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| Association Analysis of Fifteen Single Nucleotide Polymorphism(SNP) Loci with Growth Traits in Jinghai Yellow Chicken(Gallus gallus) |
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Abstract To identify single nucleotide polymorphisms (SNPs) and candidate genes affecting growth traits of Jinghai yellow chicken(Gallus gallus), a kind of chicken 60K SNP chip was used to study 396 Jinghai yellow chicken for the 15 SNPs, and the associations were analyzed between the 15 SNPs and 12 growth indexes. Linkage disequilibrium (LD) and haplotype analysis of the significant SNPs were also performed. The results showed that 9 of the 15 SNPs were identified to be associated with at least one growth trait of Jinghai yellow chicken (P＜0.05), and seven of the 9 SNPs were identified to be associated with more than one growth trait(P＜0.05). Among these SNPs, rs15497877, rs13972304, rs13553164, rs14917647 and rs13973515 were associated with body weight and average daily weight gains on both early (2~8 weeks) and late growth (10~16) stage (P＜0.05); rs316142388 and rs14917305 only had effects on the late growth stage (12~16 weeks) (P＜0.05), rs314214528 and rs13553485 only had effects on the early growth stage (2~6 weeks) (P＜0.05). The genetic parameters indicated that the average polymorphism information content (PIC) was a bit small and continue selection of Jinghai yellow chicken was possible and necessary. The result of LD and haplotype analysis showed that SNPs in the region of 173.5~175.0 Mb on chromosome one was in strong linkage disequilibrium and had high research value. Moreover, haplotype TTTCCTCAC should be valued as it accounted for 32.4% of total haplotypes. The functions of a few proximal genes including karyopherin alpha 3 (KPNA3), deleted in lymphocytic leukemia 7(DLEU7) and forkhead box O1 (FOXO1) were discussed and they were found to affect chicken growth by different ways. All these represent results not only promote the researches on SNPs having effects on growth traits of Jinghai yellow chicken, but also can benefit the utilizations for marker assisted selection (MAS) on Jinghai yellow chicken and even Chinese chickens.
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Received: 24 February 2014
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