Genetic variation at microsatellite loci in Spanish sheep

Association between the cashmere production performance, milk production performance, and body size traits and polymorphism of COL6A5 and LOC102181374 genes in Liaoning cashmere goats

The purpose of this study was to analyze the relationship between COL6A5 (collagen type VI alpha 5 chain) and LOC102181374 (alcohol dehydrogenase 1) genes and the production performance of Liaoning cashmere goats by single nucleotide polymorphism (SNP). We have searched for SNP loci of COL6A5 and LOC102181374 genes through sequence alignment and PCR experiments, and have used SPSS and SHEsis software to analyze production data. We obtained five SNP loci in total, including three SNP loci (G50985A, G51140T, G51175A) in COL6A5 gene and two SNP loci (A10067G, T10108C) in LOC102181374 gene. The genotypes G50985A (AG), G51140T (GT), G51175A (AA), A10067G (AA), and T10108C (CC) of these loci have certain advantages in improving the production performance of Liaoning cashmere goats. The haplotype combinations that can improve production performance in COL6A5 gene were H1H5:AGGGAG, H4H4:GGGGAA, and H4H4:GGGGAA. H3H3:GGCC and H2H4:AGTT were the dominant combinations in LOC102181374 gene. At G51175A and A10067G loci, we found that H1H2:AAAG and H1H3:AGAA have dominant effects. These results may provide some support for the molecular breeding of production traits in Liaoning cashmere goats.

Optimizing Microsatellite Marker Panels for Genetic Diversity and Population Genetic Studies: An Ant Colony Algorithm Approach with Polymorphic Information Content

Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, marker selection cannot rely solely on PIC. In this study, the ant colony optimization (ACO) algorithm, a widely recognized optimization method, was adopted to create an enhanced selection scheme for refining microsatellite marker panels, called the PIC-ACO selection scheme. The algorithm was fine-tuned and validated using extensive datasets of chicken (Gallus gallus) and Chinese gorals (Naemorhedus griseus) from our previous studies. In contrast to basic optimization algorithms that stochastically initialize potential outputs, our selection algorithm utilizes the PIC values of markers to prime the ACO process. This increases the global solution discovery speed while reducing the likelihood of becoming trapped in local solutions. This process facilitated the acquisition of a cost-efficient and optimized microsatellite marker panel for studying genetic diversity and population genetic datasets. The established microsatellite efficiency metrics such as PIC, allele richness, and heterozygosity were correlated with the actual effectiveness of the microsatellite marker panel. This approach could substantially reduce budgetary barriers to population genetic assessments, breeding, and conservation programs.

Selection of Cashmere Fineness Functional Genes by Translatomics

Cashmere fineness is an important index to evaluate cashmere quality. Liaoning Cashmere Goat (LCG) has a large cashmere production and long cashmere fiber, but its fineness is not ideal. Therefore, it is important to find genes involved in cashmere fineness that can be used in future endeavors aiming to improve this phenotype. With the continuous advancement of research, the regulation of cashmere fineness has made new developments through high-throughput sequencing and genome-wide association analysis. It has been found that translatomics can identify genes associated with phenotypic traits. Through translatomic analysis, the skin tissue of LCG sample groups differing in cashmere fineness was sequenced by Ribo-seq. With these data, we identified 529 differentially expressed genes between the sample groups among the 27197 expressed genes. From these, 343 genes were upregulated in the fine LCG group in relation to the coarse LCG group, and 186 were downregulated in the same relationship. Through GO enrichment analysis and KEGG enrichment analysis of differential genes, the biological functions and pathways of differential genes can be found. In the GO enrichment analysis, 491 genes were significantly enriched, and the functional region was mainly in the extracellular region. In the KEGG enrichment analysis, the enrichment of the human papillomavirus infection pathway was seen the most. We found that the COL6A5 gene may affect cashmere fineness.

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 F_ST 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.

Assessment of genetic diversity and population structure of Colombian Creole cattle using microsatellites

To establish the diversity, structure, and phylogenetic relationships among Colombian Creole cattle, six native breeds and one introduced breed were genotyped for 20 microsatellite loci. The average number of alleles per breed ranged from 7050 (Romosinuano) to 10,100 (Casanareño), and the expected heterozygosity ranged from 0.691 (San martinero) to 0.785 (Casanareño). The deviation from the Hardy-Weinberg equilibrium (HWE) was statistically significant (p < 0.05) in 59 out of 120 tests carried out in the six breeds for the 20 microsatellite loci analyzed. Colombian Creole bovine breeds have maintained a high level of genetic differentiation within the same populations (93%), and the rest is explained by differences between breeds (7%). The differentiation pattern and the genetic relationships between the Colombian Creole bovine breeds showed high consistency with the evolutionary history of each. Both the Bayesian grouping analysis and the neighbor-joining tree exhibited a reliable grouping pattern, which revealed two main groups: one comprised by the breeds Blanco Orejinegro, Hartón del Valle, Costeño Con Cuernos, Romosinuano, and San Martinero, and the other one by the Creole breed Casanareño and Zebu. These were probably caused by different historical, reproductive, and geographic isolation precedents, as well as by different levels of inbreeding. This study will help understand the genetic characteristics of Colombian Creole cattle and will benefit future conservation programs.

Review on small ruminant conservation status and prospects in India

Small ruminants always play a major role in the agricultural economy of India. They provide livelihoods to numerous small and marginal farmers. The diversity of small ruminant population is enormous in the country which contributes to agrarian economy. However, the genetic variety is now at risk due to indiscriminate cross-breeding, and change is farmer's preference towards high-producing breeds. The population statistics is showing a declining trend for the past several years. During time of climate change and outbreak of novel diseases, this genetic diversity is important as consumer preferences and climate is bound to change in future. So to ensure fitness and vitality in future populations of food-producing animals, and to keep genetic options open, access to greater diversity of genetic material will always be required. The native breeds of the country also possess several characteristics of disease tolerance, high fecundity and specific products which make them unique in their own aspect. Hence, conservation programmes should be adopted to maintain this large diversity of small ruminants. It may involve tradition practices followed by pastoralists or modern reproductive technologies like MOET. The government has taken several steps towards conservation and national institutes like NBAGR works for evaluation and conservation of native genetic diversity. However, better awareness among famers and improving of conservational approaches will go a long way in sustainable management of sheep and goat genetic resources.

Two ovine mitochondrial DNAs harboring a fifth 75/76 bp repeat motif without altered gene expression in Northern Spain

The Basque Country is home to the Latxa sheep breed, which is divided in several varieties such as Latxa Black Face (LBKF) and Latxa Blonde Face (LBLF). Mitochondrial DNA control region analysis of 174 male sheep (97 LBKF and 77 LBLF) was performed with the objective of characterizing the maternal lineages of these two varieties that are the basis to produce the cheese with Idiazabal quality label. The percentage of unique haplotypes was 77.32% in LBKF and 67.53% in LBLF. Most of the individuals were classified into B haplogroup (98.85%), while A haplogroup was much less frequent. Two Latxa individuals (one LBKF and one LBLF), both belonging to B haplogroup, displayed an additional 75/76 bp tandem repeat motif. Only 33 other sequences with this repeat motif were found among 11 061 sheep sequences included in the GenBank database. Gene expression was analyzed in peripheral blood leukocytes since the additional 75/76 bp repeat motif falls within ETAS1, a domain with a possible function in regulation of replication and transcription. The mRNA expression from four mitochondrial genes (COI, cyt b, ND1, and ND2) was analyzed in the two individuals of this study with a fifth repeat motif and in four without it. Although lower transcription was observed when the additional 75/76 bp repeat motif was present, no statistically significant differences were observed. Therefore, the variation in the number of the 75/76 repeat motif does not seem to modify the gene expression rate in mitochondrial genes.

Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep

Background

Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (N_e), heterozygosity, fixation index (F_ST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates.

Methods

In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r² and D′), N_e, heterozygosity, F_ST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP).

Results

Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller N_e than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest F_ST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection.

Conclusions

This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0169-6) contains supplementary material, which is available to authorized users.

Bottleneck study and genetic structure of Iranian Caspian horse population using microsatellites

Genetic diversity within the Iranian Caspian horse was evaluated using 8 different microsatellite pairs on 45 Caspian horse blood samples. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks, if any, in this breed. The number of alleles per locus varied from 3 to 5 with mean value of 4.125. All markers have relatively high PIC value (> 0.6), observed heterozygosity; 0.9433, expected Levene's heterozygosity 0.6856 and expected Nei's heterozygosity equal to 0.6762. This study indicated the existence of substantial genetic diversity in the Caspian horse. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A mode-shifted distribution, significant heterozygote excess on the basis of different mutation models, as revealed from Sign, Standardized differences and Wilcoxon rank tests suggested that there was recent bottleneck in the existing Caspian horse. Urgent conservational strategies on this population, is recommended.

Genetic diversity and bottleneck studies in the Marwari horse breed

Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (-/+ s.e.) allelic diversity was 5.9 (-/+ 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (-/+ s.e.) effective number of alleles (3.3 -/+ 1.27), observed heterozygosity (0.5306 -/+ 0.22), expected Levene's heterozygosity (0.6612 -/+ 0.15), expected Nei's heterozygosity (0.6535 -/+ 0.14), and polymorphism information content (0.6120 -/+ 0.03). Low values of Wright's fixation index, F(IS) (0.2433 -/+ 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal 'L' shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant M ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.