Development of High-Density SNP Markers for Evaluating Genetic Diversity
and Population Structure in Pingwu Red Chicken
Abstract
Broilers supply humans with an abundance of high-quality chicken, and
the utilization of local poultry genetic variety is crucial for the
development of high-performing and efficient broiler breeders. Pingwu
red chicken is an outstanding native poultry genetic resource in Sichuan
Province, yet research on Pingwu red chicken DNA polymorphism lags
behind that of standard broiler breeds. To uncover the genetic variety
of Pingwu red chickens, blood genomic DNA from 18 Pingwu red chickens
was extracted, and high-throughput locus-specific amplified fragment
sequencing (SLAF-seq) was utilized for SNP marker analysis and
phylogenetic tree construction. To investigate the genetic evolutionary
relationship of Pingwu red chickens, a total of 952,944 high-quality
SNPs (integrity > 0.5 and MAF > 0.05) and SLAF
fragments were gathered, according to the study. This study successfully
uncovered the genetic foundation of Pingwu red chicken, indicating the
existence of three tiny clusters across all samples. Specific-length
amplified fragment sequencing (SLAF-seq) is a high-resolution technique
for identifying and genotyping de novo SNPs. This study concludes that
slaf-seq is an effective method for revealing the genetic variety of
Pingwu red chickens and provides a scientific basis for its use in
Pingwu red chicken evolution.