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

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

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

A predictive assessment of genetic correlations between traits in chickens using markers

International audienceAbstractBackgroundGenomic selection has been successfully implemented in plant and animal breeding programs to shorten generation intervals and accelerate genetic progress per unit of time. In practice, genomic selection can be used to improve several correlated traits simultaneously via multiple-trait prediction, which exploits correlations between traits. However, few studies have explored multiple-trait genomic selection. Our aim was to infer genetic correlations between three traits measured in broiler chickens by exploring kinship matrices based on a linear combination of measures of pedigree and marker-based relatedness. A predictive assessment was used to gauge genetic correlations.MethodsA multivariate genomic best linear unbiased prediction model was designed to combine information from pedigree and genome-wide markers in order to assess genetic correlations between three complex traits in chickens, i.e. body weight at 35 days of age (BW), ultrasound area of breast meat (BM) and hen-house egg production (HHP). A dataset with 1351 birds that were genotyped with the 600 K Affymetrix platform was used. A kinship kernel (K) was constructed as K = λG + (1 − λ)A, where A is the numerator relationship matrix, measuring pedigree-based relatedness, and G is a genomic relationship matrix. The weight (λ) assigned to each source of information varied over the grid λ = (0, 0.2, 0.4, 0.6, 0.8, 1). Maximum likelihood estimates of heritability and genetic correlations were obtained at each λ, and the “optimum” λ was determined using cross-validation.ResultsEstimates of genetic correlations were affected by the weight placed on the source of information used to build K. For example, the genetic correlation between BW–HHP and BM–HHP changed markedly when λ varied from 0 (only A used for measuring relatedness) to 1 (only genomic information used). As λ increased, predictive correlations (correlation between observed phenotypes and predicted breeding values) increased and mean-squared predictive error decreased. However, the improvement in predictive ability was not monotonic, with an optimum found at some 0 < λ < 1, i.e., when both sources of information were used together.ConclusionsOur findings indicate that multiple-trait prediction may benefit from combining pedigree and marker information. Also, it appeared that expected correlated responses to selection computed from standard theory may differ from realized responses. The predictive assessment provided a metric for performance evaluation as well as a means for expressing uncertainty of outcomes of multiple-trait selection

Using PCR-SSCP technique to investigate polymorphism of leptin gene in Kermani sheep

شناسایی ژنهاي موثر بر تعادل انرژي، تولید شیر و مصرف خوراك از علاقهمنديهاي اخیر پژوهشگران اصلاح نژاداست. در ایران علی رغم وجود منابع غنی حیوانی، تلاشهاي اندکی براي شناسایی ژنهاي کنترل کنندهي صفات درآنها صورت گرفته است. بنابراین، شناسایی ژنهاي کاندیداي موثر بر صفات اقتصادي میتواند به اصلاح نژاد گوسفنددر کشور کمک شایانی نماید. در این تحقیق براي بررسی چند شکلی ژن لپتین از 120 رأس گوسفند نر و مادهي کرمانیایستگاه اصلاح نژاد شهر بابک خونگیري شد. پس از استخراج DNA با استفاده از کیت استخراج استاندارد، واکنشزنجیرهاي پلیمراز براي تکثیر قطعهي 275 جفت بازي از اگزون سوم این ژن انجام شد. پس از تعیین چند شکلی فضاییتکرشتهاي، محصولات PCR ،الگوهاي باندي مربوط به ژن لپتین با استفاده از ژل آکریل آمید و رنگ آمیزي نیترات،A/B/F ،A/B/E ،A/B/C ،A/C ،A/B ،C/C ،A/A الگوي 10 ،مطالعه مورد نمونهي در لپتین ژن براي. آمد بدست، نقرهF/C/A ،E/D/B/A وF/C/B/A بدست آمد که نشان دهندهي چندشکلی بالاي در ژن لپتین گوسفندان نژاد کرمانی می-باشد

Effects of the myostatin F94L substitution on beef traits

This study investigated the effects of a SNP in the myostatin gene (MSTN or growth differentiation factor 8, GDF8) on birth, growth, carcass, and beef quality traits in Australia (Aust.) and New Zealand (NZ). The SNP is a cytosine to adenine transversion in exon 1, causing an amino acid substitution of leucine for phenylalanine94 (F94L). The experiment used crosses between the Jersey and Limousin breeds, with the design being a backcross using first-cross bulls of Jersey x Limousin or Limousin x Jersey breeding, mated to Jersey and Limousin cows. Progeny were genotyped for the myostatin SNP and phenotyped in Aust., with finishing on feedlot (366 calves, over 3 birth years) and in NZ with finishing on pasture (416 calves, over 2 birth years). The effect of the F94L allele (A allele) on birth and growth traits was not significant. The F94L allele in Limousin backcross calves was associated with an increase in meat weight (7.3 and 5.9% of the trait mean in Aust. and NZ, respectively, P < 0.001), and a reduction in fat depth (–13.9 and –18.7% of the trait means on live calves (600 d) and carcasses, respectively, Aust. only, P < 0.001), intramuscular fat content (–8.2% of the trait mean in Aust., P < 0.05; –7.1% in NZ, not significant), total carcass fat weight (–16.5 and –8.1% of the trait mean, Aust. and NZ; P < 0.001 and P < 0.05, respectively). Meat tenderness, pH, and cooking loss of the M. longissimus dorsi were not affected by the F94L variant. In the Jersey backcross calves, additive and dominance effects were confounded because the F94L allele was not segregating in the Jersey dams. The combined effects, however, were significant on LM area (4.4% in both Aust., P < 0.05, and NZ, P < 0.01), channel fat (–11.7%, NZ only, P < 0.01), rib fat depth (–11.2%, NZ only, P < 0.05), and carcass fat weight (–7.1%, NZ only, P < 0.05). The results provide strong evidence that this myostatin F94L variant provides an intermediate and more useful phenotype than the more severe double-muscling phenotype caused by knockout mutations in the myostatin gene.A. K. Esmailizadeh, C. D. K. Bottema, G. S. Sellick, A. P. Verbyla, C. A. Morris, N. G. Cullen and W. S. Pitchfor

Out of Southern East Asia of the brown rat revealed by large-scale genome sequencing

The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat