litter size

Milk production and reproductive traits are important economic traits in goat. The different approaches including candidate gene mapping and genome-wide association studies (GWAS) are now implemented in goats in an attempt to identify the molecular mechanisms affecting these economically important traits. The gene ontology (GO) analysis gives a controlled vocabulary for describing attributes of genes and gene products. Kyoto Encyclopedia of Genes and Genomes (KEGG) provides the mythology for the careful examination of gene functions in respect of networks of genes and molecules. Gene network analysis can also identify paths and processes shared by candidate genes. The purpose of the present study was to bioinformatics analysis (GO, path enrichment, and network analysis of the effects of protein-protein interaction) of genes effective in litter size and milk production in goat.

Candidate genes associated with studied traits were retrieved from literature review, review of candidate gene studies, GWAS and NCBI database. GO analysis and enrichment analysis of the signaling pathways of KEGG were performed using online database of G: Profiler. The String database was used to infer the network of protein-protein interactions (PPI) and the selection of performance module. Cytoscape software was used to draw the resultant networks of protein-protein interactions. Finally, cytoHubba was used to identify Hub genes.

GO analysis for litter size showed that, for molecular function the candidates genes enriched in signaling receptor binding, signaling receptor active activity, hormone activity, protein binding and transforming growth factor beta receptor activity. The effect of the transforming growth factor β (TGF-β) family on fertility and reproduction, embryonic development, organogenesis, and uterine growth and function is remarkable in a wide range of organisms. In mammals, even early stages of reproductive development, including male and female germline specification, are controlled by TGF-β-related proteins. Hormone binding play an important role in fertility and reproduction. Sex hormone-binding globulin (SHBG), specifically bound to the biologically active androgens and estrogens that are key regulators of the reproductive organs as well as other sex-differentiated tissues such as muscle, adipose tissue, and bone. KEGG analysis also identified some signaling pathways including ، PI3K-Akt signaling pathway، TGF-beta signaling pathway and ovarian steroidogenesis which are significantly associated with litter size. GO analysis for 33 candidate genes related to milk production traits identified only one GO category for biological process namely linoleic acid metabolic process.

In this study, we identified several significant biological and signaling pathways that can be used to better understand the biological processes associated with litter size and milk production in goats.

Artificial and natural selection not only increases the frequency of new-useful mutations but also remains some signals throughout the genome. Since these regions often control economically important traits, identifying and tracking these regions is the most important subject in animal genetics. Also, natural and artificial selection related to adaptation and economic traits, such as litter size, results in changes at the genomic level which leads to the appearance of selection signatures. Several tests including the linkage disequilibrium-based approach, site frequency spectrum, and population differentiation-based approach have been developed to explore the footprints of selection in the genome. Domestication and selection have significantly changed the behavioral and phenotypic traits in modern domestic animals. The selection of animals by humans left detectable signatures on the genome of modern sheep. The identification of these signals can help us to improve the genetic characteristics of economically important traits in sheep. Over the last decade, interest in the detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. This study aimed to identify selection signature regions and candidate genes related to adaptation and the number of lambs born.
To identify the signatures of selection in Iranian native sheep and Egyptian breeds, genomic information of 96 native sheep (including 96 Zandi) and 107 Egyptian sheep (including 59 Barki and 48 Rahmani) were used. The genomic information of foreign breeds was extracted from the Dryad database (https://dryad.com/articles/dataset). To determine the genotype of the samples, Illumina Bead Chip 50K was used. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. After the quality control of the data, the hapFLK statistical method, with hapFLK v1.4 software, was used to identify selection signatures. The genomic version of the Oar_v4.0 database in NCBI was used for detecting the genomic position of single nucleotide polymorphisms (SNPs) in the sheep genome. Candidate genes were identified by SNPs located at 0.1% upper range of hapFLK using BioMart software in ensemble 109. Then, using the PANTHER database, the general biological function of the genes was checked. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics, and the QTLs in the selected region were extracted using the Animal Genome database, and the genes were compared with other research. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.
Based on the results of hapFLK, by comparing the Zandi population with Egyptian breeds (Barki and Rahmani), seven genomic regions on chromosomes 1, 2 (three regions), 10, 25, and 26 were identified. Candidate genes of DNAJB4, FNDC3B, GULP1, ACVR1, and FGF9 were in these regions. Further investigation using bioinformatics tools showed these genomic regions overlapped with the immune system, adaptation, litter size, and lipid and muscle metabolism.
The results of this study may provide an important source to facilitate the identification of genomic regions and then, the genes affecting economically important traits in the sheep industry. However, it will be necessary to carry out more association and functional studies to demonstrate the implications of these genes. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved.

G-protein-coupled receptor (GPR54) is one of the known gene affecting fecundity. This gene  affects  the ovulation rate and litter size performance. A total of 160 animals including Sanjabi (n=100) and Ghezel (n=60) were used to identify polymorphisms of GPR54 gene and  their influence on litter size. Genomic DNA was extracted by commercial DNA kit. The genotypic patterns were detected using the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). The genotypic patterns frequencies for three detected patterns in Sanjabi sheep were 54.93, 17.59 and 17.59 percent, and for two detected patterns of Ghezel were 41.86, 58.14 percent, respectively. Significant association (P<0.05) was identified between detected genotypes with litter size in Sanjabi, but no significant association (P>0.05) was found between detected polymorphisms with litter size in Ghezel sheep. Although the  results showed that the detected polymorphisms  in this gene can be used as a marker for twinning in Sanjabi sheep but,  it may be necessary to carry out further studies with larger sample sizes to find an exact correlation between GPR54 gene variants and fecundity trait.

In this study, data from 1882 ewes, including 3351 lambs born, was used as litter size trait in Afshari sheep breed. The data were collected from 2000 to 2016 by the research station at Zanjan University. The data were analyzed by ASReml software via threshold model in six different models. Fixed effects of year and season, age of ewe, number of parturition and genetic group [at five levels including pure Afshari, 50% Afshari (F1), 75% Afshari (B1), 87.5% Afshari (B2) and 93.75% Afshari (B3)] were significant (P<0.05). Heritability and repeatability were estimated to be as 0.08 and 0.17, respectively. Genetic trends of this trait, in two periods between 2000 to 2006, before the gene introgression design as first period, and from 2007 to 2016, after the introgression as second period, were 0.004 (P>0.05) and 0.059 (P<0.05), respectively. Also, the phenotypic trends were 1.37 (P>0.05) and 1.69 (P<0.05) for two periods, respectively. The results showed that the FecB gene transfer increased the litter size. Consequently, because of the direct relationship between the more profitability of flock and the increase in the number of lambs born, the gene transfer design will be followed and more welcomed by sheep breeders. Therefore, genetic parameters and genetic trends estimation of litter size in this flock can be effective for developing continues genetic breeding strategy.

The purpose of this study was to evaluate traditional, genomic, gene-assisted traditional selection and gene-assisted genomic selection methods for introgression a major gene in sheep population to improve the litter size trait using computer simulation. In this regard, a trait with heritability of 0.1, including two chromosomes each with a length of 100 cM, was simulated. On chromosome 1, a single QTL as the major gene was created that accounted for 40% of the total genetic variance. This QTL was located in the position of 25.7 cM. In breed A and B, animals were selected based for favorable and unfavorable to create two breeds that has been fixed for opposite alleles. Using the gene introgression approach, the favorable allele in breed A was insert to breed B and the new population was evaluated for genetic gain, accuracy of evaluation, frequencies of favorable allele and inbreeding rate. After five backcrossing generations, genetic gain in GasGenomic and Genomic methods was 26 and 62 percent higher than GasClassic and Classic methods, respectively. The frequency of favorable allele after five generations in Classic, Genomic, GasClassic and GasClassic was 0.387, 0.778, 0.965 and 0.975, respectively. The results of this study showed that if the goal is only introgression a major gene into an indigenous breed, by using gene-assisted classic selection, the frequency of a major gene can also be increased as much as obtain by the gene-assisted genomic selection.

This research was conducted to find association of genetic variation in exon 1 and 3 of the follicle stimulating hormone beta (FSHB) subunit gene and litter size in Baluchi sheep. DNA was extracted using modified salting out method and polymerase chain reaction was used to amplify a fragment of 220 bp of exon 1 and a fragment of 427 bp of exon 3 along with a part of intron 2. Two methods of PCR-SSCP and DNA sequencing were used for identification the different genotypes, While no polymorphism was found for exon 3, the present study identified 3 novel nucleotide polymorphisms in exon 1 of ovine FSHB gene, resulted 7 banding patterns which significantly influenced total and average number of labs across all parties. Results also showed significant association (p

GDF9 gene is one of the most important effective factors on litter size in sheep. Thus, the aim of the present study was to detect single nucleotide polymorphisms (SNPs) available in exon 2 of GDF9 gene in pure and crossbred of Pakistani sheep using PCR-SSCP. Hence, blood samples were collected from 30 Pakistani sheep, 17 crossbred sheep (Pakistani rams × LoriBakhtiari) and 7 crossbred sheep (Pakistani rams × Kermani ewes) and genomic DNA was extracted using salting-out method. A 634 bp fragment was amplified using one specific primer pairs using polymerase chain reaction. After single stranded conformation polymorphism (SSCP) of PCR products, band patterns of GDF9 gene were observed on 8% polyacrylamide gel stained with silver-nitrate method. In total, 4 banding patterns 1, 2, 3 and 4 were obtained with frequencies of 0.193, 0.129, 0.371 & 0.407, respectively. The sequencing results were led to identification of 3 mutations in 443, 477 and 721 nucleotide situations of GDF9 gene in the studied populations.

Five microsatellite markers BM1329, OarAE101, BM143, BM4621 and BM415 which were closely linked to the fecundity gene FecB in Booroola sheep were chosen based on their high conservatism in the closest species and were analyzed for polymorphisms and also their correlation with the litter size of a goat. Observed results showed four microsatellite loci show polymorphism in the present study. However, BM4621 locus was monomorphic. The range of allele size of BM1329, OarAE101, BM143 and BM415 were 180 to 216 to 112, 102 to 112 and 198 to 200 in goat respectively. The alleles of the greatest frequency for of BM1329, OarAE101, BM143 and BM415 were 212, 99, 108 and 200bp respectively. Polymorphism information content (Nei Index) for BM1329, OarAE101, BM143 and BM415 were 0.82, 0.82, 0.72 and 0.49 respectively. Mean number of allele, Observed Heterozygosis, PIC and Shannon information index were 4.75 ± 2.2, 0.36 ± 0.12, 0.71 ± 0.15 and 1.41 ± 0.52 respectively. The litter size for first lambing for investigated loci were significantly different (p

This study was carried out to identify polymorphisms of BMP15, GDF9 and BMPRIB genes in cross- bred of Romanov×shal sheep. For this reason 79 blood samples were collected from a flock in Gonbad kavous city in Golestan province. DNA was extracted using modified salting out method. Polymerase chain reaction was done by specific primers for amplification of two fragments with 141and 153 bp from exon 2 of BMP15, one fragment with 190 bp from BMPR-IB gene and two fragment with 462 bp, 139bp from exon 1and 2 of GDF9 genes, respectively. The results obtained from digested PCR products did not confirm the existence of mutation in BMp15, BMPR-1B and in exon 2 of GDF9 marker site. While, polymorphism was observed in exon 1 of GDF9 marker site and the heterozygotes were estimated as 0.11 in this population.

For decreasing the number of breeding ewes on pastures and prevention of demolition pastures, it seems that animal breeding programs are benefit for identifying effective candidate genes on litter size in Iranian sheep breeds and using those. The TGFβ family genes are one of the most important effective factors on litter size in sheep. The GDF9 gene is one of the most important members from this family. The aim of the present study was to identify available mutations in exon 2 of GDF9 gene in crossbred sheep (Romanov rams × Lori-Bakhtiari ewes) using PCR-SSCP. In this study, after extraction genomic DNA from blood samples of 36 crossbred animals with 3-6 months old (17 males and 19 females), the first region (from 5’ end) of exon 2 (634bp segments) of GDF9 gene was amplified using PCR. The single stranded conformation polymorphism (SSCP) patterns of PCR products were studied using acrylamide gel electrophoresis and silver staining method and then from any pattern one sample sequenced. In the studied population, 3 banding patterns 1, 2, and 3 obtained with frequencies of 0.305, 0.584 and 0.111, respectively. The sequencing results showed presence of 4 mutations (471, 477, 520 and 721 situations) in the studied population.

For decreasing the numberofbreedingewes onpastures and prevention of demolition pastures, Animal breedingprograms are necessary on genes with major effects on litter size in Iranian sheep breeds for Identify effective candidate genes on these economical traits. The GDF9 gene is one of the most important effective factors on litter size in sheep. The aim of the present study was to identify G2, G3 and G4 mutations in exon 2 of GDF9 gene in crossbred sheep (Romanov rams×Kermani ewes) using PCR-SSCP. Blood samples were collected from jugular vein of 121 crossbred individuals. Genomic DNA was extracted using salting-out method. Partial region of exon 2 (633 bp segments) of GDF9 gene was amplified with designed specific primers. The single stranded conformation polymorphism (SSCP) patterns of PCR products were studied using acrylamide gel electrophoresis and silver-nitrate staining method. Finally, we obtained 5 banding patterns 1, 2, 3, 4 and 5 with frequencies of 0.314, 0.024, 0.289, 0.232 & 0.141, respectively. The sequencing results showed presence 5 mutations in the studied population.

Recently, mutations with major influence on ovulation rate and litter size were identified in TGFβ superfamily ligands and receptors. This study was conducted to identify polymorphisms in GDF9 and BMP15 genes in Dalagh sheep breed. One hundred mature ewes from two flocks in Golestan province were genotyped for the GDF9 (G1) and BMP15 (B4) variants. Two fragments of 462bp and 153bp of GDF9 and BMP15 genes were amplified by PCR-RFLP method. PCR product was digested using HhaI and DdeI endonuclease restriction enzymes. The results of the digested PCR products, did not confirm mutation at position B4 but Polymorphism was observed at G1position. The heterozygote genotype frequency in the population was estimated at 15%.

Genetic parameters for litter size trait in Makuie sheep were estimated using Bayesian method and different models. For this purpose, six threshold models were fitted. Different models with direct genetic effects, maternal and permanent environmental effects were implemented. Effects after significance test (P<0.05) by logistic procedure of SAS software were included in these models (herd and year of lambing). Variance components of litter size trait were estimated by Thrgibbs1f90 software. The most appropriate model was determined based on deviance information criterion (DIC). Model 4 was recognized as the best model for the genetic analysis of litter size trait in Makuie sheep. The meanof the posterior distribution of estimated additive and maternal heritability for best model (model 4) were 0.03% (0.004) and 0.109(0.017), respectively. Estimated genetic parameters of litter size in this studyshowed that for genetic gain in this trait more attention should be paid to maternal effect and improve environmental condition.

The present study was carried out to estimate genetic and phenotypic parameters for litter size trait in Mehrabani sheep by threshold model. Data file included the litter size of 5069 ewes which collected from 1994 to 2010 at Mehrabani sheep breeding center under supervision of Agriculture-Jahad Organization of Hamedan. The pedigree file consisted of the information of animals burned which were born from 1987 to 2010. The number of lambs per ewe were used as, repeated records. The effects of herd, year, and lambing time were fitted in the model as fixed effects. The significance of fixed effects was examined using Logistic procedure of SAS software. The analysis for trait was carried out, using the Thrgibbs1f90 program. Estimates of direct heritability, maternal heritability and repeatability were 0.039, 0.11 and 0.057, respectively. The low estimations of direct heritability, maternal heritability and repeatability were obtained in the current study for litter size trait. It indicates that selection based on the ewe’s own performance may result in slow genetic improvement.