QTL Express: mapping quantitative trait loci in simple and
  complex pedigrees

Seaton, G. G. R.; Haley, Chris; Knott, Sara; Kearsey, M. J.; Visscher, Peter M.

doi:10.1093/bioinformatics/18.2.339

Cited by 437 publications

(328 citation statements)

References 8 publications

(4 reference statements)

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“…All analyses were carried out with QTL express (Seaton et al, 2002). Family and farm was included as fix effects for both gestation length and maternal ability related traits.…”

Section: Discussionmentioning

confidence: 99%

A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

Chen

Guo

Zhang

et al. 2010

Animal

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Gestation length and maternal ability are important to improve the sow reproduction efficiency and their offspring survival. To map quantitative trait loci (QTL) for gestation length and maternal ability related traits including piglet survival rate and average body weight of piglets at weaning, more than 200 F 2 sows from a White Duroc 3 Erhualian resource population were phenotyped. A genome-wide scan was performed with 194 microsatellite markers covering the whole pig genome. QTL analysis was carried out using a composite regression interval mapping method via QTL express. The results showed that total number of born piglets was significantly correlated with gestation length (r 5 20.13, P , 0.05). Three QTL were detected on pig chromosome (SSC)2, 8 and 12 for gestation length. The QTL on SSC2 achieved the 5% genome-wide significant level and the QTL on SSC8 was consistent with previous reports. Four suggestive QTL were identified for maternal ability related traits including 1 QTL for survival rate of piglets at weaning on SSC8, 3 QTL for average body weight of piglet at weaning on SSC3, 11 and 13.

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“…All analyses were carried out with QTL express (Seaton et al, 2002). Family and farm was included as fix effects for both gestation length and maternal ability related traits.…”

Section: Discussionmentioning

confidence: 99%

A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

Chen

Guo

Zhang

et al. 2010

Animal

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“…The QTL analysis was performed using the F2 least squares interval mapping method and the QTL Express software program [45]. Hatch (1-7) was included as a fixed effect in the model for all traits.…”

Section: Discussionmentioning

confidence: 99%

Identification of quantitative trait loci associated with bone traits and body weight in an F2 resource population of chickens

2005

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-Bone fractures at the end of lay are a significant problem in egg-laying strains of hens. The objective of the current study was to identify quantitative trait loci (QTL) associated with bone mineralization and strength in a chicken resource population. Layer (White Leghorn hens) and broiler (Cobb-Cobb roosters) lines were crossed to generate an F2 population of 508 hens over seven hatches, and 26 traits related to bone integrity, including bone mineral density (BMD) and content (BMC), were measured. Genotypes of 120 microsatellite markers on 28 autosomal groups were determined, and interval mapping was conducted to identify QTL regions. Twenty-three tests representing three chromosomal regions (chromosomes 4, 10 and 27) contained significant QTL that surpassed the 5% genome-wise threshold, and 47 tests representing 15 chromosomes identified suggestive QTL that surpassed the 5% chromosome-wise threshold. Although no significant QTL influencing BMD and BMC were detected after adjusting for variation in body weight and egg production, multiple suggestive QTL were found. These results support previous experiments demonstrating an important genetic regulation of bone strength in chickens, but suggest the regulation may be due to the effects of multiple genes that each account for relatively small amounts of variation in bone strength.bone mineral density / chickens / QTL / osteoporosis

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“…Reported estimates for a and d were those obtained at the location with the highest F ratio. 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).…”

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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QTL Express: mapping quantitative trait loci in simple and complex pedigrees

Cited by 437 publications

References 8 publications

A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population

Identification of quantitative trait loci associated with bone traits and body weight in an F2 resource population of chickens

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

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