Haplotype‐based genome‐wide association studies reveal new loci for haematological and clinical–biochemical parameters in Large White pigs

Bovo, Samuele; Ballan, Mohamad; Schiavo, Giuseppina; Gallo, M.; Dall’Olio, Stefania

doi:10.1111/age.12959

Cited by 10 publications

(12 citation statements)

References 27 publications

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“…It is also clear that alleles (haplotypes) with low MAF could potentially identify falsepositive QTL regions. However, higher estimated genomic heritability of the haplotype analysis in this breed might indicate that most of the haplotype-detected QTL regions are actually true QTL regions, as we already reported in another study using a similar approach (Bovo et al 2020a). Moreover, the low MAF at several QTL regions in this breed (captured by the haplotypes; Fig.…”

Section: Discussionsupporting

confidence: 61%

“…GWAS may benefit from utilising haplotypes instead of SNPs to establish marker‐phenotype associations (Lorenz et al 2010 ; Barendse 2011 ). We recently demonstrated that by using haplotypes in GWAS it is possible to detect genomic regions affecting targeted phenotypes that could not be detected with a single‐marker approach and vice versa (Bovo et al 2019 , 2020a ). The additional information that could be extracted might be dependent on the particular mutational and recombination history between QTL alleles and the genotyped markers, which in turn, might be affected by possible ascertainment biases derived by the construction of the SNP genotyping panels used in the studies.…”

Section: Introductionmentioning

confidence: 99%

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Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds

et al. 2021

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Summary The number of teats is a reproductive‐related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single‐marker and haplotypes‐based genome‐wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype‐based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single‐marker and haplotype‐based genome‐wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs.

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Section: Discussionsupporting

confidence: 61%

Section: Introductionmentioning

confidence: 99%

Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds

et al. 2021

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“…First QTL were detected using microsatellites (e.g., [ 26 , 27 ]) or concentrated on particular genes (e.g., [ 28 – 30 ]). Other studies to detect immune relevant QTL vary widely in treatment, methods of phenotype determination and breed (e.g., [ 10 , 31 – 37 ]). In addition, different ages and developmental stages are covered, limiting the comparability of the studies.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide associations for immune traits in two maternal pig lines

et al. 2021

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Background In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and inflammation. Previous studies have shown moderate to high heritabilities in most of these traits. However, the genetic background of health and robustness of pigs needs to be extensively clarified. The objective of this study was to identify genomic regions with a biological relevance for the immunocompetence of piglets. Genome-wide Association Studies (GWAS) in 535 Landrace (LR) and 461 Large White (LW) piglets were performed, investigating 20 immune relevant traits. Besides the health indicators of the complete and differential blood count, eight different cytokines and haptoglobin were recorded in all piglets and their biological dams to capture mediating processes and acute phase reactions. Additionally, all animals were genotyped using the Illumina PorcineSNP60v2 BeadChip. Results In summary, GWAS detected 25 genome-wide and 452 chromosome-wide significant SNPs associated with 17 immune relevant traits in the two maternal pig lines LR and LW. Only small differences were observed considering the maternal immune records as covariate within the statistical model. Furthermore, the study identified across- and within-breed differences as well as relevant candidate genes. In LR more significant associations and related candidate genes were detected, compared with LW. The results detected in LR and LW are partly in accordance with previously identified quantitative trait loci (QTL) regions. In addition, promising novel genomic regions were identified which might be of interest for further detailed analysis. Especially putative pleiotropic regions on SSC5, SSC12, SSC15, SSC16 and SSC17 are of major interest with regard to the interacting structure of the immune system. The comparison with already identified QTL gives indications on interactions with traits affecting piglet survival and also production traits. Conclusion In conclusion, results suggest a polygenic and breed-specific background of immune relevant traits. The current study provides knowledge about regions with biological relevance for health and immune traits. Identified markers and putative pleiotropic regions provide first indications in the context of balancing a breeding-based modification of the porcine immune system.

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“…Although the same algorithm to obtain the haplotype blocks was used in our study and in Veroneze et al (2013), they used a threshold of at least 3 SNPs (we used 2). On the other hand, the number of haplotype blocks identified in our population was smaller than the number of haplotype blocks identified in a Large White population of 21,296 (Bovo et al, 2020). LD is expected to be lower in crossbred populations and, consequently, the number of haplotype blocks is also expected to be smaller than in purebred lines (Fu et al, 2015).…”

Section: Identification Of Haplotypescontrasting

confidence: 66%

Genetic and phenotypic indicator traits for reproductive performance in commercial sows

Sanglard¹,

Leticia²

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Haplotype‐based genome‐wide association studies reveal new loci for haematological and clinical–biochemical parameters in Large White pigs

Cited by 10 publications

References 27 publications

Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds

Single‐marker and haplotype‐based genome‐wide association studies for the number of teats in two heavy pig breeds

Genome-wide associations for immune traits in two maternal pig lines

Genetic and phenotypic indicator traits for reproductive performance in commercial sows

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