Analysis of bovine growth hormone gene polymorphism of local and Holstein cattle breeds in Kerman province of Iran using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP)

Bovine growth hormone (bGH) gene is a part of the multiple gene family that contains prolactin and placental lactogens. Also, variations in introns have potential usefulness as genetic markers and could help in the genetic improvement of populations. Genomic DNA was isolated from blood samples of two local herds (53 animals) and two Holstein herds (50 animals). Genomic DNA samples were genotyped for the GHI-AluI polymorphism by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). A 211 bp (bGH) gene exon 5 segment was amplified by PCR using bovine specific primers. RFLPs in this segment were studied using AluI restriction enzyme. The frequencies of V and L alleles in the local and Holstein herds were 0.2 and 0.65, respectively. For both herds, significant difference from the Hardy-Weinberg equilibrium was observed.Key words: Growth hormone, polymorphism, polymerase chain reaction restriction fragment length polymorphism, local herds, Holstein herds

Association of the exon 9 single nucleotide polymorphism of CAPN1 with beef tenderness

The document attached has been archived with permission from the Association for the Advancement of Animal Breeding and Genetics.Initial data analysis from both the University of Adelaide’s Davies Cattle Gene Mapping and the New Zealand AgResearch Cattle Gene Mapping Projects showed a tenderness quantitative trait locus (QTL) on BTA29. Based on its function and location, the gene for micromolar calcium-activated neutral protease or calpain gene (CAPN1) was considered to be a strong positional candidate for the observed QTL effects. The objective of this study was to assess the association of a previously reported single nucleotide polymorphism (SNP) in Exon 9 of CAPN1 with the tenderness of M. longissimus dorsi (LD) and M. semitendinosus (ST) muscles in Bos taurus. The SNP (base 5709) causes the amino acid substitution of alanine for glycine316 [superscript] in the μ-calpain enzyme. Results demonstrated that the Exon 9 SNP was significantly associated with tenderness of both ST and LD muscles (P<0.01). Animals with the GG genotype showed higher (P<0.01) shear force values compared with CC genotypes (15% and 11% on day 1 and 14% and 11% on day 26 in LD and ST, respectively). The paternal allele encoding glycine at position 316 was associated with decreased meat tenderness relative to the allele encoding alanine at position 316. The equivalent maternal allele for CAPN1 Exon 9 was significantly associated with decreased tenderness of LD at four cook times and ST at day 1

QTL for meat colour and pH IN Bos Taurus cattle

The document attached has been archived with permission from the Association for the Advancement of Animal Breeding and Genetics.An experimental cattle backcross between the Jersey and Limousin breeds was performed in Australia and New Zealand to map quantitative trait loci (QTL) for diverse production traits. Six crossbred sires and their progeny were genotyped for 253 informative microsatellite markers covering the 29 bovine autosomes. This study reports the results for meat colour and pH recorded on 355 backcross animals in Australia. Results of the genome scan using regression interval mapping revealed evidence for QTL (<5% chromosome-wise level) on BTA10, 18, 19, and 27 for meat colour and BTA2, 3, 5, 6, 11, 12, 13, 16, 24 and 27 for meat pH. A number of detected QTL were mapped to genomic regions likely to contain the 'RN' or 'RYR1' genes, which are known to affect meat quality traits in pigs

Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway

Paternal Origins and Migratory Episodes of Domestic Sheep

Deng et al. show that domestic sheep harbor four Y chromosome lineages and early expansions of sheep were associated with the segregation of primitive and fat-tailed phenotypes as well as traits selected for different purposes

The origin of domestication genes in goats

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically

Paternal Origins and Migratory Episodes of Domestic Sheep

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (similar to 16.10x) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, similar to 121.2 million single nucleotide polymorphisms, similar to 61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3 '-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep

AdaptMap: exploring goat diversity and adaptation

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