Genotyping and Sequencing Technologies in Population Genetics and Genomics

Assessment of genetic diversity among native Algerian rabbit populations using microsatellite markers

Having higher adaptability against abiotic stress, which is characterized in rural areas in developing countries, local farm animal genetic resources (FAGRs) are increasingly precarious for random and unsystematic crossing with exotic breeds. In this study, 85 microsatellite loci were utilized to assess genetic diversity among native Algerian rabbits (NARs) sampled from an area of 753 km (from north to south) and 919 km (from east to west). Those distances covered 25 significant geographical points in seven rural areas (El Taref, Mostaganem, Sidi Bel Abbès, M'Sila, Dar Chioukh, Faidh El Botma, and Laghouat). A total of 558 alleles were observed in this study. The highest genetic diversity was registered in the southern direction among NAR populations. The mean number of alleles per locus (MNa) and the inbreeding coefficient (F IS ) were highest in Laghouat (4.482 and 0.232), while they were lowest in El Taref (4.000 and 0.149). In the current study, the number of private alleles (Pa) ranged from 9 to 23. In addition, the average of observed heterozygosity (0.427) was lower than the expected value (0.524) due to high levels of inbreeding. The discriminant analysis of principal components (DAPC), the neighbor-joining tree (NJ), and the analysis of STRUCTURE software confirmed the classification of populations according to geographical zones into four main groups (east, west, south, and middle). The results of the current study are useful for breeding improvement and conservation plan research in relation to local animal genetic resources in Algeria.

Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep

In developing countries, the use of simple and cost-efficient molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique, also called restriction enzyme- reduced representational sequencing, is an efficient, cost-effective method for simultaneous discovery and genotyping of many markers. In the present study, we applied a two-enzyme GBS protocol (PstI/MspI) to discover and genotype SNP markers among 197 Tunisian sheep samples. A total of 100 333 bi-allelic SNPs were discovered and genotyped with an SNP call rate of 0.69 and mean sample depth 3.33. The genomic relatedness between 183 samples grouped the samples perfectly to their populations and pointed out a high genetic relatedness of inbred subpopulation reflecting the current adopted reproductive strategies. The genome-wide association study contrasting fat vs. thin-tailed breeds detected 41 significant variants including a peak positioned on OAR20. We identified FOXC1, GMDS, VEGFA, OXCT1, VRTN and BMP2 as the most promising for sheep tail-type trait. The GBS data have been useful to assess the population structure and improve our understanding of the genomic architecture of distinctive characteristics shaped by selection pressure in local sheep breeds. This study successfully investigates a cost-efficient method to discover genotypes, assign populations and understand insights into sheep adaptation to arid area. GBS could be of potential utility in livestock species in developing/emerging countries.

Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans

Genome-level sequencing is the next step in understanding species-level relationships within Anthozoa (soft corals, anemones, stony corals, and their kin) as morphological and PCR-directed (single-locus) sequencing methods often fall short of differentiating species. The sea anemone genus Metridium is a common northern temperate sea anemone whose species are difficult to differentiate using morphology alone. Here we use Metridium as a case study to confirm the low level of information available in six loci for species differentiation commonly sequenced for Actiniaria and explore and compare the efficacy of ddRAD and sequence-capture methods in species-level systematics and biogeographic studies. We produce phylogenetic trees from concatenated datasets and perform DAPC and STRUCTURE analyses using SNP data. The six conventional loci are not able to consistently differentiate species within Metridium. The sequence-capture dataset resulted in high support and resolution for both current species and relationships between geographic areas. The ddRAD datasets displayed ambiguity among species, and support between major geographic groupings was not as high as the sequence-capture datasets. The level of resolution and support resulting from the sequence-capture data, combined with the ability to add additional individuals and expand beyond the genus Metridium over time, emphasizes the utility of sequence-capture methods for both systematics and future biogeographic studies within anthozoans. We discuss the strengths and weaknesses of the genomic approaches in light of our findings and suggest potential implications for the biogeography of Metridium based on our sampling.