Acta Veterinaria et Zootechnica Sinica ›› 2024, Vol. 55 ›› Issue (2): 502-514.doi: 10.11843/j.issn.0366-6964.2024.02.009

• ANIMAL GENETICS AND BREEDING • Previous Articles     Next Articles

Investigating the Influencing Factors of Egg Laying Performance in Wenchang Chickens Based on Whole Genome Resequencing

REN Yuwei1, CHEN Xing2, LIN Yanning1, HUANG Xiaoxian1, HONG Lingling1, WANG Feng1, SUN Ruiping1, ZHANG Yan1, LIU Hailong1, ZHENG Xinli1*, CHAO Zhe1*   

  1. 1. Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
    2. Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan 430000, China
  • Received:2023-07-04 Online:2024-02-23 Published:2024-02-27

Abstract: The purpose of this project was to study the features of the evolution process of Wenchang chickens, to understand the factors affecting the egg production performance, and to provide the basis for the breeding of improved breeds of Wenchang chickens. Blood samples of 3 mL from 35 Wenchang chickens (35 weeks of age, 15 cocks and 20 hens) and 30 Jianghan chickens (35 weeks of age, 10 cocks and 20 hens) were collected, and DNA was extracted, which was used to construct libraries for sequencing by whole genome resequencing (WGS) method. Firstly, the original sequencing data was filtered by trimmomatic software to obtain high-quality sequences for comparison with chicken reference genome. The variation sites was extracted by GATK software, parameters was set for quality control to remove low quality and false positive variation sites, and further snpEff was used to annotate the gene structure and function of filtered SNPs. Then, the population structure difference between Wenchang chickens and Jianghan chickens were compared, and the ranges of Fst top 1%,top 5%, ROD top 1%,top 5%, Tajima's D bottom 1% and Bottom 5% were set to screen the selected regions, and the genes in these regions were enriched functionally. The results showed as follows: 1) A total of 1.05 Tb clean data was obtained for Wenchang chickens, with an average of 29.97 Gb (~28×) per sample; A total of 1.10 Tb of clean data was obtained for Jianghan chicken, with approximately 36.72 Gb (~35×) of each sample. The average mapping rate was more than 98%. 2) The total number of gene structure annotations in both populations was intron>intergene region>upstream and downstream regulatory region>coding region; Phylogenetic tree and principal component analysis showed that Wenchang chickens and Jianghan chickens were distant relatives. The degree of linkage disequilibrium of Wenchang chickens was lower than that of Jianghan chickens. 3) The enrichment pathways of genes related to egg production performance were mainly focused on the metabolic pathways of 3 essential amino acids (valine, leucine, isoleucine), calcium ion deposition, metallopeptidase antioxidant, adrenalin and prolactin receptor activities, and the genes in these pathways were located in strongly selected regions. In summary, the factors influencing the laying performance of Wenchang chickens mainly include essential amino acid metabolism, mineral deposition and antioxidant, endocrine hormone secretion. The 3 factors were strongly selected in the evolutionary process, and they played important roles in regulating egg production performance. The study of egg production mechanism from evolutionary molecular genetics can not only promote the understanding of the evolutionary characteristics of Wenchang chickens, but also help to accelerate the breeding of high-yield laying hens.

Key words: Wenchang chickens, whole genome resequencing(WGS), genetic selection, laying performance, influencing factors

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