Mitochondrial genome sequencing reveals mitochondrial single nucleotide polymorphisms and DNA haplotypes associated with egg-laying performance in chickens.

The relationship between mitochondrial single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) haplotypes and production performance in poultry has been widely reported. Here, the study aimed to investigate the association between mitochondrial SNPs or mtDNA haplotypes and egg-laying performance in Jingmen black-feathered green-shelled laying hens. Egg-laying performance data, including age at first egg (AE) and total egg number by 300 days of age (TE), were collected from 474 hens. Whole mitochondrial genome sequencing was performed using blood-derived DNA to identify mitochondrial SNPs and mtDNA haplotypes, and their associations with egg-laying performance were subsequently evaluated. A total of 101 SNPs were identified in this study. These SNPs were classified into 3 major linkage groups (A, B, and C) and 5 minor subgroups (D-H). Linkage groups A, F and H were significantly associated with TE in hens. The SNP site exerting the strongest effect on TE was 15944C/A/T; hens carrying the A genotype at this locus produced the highest number of eggs by 300 days of age (103.23 eggs), with a maximum SNP effect value of 15.96 eggs and the relative phenotypic difference of 15.46%. Haplotypes within the COX1, ND5 and d-loop region/MIT were significantly associated with TE. The haplotype exerting the strongest effect on total egg number by 300 days of age was identified across the d-loop region and comprised 14 SNPs. Hens carrying the L5 haplotype produced the highest number of eggs by 300 days of age (103.23 eggs), with a maximum SNP effect value of 16.15 eggs and the relative phenotypic difference of 15.65%. However, no mitochondrial SNPs or mtDNA haplotypes were significantly associated with AE. In conclusion, this study not only fills the knowledge gap regarding mitochondrial SNPs and mtDNA haplotypes in Jingmen black-feathered green-shelled laying hens, but also identifies SNPs and haplotypes associated with egg-laying performance, providing an important theoretical basis for the future selection of high-producing hens using mitochondrial genetic markers.