SNP mapping of QTL affecting growth and fatness on chicken GGA1

Rao, Yanghui; Shen, Xu; Xia, Mengna; Luo, Chenglong; Nie, Qinghua; Zhang, Dexiang; Zhang, Xiquan

doi:10.1051/gse:2007022

Cited by 9 publications

(7 citation statements)

References 23 publications

(11 reference statements)

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“…The novel QTLs identified could be false positives, exclusive to our population, or a consequence of the number of animals and the higher SNP density compared to other QTL mapping studies for abdominal fat and skin traits in chickens [ 5 , 8 – 14 ]. The PPA (ranging from 0.83 to 0.93) and the proportion of the genetic variance explained by the novel QTLs (ranging from 0.58 to 1.49) suggest that these novel QTL are not false positives.…”

Section: Discussionmentioning

confidence: 99%

“…Some studies have been conducted to map genomic quantitative trait loci (QTLs) associated with variation in abdominal fat [ 5 , 9 – 13 ], and skin traits [ 9 , 14 ]. However, most previously published QTLs were mapped using low density of markers (ranging from 102 to 410 markers), and the detected intervals spanned tens of centimorgans (cM) [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

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A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

et al. 2018

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BackgroundExcess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken’s carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds.ResultsABF and SKIN are moderately heritable traits in our broiler population with estimates ranging from 0.23 to 0.33. Using a high density SNP panel (355,027 informative SNPs), we detected nine unique QTLs that were associated with these fat traits. Among these, four QTL were novel, while five have been previously reported in the literature. Thirteen PCGs were identified that might regulate fat deposition in these QTL regions: JDP2, PLCG1, HNF4A, FITM2, ADIPOR1, PTPN11, MVK, APOA1, APOA4, APOA5, ENSGALG00000000477, ENSGALG00000000483, and ENSGALG00000005043. We used sequence information from founder animals to detect 4843 SNPs in the 13 PCGs. Among those, two were classified as potentially deleterious and two as high impact SNPs.ConclusionsThis study generated novel results that can contribute to a better understanding of fat deposition in chickens. The use of high density array of SNPs increases genome coverage and improves QTL resolution than would have been achieved with low density. The identified PCGs were involved in many biological processes that regulate lipid storage. The SNPs identified in the PCGs, especially those predicted as potentially deleterious and high impact, may affect fat deposition. Validation should be undertaken before using these SNPs for selection against carcass fat accumulation and to improve feed efficiency in broiler chicken production.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4779-6) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

et al. 2018

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“…The ADG was calculated based on the difference between the current BW and the BW of two weeks ago for 1–14, 15–28, 29–42, 43–56, 57–70, and 71–84 d of age (ADG14, ADG28, ADG42, ADG56, ADG70, and ADG84). For example, ADG28 was calculated as (BW28 – BW14)/14 and represented the net daily weight increase during the period of 15–28 d. All 489 F2 individuals (252 males and 237 females) were slaughtered and measured for BMW (g), LMW (g), and WW (g) at 90 d of age [13], [37].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Study Identified a Narrow Chromosome 1 Region Associated with Chicken Growth Traits

et al. 2012

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Chicken growth traits are important economic traits in broilers. A large number of studies are available on finding genetic factors affecting chicken growth. However, most of these studies identified chromosome regions containing putative quantitative trait loci and finding causal mutations is still a challenge. In this genome-wide association study (GWAS), we identified a narrow 1.5 Mb region (173.5–175 Mb) of chicken (Gallus gallus) chromosome (GGA) 1 to be strongly associated with chicken growth using 47,678 SNPs and 489 F2 chickens. The growth traits included aggregate body weight (BW) at 0–90 d of age measured weekly, biweekly average daily gains (ADG) derived from weekly body weight, and breast muscle weight (BMW), leg muscle weight (LMW) and wing weight (WW) at 90 d of age. Five SNPs in the 1.5 Mb KPNA3-FOXO1A region at GGA1 had the highest significant effects for all growth traits in this study, including a SNP at 8.9 Kb upstream of FOXO1A for BW at 22–48 d and 70 d, a SNP at 1.9 Kb downstream of FOXO1A for WW, a SNP at 20.9 Kb downstream of ENSGALG00000022732 for ADG at 29–42 d, a SNP in INTS6 for BW at 90 d, and a SNP in KPNA3 for BMW and LMW. The 1.5 Mb KPNA3-FOXO1A region contained two microRNA genes that could bind to messenger ribonucleic acid (mRNA) of IGF1, FOXO1A and KPNA3. It was further indicated that the 1.5 Mb GGA1 region had the strongest effects on chicken growth during 22–42 d.

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“…Recently, there has been some success in explaining body condition variation using genetic markers by exploring the correlation between body condition or body fat and genetic markers in controlled crosses (QTL analysis) (e.g. Abasht et al 2006;Moghadam et al 2007;Rao et al 2007;Kü ttner et al 2011). However, this method is laborious and difficult to achieve in nonmodel organisms that cannot be kept and crossed in laboratory conditions.…”

Section: Introductionmentioning

confidence: 99%

Genetic polymorphism in dopamine receptor D4 is associated with early body condition in a large population of greater flamingos, Phoenicopterus roseus

Gillingham¹,

Béchet²,

Geraci³

et al. 2012

Molecular Ecology

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Body condition is an important determinant of fitness in many natural populations. However, as for many fitness traits, the underlying genes that regulate body condition remain elusive. The dopamine receptor D4 gene (DRD4) is a promising candidate as dopamine is known to play an important role in the regulation of food intake and the metabolism of both glucose and lipids in vertebrates. In this study, we take advantage of a large data set of greater flamingos, Phoenicopterus roseus, to test whether DRD4 polymorphism predicts early body condition (EBC) while controlling for whole-genome effects of inbreeding and outbreeding using microsatellite multilocus heterozygosity (MLH). We typed 670 of these individuals for exon 3 of the homologue of the human DRD4 gene and 10 microsatellite markers. When controlling for the effects of yearly environmental variations and differences between sexes, we found strong evidence of an association between exon 3 DRD4 polymorphisms and EBC, with 2.2-2.3% of the variation being explained by DRD4 polymorphism, whereas there was only weak evidence that MLH predicts EBC. Because EBC is most likely a polygenic trait, this is a considerable amount of variation explained by a single gene. This is to our knowledge, the first study to show an association between exon 3 DRD4 polymorphism and body condition in non-human animals. We anticipate that the DRD4 gene as well as other genes coding for neurotransmitters and their receptors may play an important role in explaining variation in traits that affect fitness.

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SNP mapping of QTL affecting growth and fatness on chicken GGA1

Cited by 9 publications

References 23 publications

A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Genome-Wide Association Study Identified a Narrow Chromosome 1 Region Associated with Chicken Growth Traits

Genetic polymorphism in dopamine receptor D4 is associated with early body condition in a large population of greater flamingos, Phoenicopterus roseus

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