Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs

Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs.Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify the selection signatures. To do so, the population differentiation measure, Weir-Cockerham’s F<sub>st</sub> was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features.Results: Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response to oxygen-containing compound and generation of neurons were the most enriched GO.Conclusion: The selection signatures of the JNP were identified through the population differentiation statistic. The genes with possible selection signatures are expected to play a role in JNP’s unique pork quality.

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A genome-wide scan for diversifying selection signatures in selected horse breeds

PLoS ONE ◽

10.1371/journal.pone.0210751 ◽

2019 ◽

Vol 14 (1) ◽

pp. e0210751 ◽

Cited By ~ 22

Author(s):

Artur Gurgul ◽

Igor Jasielczuk ◽

Ewelina Semik-Gurgul ◽

Klaudia Pawlina-Tyszko ◽

Monika Stefaniuk-Szmukier ◽

...

Keyword(s):

Selection Signatures ◽

Diversifying Selection ◽

Genome Wide ◽

A Genome ◽

Genome Wide Scan

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Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

Animals ◽

10.3390/ani10030524 ◽

2020 ◽

Vol 10 (3) ◽

pp. 524 ◽

Cited By ~ 3

Author(s):

Sangang He ◽

Jiang Di ◽

Bing Han ◽

Lei Chen ◽

Mingjun Liu ◽

...

Keyword(s):

Candidate Genes ◽

Average Length ◽

Inbreeding Coefficient ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Genotyping Array ◽

Genome Region ◽

Genome Wide ◽

Genomic Regions ◽

Genome Wide Scan

In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.

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