Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Wang, Xiaopeng; Li, Guixin; Ruan, Donglin; Zhuang, Zhanwei; Ding, Rongrong; Quan, Jianping; Wang, Shiyuan; Jiang, Yongchuang; Huang, Jinyan; Gu, Tao; Hong, Linjun; Zheng, Enqin; Li, Zicong; Cai, Guangyan; Wu, Zhenfang; Yang, Jie

doi:10.3389/fvets.2022.832633

Cited by 10 publications

(8 citation statements)

References 77 publications

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“…On the one hand, this may be due to the sample bias, whereas on the other hand, the difference may result from the two Duroc lines experiencing different selection directions and intensities. The later hypothesis was in line with our previous studies that S22 had more strong selection on the production performance than S21 pigs ( 34 ), and S21 may have a special selection for reproduction and S22 may have a special selection for immunity ( 43 ). In the breeding program, superior individuals always had more mating opportunities than inferior individuals, which may reduce the number of harmful ROHs in the population.…”

Section: Discussionsupporting

confidence: 86%

“…The number of significantly adverse ROHs on the economic traits (except for BFT) of S21 was larger than that of S22 pigs. The population inbreeding coefficient may be positively correlated with the number of adverse ROHs; however, our previous study found that S21 pigs had lower inbreeding levels than S22 pigs ( 43 ). On the one hand, this may be due to the sample bias, whereas on the other hand, the difference may result from the two Duroc lines experiencing different selection directions and intensities.…”

Section: Discussionmentioning

confidence: 81%

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Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Wang

Yang

et al. 2022

Front. Vet. Sci.

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Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 81%

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Wang

Yang

et al. 2022

Front. Vet. Sci.

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“…Cinta Sense and Mora Romagnola showed ROH islands already found in previous studies (Schiavo, Bovo, Bertolini, et al, 2020;Wang et al, 2022), including genes related to productive traits (Puig-Oliveras et al, 2014) and reproductive traits (Chen et al, 2019;He et al, 2017;Nonneman et al, 2016;Schneider et al, 2015). Large White and Pietrain also evidenced ROH islands previously reported with a high percentage in the same breeds (Gorssen et al, 2019;Schiavo, Bovo, Bertolini, et al, 2020).…”

Section: Roh and Rohet Islandssupporting

confidence: 73%

Genome‐wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

et al. 2023

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Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome‐wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity‐rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health‐related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.

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“…Nevertheless, none of these mechanisms can fully explain the presence of no-ROH regions, therefore other mechanisms and their combinations are likely involved. It can also be assumed that the no-ROH regions detected in this study are ROH cold spots, as described by, e.g., Wang et al [ 67 ]. These cold spot regions were suggested to be produced through high recombination rates and are likely enriched for variants with severe adverse effects on fitness in homozygotes [ 9 ].…”

Section: Discussionmentioning

confidence: 97%

Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types

Szmatoła

Gurgul

Jasielczuk

et al. 2022

Animals

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The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ROH islands, which may be signals of recent selection events. Eight to fourteen ROH islands were identified per breed, which spanned multiple genes. Many were involved in important horse breed characteristics, including WFIKNN2, CACNA1G, STXBP4, NOG, FAM184B, QDPR, LCORL, and the zinc finger protein family. Regions of the genome with zero ROH occurrences were also of major interest in specific populations. Depending on the breed, we detected between 2 to 57 no-ROH regions and identified 27 genes in these regions that were common for five breeds. These genes were involved in, e.g., muscle contractility (CACNA1A) and muscle development (miR-23, miR-24, miR-27). To sum up, the obtained results can be furthered analyzed in the topic of identification of markers unique for specific horse breed characteristics.

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Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Cited by 10 publications

References 77 publications

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs

Genome‐wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types

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