SNV and haplotype analysis reveals new CSRP1 variants associated with growth and carcass traits

The cysteine and glycine-rich protein 1 and 2 genes (CSRP1 and CSRP2) are an effective growth factor in promoting skeletal muscle growth in vitro and vivo. However, in cattle, the information on the CSRP1 and CSRP2 genes is very limited. The aim of this study was to examine the association of the CSRP1 and CSRP2 variants with growth and carcass traits in cattle breeds. Three single nucleotide variants (SNVs) were identified within the bovine CSRP1 gene, whereas CSRP2 gene has not detected any SNVs, using DNA pooled sequencing, PCR-RFLP, and forced PCR-RFLP methods. These SNVs include g. 801T>C (Intron 2), g. 46T>C (Exon 3) and g. 99C>G (Intron 3). Besides, we also investigated haplotype frequencies and linkage disequilibrium (LD) coefficients for three SNVs in all study populations. LD and haplotype structure of CSRP1 were different between breeds. The result of haplotype analysis demonstrated eight haplotype present in QC (Qinchuan) and one haplotype in CH (Chinese Holstein). Only haplotype 1 (TTC), shared by all two populations, comprised 10.74% and 100.00%, of all haplotypes observed in QC and CH, respectively. Haplotype 5 (CTC) had the highest haplotype frequencies in QC (30.98%) and haplotype 1 had the highest haplotype frequencies in CH (100.00%). The statistical analyses indicated that one single SNV and 19 combined haplotypes were significantly or highly significantly associated with growth and carcass traits in the QC cattle population (P < 0.05 or P < 0.01). Quantitative real-time PCR (qRT-PCR) analyses showed that the bovine CSRP1 and CSRP2 genes were widely expressed in many tissues. The results of this study suggest that the CSRP1 gene possibly is a strong candidate gene that affects growth and carcass traits in the Chinese beef cattle breeding.     

Rhh: an R extension for estimating multilocus heterozygosity and heterozygosity-heterozygosity correlation

Individual multilocus heterozygosity estimates based on a limited number of loci are expected to correlate only weakly with the inbreeding level of an individual. Before using multilocus heterozygosity estimates in studies of inbreeding, their ability to capture information on inbreeding in the given setting should be tested. A convenient method for this is to compute the heterozygosity-heterozygosity correlation, i.e. the mean correlation between multilocus heterozygosity estimates calculated from random samples of loci, which should be positive if multilocus heterozygosity carries a signature of inbreeding. Rhh is an extension package for the statistical software r that estimates this correlation and calculates three measures of individual multilocus heterozygosity: homozygosity by loci, internal relatedness and standardized heterozygosity. The extension package is available through the CRAN (http://cran.r-project.org) and has a homepage at http://www.helsinki.fi/biosci/egru/research/software.     

Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions

Background

Genome signatures of artificial selection in U.S. Jersey cattle were identified by examining changes in haplotype homozygosity for a resource population of animals born between 1953 and 2007. Genetic merit of this population changed dramatically during this period for a number of traits, especially milk yield. The intense selection underlying these changes was achieved through extensive use of artificial insemination (AI), which also increased consanguinity of the population to a few superior Jersey bulls. As a result, allele frequencies are shifted for many contemporary animals, and in numerous cases to a homozygous state for specific genomic regions. The goal of this study was to identify those selection signatures that occurred after extensive use of AI since the 1960, using analyses of shared haplotype segments or Runs of Homozygosity. When combined with animal birth year information, signatures of selection associated with economically important traits were identified and compared to results from an extended haplotype homozygosity analysis.

Results

Overall, our results reveal that more recent selection increased autozygosity across the entire genome, but some specific regions increased more than others. A genome-wide scan identified more than 15 regions with a substantial change in autozygosity. Haplotypes found to be associated with increased milk, fat and protein yield in U.S. Jersey cattle also consistently increased in frequency.

Conclusions

The analyses used in this study was able to detect directional selection over the last few decades when individual production records for Jersey animals were available.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1500-x) contains supplementary material, which is available to authorized users.     

High-throughput sequencing to decipher the genetic heterogeneity of deafness

Identifying genes causing non-syndromic hearing loss has been challenging using traditional approaches. We describe the impact that high-throughput sequencing approaches are having in discovery of genes related to hearing loss and the implications for clinical diagnosis.     

Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century

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No postcopulatory selection against MHC‐homozygous offspring: Evidence from a pedigreed captive rhesus macaque colony

The heterozygosity status of polymorphic elements of the immune system, such as the major histocompatibility complex (MHC), is known to increase the potential to cope with a wider variety of pathogens. Pre‐ and postcopulatory processes may regulate MHC heterozygosity. In a population where mating occurs among individuals that share identical MHC haplotypes, postcopulatory selection may disfavour homozygous offspring or ones with two MHC haplotypes identical to its mother. We tested these ideas by determining the incidence of MHC‐heterozygous and MHC‐homozygous individuals in a pedigreed, partially consanguineous captive rhesus monkey colony. Bayesian statistics showed that when parents share MHC haplotypes, the distribution of MHC‐heterozygous and MHC‐homozygous individuals significantly fitted the expected Mendelian distribution, both for the complete MHC haplotypes, and for MHC class I or II genes separately. Altogether, we found in this captive colony no evidence for postcopulatory selection against MHC‐homozygous individuals. However, the distribution of paternally and maternally inherited MHC haplotypes tended to differ significantly from expected. Individuals with two MHC haplotypes identical to their mother were underrepresented and offspring with MHC haplotypes identical to their father tended to be overrepresented. This suggests that postcopulatory processes affect MHC haplotype combination in offspring, but do not prevent low MHC heterozygosity.     

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive,non‐random SNP heterozygosity

Local breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350‐year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high‐density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62–90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r² = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.