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| Identification of PPP3CA Gene SNP and Its Association Analysis withGrowth Traits in Weining Chickens (Gallus gallus) |
| ZHAO Zhong-Long1, RAN Guang-You1, ZHANG Yong1*, ZHANG Xi-Ben2, WANG Zhi-Wei1, AI Zhao-Bi1, YANG Run-Qian1, LI Wei-Bo2, CHEN Ze-Lin2, YE Hong-Ying2 |
1 College of Animal Science/Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China;
2 Bijie City Academy of Agricultural Sciences, Bijie 551700, China |
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Abstract The Weining chicken (Gallus gallus) is one of the valuable local poultry genetic resources inGuizhou province. It is of great significance for the genetic improvement and molecular marker-assisted breeding of Weining chickens to study their growth traits and uncover their genetic effects using candidate genes. In this study, a total of 113 Weining chickens (58 males and 55 females) aged 300 days were selected asthe study subjects. PCR amplification and direct sequencing were used to identify the SNP locus of PPP3CAgene. Excel was used to calculate genotype frequency, allele frequency, effective allele number and polymorphism information content of each site, and to analyze whether each mutation site was in Hardy- Weinberg equilibrium state. The secondary structure analysis of mRNAs was performed using RNA fold online software. SPSS 27.0 was used to analyze the association between genotypes of different polymorphicloci and body size indexes. The results showed that 3 SNP sites were found on exon 6 of PPP3CA gene inWeining chickens, namely g. 151368C>T, g. 151389T>C and g. 151402T>G, among which missense mutation occurred at g.151368C>T site, resulting in the conversion of arginine at position 206 on mRNA to tryptophan. g. 151402T>G site missense mutation resulting in the conversion of isoleucine at position 216 to tryptophan. Linkage disequilibrium analysis showed that there was a strong linkage disequilibrium effect between g.151389T>C and g. 151368C>T, g. 151402T>G. The χ2 test showed that g. 151368C>T and g. 151389T>C matched Hardy-Weinberg equilibrium, while g. 151402T>G deviated from Hardy-Weinberg equilibrium. At the g.151402T>G site, association analysis showed that TT and GG individuals had significantly higher bodyweight, body slope length, and chest width than TG individuals (P<0.05), TT individuals had significantlyhigher chest depth than GG and TG individuals (P<0.05), GG individuals had significantly higher chest depth than TG individuals (P<0.05), and TT and GG individuals had extremely significantly longer keel and shank length than TG individuals (P<0.01). Individuals of the TT and GG types had considerably larger tibia girth than those of the TG type (P<0.05). Haplotype and diplotype analysis of 3 SNPs showed that there were 4haplotypes and 8 diplotypes. Among them, diplotype H2H3 (TCTCTT) and H1H1 (TTCCGG) could be used as molecular marker sites to improve keel length, shank length and shank girth. This study provides a scientific basis for molecular marker-assisted selection for growth traits of Weining chickens.
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Received: 24 June 2024
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Corresponding Authors:
*gzdxzy2020@163.com
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