Genome‐wide association analysis for growth, muscularity and meat quality in Piétrain pigs

Stratz, Patrick; Wellmann, Robin; Preuß, Siegfried; Wimmers, Klaus; Bennewitz, Jörn

doi:10.1111/age.12133

Cited by 15 publications

(24 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genomic tools are increasingly important in livestock conservation and selection (Lenstra et al 2012). Pietrain is under strong management regarding pig performance; therefore, clear selection signals are present in the population (Stratz et al 2014). We have shown that selection signatures are weakened when the focus is solely on optimizing diversity.…”

Section: Impact Of Management On Selection Goalsmentioning

confidence: 89%

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

et al. 2015

View full text Add to dashboard Cite

Conservation and breeding programs aim at maintaining the most diversity, thereby avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, the most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequencing data and use them in population management. We analyzed the resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analyzing the demographic history of Sus cebifrons, we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analyzed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness, and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved the best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programs.

show abstract

Section: Impact Of Management On Selection Goalsmentioning

confidence: 89%

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

et al. 2015

View full text Add to dashboard Cite

show abstract

“…The same filtering criteria as in Stratz et al . () were used to compare the results of both studies. Genotypes from individuals were filtered with respect to call rate (removal of SNPs with a call rate less than 95%), parent–progeny conflicts (removal of SNPs with parent–progeny conflict greater than 2%), MAF (exclusion of SNP with a minor allele frequency less than 3%) and significant deviation from the Hardy–Weinberg equilibrium (p ‐ value < 0.0001).…”

Section: Methodsmentioning

confidence: 99%

“…It can be speculated that sites in the genome at which we know selection has occurred (Stratz et al . ) coincide with selective sweeps (Qanbari et al . ).…”

Section: Introductionmentioning

confidence: 90%

“…() for genomic selection and by Stratz et al . () for association analysis. In the study of Stratz et al .…”

Section: Introductionmentioning

confidence: 99%

“…In the study of Stratz et al . (), around 500 progeny‐tested sires from three different breeding organizations were genotyped with 60 k PorcineSNP60 BeadChip SNPs. After data filtering, around 48 k SNPs were used.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs

Stratz

Wimmers

Meuwissen

et al. 2014

J Animal Breeding Genetics

Self Cite

View full text Add to dashboard Cite

The aim of this study was to study the population structure, to characterize the LD structure and to define core regions based on low recombination rates among SNP pairs in the genome of Piétrain pigs using data from the PorcineSNP60 BeadChip. This breed is a European sire line and was strongly selected for lean meat content during the last decades. The data were used to map signatures of selection using the REHH test. In the first step, selection signatures were searched genome-wide using only core haplotypes having a frequency above 0.25. In the second step, the results from the selection signature analysis were matched with the results from the recently conducted genome-wide association study for economical relevant traits to investigate putative overlaps of chromosomal regions. A small subdivision of the population with regard to the geographical origin of the individuals was observed. The extent of LD was determined genome-wide using r(2) values for SNP pairs with a distance ≤5 Mb and was on average 0.34. This comparable low r(2) value indicates a high genetic diversity in the Piétrain population. Six REHH values having a p-value < 0.001 were genome-wide detected. These were located on SSC1, 2, 6 and 17. Three positional candidate genes with potential biological roles were suggested, called LOC100626459, LOC100626014 and MIR1. The results imply that for genome-wide analysis especially in this population, a higher marker density and higher sample sizes are required. For a number of nine SNPs, which were successfully annotated to core regions, the REHH test was applied. However, no selection signatures were found for those regions (p-value < 0.1).

show abstract

Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs

et al. 2015

View full text Add to dashboard Cite

Meat quality traits have economically significant impacts on the pig industry, and can be improved using molecular approaches in pig breeding. Since 1994 when the first genome-wide scan for quantitative trait loci (QTLs) in pig was reported, over the past two decades, numerous QTLs have been identified for meat quality traits by family based linkage analyses. However, little is known about the genetic variants for meat quality traits in Chinese purebred or outbred populations. To unveil it, we performed a genome-wide association study for 10 meat quality traits in Chinese purebred Laiwu pigs. In total, 75 significant SNPs (P < 1.01 × 10(-6)) and 33 suggestive SNPs (P < 2.03 × 10(-5)) were identified. On SSC12, a region between 56.22 and 61.49 Mb harbored a cluster of SNPs that were associated with meat color parameters (L*, lightness; a*, redness; b*, yellowness) and moisture content of longissimus muscle (LM) and semimembranosus muscle at the genome-wide significance level. A region on SSC4 also has pleiotropic effects on moisture content and drip loss of LM. In addition, this study revealed at least five novel QTLs and several candidate genes including 4-linked MYH genes (MYH1, MYH2, MYH3, and MYH13), MAL2, LPAR1, and PRKAG3 at four significant loci. Except for the SSC12 QTL, other QTLs are likely tissue-specific. These results provide new insights into the genetic basis of meat quality traits in Chinese Laiwu pigs and some significant SNPs reported here could be incorporated into the selection programs involving this breed.

show abstract

Genome‐wide association analysis for growth, muscularity and meat quality in Piétrain pigs

Cited by 15 publications

References 28 publications

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Investigations on the pattern of linkage disequilibrium and selection signatures in the genomes of German Piétrain pigs

Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs

Contact Info

Product

Resources

About