Sheep farming plays an important economic role, and it contributes to the livelihoods of many rural poor in several regions worldwide and particularly in Tunisia. Therefore, the steady improvement of ewes’ reproductive performance is a pressing need. The MTNR1A gene has been identified as an important candidate gene that plays a key role in sheep reproduction and its sexual inactivity. It is involved in the control of photoperiod-induced seasonality mediated by melatonin secretion. The aim of this study was to identify SNPs in the MTNR1A gene in two Tunisian breeds, Barbarine (B) and Queue Fine de l’Ouest (QFO). DNA extracted from the blood of 77 adult ewes was sequenced. Selected ewes were exposed to adult fertile rams. A total of 26 SNPs were detected; 15 SNPs in the promoter region and 11 SNPs in the exon II were observed in both (B) and (QFO) breeds. The SNP rs602330706 in exon II is a novel SNP detected for the first time only in the (B) breed. The SNPs rs430181568 and rs40738822721 (SNP18 and SNP20 in our study, respectively) were totally linked in this study and can be considered a single marker. DTL was associated with SNP18 and SNP20 in (B) ewes (p < 0.05); however, no significant difference was detected between the three genotypes (G/G, G/A, and A/A) at these two SNPs. Fertility rate and litter size parameters were not affected by SNP18 and SNP20. There was an association between these two polymorphisms and (B) lambs’ birth weights (p < 0.05). Furthermore, the ewes with the A/A genotype gave birth to lambs with a higher weight compared to the other two genotypes for this breed (p < 0.05). There was not an association between SNP 18 and SNP20 and (QFO) ewes’ reproductive parameters. These results might be considered in future sheep selection programs for reproductive genetic improvement.

Background:X-chromosome short tandem repeat (X-STR) markers have shown a great capability in forensic identity investigations and paternity testing involving kinship analysis. Material and methods:In the current study, the distribution of 12 X-STR loci (DXS10148, and HPRTB) located in four linkage groups (LG)s was evaluated using Investigator ® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males, and 95 females) from the central region of the Saudi Arabia in order to create a DNA database. Results:No significant difference was recorded in the allele frequencies of males and females.Our results indicated that DXS10146 locus was the most informative with 21 alleles while DXS8378 locus was the least with 5 alleles. Hardy-Weinberg equilibrium (HWE) was applied and confirmed for all loci in the female samples, except for DXS10074, DXS10101, DXS10135 and DXS10148 (p > 0.05/12 = 0.0042). Forensic parameters showed that all X-STRs loci either as individual markers or as linkage groups provide genetic information with high discrimination that is appropriate for forensic purposes with Paternity Informed Consent (PIC), Power of exclusion (PE), and Paternity index (PI) varied from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. A significant Linkage disequilibrium (LD) with p-value after Bonferroni correction p ≤ 0.05/66= 0.0008 was observed for 17 pairs of loci in male samples and 4 pairs of loci in female. In the male group, LG3 showed relatively high values of Haplotype diversity (HD). This indicated that these LGs were quite informative in the studied Saudi group and would have high application value in forensic sciences. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically close to the Egyptian and Emirati populations and distant to the Turkish population. Genetic distances were represented in a non-metric MDS plot representing that Saudis cluster with Middle East populations and are clearly separated from European and East Asian populations. Conclusion:The current study revealed that Investigator® Argus 12 X-STR kit would support forensic application, kinship testing involving female offspring, and human identification in Saudi populations.

Next-Generation Sequencing allows for quick and precise sequencing of multiple genes concurrently. Recently, this technology has been employed for the identification of novel gene mutations responsible for disease manifestation among breast cancer (BC) patients, the most common type of cancer amongst Arabian women, and the major cause of disease-associated death in women worldwide. Genomic DNA was extracted from the peripheral blood of 32 Saudi Arabian BC patients with histologically confirmed invasive BC stages I-III and IV, as well from 32 healthy Saudi Arabian women using a QIAamp ® DNA Mini Kit. The isolated DNA was quantified using a Qubit™ dsDNA BR Assay Kit with a Qubit 2.0 Fluorometer. Ion semiconductor sequencing technology with an Ion S5 System and AmpliSeq™ Cancer Hotspot Panel v2 were utilized to analyze ~2,800 mutations described in the Catalogue of Somatic Mutations in Cancer from 50 oncogenes and tumor suppressor genes. Ion Reporter Software v.5.6 was used to evaluate the genomic alterations in all the samples after alignment to the hg19 human reference genome. The results showed that out of the 50 genes, 26 mutations, including 17 (65%) missense point mutations (single nucleotide variants), and 9 (35%) frameshift (insertion/deletion) mutations, were identified in 11 genes across the cohort in 61 samples (95%). Mutations were predominantly focused on two genes, PIK3CA and TP53, in the BC genomes of the sample set. PIK3CA mutation, c.1173A>G located in exon 9, was identified in 15 patients (46.9%). The TP53 mutations detected were a missense mutation (c.215C>G) in 26 patients (86.70%) and 1 frameshift mutation (c.215_216insG) in 1 patient (3.33%), located within exon 3 and 5, respectively. This study revealed specific mutation profiles for every BC patient, Thus, the results showed that Ion Torrent DNA Sequencing technology may be a possible diagnostic and prognostic method for developing personalized therapy based on the patient's individual BC genome.

Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10−2) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1–20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father–son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates.

The last three decades have seen rapid advances in the field of short tandem repeats (STRs) genotyping technology. Autosomal STRs have emerged as a powerful tool in forensic identification and paternity investigations. The indigenous population of Saudi Arabia is irregularly distributed and has historically been organized into geographically distinct groups or tribes of patrilineal descent. So far, there has been no detailed investigation of the southern region Saudi population to assist in the interpretation of DNA-based forensic evidence and in the construction of DNA database. The objective of this study is to investigate the genetic structure in 154 unrelated healthy Saudi subjects within three generations from the southern Saudi regions using a GlobalFiler™ PCR Amplification kit. Intra- and Inter-population genetic diversity as well as the forensic genetics parameters were analyzed. Our results showed that SE33 and TPOX loci were the most and the least polymorphic loci, respectively. The PIC, PE, TPI, Ho and He varied from 0.56116 (TPOX) to 0.94393 (SE33), 0.26638 (TPOX) to 0.83859 (SE33), 1.1875 (TPOX) to 6.33333 (SE33), 0.57894 (TPOX) to 0.92105 (SE33) and 0.6169 (TPOX) to 0.952 (SE33), respectively. The highest PM was observed for D22S1045 (0.223944) and the highest PD for SE33 (0.98935). The combined PD was 99.99999999% and the combined PM was equal to 3.19021E-25. Phylogenetic parameters showed that the southern region Saudi population had the closest genetic relationship with the Saudi, Emirati, Kuwaiti, and Bahraini populations. The study offers some important insights into the southern region Saudi population structure using GlobalFiler™ PCR Amplification kit.