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| Genome-wide Association Studies on Growth and Carcass Traits in Ninghai Yellow Chickens (Gallus gallus domesticus) and Guangxi Yellow Chickens Based on 600 K SNP Chips Technology |
| TAN Yu-Ge1, CAO Hai-Yue1, DONG Xin-Yang1, Mao Hai-Guang1, LU Lei2, JIANG Jun-Bao2, MA You-Zhi1, YIN Zhao-Zheng1,* |
1 College of Animal Science, Zhejiang University, Hangzhou 310058, China;
2 Ningbo Zhenning Animal Husbandry Co., Ltd, Ningbo 315000, China |
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Abstract As a crucial approach to detect candidate genes of important economic straits, GWAS (genome-wide association study) is used for identifying complex functional genes of straits on genomic level. To identify molecular markers and candidate genes associated with growth and carcass straits, a multibreed GWAS was performed based on growth and carcass trait phenotypes with the 600 K SNP array in Ninghai yellow chickens (Gallus gallus domesticus) and Guangxi yellow chickens. The statistics of the minimum, maximum, mean, standard deviation and coefficient of the growth traits and carcass traits of Ninghai yellow and Guangxi yellow chickens were made , which found that there were significant differences (P<0.01) in the body weight at 8 weeks old and 16 weeks old and slaughter rate in the 2 breeds . As shown in present study, the variation coefficients of abdominal fat weight and abdominal fat rate were the highest. Followed by body weight at 0, 8 and 16 weeks, slaughter rate, semi-eviscerated rate and eviscerated rate. The result of principal component analysis showed that there was no significant subgroup structure in the 2 chicken populations, respectively. The Quantile-Quantile (QQ) graph showed that the actual value of each character was basically consistent with the expected value. Finally, Manhattan plots of growth traits and carcass traits showed that the presence of loci on multiple chromosomes of 2 breeds of chickens was significantly correlated with growth traits and carcass traits, respectively. The SNPs that significantly associated with phenotypic traits were identified by a general linear model. Four SNPs (rs313150871, rs314661053, rs313314400 and rs314694861)on G. gallus domesticus (GGA)3, 5, 8, and 11, and 3 SNPs (rs313989383, rs317888074 and rs313384732) on GGA 2, 5, and 9 were found to be significantly associated with growth and carcass traits, respectively. Only one SNP (rs313384732) on GGA 5 at 11.80 Mb was significantly associated with 2 traits (semi-eviscerated weight, eviscerated weight). In particular, a region of GGA 5 between 8.98 and 11.80 Mb was associated with multiple traits (i.e. BW at hatching, semi-eviscerated weight, and eviscerated weight). Four proximal genes (adrenomedullin, ADM; ATP/GTP binding protein like 4, AGBL4; activating signal cointegrator 1 complex subunit3, ASCC3; wilms tumor 1 interacting protein, WTIP) for growth traits and 3 proximal genes (phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha, PIK3C2A; mitogen-activated protein kinase kinase kinase 13, MAP3K13; and LOC101747362 (uncharacterized gene)) for carcass traits were detected. The findings would be helpful to reveal the genetic effects of traits and marker-assisted selection.
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Received: 03 March 2019
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Corresponding Authors:
* , yzhzh@zju.edu.cn
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