Imputation-based fine-mapping suggests that most QTL in an outbred chicken Advanced Intercross Line are due to multiple, linked loci

AbstractThe Virginia chicken lines have been divergently selected for juvenile body-weight for more than 50 generations. Today, the high-and low-weight lines show a 12-fold difference for the selected trait, 56-day body-weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several Quantitative Trait Loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the haplotype-diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker-density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to detect associations to 56-day body-weight. The approach revealed several statistically and population-structure independent associations and increased the resolution of most QTL. Further, most QTL were also found to contain multiple independent associations, implying a complex underlying architecture due to the combined effects of multiple, linked loci on independent haplotypes that still segregate in the selected lines.Article summaryAfter 50 generations of bi-directional selection, the Virginia chicken lines display a 12-fold difference in bodyweight at 56 days of age. Birds from the high and low selected lines were crossed to found an Advanced Intercross Line, which has been maintained for 9 generations. Using high-density genotypes of the founders, we imputed genotypes in intercross birds that were only genotyped for a sparse set of markers. Using single and multi-marker association analyses, we replicated nine known body-weight QTL. Multiple statistically independent associations were revealed in eight of the QTL, suggesting that most are caused by multiple linked loci.

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P5035 Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass in a chicken advanced intercross line

Journal of Animal Science ◽

10.2527/jas2016.94supplement4132a ◽

2016 ◽

Vol 94 (suppl_4) ◽

pp. 132-133

Author(s):

S. Lyu ◽

D. Arends ◽

M. K. Nassar ◽

G. A. Brockmann

Keyword(s):

Muscle Mass ◽

Fine Mapping ◽

Chromosome 4 ◽

Advanced Intercross Line ◽

Distal Chromosome

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Mapping of quantitative trait loci influencing daily body weight gain (DBWG) on chromosome 6 in German Holstein population

Biotechnology in Animal Husbandry ◽

10.2298/bah0602035r ◽

2006 ◽

Vol 22 (1-2) ◽

pp. 35-46 ◽

Cited By ~ 1

Author(s):

M. Reißmann ◽

P. Reinecke ◽

U. Müller ◽

S. Abdel-Rahman

Keyword(s):

Body Weight ◽

Weight Gain ◽

Fine Mapping ◽

Marker Assisted Selection ◽

Growth Traits ◽

Body Weight Gain ◽

Chromosome 6 ◽

Production Traits ◽

Daily Body Weight ◽

Holstein Population

Twelve microsatellite markers on chromosome 6 were analyzed in German Holstein population to detect and locate QTL affecting daily body weight gain (DBWG). The results indicate promising location for QTL controlling daily body weight gain trait on chromosome 6. Where, three markers BMS2508 BM3026 and TGLA37 at three different positions in a distance 15.2 cM on BTA6 were associated with significant effects for daily body weight gain trait (DBWG). Comparison between this finding and previously identified QTL support the location of a QTL for growth traits on chromosome 6, where a significant QTL for birth and yearling weight was previously identified on chromosome 6 tightly close to marker BM3026. Finding from this study could be used in subsequent fine-mapping work and applied to marker-assisted selection (MAS) of production traits.

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Fine-mapping quantitative trait loci affecting murine external ear tissue regeneration in the LG/J by SM/J advanced intercross line

Heredity ◽

10.1038/hdy.2013.133 ◽

2014 ◽

Vol 112 (5) ◽

pp. 508-518 ◽

Cited By ~ 17

Author(s):

J M Cheverud ◽

H A Lawson ◽

K Bouckaert ◽

A V Kossenkov ◽

L C Showe ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Tissue Regeneration ◽

Fine Mapping ◽

Quantitative Trait ◽

External Ear ◽

Advanced Intercross Line ◽

Trait Loci

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Fine-mapping QTLs and the validation of candidate genes for Aluminum tolerance using a high-density genetic map

Plant and Soil ◽

10.1007/s11104-019-04261-0 ◽

2019 ◽

Vol 444 (1-2) ◽

pp. 119-137 ◽

Cited By ~ 1

Author(s):

Zhandong Cai ◽

Yanbo Cheng ◽

Peiqi Xian ◽

Rongbin Lin ◽

Qiuju Xia ◽

...

Keyword(s):

Candidate Genes ◽

Genetic Map ◽

Fine Mapping ◽

Aluminum Tolerance ◽

High Density

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QTL fine mapping for intramuscular fat and fatty acid composition using high-density SNP chip array on SSC12 in Korean native pig × Yorkshire F2 population

Czech Journal of Animal Science ◽

10.17221/50/2018-cjas ◽

2019 ◽

Vol 64 (No. 4) ◽

pp. 180-188

Author(s):

Sangwook Kim ◽

Byeonghwi Lim ◽

Kwansuk Kim ◽

Kyoungtag Do

Keyword(s):

Fatty Acid Composition ◽

Fatty Acid ◽

Candidate Genes ◽

Acid Composition ◽

Fine Mapping ◽

Intramuscular Fat ◽

Economic Benefits ◽

High Density ◽

Chromosome 12 ◽

Qtl Fine Mapping

Intramuscular fat (IMF) and fatty acid composition are characteristics that are used as important indicators of evaluating high quality pork and contribute to the economic benefits of the pig farming industry. In this study, quantitative trait loci (QTL) fine mapping of chromosome 12 was performed in a population of F2 intercross between Yorkshire (YS) and Korean native pigs (KNPs) by adopting combined linkage and linkage disequilibrium method using high-density SNP chips. QTLs for IMF (H3GA0034813 to H3GA0034965) and oleic acid (C18:1) (ASGA0054380 to ALGA0066299) were located at 120 cM (54.112–57.610 kb) and 85 cM (36.097–38.601 kb), respectively, within chromosome 12 (Sscrofa11.1 genomic reference). In addition, 31 candidate genes present within the IMF QTL region and 28 candidate genes existing within C18:1 QTL region were chosen. In order to understand the function of these candidate genes at the molecular level, these candidate genes were functionally categorized by studying gene ontology and analyzing network and pathway. Among the 59 candidate genes within the region of IMF QTL and C18:1 QTL, five (MYH1, MYH2, MYH4, ACACA, and RPS6KB1) directly interacting candidate genes were found. Furthermore, the RPS6KB1 gene was assumed to be an important candidate gene that is involved in leptin and insulin signaling pathway and participates in controlling adipogenic differentiation, fat deposition, and fatty acid composition, which is related to obesity of pigs.

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Oral contraception in diabetic women. Diabetes control, serum and high density lipoprotein lipids during low-dose progestogen, combined oestrogen/progestogen and non-hormonal contraception

Acta Endocrinologica ◽

10.1530/acta.0.0980246 ◽

1981 ◽

Vol 98 (2) ◽

pp. 246-251 ◽

Cited By ~ 22

Author(s):

Thomas Rådberg ◽

Anders Gustafson ◽

Asbjörn Skryten ◽

Kirsten Karlsson

Keyword(s):

Body Weight ◽

Lipid Metabolism ◽

High Density Lipoprotein ◽

Density Lipoprotein ◽

Insulin Requirement ◽

High Density ◽

Diabetes Control ◽

Insulin Dosage ◽

Urinary Glucose ◽

Insulin Dependent

Abstract. Thirtyeight women with insulin-dependent diabetes were randomly allocated to contraception with either a progestogen only (Lynestrenol 0.5 mg daily) (LYN), a combined oral contraceptive (OC) (Ethinyl oestradiol 50 μg + Lynestrenol 2.5 mg) (EE + LYN) or a non-hormonal intrauterine device (IUD). Diabetes control (i.e. insulin dosage, blood and urinary glucose and body weight) and the lipid concentration in serum and in high density lipoprotein (HDL) were assessed before and during six months use of the respective contraceptives. In the LYN group urinary glucose excretion increased 10% in spite of unchanged blood glucose, body weight and insulin requirement. All serum lipids decreased; triglycerides by 40% (P < 0.01), cholesterol by 13% (P < 0.01) and phospholipids by 12% (P = 0.06), without alteration of HDL lipids. In the group using combined OC (EE + LYN) the insulin requirement increased by 7% (P < 0.01) without any change in body weight or blood and urinary glucose. Serum as well as HDL lipids remained unchanged. In the IUD group neither diabetes control nor serum or HDL lipids were altered. It is concluded that in insulin-dependent diabetics the progestogen (LYN) has little influence on diabetes control but has a marked, though probably not adverse, effect on lipid metabolism. The combined OC (EE + LYN) may impair glucose homeostasis slightly but has little influence on serum or HDL lipids. These findings seem to differ from those obtained in non-diabetics during administration of contraceptive steroids and these differences suggest that absence of endogenous insulin production enhances the effects of progestogen and reduces the effects of synthetic oestrogens on lipid metabolism.

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High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut

Plant Biotechnology Journal ◽

10.1111/pbi.12930 ◽

2018 ◽

Vol 16 (11) ◽

pp. 1954-1967 ◽

Cited By ~ 29

Author(s):

Gaurav Agarwal ◽

Josh Clevenger ◽

Manish K. Pandey ◽

Hui Wang ◽

Yaduru Shasidhar ◽

...

Keyword(s):

Disease Resistance ◽

Candidate Gene ◽

Genetic Map ◽

Fine Mapping ◽

Gene Discovery ◽

High Density ◽

Whole Genome ◽

Genome Resequencing ◽

Whole Genome Resequencing

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SELECTION FOR SERUM CHOLESTEROL, VOLUNTARY PHYSICAL ACTIVITY, 56-DAY BODY WEIGHT AND FEED INTAKE IN RANDOMBRED MICE. II. CORRELATED RESPONSES

Canadian Journal of Genetics and Cytology ◽

10.1139/g81-060 ◽

1981 ◽

Vol 23 (3) ◽

pp. 545-555 ◽

Cited By ~ 8

Author(s):

E. A. Dunnington ◽

J. M. White ◽

W. E. Vinson

Keyword(s):

Physical Activity ◽

Body Weight ◽

Serum Cholesterol ◽

Feed Intake ◽

High Weight ◽

Control Line ◽

High Intake ◽

Low Weight ◽

Voluntary Physical Activity ◽

High Feed

Randomly bred ICR mice were selected for five generations for high and low serum cholesterol (SC), voluntary physical activity, 56-day body weight and feed intake. An unselected, randomly bred control line was maintained with each pair of selection lines. Significant increases in mature body weight occurred in males of high weight and high intake lines and in females of high SC, high weight and high intake lines. Significant decreases in mature body weights occurred in males of low weight line and in females of low SC and low weight lines. Both high and low selected SC lines had greater (P<0.05) activity scores and consumed more feed than the SC control. Mice selected for high activity consumed more (P<0.05) feed than mice selected for low activity. Mice selected for high 56-day body weight consumed more (P<0.05) feed and had higher SC than mice selected for low 56-day body weight. Mice selected for high feed intake were heavier (P<0.05) and more active (P<0.05) than low feed intake mice but had significantly lower SC levels.

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