Multiple Origins and Genomic Basis of Complex Traits in Sighthounds.

Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.

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 (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼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.

Impact of inclusion non-additive effects on genome-wide association and variance's components in Scottish black sheep.

CONTEXT: It's well-documented that most economic traits have a complex genetic structure that is controlled by additive and non-additive gene actions. Hence, knowledge of the underlying genetic architecture of such complex traits could aid in understanding how these traits respond to the selection in breeding and mating programs. Computing and having estimates of the non-additive effect for economic traits in sheep using genome-wide information can be important because; non-additive genes play an important role in the prediction accuracy of genomic breeding values and the genetic response to the selection. AIM: This study aimed to assess the impact of non-additive effects (dominance and epistasis) on the estimation of genetic parameters for body weight traits in sheep. METHODS: This study used phenotypic and genotypic belonging to 752 Scottish Blackface lambs. Three live weight traits considered in this study were included in body weight at 16, 20, and 24 weeks). Three genetic models including additive (AM), additive + dominance (ADM), and additive + dominance + epistasis (ADEM), were used. KEY RESULTS: The narrow sense heritability for weight at 16 weeks of age (BW16) were 0.39, 0.35, and 0.23, for 20 weeks of age (BW20) were 0.55, 0.54, and 0.42, and finally for 24 weeks of age (BW24) were 0.16, 0.12, and 0.02, using the AM, ADM, and ADEM models, respectively. The additive genetic model significantly outperformed the non-additive genetic model (p < 0.01). The dominance variance of the BW16, BW20, and BW24 accounted for 38, 6, and 30% of the total phenotypic, respectively. Moreover, the epistatic variance accounted for 39, 0.39, and 47% of the total phenotypic variances of these traits, respectively. In addition, our results indicated that the most important SNPs for live weight traits are on chromosomes 3 (three SNPS including s12606.1, OAR3_221188082.1, and OAR3_4106875.1), 8 (OAR8_16468019.1, OAR8_18067475.1, and OAR8_18043643.1), and 19 (OAR19_18010247.1), according to the genome-wide association analysis using additive and non-additive genetic model. CONCLUSIONS: The results emphasized that the non-additive genetic effects play an important role in controlling body weight variation at the age of 16-24 weeks in Scottish Blackface lambs. IMPLICATIONS: It is expected that using a high-density SNP panel and the joint modeling of both additive and non-additive effects can lead to better estimation and prediction of genetic parameters.

Comparison of genetic diversity and phylogenetic structure of BRCA1 gene of some domestic and wild sheep breeds in different countries.

BRCA1 gene plays an important role in DNA damage repair, cell cycle, and transcription process regulation; hence it's called gate keeper. The current research aims to perform bioinformatics analyzes of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 14 countries using the NCBI genome database. The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. The number of mutations, nucleotide diversity, and haploid diversity were also analyzed using Dnaspv5 software. The analyses showed 296 polymorphisms, which led to the creation of 45 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences among breeds were estimated as 0.259 and 0.052, respectively. The average genetic distance within the population of countries was calculated as 0.052. The amount of sequence conservation in this research was 0.313 on average, which indicates the high polymorphism of this gene and the emergence of new proteins. Tajima's D value in Tajima's neutrality test was -2.421, which was significant (p < 0.05). One of the reasons for the high genetic diversity in Iran's wild sheep population is the existence of forests and open environments, which prevent genetic drift and reduce inbreeding.

Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens.

BACKGROUND: Understanding how evolutionary forces relating to climate have shaped the patterns of genetic variation within and between species is a fundamental pursuit in biology. Iranian indigenous chickens have evolved genetic adaptations to their local environmental conditions, such as hot and arid regions. In the present study, we provide a population genome landscape of genetic variations in 72 chickens representing nine Iranian indigenous ecotypes (Creeper, Isfahan, Lari, Marand, Mashhad, Naked neck, Sari, Shiraz and Yazd) and two commercial lines (White Leghorn and Arian). We further performed comparative population genomics to evaluate the genetic basis underlying variation in the adaptation to hot climate and immune response in indigenous chicken ecotypes. To detect genomic signatures of adaptation, we applied nucleotide diversity (θπ) and FST statistical measurements, and further analyzed the results to find genomic regions under selection for hot adaptation and immune response-related traits. RESULTS: By generating whole-genome data, we assessed the relationship between the genetic diversity of indigenous chicken ecotypes and their genetic distances to two different commercial lines. The results of genetic structure analysis revealed clustering of indigenous chickens in agreement with their geographic origin. Among all studied chicken groups, the highest level of linkage disequilibrium (LD) (~ 0.70) was observed in White Leghorn group at marker pairs distance of 1 Kb. The results from admixture analysis demonstrated evidence of shared ancestry between Arian individuals and indigenous chickens, especially those from the north of the country. Our search for potential genomic regions under selection in indigenous chicken ecotypes revealed several immune response and heat shock protein-related genes, such as HSP70, HSPA9, HSPH1, HSP90AB1 and PLCB4 that have been previously unknown to be involved in environmental-adaptive traits. In addition, we found some other candidate loci on different chromosomes probably related with hot adaptation and immune response-related traits. CONCLUSIONS: The work provides crucial insights into the structural variation in the genome of Iranian indigenous chicken ecotypes, which up to now has not been genetically investigated. Several genes were identified as candidates for drought, heat tolerance, immune response and other phenotypic traits. These candidate genes may be helpful targets for understanding of the molecular basis of adaptation to hot environmental climate and as such they should be used in chicken breeding programs to select more efficient breeds for desert climate.

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep.

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Large-scale genomic analysis reveals the genetic cost of chicken domestication.

BACKGROUND: Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. RESULTS: We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. CONCLUSION: This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations.

Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.

Genome-wide DNA arrays profiling unravels the genetic structure of Iranian sheep and pattern of admixture with worldwide coarse-wool sheep breeds.

Archaeological and genetic evidence show that sheep were originally domesticated in area around the North of Zagros mountains, North-west of Iran. The Persian plateau exhibits a variety of native sheep breeds with a common characteristic of coarse-wool production. Therefore, knowledge about the genetic structure and diversity of Iranian sheep and genetic connections with other sheep breeds is of great interest. To this end, we genotyped 154 samples from 11 sheep breeds distributed across Iran with the Ovine Infinium HD SNP 600 K BeadChip array, and analyzed this dataset combined with the retrieved data of 558 samples from 19 worldwide coarse-wool sheep breeds. The average genetic diversity ranged from 0.315 to 0.354, while the FST values ranged from 0.016 to 0.177 indicating a low differentiation of Iranian sheep. Analysis of molecular variance showed that 90.21 and 9.79% of the source of variation were related to differences within and between populations, respectively. Our results indicated that the coarse-wool sheep from Europe were clearly different from those of the Asia. Accordingly, the Asiatic mouflon was positioned between Asian and European countries. In addition, we found that the genetic background of Iranian sheep is present in sheep from China and Kyrgyzstan, as well as India. The revealed admixture patterns of the Iranian sheep and other coarse-wool sheep breeds probably resulted from the expansion of nomads and through the Silk Road trade network.

Genomic and Phenotypic Analyses Reveal Mechanisms Underlying Homing Ability in Pigeon.

The homing pigeon was selectively bred from the domestic pigeon for a homing ability over long distances, a very fascinating but complex behavioral trait. Here, we generate a total of 95 whole genomes from diverse pigeon breeds. Comparing the genomes from the homing pigeon population with those from other breeds identifies candidate positively selected genes, including many genes involved in the central nervous system, particularly spatial learning and memory such as LRP8. Expression profiling reveals many neuronal genes displaying differential expression in the hippocampus, which is the key organ for memory and navigation and exhibits significantly larger size in the homing pigeon. In addition, we uncover a candidate gene GSR (encoding glutathione-disulfide reductase) experiencing positive selection in the homing pigeon. Expression profiling finds that GSR is highly expressed in the wattle and visual pigment cell layer, and displays increased expression levels in the homing pigeon. In vitro, a magnetic field stimulates increases in calcium ion concentration in cells expressing pigeon GSR. These findings support the importance of the hippocampus (functioning in spatial memory and navigation) for homing ability, and the potential involvement of GSR in pigeon magnetoreception.

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes.

BACKGROUND: Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (FST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. RESULTS: Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). CONCLUSIONS: Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations.

Mammary tissue transcriptomic analysis for construction of integrated regulatory networks involved in lactogenesis of Ovis aries.

The mammary gland experiences vast changes between the onset of lactation and pregnancy. This remodeling involves different functions such as lactation that is controlled by innumerable regulators and various gene networks which are still not completely understood. MicroRNAs (miRNAs) are one of the important non-coding gene regulators which control an extensive range of biological processes. Thus, exploring miRNAs functions is important for solving gene regulation complexity. The main purpose in the present study is to identify the various gene regulative integrated networks involved in lactation progress in mammary gland. We analyzed ovine mammary tissue data sets which included expression profiles of mRNA (genes) and miRNAs related to six ewes in different days of lactation and nutritional treatments. We combined two different types of information: the network that is module inference by mRNAs (RNA-seq data), miRNAs and transcription factors (TFs) expression matrix and prediction of targets via computational methods. To discover the miRNAs regulatory function, 134 modules were predicted by using gene expression data and 14 TFs and 20 miRNAs were allocated to these predicted modules. By applying this integrated computation-based method, 38 miRNA-modules and 35 TF-module interactions were identified from ovine mammary tissue data during lactogenesis. A lot of these modules were involved in lipid and protein metabolism, as well as steroids and vitamin biosynthesis, which would play key roles in mammary tissue and lactation development. These results present new information about the regulatory procedures at the miRNAs and TF levels throughout lactation.

Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle.

Milk production and composition are the most economically important traits affecting profitability in dairy cattle. In this study, we aimed at detecting signatures of positive selection in Kenana, known as one of the high milk production African indigenous zebu cattle, using next-generation sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (Pi). Further analysis showed that several candidate genes such as CSN3, IGFBP-2, RORA, ABCG2, B4GALT1 and GHR are positively selected for milk production traits in Kenana cattle. The candidate genes and enriched pathways identified in this study may provide a basis for future genome-wide association studies and investigations into genomic targets of selection in dairy cattle.

Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony.

BACKGROUND: Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for heights at withers and body sizes. Debao pony (DBP), a famous Chinese horse, is known for its small body size and lives in Guangxi mountains of southern China. In this study, we employed comparative population genomics to study the genetic basis underlying the small body size of DBP breed based on the whole genome sequencing data. To detect genomic signatures of positive selection, we applied three methods based on population comparison, fixation index (FST), cross population composite likelihood ratio (XP-CLR) and nucleotide diversity (θπ), and further analyzed the results to find genomic regions under selection for body size-related traits. RESULTS: A number of protein-coding genes in windows with the top 1% values of FST (367 genes), XP-CLR (681 genes), and log2 (θπ ratio) (332 genes) were identified. The most significant signal of positive selection was mapped to the NELL1 gene, probably underlies the body size and development traits, and may also have been selected for short stature in the DBP population. In addition, some other loci on different chromosomes were identified to be potentially involved in the development of body size. CONCLUSIONS: Results of our study identified some positively selected genes across the horse genome, which are possibly involved in body size traits. These novel candidate genes may be useful targets for clarifying our understanding of the molecular basis of body size and as such they should be of great interest for future research into the genetic architecture of relevant traits in horse breeding program.

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication.

BACKGROUND: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS: Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS: Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.

Correction to: The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau.

AbstractIn the original publication of this article [1], the colors of the Fig. 1 are wrong, and are revised in the updated figure below.

The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau.

BACKGROUND: The ability to digest dietary lactose is associated with lactase persistence (LP) in the intestinal lumen in human. The genetic basis of LP has been investigated in many populations in the world. Iran has a long history of pastoralism and the daily consumption of dairy products; thus, we aim to assess how LP has evolved in the Iranian population. We recruited 400 adult individuals from seven Iranian ethnic groups, from whom we investigated their lactose tolerance and screened the genetic variants in their lactase gene locus. RESULTS: The LP frequency distribution ranged from 0 to 29.9% in the seven Iranian ethnic groups with an average value of 9.8%. The variants, - 13910*T and - 22018*A, were significantly associated with LP phenotype in Iranians. We found no evidence of hard selective sweep for - 13910*T and - 22018*A in Persians, the largest ethnic group of Iran. The extremely low frequency of - 13915*G in the Iranian population challenged the view that LP distribution in Iran resulted from the demic diffusion, especially mediated by the spread of Islam, from the Arabian Peninsula. CONCLUSIONS: Our results indicate the distribution of LP in seven ethnic groups across the Iranian plateau. Soft selective sweep rather than hard selective sweep played a substantial role in the evolution of LP in Iranian populations.

Whole-genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse.

The primary objective of most horse breeding operations was to maximize reproductive efficiency and minimize the cost of producing live foals. Here, we compared individual horses from the Thoroughbred population (n = 17), known as a horse breed with poor reproductive performance, with other six horse populations (n = 28), to detect genomic signatures of positive selection underlying of reproductive traits. A number of protein-coding genes with significant (p-value <.01) higher FST values (616 genes) and a lower value for nucleotide diversity (π) (310 genes) were identified. The results of our study revealed some candidate genes such as IGFBP2, IGFBP5, GDF9, BRINP3 and GRID1 are possibly associated with functions influencing reproductive traits. These genes may have been under selection due to their essential roles in reproduction performance in horses. The candidate selected genes identified in this work should be of great interest for future research into genetic architecture of traits relevant to horse breeding programmes.

Performance of pedigree and various forms of marker-derived relationship coefficients in genomic prediction and their correlations.

In recent years, with development and validation of different genotyping panels, several methods have been proposed to build efficient similarity matrices among individuals to be used for genomic selection. Consequently, the estimated genetic parameters from such information may deviate from their counterpart using traditional family information. In this study, we used a pedigree-based numerator relationship matrix (A) and three types of marker-based relationship matrices ( G ) including two identical by descent, that is G K and G M and one identical by state, G V as well as four Gaussian kernel ( GK ) similarity kernels with different smoothing parameters to predict yet to be observed phenotypes. Also, we used different kinship matrices that are a linear combination of marker-derived IBD or IBS matrices with A, constructed as K = λ G + 1 - λ A , where the weight ( λ ) assigned to each source of information varied over a grid of values. A Bayesian multiple-trait Gaussian model was fitted to estimate the genetic parameters and compare the prediction accuracy in terms of predictive correlation, mean square error and unbiasedness. Results show that the estimated genetic parameters (heritability and correlations) are affected by the source of the information used to create kinship or the weight placed on the sources of genomic and pedigree information. The superiority of GK-based model depends on the smoothing parameters (θ) so that with an optimum θ value, the GK-based model statistically yielded better performance (higher predictive correlation, lowest MSE and unbiased estimates) and more stable correlations and heritability than the model with IBD, IBS or A kinship matrices or any of the linear combinations.

Genetic structure of Iranian indigenous sheep breeds: insights for conservation.

Genetic structure and genetic diversity levels of indigenous Iranian sheep breeds are not clear, despite the interest this region has in itself as an important center for domestication of livestock. Early population genetic studies have reported high levels of diversity among Iranian sheep breeds until recently, when high admixture levels and genetic homogeneity have been detected. The rapid reduction of diversity observed in Iranian breeds might be due to an increasing trend of intensive crossbreeding practices or even total replacement of native breeds by highly specialized and productive ones. From a conservative perspective, this situation is highly concerning; thus, it might be wise to consider a conservation program in Iran to preserve the original genetic diversity in native sheep breeds. In this study, a total of 1065 animals with the purest morphological features representing 24 Iranian indigenous sheep breeds were sampled, corresponding to ancestral breed diversity. These samples were genotyped for 17 microsatellite loci in order to (1) determine the native ancestral diversity of Iranian breeds, (2) define the degree of genetic relationship among studied breeds, and (3) assess conservation priorities among defined groups. Our results showed no recent loss of diversity, but high genetic diversity levels for indigenous sheep breeds in Iran. Indeed, the analysis of conservation priorities pointed out the importance of 8 breeds for maintaining Iranian sheep breeds' maximum genetic diversity. Thus, under a genetic perspective, these 8 breeds should be the ones included into conservation programs for restocking endangered areas.