Increased heterozygosity in low-pass sequencing data allows identification of blood chimeras in cattle

From cytogenetics to cytogenomics: a new era in the diagnosis of chromosomal abnormalities in domestic animals

Identification of chromosomal abnormalities is an important issue in animal breeding and veterinary medicine. Routine cytogenetic diagnosis of domestic animals began in the 1960s with the aim of identifying carriers of centric fusion between chromosome 1 and 29 in cattle. In the 1970s, chromosome banding techniques were introduced, and in the 1980s, the first cytogenomic techniques, based on the development of locus- and chromosome-specific probes, were used. Since the beginning of the twenty-first century, molecular techniques (such as polymorphism of microsatellite markers, droplet digital PCR, SNP microarrays, and whole genome sequencing) have begun to be widely used in animal breeding. This review is focused on the cytogenomic diagnosis of chromosome abnormalities in cattle, horses, pigs, dogs, and cats. We show that these approaches are very useful in large-population screening studies of the prevalence of aneuploidies (mainly of sex chromosomes) and structural rearrangements (centric fusions and reciprocal translocations).

Assessment of genome complementarity in three beef-on-dairy crossbreds reveals sire-specific effects on production traits with comparable rates of genomic inbreeding reduction

BACKGROUND

Crossbreeding beef bulls with dairy cows can improve the economic value and fitness of calves not entering dairy production owing to increased meat yield and heterosis. However, outcrossing might reduce the dosage of alleles that confer local adaptation or result in a higher risk of dystocia due to increased calf size. Given the clear phenotypic differences between beef breeds, the varying phylogenetic distances between beef and dairy breeds, and the genomic variations within breeds, the attainable economic and fitness gains of calves will strongly depend on the selection of sires for crossing. Thus, the aim of this study was to assess genome complementarity between Angus (AAN), Limousin (LIM), or Simmental (SIM) beef bulls and Brown Swiss (BSW) dairy cows by quantifying genomic inbreeding reduction in F1 crosses and identifying genes potentially under BSW-specific selection that might be affected by outcrossing.

RESULTS

Low-pass sequencing data from 181 cows, 34 bulls, and 301 of their F1 progeny, and body weight and carcass composition measurements of 248 F1s were obtained. The high genomic inbreeding levels detected in the BSW cows were substantially reduced in the crossbreds, with only minor differences between the sire breeds. In the BSW cows, 585 candidate genes under selection were identified, overrepresenting genes associated with milk, meat and carcass, and production traits. Only a few genes were strongly differentiated at nonsynonymous variants between the BSW and beef breeds, including four tightly clustered genes (FAM184B, NCAPG, DCAF16, and LCORL) nearly fixed for alternate alleles in the BSW cows but mostly heterozygous or homozygous for the reference alleles in the AAN and LIM bulls. The alternate allele dosage at these genes significantly correlated with reduced carcass weight and protein mass in F1s.

CONCLUSION

Some of the few genes that were highly divergent between the BSW and beef breeds at nonsynonymous variants were likely under strong selection for reduced carcass weight in the BSW breed, potentially due to trade-offs between beef and dairy productions. As alleles with opposing effects still segregate in beef cattle, marker-assisted selection of mating pairs may be used to modulate the desired phenotypes and simultaneously decrease genomic inbreeding.

Specificity of Key Sex Determination Genes in a Mammal with Ovotestes: The European Mole Talpa europaea

Here, for the first time, the structure of genes involved in sex determination in mammals (full Sry and partial Rspo1, Eif2s3x, and Eif2s3y) was analyzed for the European mole Talpa europaea with ovotestes in females. We confirmed male-specificity for Eif2s3y and Sry. Five exons were revealed for Rspo1 and the deep similarity with the structure of this gene in T. occidentalis was proved. The most intriguing result was obtained for the Sry gene, which, in placental mammals, initiates male development. We described two exons for this canonically single-exon gene: the first (initial) exon is only 15 bp while the second exon includes 450 bp. The exons are divided by an extended intron of about 1894 bp, including the fragment of the LINE retroposon. Moreover, in chromatogram fragments, which correspond to intron and DNA areas, flanking both exons, we revealed double peaks, similar to heterozygous nucleotide sites of autosomal genes. This may indicate the existence of two or more copies of the Sry gene. Proof of copies requires an additional in-depth study. We hypothesize that unusual structure and possible supernumerary copies of Sry may be involved in ovotestes formation.

The 'communicatome' of pregnancy: spotlight on cellular and extravesicular chimerism

Communication via biological mediators between mother and fetus are key to reproductive success and offspring's future health. The repertoire of mediators coding signals between mother and fetus is broad and includes soluble factors, membrane-bound particles and immune as well as non-immune cells. Based on the emergence of technological advancements over the last years, considerable progress has been made toward deciphering the "communicatome" between fetus and mother during pregnancy and even after birth. In this context, pregnancy-associated chimerism has sparked the attention among immunologists, since chimeric cells-although low in number-are maintained in the allogeneic host (mother or fetus) for years after birth. Other non-cellular structures of chimerism, e.g. extracellular vesicles (EVs), are increasingly recognized as modulators of pregnancy outcome and offspring's health. We here discuss the origin, distribution and function of pregnancy-acquired microchimerism and chimeric EVs in mother and offspring. We also highlight the pioneering concept of maternal microchimeric cell-derived EVs in offspring. Such insights expand the understanding of pregnancy-associated health or disease risks in mother and offspring.