Dissecting the genetic architecture of complex traits and its impact on genetic improvement programs: lessons learnt from the Virginia chicken lines

Pettersson, Mats E.; Carlborg, Örjan

doi:10.1590/s1516-35982010001300028

Cited by 3 publications

(2 citation statements)

References 7 publications

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“…Over the course of long-term bidirectional selection, the Virginia body weight lines have experienced significant changes impacting behavioral, neurological, metabolic, and developmental processes (Dunnington and Siegel 1996). With a concerted effort to understand the fundamental genomics underlying these changes, we have employed linkage and association mapping, selective-sweep analyses using high-density SNP data and pooled genome sequencing across generations of the selected lines, relaxed lines, and a derived advanced intercross line (Wahlberg et al 2009; Johansson et al 2010; Pettersson and Carlborg 2010; Besnier et al 2011; Pettersson et al 2011; Ahsan et al 2013; Pettersson et al 2013; Sheng et al 2015; Brandt et al 2016). It has become clear that the difference in body weight between the selected lines relies on small to moderate effects from many loci, with the most recent analysis revealing 20 contributing loci (Zan et al 2017).…”

Section: Discussionmentioning

confidence: 99%

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Lillie

Honaker

Siegel

et al. 2019

G3 Genes|Genomes|Genetics

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Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line divergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the example of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.

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Section: Discussionmentioning

confidence: 99%

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Lillie

Honaker

Siegel

et al. 2019

G3 Genes|Genomes|Genetics

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“…The development of the chicken 600k SNP array 4 facilitates efficient screening for causal loci and genes with relevance to target traits due to the uniform coverage across chromosomes and the inclusion of markers within coding regions. Despite the large number of findings by GWAS, understanding of the genetic architecture of BW in chicken remains limited 5 , since only a small number of positional candidate genes are confirmed as truly functionally relevant to the trait (e.g. HDAC2 and GNPDA2 6,7 ).…”

Section: Introductionmentioning

confidence: 99%

Discovery and characterization of functional modules associated with body weight in broilers

Tarsani

Kranis

Maniatis

et al. 2019

Sci Rep

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Aim of the present study was to investigate whether body weight (BW) in broilers is associated with functional modular genes. To this end, first a GWAS for BW was conducted using 6,598 broilers and the high density SNP array. The next step was to search for positional candidate genes and QTLs within strong LD genomic regions around the significant SNPs. Using all positional candidate genes, a network was then constructed and community structure analysis was performed. Finally, functional enrichment analysis was applied to infer the functional relevance of modular genes. A total number of 645 positional candidate genes were identified in strong LD genomic regions around 11 genome-wide significant markers. 428 of the positional candidate genes were located within growth related QTLs. Community structure analysis detected 5 modules while functional enrichment analysis showed that 52 modular genes participated in developmental processes such as skeletal system development. An additional number of 14 modular genes ( GABRG1, NGF, APOBEC2, STAT5B, STAT3, SMAD4, MED1, CACNB1, SLAIN2, LEMD2, ZC3H18, TMEM132D, FRYL and SGCB ) were also identified as related to body weight. Taken together, current results suggested a total number of 66 genes as most plausible functional candidates for the trait examined.

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Bidirectional selection for body weight on standing genetic variation in a chicken model

Lillie

Honaker

Siegel

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. Using pooled genome resequencing of paired generations of these lines, we reveal the within and between-line genomic signatures of selection. At 55 generations of divergent selection, 14.2% of the genome showed extreme differentiation between the selected lines were contained within 395 genomic regions. The lines often displayed a duality of the sweep signatures: an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consist of short, distinct haploblocks of variable between-line divergence. Formed during what probably was a complex history of bottlenecks, inbreeding, and introgressions, these mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.

show abstract

Dissecting the genetic architecture of complex traits and its impact on genetic improvement programs: lessons learnt from the Virginia chicken lines

Cited by 3 publications

References 7 publications

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Discovery and characterization of functional modules associated with body weight in broilers

Bidirectional selection for body weight on standing genetic variation in a chicken model

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