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

Abstract

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.

Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations

“…On the other hand, low-coverage sequencing approaches, including GBS, may produce missing data and cause under-calling of heterozygotes due to the limited number of reads and uneven coverage capturing information for only one allele in a heterozygote, causing its misidentification as a homozygote [54,55]. Obtained average read depth across SNPs and samples and call rate are similar to previous studies in livestock [53,56] and wild animal species [30,57,58].…”

“…GBS is a simplified reduced-representation sequencing approach similar to RAD sequencing that is popular in animal and plant genetics as a low-cost alternative to whole genome sequencing and SNP genotyping microarrays [48][49][50][51]. As previous studies have shown, GBS can be successfully applied in population genetics [51], animal breeding and genomic selection [29,52] or genome-wide association studies [53]. On the other hand, low-coverage sequencing approaches, including GBS, may produce missing data and cause under-calling of heterozygotes due to the limited number of reads and uneven coverage capturing information for only one allele in a heterozygote, causing its misidentification as a homozygote [54,55].…”

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

“…Indeed, ( 21 ) suggests direct contact between Balkan and some southern Italian breeds such as Barbaresca and Laticauda breeds which are known to have been influenced by NA fat-tailed Barbary sheep ( 50 ). Global-scale genetic diversity shows that Maghrebin sheep breeds overlap genetically with each other, reflecting global genetic homogenization and weak genetic structure among Maghreb sheep stocks ( 6 , 25 , 51 ). However, the differentiation of overall Maghrebin from Egyptian and Libyan sheep with affinity to Middle Eastern and Asian breeds may suggest two complementary hypotheses.…”