Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens

Abstract

Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (p < .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.

Keywords:

• Chicken
• mtDNA
• SNPs
• association
• body measurement traits

Acknowledgements

The authors thank Shandong Jinqiu Agriculture and Animal Husbandry Technology Co. LTD in Wenshang county, Shandong province for help with samples.

Author contributions

HT designed the study. DW, JT and SL collected the sample and performed the experiments. DW and CN analyzed and interpreted the data. DW, HT, QZ and WW drafted the manuscript.

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Data availability statement

Necessary data generated during this study are included in this published article and its supplementary information files.

Additional information

Funding

The research was supported by National Natural Science Foundation of China (31872344, 32102526 and 32002172), Shandong Provincial Key Project for R&D (2019LYXZ004), Shandong ‘Double Tops’ Program (SYL2017YSTD12), China Postdoctoral Science Foundation (2020M682217), Shandong Provincial Natural Science Foundation (ZR2020QC176 and ZR2020QC175) and Shandong Provincial Postdoctoral Program for Innovative Talent.