Moringa oleifera, commonly known as the horseradish (drumstick tree), is a fast-growing, mineral-rich evergreen tree in the family Moringaceae, with wide applications in herbal medicine, agriculture, and livestock production. Despite its importance, genomic resources remain limited, with only one public draft assembly previously available. This study presents a de novo draft genome of Moringa oleifera from Pakistan, sequenced by the Illumina HiSeq platform using paired-end libraries. The assembly comprises ~205.2 Mb across 13,872 scaffolds (N50 = 17,279 bp) and includes 26,215 predicted protein-coding genes. Assembly quality, supported by completeness assessments, indicates the recovery of 83.9% of embryophyte BUSCOs and 84.68% of CEGMA core genes. This Pakistan-origin reference fills a vital geographic and technical gap for M. oleifera, enabling robust functional annotation and comparative analysis in the Moringa genus. It provides an immediate foundation for marker development and downstream applications in molecular breeding, biotechnology, and stress adaptation research. Keywords: Moringa oleifera, genome, assembly, annotation, Pakistan

Pakistan is the 2nd largest country in buffalo population in the world. The current population of buffalo in Pakistan is 45.0 million heads whereas the current world buffalo population is 200 million heads. Pakistan is home to one of the best buffalo breeds in the world i.e., Nili, Ravi, Nili-Ravi, Kundi, and Azi Khaili. Moreover, Pakistan is ranked 2nd largest buffalo-milk-producing country in the world. Keeping in consideration, the tremendous role and importance of buffalo, the current study aims to provide a comprehensive overview of the important genetic studies conducted up till now and the need to apply the latest genomic tools, gene editing, and reproductive biotechnologies for the improvement of these native buffalo breeds. The current research is limited to a few diversity studies, basic phylogenetics, evolution, and genetic characterization using only a few loci and phenotypic studies of limited productive traits. The current picture is gloomy as proper genetic characterization and diversity study of these breeds has never been made using reliable, accurate, and advanced genomic techniques. In a developing country like Pakistan where there is no comprehensive data collection coupled with scattered farming without any organized breeding system; genomic selection, gene editing, and application of advanced reproductive biotechnology techniques are the most promising techniques for rapid and sustainable development in the productive and reproductive potential of our Black Gold. Advancement in the methods of genotyping using commercially available SNP Chips at affordable prices along with improvements in reproductive biotechnology and genome editing techniques will provide the framework for the true genetic exploration and optimal utilization of precious native buffalo breeds potential. Conclusively, these techniques have great potential to revolutionize the world's buffalo population.

Indigenous cattle breeds in Asia are highly adapted to their local environments providing essential commodities such as meat, milk and draught power while also playing a key role in traditional ceremonies, and sports. Despite ongoing efforts to characterize and conserve these breeds, the increasing trend of indiscriminate crossbreeding of Zebu cattle with high-yielding taurine breeds, threatens their genetic diversity. This study investigates the population structure, inbreeding levels, effective population size, gene flow and identification of selection footprints of Asian Zebu (Bos indicus) cattle. Using an Axiom 60 K SNP chip, we analyzed genotypes from 1303 cattle across 36 populations in nine countries, including seven taurine outgroups and 29 Zebu populations from Bangladesh, Cambodia, India, Myanmar, Pakistan, and Sri Lanka. Zebu populations demonstrated moderate genetic diversity, with heterozygosity levels averaging 0.356, inbreeding coefficients ranging from 0.026 to 0.074 and genetic differentiation (FST) varied between 0.01 and 0.11. Breed clusters aligned closely with their geographic locations except for Achai (Pakistan) and Baru Harak (Sri Lanka) breeds that appeared in both Zebu and taurine clusters indicating evidence of taurine admixture. Genomic analyses identified regions under selection using extended haplotype homozygosity (EHH) and fixation index (FST) methods. Candidate genes associated with key biological functions related to environmental responsiveness, including heat tolerance (HSP90AA1), immunity (RIPK3), metabolism and fertility (REC8, CLIC4, TSSK4), were identified, reflecting adaptive traits critical for Zebu survival and utility across diverse environments. These findings provide valuable insights for conservation and management strategies aimed at preserving the unique genetic diversity of Asian Bos indicus breeds.

We analyzed the complete mitochondrial DNA displacement-loop (D-loop) and the cytochrome b (cyt b) gene of ten Pakistani domestic goat breeds ( Capra hircus ). The sequence analysis showed 209 variable sites in goat breeds and each haplotype was unique. All the haplotypes were rich in A/T content. Analysis of variable sites revealed 178 transitions and 31 transversions. Out of 178 transitions 81 were A↔G and 97 were C↔T. Of the 31 transversions, 2 were heteromorphic transversion G→T/C and T→G/C, one transversion also showed a pattern of transition. The ratio between transitions to transversion was 8.5:1.5. The phylogenetic analyses and sequence divergence (SD) established two major distinct mt-lineages termed as A, B. An A mt-lineage is further branched into three clades A1, A2, A3. This suggested that at least two different strains of wild Capra might have been the source of the modern domestic goats. Phylogenetic analysis of all haplotypes of this research work was performed with some reported haplotypes of Capra hircus and wild goats. Origin of domestication seemed to be from Europe, Asia and Africa. Our haplotypes have close relationship with Cashmiree breed, inner Mangolia and probably have originated from wild Capra aegagrus .

Interleukin 2 (IL-2) is produced by activated T cells and play important role in immune response against antigen. It acts in both autocrine and paracrine manner. It can stimulate B cells and various other phagocytic cells like monocytes, lymphokine-activated killer cells and natural killer cells. Acting in autocrine fashion, IL-2 protein plays a crucial role in proliferation of T cells. IL-2 triggers the release of pro and anti- inflammatory cytokines by activating several pathways. In present study, exon 1 of IL-2 gene of four local Pakistani breeds (Dera Din Panah, Beetal, Nachi and Kamori) was amplified by using reported ovine IL-2 primers. Amplified products of 4 breeds of goat were bidirectionally sequenced to decipher polymorphisms. Only a single substitution (T -> A) was found in non-coding region of IL-2 gene. Comparison of IL-2 gene sequence of all four breeds with other goat breeds showed high similarity in sequence. Phylogenetic analysis of our local breeds with other mammals showed that IL-2 was highly variable. This high substitution rate could be due to changed selective pressure. These rapid changes may also lead to the changes in the functions of immune system.

Abstract Bovidae and Cervidae are the most important families of mammals. Due to unusual human interference, extraordinary utilization of natural resources, uncontrolled and unplanned hunting, and other unfavorable environmental conditions, some of these wild species are on the verge of extinction. Genetic variations provide the base material for animal survival from the evolutionary perspective, which is vital for the conservation of animals, particularly endangered species that, if not be protected, will soon be extinct. Therefore, the current study was planned to investigate the molecular phylogeny and genetic diversity of Bovidae (Boselaphus tragocamelus, Antilope cervicapra) and Cervidae (Axis axis, Axis porcinus) families of wild deer in Pakistan using the collective effect of mitochondrial cytochrome B, C and D-loop regions. For genetic diversity study, we collected 25 unrelated wild deer blood samples from all four species in EDTA-containing vacutainers. Genomic DNA was extracted using phenol-chloroform method of DNA extraction. PCR was performed for amplification of cytochrome B, C, and D loop genes, and sequencing of the PCR products was performed at Foster City, CA, USA. In this study, we found evidence for a significant reduction in genetic diversity of the members of Bovidae and Cervidae from different regions of Pakistan. Both allelic richness and observed heterozygosity were lower in these populations compared to the larger populations from other regions of the world. The findings of current study revealed that the distribution of studied species inclined more towards endangered, which is alarming and demands immediate measures for their conservation.

The blue peafowl from the genus Pavo is the largest species among both of its wild and domestic types, which is widely distributed in the habitats of Pakistan, India, Nepal, Sri Lanka and Bangladesh. The aim of this study is to have an insight of molecular diversity and phylogenetic analysis of Pavo cristatus on the basis of mitochondrial D-loop region. A total of six samples were collected from the Lahore Zoo and Safari Park Lahore. The whole genome was extracted by using standard protocol with minor modification. PCR amplification was done by using a set of mitochondrial D loop primer. Codon Code Aligner 5.1.5 was used for the sequence alignment and data analysis. Three C/T heterozygous loci were found at position 168, 170 and 223. One A/G heterozygous locus was observed at position 234. One insertion of A at 137, one transversion C>G at 190 and three transition mutation were observed at position 206, 222 and 236 respectively. Phylogenetic analysis was performed with the help of MEGA 6 software using neighbor joining method which revealed that our individuals are closely related with the Japanese Pavo cristatus. Moreover, this Japanese and Pakistan species sharing their common ancestor. Our samples are clearly placed themselves in one clade while all other related species are in another clade which predict the substantial divergence between Pakistani and other studies D loop regions of peacocks.

Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.

The present study reports the population structure, genetic admixture and phylogeography of cattle breeds of Sri Lanka viz. Batu Harak, Thawalam and White cattle. Moderately high level of genetic diversity was observed in all the three Sri Lankan zebu cattle breeds. Estimates of inbreeding for Thawalam and White cattle breeds were relatively high with 6.1% and 7.2% respectively. Genetic differentiation of Sri Lankan Zebu (Batu Harak and White cattle) was lowest with Red Sindhi among Indus Valley Zebu while it was lowest with Hallikar among the South Indian cattle. Global F statistics showed 6.5% differences among all the investigated Zebu cattle breeds and 1.9% differences among Sri Lankan Zebu breeds. The Sri Lankan Zebu cattle breeds showed strong genetic relationships with Hallikar cattle, an ancient breed considered to be ancestor for most of the Mysore type draught cattle breeds of South India. Genetic admixture analysis revealed high levels of breed purity in Lanka White cattle with >97% Zebu ancestry. However, significant taurine admixture was observed in Batu Harak and Thawalam cattle. Two major Zebu haplogroups, I1 and I2 were observed in Sri Lankan Zebu with the former predominating the later in all the three breeds. A total of 112 haplotypes were observed in the studied breeds, of which 50 haplotypes were found in Sri Lankan Zebu cattle. Mismatch analysis revealed unimodal distribution in all the three breeds indicating population expansion. The sum of squared deviations (SSD) and raggedness index were non-significant in both the lineages of all the three breeds except for I1 lineage of Thawalam cattle (P<0.01) and I2 lineage of Batu Harak cattle (P<0.05). The results of neutrality tests revealed negative Tajima’s D values for both the lineages of Batu Harak (P>0.05) and White cattle (P>0.05) indicating an excess of low frequency polymorphisms and demographic expansion. Genetic dilution of native Zebu cattle germplasm observed in the study is a cause for concern. Hence, it is imperative that national breeding organizations consider establishing conservation units for the three native cattle breeds to maintain breed purity and initiate genetic improvement programs.