A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond

Abstract

Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1–5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

“…In recent years, due to the extensive utilization of SNP microarray gene chip and whole-genome resequencing technologies [8][9][10][11], research into ROHs based on livestock and poultry genomic information has been increasing. This includes research on various species, such as goats [12][13][14], sheep [15][16][17], cattle [7,18,19], pigs [3,20,21], chickens [22][23][24] and so on. Genomic regions that were abundant with ROHs were defined as ROH islands, potentially signaling selection sweeps.…”

“…Genomic regions that were abundant with ROHs were defined as ROH islands, potentially signaling selection sweeps. For instance, in cattle, pigs and sheep, some ROH islands have been discovered to correlate with genes related to reproduction, immune function and local adaptability [13,16,18,20]. ROHs also can be utilized as a useful tool to evaluate genetic diversity and inbreeding, providing insights into both recent and ancient inbreeding through the analysis of short and long ROH segments, respectively [25].…”

Classification of breed combinations for slaughter pigs based on genotypes—modeling DNA samples of crossbreeds as fuzzy sets from purebred founders

“…Most methods used to infer breed combinations in pig populations with genomic data were originally developed for inferring human ancestry. ADMIXTURE ( Alexander et al, 2009 ) is one of the most popular methods used to classify individuals with an unknown ancestry into discrete populations and was developed for human populations but has been used extensively in pigs to trace commercial ( Huang et al, 2014 ) or indigenous pig breeds ( Mujibi et al, 2018 ; Dadousis et al, 2022 ; Kim et al, 2022 ; Yin et al, 2023 ). Principal component-based algorithms for determining the ancestry have also been developed, such as PCAdmix ( Brisbin et al, 2012 ), and applied in pig populations ( Schleimer et al, 2022 ).…”