# Genetic Diversity Evaluation of Shanghai Local Pig Breeds Using Liquid-Phase Chip Technology

## TL;DR

This study uses a new DNA chip to assess genetic diversity in five local pig breeds in Shanghai, helping improve breeding strategies to conserve these populations.

## Contribution

A novel 60K SNP liquid-phase chip ('Shenxin I') was developed and applied for genetic evaluation of local pig breeds.

## Key findings

- PD and FJ breeds showed higher inbreeding levels based on genomic data.
- Optimized mating reduced inbreeding and increased genetic diversity in the Meishan population.
- Molecular pedigree construction and genomic analysis improved conservation effectiveness.

## Abstract

This study employed genotyping by target sequencing (GBTS) genotyping technology to conduct genetic evaluations of conservation populations for five local pig breeds in the Shanghai region of China, providing theoretical guidance for optimizing breeding strategies within these populations.

This study developed a 60K single-nucleotide polymorphism (SNP) liquid-phase chip (‘Shenxin I’) based on genotyping by target sequencing (GBTS) technology. The chip was used to genotype 1451 individuals spanning five conserved local pig breeds: Fengjing (FJ), Meishan (MMS), Pudong White (PD), Shaowutou (SW), and Shanghai White (SHW), and newborn purebred Meishan offspring (MMS_New). The study assessed the genetic diversity, population structure, and genomic breed composition (GBC) of these breeds. The GBC analysis provided insights into genomic introgression within admixed individuals. Results indicate that PD and FJ breeds exhibited the higher fraction of the genome covered by runs of homozygosity (FROH) and slower linkage disequilibrium (LD) decay rate, suggesting higher genetic inbreeding level in these two breeds. The study conducted genetic distance of identity-by-state (IBS) analysis and molecular pedigree construction for the MMS population. Subsequently, purebred mating was implemented by selecting boars from different pedigrees to mate with sows and excluding individuals with high inbreeding coefficients from the breeding program. This resulted in a significant reduction in the overall inbreeding level of the born progeny and an increase in genetic diversity compared to the original population. Consequently, the study concludes that utilizing liquid-phase chip technology for genotyping, constructing molecular pedigrees, and optimizing mating combinations in small populations of locally conserved pig breeds contributes to enhancing the conservation effectiveness.