The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study

Sun, Yanfa; Zhao, Guiping; Liu, Ranran; Zheng, Maiqing; Hu, Yaodong; Wu, Dan; Zhang, Lei; Li, Peng; Wen, Jie

doi:10.1186/1471-2164-14-458

Cited by 109 publications

(96 citation statements)

References 52 publications

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“…To correct for population stratification, the first MDS component was used as a covariate in the model as suggested (Price et al 2006; Gu et al 2011; Sun et al 2013). …”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Linkage Analysis and Association Study Identifies Loci for Polydactyly in Chickens

Sun

Liu

Zhao

et al. 2014

G3 Genes|Genomes|Genetics

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Polydactyly occurs in some chicken breeds, but the molecular mechanism remains incompletely understood. Combined genome-wide linkage analysis and association study (GWAS) for chicken polydactyly helps identify loci or candidate genes for the trait and potentially provides further mechanistic understanding of this phenotype in chickens and perhaps other species. The linkage analysis and GWAS for polydactyly was conducted using an F2 population derived from Beijing-You chickens and commercial broilers. The results identified two QTLs through linkage analysis and seven single-nucleotide polymorphisms (SNPs) through GWAS, associated with the polydactyly trait. One QTL located at 35 cM on the GGA2 was significant at the 1% genome-wise level and another QTL at the 1% chromosome-wide significance level was detected at 39 cM on GGA19. A total of seven SNPs, four of 5% genome-wide significance (P < 2.98 × 10−6) and three of suggestive significance (5.96 × 10−5) were identified, including two SNPs (GGaluGA132178 and Gga_rs14135036) in the QTL on GGA2. Of the identified SNPs, the eight nearest genes were sonic hedgehog (SHH), limb region 1 homolog (mouse) (LMBR1), dipeptidyl-peptidase 6, transcript variant 3 (DPP6), thyroid-stimulating hormone, beta (TSHB), sal-like 4 (Drosophila) (SALL4), par-6 partitioning defective 6 homolog beta (Caenorhabditis elegans) (PARD6B), coenzyme Q5 (COQ5), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, etapolypeptide (YWHAH). The GWAS supports earlier reports of the importance of SHH and LMBR1 as regulating genes for polydactyly in chickens and other species, and identified others, most of which have not previously been associated with limb development. The genes and associated SNPs revealed here provide detailed information for further exploring the molecular and developmental mechanisms underlying polydactyly.

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“…To correct for population stratification, the first MDS component was used as a covariate in the model as suggested (Price et al 2006; Gu et al 2011; Sun et al 2013). …”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Linkage Analysis and Association Study Identifies Loci for Polydactyly in Chickens

Sun

Liu

Zhao

et al. 2014

G3 Genes|Genomes|Genetics

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“…AGRP 유전자는 육질 및 보수력과 연관된 연구결과는 보 고되지 않았으며, 주로 닭과 쥐 실험에서 성장과 지방산의 축적에 관련한 유전자로 보고되고 있다 (Dunn et al, 2013;Sun et al, 2013). FTO 유전자는 Fan et al(2010) (Sammel et al, 2002;Mancini and Hunt, 2005).…”

Section: Zeng Et Al(2011)은 Xinghua와 Recessive White Leghorn을unclassified

Quantitative Trait Locus and Association Studies affecting Meat Colors in Chicken : Review

Seo¹,

Lee²

2015

Korean Journal of Poultry Science

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Recently, livestock breeding is more focused on the meat quality rather than meat quantity, mainly due to the improvement of consumers' income. Among the meat quality traits, meat color is one of very important traits because meat color is the first selection criterion from the consumers in the market. Most of the economically important traits have continuous variations and these are called quantitative traits. the genomic locations affecting these traits are called quantitative trait locus (QTL), which is mostly controlled by many genes having small effects. In this study, the recent QTL and candidate gene studies were reviewed in order to meet the consumers' demand for the future market. In the chicken QTL database, three traits are related with meat colors, namely breast color (Bco), meat color (Mco), drip loss (DL) and pH. The identified number of QTLs is 33 from 13 chromosomal regions. In these QTL regions, 14 candidate genes were identified; Eight for meat color (APP, BCMO1, COL1A2, FTO, KPNA2, PSMD12, G0S2, FTSJ3), two for drip loss (AGRP, FTO) and four for pH (GALNT1, PCDH19, DIAPH1, SPP2). These QTLs and candidate genes need to be confirmed and fine mapping is ultimately needed for identification of causative variations. The recently developed chicken resource population using Korean native chicken can be used for the improvement of meat quality traits, which increase the value that needed in the chicken industry. 식육의 색은 육제품으로써 소비자의 선택을 받을 때 가장 먼저 선택의 기준이 되는 관능 형질의 하나이기 때문에, 육 색은 제품의 상품성과 판매에 직결되어 경제적으로 매우 중 요한 형질이라고 볼 수 있다 (Mancini and Hunt, 2005). 기존 의 육색에 대한 연구는 식육의 수분이 포함된 정도인 보수 력에 영향을 받고, 이러한 보수력의 차이는 사후강직시에 일 어나는 pH 변화와도 밀접한 관련이 있는 것으로 보고된 바 있다 (Fletcher, 1999;Qiao et al., 2001;Huff-Lonergan and Lonergan, 2005). 또한, 이러한 결과는 수분이 많고 창백한 색깔의 PSE 육이나, 수분이 적고 어두운 색깔의 DFD 육과의 association이 보고되기도 하였다 (Fletcher, 1999;Barbut et al., 2008). 이러한 연구는 오래전부터 닭을 포함한 소와 돼지의 연구에서 식육의 품질을 개선하기 위해 형질간의 관련성을 확인하기도 하였고, 최근에는 많은 수의 마커를 이용한 genome-wide mapping 연구가 발전하면서 육색의 원인 유전자 를 탐색하는 연구가 수행되기 시작했다 (Groenen et al., 2009;Gu et al., 2011).Genome-wide QTL mapping(GWL)과 Genome-wide association(GWA) 연구는 질적 표현형질이 아닌 양적 표현형질 에 대해서 유전체 전반에 걸쳐 고루 분포되어 있는 유전자

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“…In previous studies, an F2 resource population derived from a cross between Beijing‐You (BJY) and a commercial rapidly growing broiler line has been constructed for identifying loci and candidate genes related with meat quality traits (Sun et al . ,b), shank length (Sun et al . ,b), polydactyly (Sun et al .…”

Section: Introductionmentioning

confidence: 99%

“…,b), shank length (Sun et al . ,b), polydactyly (Sun et al . ) and physical appearance traits (accept from G3).…”

Section: Introductionmentioning

confidence: 99%

Genomewide association study of immune traits in chicken F2 resource population

Sun

et al. 2016

J Animal Breeding Genetics

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Immune traits play pivotal roles in animal immune capacity development and disease resistance. Single nucleotide polymorphisms (SNPs) are common forms of genetic variations among individuals, which are thought to account for the majority of inherited phenotypic variations. In this study, we performed genomewide association, using the Illumina 60K SNP BeadChip studies to detect molecular markers and candidate genes associated with immune traits in an F2 population. Sixteen immune traits were measured. We identified 85 significant SNPs (p < 2.98 × 10(-6) ) with 5% as the genomewide significance threshold, 380 SNPs of suggestive significance (p < 5.96 × 10(-5) ) from simple model (general linear model, GLM) and 15 SNPs of suggestive significance (p < 5.96 × 10(-5) ) from the compressed mixed linear model (MLM), which were also found in GLM (six significant SNPs and seven suggestive SNPs). Three significant SNPs (GGaluGA151406, Gga_rs14554319 and Gga_rs13593979) and candidate genes (LYRM4 and KTN1) were found to be associated with avian influenza antibody titres, and the first two SNPs are from the results of two-model analysis. For the immune organs, through the analysis of GLM, 19 SNPs were found to be significantly associated with the thymus weight, 61 SNPs were significantly associated with the bursa of Fabricius weight, six of which were located within a 34-Mb region (125 846 474-159 649 698 bp) on chicken chromosome 1 (GGA1). A candidate region relevant to haematological traits from GLM was found in GGA4 and 9 loci were located on it. Three loci (GGaluGA348521, Gga_rs16098446 and GGaluGA348518) within 179 kb (16 286 868-16 466 134 bp) on GGAZ from GLM provided evidence that this genomic segment may be relevant to red blood cell volume distribution width (RDW). Our study provides a list of significant SNPs and candidate genes that will be valuable information for unveiling the underlying molecular mechanism of immune regulation.

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The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study

Cited by 109 publications

References 52 publications

Genome-Wide Linkage Analysis and Association Study Identifies Loci for Polydactyly in Chickens

Genome-Wide Linkage Analysis and Association Study Identifies Loci for Polydactyly in Chickens

Quantitative Trait Locus and Association Studies affecting Meat Colors in Chicken : Review

Genomewide association study of immune traits in chicken F2 resource population

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