping of quantitative trait loci in an outbred pedigree of loblolly pine

Knott, Sara; Neale, David B.; Sewell, Mitchell M.; Haley, Chris

doi:10.1007/s001220050482

Cited by 278 publications

(398 citation statements)

References 7 publications

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“…The analyses were carried out using the QTLExpress software (Seaton et al, 2002). Significance thresholds were empirically determined at the chromosome level, by performing 1000 permutations of the trait values against the genotypes, and the genomewide levels were obtained applying an approximate Bonferroni correction (Knott et al, 1998). Chromosome-wide thresholds slightly varied depending on chromosomes and traits but they were on average equal to F 5 7.6 and 5.4, respectively, with two (autosomes) and one (chromosome X) degrees of freedom in the numerator.…”

Section: Statistical Analysesmentioning

confidence: 99%

Detection of quantitative trait loci for teat number and female reproductive traits in Meishan × Large White F2 pigs

Bidanel

Rosendo

Iannuccelli

et al. 2008

Animal

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A quantitative trait locus (QTL) analysis of female reproductive data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. Six F1 boars and 23 F1 sows, progeny of six LW boars and six MS sows, produced 573 F2 females and 530 F2 males. Six traits, i.e. teat number (TN), age at puberty (AP), ovulation rate (OR), weight at mating (WTM), number of viable embryos (NVE) and embryo survival (ES) at 30 days of gestation were analysed. Animals were genotyped for a total of 137 markers covering the entire porcine genome. Analyses were carried out based on interval mapping methods, using a line-cross (LC) regression and a half-full sib (HFS) maximum likelihood test. Genome-wide (GW) highly significant (P , 0.001) QTL were detected for WTM on SSC 7 and for AP on SSC 13. They explained, respectively, 14.5% and 8.9% of the trait phenotypic variance. Other GW significant (P , 0.05) QTL were detected for TN on SSC 3, 7, 8, 16 and 17, for OR on SSC 4 and 5, and for ES on SSC 9. Two additional chromosome-wide significant (P , 0.05) QTL were detected for TN, three for WTM, four for AP, three for OR, three for NVE and two for ES. With the exception of the two above-mentioned loci, the QTL explained from 1.2% to 4.6% of trait phenotypic variance. QTL alleles were in most cases not fixed in the grand-parental populations and Meishan alleles were not systematically associated with higher reproductive performance.

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Section: Statistical Analysesmentioning

confidence: 99%

Detection of quantitative trait loci for teat number and female reproductive traits in Meishan × Large White F2 pigs

Bidanel

Rosendo

Iannuccelli

et al. 2008

Animal

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“…The presence of imprinting effects was investigated as suggested by Knott et al [25] by adding a third effect in the model in order to test the differences between the two classes of heterozygotes, defined according to the paternal or maternal origin of grandparental (MS or LW) alleles. This model was first contrasted with a no QTL model (F test with 3 d.f.…”

Section: Statistical Analysesmentioning

confidence: 99%

Detection of�quantitative trait loci for�carcass composition traits in pigs

et al. 2002

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-A quantitative trait locus (QTL) analysis of carcass composition data from a threegeneration experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. A total of 488 F2 males issued from six F1 boars and 23 F1 sows, the progeny of six LW boars and six MS sows, were slaughtered at approximately 80 kg live weight and were submitted to a standardised cutting of the carcass. Fifteen traits, i.e. dressing percentage, loin, ham, shoulder, belly, backfat, leaf fat, feet and head weights, two backfat thickness and one muscle depth measurements, ham + loin and back + leaf fat percentages and estimated carcass lean content were analysed. Animals were typed for a total of 137 markers covering the entire porcine genome. Analyses were performed using a line-cross (LC) regression method where founder lines were assumed to be fixed for different QTL alleles and a half/full sib (HFS) maximum likelihood method where allele substitution effects were estimated within each half-/full-sib family. Additional analyses were performed to search for multiple linked QTL and imprinting effects. Significant gene effects were evidenced for both leanness and fatness traits in the telomeric regions of SSC 1q and SSC 2p, on SSC 4, SSC 7 and SSC X. Additional significant QTL were identified for ham weight on SSC 5, for head weight on SSC 1 and SSC 7, for feet weight on SSC 7 and for dressing percentage on SSC X. LW alleles were associated with a higher lean content and a lower fat content of the carcass, except for the fatness trait on * Correspondence and reprints E-mail: milan@toulouse.inra.fr, bidanel@dga.jouy.inra.fr 706 D. Milan et al. SSC 7. Suggestive evidence of linked QTL on SSC 7 and of imprinting effects on SSC 6, SSC 7, SSC 9 and SSC 17 were also obtained. pig / gene mapping / quantitative trait locus / carcass composition

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“…The analyzed body composition traits are listed in Table 2. The significance thresholds were derived empirically by a permutation test with 10 000 permutations as described by Churchill and Doerge (1994) and the marker information contents were calculated according to Knott et al (1998) as implemented in GridQTL.…”

Section: Discussionmentioning

confidence: 99%

Evidence for additional functional genetic variation within the porcine IGF2 gene affecting body composition traits in an experimental Piétrain × Large White/Landrace cross

Boysen

Tetens

Thaller

2011

Animal

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The aim of this study was to test for the existence of causative genetic variation affecting body composition traits within or adjacent to the porcine insulin-like growth factor 2 (IGF2) gene beyond the known IGF2-intron3-G3072A mutation. A focussed quantitative trait loci analysis using four microsatellite markers within the telomeric region of porcine chromosome 2p was conducted in a large resource population comprising 2741 F2 offspring. The analysis of two subsets of animals that were alternatively homozygous for the in3G3072A mutation provides evidence for additional genetic variation significantly contributing to the overall quantitative trait nucleotide variance within our population.

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Multiple marker mapping of quantitative trait loci in an outbred pedigree of loblolly pine

Cited by 278 publications

References 7 publications

Detection of quantitative trait loci for teat number and female reproductive traits in Meishan × Large White F2 pigs

Detection of quantitative trait loci for teat number and female reproductive traits in Meishan × Large White F2 pigs

Detection of�quantitative trait loci for�carcass composition traits in pigs

Evidence for additional functional genetic variation within the porcine IGF2 gene affecting body composition traits in an experimental Piétrain × Large White/Landrace cross

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