DNA polymorphisms of FGFBP1, leptin, κ-casein, and αs1-casein genes and their association with reproductive performance in dromedary she-camels

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data

Copy number variants (CNVs) are structural variants within the eukaryotic genome that vary among individuals of a species. These variants have been associated with different phenotypic traits, making them a valuable consideration as markers for designing breeding programmes. In this study, whole genome sequence data of 60 dromedary camel samples originating from the Arabian Peninsula were analyzed to construct a comprehensive dromedary CNV map. Utilizing four CNV callers employing read-depth, split-read and paired-end mapping approaches, a total of 37,519 CNV events (17,847 deletions and 19,672 duplications) were called on the dromedary autosomes. These CNV events were merged into 2,557 regions, categorized as 1,322 losses, 122 gains, and 1,113 "mixed regions" comprising both types. The cumulative size of the CNV regions amounted to 22.5 Mb, covering roughly 1.16% of the dromedary autosomes. Approximately 32% of the defined CNV regions (comprising 60% losses, 18% gains, and 0.27% mixed regions) were found in ≥ 90% of the dromedary samples, classifying them as prevalent regions. Genes with biological functions related to the different adaptive physiologies of dromedary camels, such as fertility, heat stress, musculoskeletal development, and fat metabolism, were overlapping with or in close proximity to ~ 68% of the defined CNV regions, demonstrating their potential role in dromedaries' physiology. This study presents the first comprehensive CNV map of dromedary camels and builds on the present knowledge in understanding the genetic structure of this species.

Identification of novel genetic loci related to dromedary camel (Camelus dromedarius) morphometrics, biomechanics, and behavior by genome-wide association studies

In the realm of animal breeding for sustainability, domestic camels have traditionally been valued for their milk and meat production. However, key aspects such as zoometrics, biomechanics, and behavior have often been overlooked in terms of their genetic foundations. Recognizing this gap, the present study perfomed genome-wide association analyses to identify genetic markers associated with zoometrics-, biomechanics-, and behavior-related traits in dromedary camels (Camelus dromedarius). 16 and 108 genetic markers were significantly associated (q < 0.05) at genome and chromosome-wide levels of significance, respectively, with zoometrics- (width, length, and perimeter/girth), biomechanics- (acceleration, displacement, spatial position, and velocity), and behavior-related traits (general cognition, intelligence, and Intelligence Quotient (IQ)) in dromedaries. In most association loci, the nearest protein-coding genes are linkedto neurodevelopmental and sensory disorders. This suggests that genetic variations related to neural development and sensory perception play crucial roles in shaping a dromedary camel's physical characteristics and behavior. In summary, this research advances our understanding of the genomic basis of essential traits in dromedary camels. Identifying specific genetic markers associated with zoometrics, biomechanics, and behavior provides valuable insights into camel domestication. Moreover, the links between these traits and genes related to neurodevelopmental and sensory disorders highlight the broader implications of domestication and modern selection on the health and welfare of dromedary camels. This knowledge could guide future breeding strategies, fostering a more holistic approach to camel husbandry and ensuring the sustainability of these animals in diverse agricultural contexts.

DNA polymorphisms and expression profile of immune and antioxidant genes as biomarkers for reproductive disorders tolerance/susceptibility in Baladi goat

The objective of this study was to explore single nucleotide polymorphisms (SNPs) and gene expression of immune and antioxidant markers associated with reproductive disorders in Baladi goats. A total of one hundred adults Baladi does were allocated into two equal-sized groups: normal reproductive performance and does have a history of reproductive disorders. DNA sequencing of PRLR (304-bp), LTF (904-bp), TLR2 (420-bp), TLR4 (335-bp), CLA-DRB3.2 (285-bp), SOD3 (735-bp), CAT (1526-bp), GPX4 (782-bp), and GST (690-bp) revealed SNPs associated with reproductive disorders tolerance/susceptibility in investigated does. Nonetheless, DNA sequencing of beta defensin (483-bp), CCL5 (840-bp), and ATOX1 (374-bp) genes elicited a monomorphic pattern. Levels of PRLR, LTF, TLR2, TLR4, CLA-DRB3.2, beta defensin, and CCL5 genes were significantly up-regulated in does affect with reproductive disorders than tolerant ones; while SOD3, CAT, GPX4, GST and ATOX1 genes pattern elicited an opposite trend. The results herein confirmed the potential significance of SNPs in immune and antioxidant genes as genetic markers for reproductive disorders tolerance/susceptibility in Baladi does. The Gene expression profile of investigated genes could be also used as proxy biomarkers for the prediction of the most susceptible risk time for disease occurrence and for building up an effective management protocol.

DNA Polymorphisms and mRNA Levels of Immune Biomarkers as Candidates for Inflammatory Postpartum Disorders Susceptibility in Italian Buffaloes

The immunological genes that may interact with inflammatory postpartum diseases in Italian buffaloes were examined in this study. A total number of 120 female Italian buffaloes (60 normal and 60 with inflammatory reproductive diseases) were employed. Each buffalo's jugular vein was pierced to get five milliliters of blood. To obtain whole blood and extract DNA and RNA, the blood was placed within tubes containing sodium fluoride or EDTA anticoagulants. The immunological (IKBKG, LGALS, IL1B, CCL2, RANTES, MASP2, HMGB1, and S-LZ) genes' nucleotide sequence differences between healthy buffaloes and buffaloes affected by inflammatory reproductive diseases were found by employing PCR-DNA sequencing. According to Fisher's exact test (p ˂ 0.01), there were noticeably different probabilities of all major nucleotide changes spreading among buffalo groups with and without reproductive problems. Buffaloes were significantly more likely to express the examined genes when they had inflammatory reproductive diseases. The outcomes might support the significance of these markers' nucleotide variations and gene expression patterns as indicators of the prevalence of inflammatory reproductive disorders and provide a workable buffalo management policy.

Applications of Omics Technology for Livestock Selection and Improvement

Conventional animal selection and breeding methods were based on the phenotypic performance of the animals. These methods have limitations, particularly for sex-limited traits and traits expressed later in the life cycle (e.g., carcass traits). Consequently, the genetic gain has been slow with high generation intervals. With the advent of high-throughput omics techniques and the availability of multi-omics technologies and sophisticated analytic packages, several promising tools and methods have been developed to estimate the actual genetic potential of the animals. It has now become possible to collect and access large and complex datasets comprising different genomics, transcriptomics, proteomics, metabolomics, and phonemics data as well as animal-level data (such as longevity, behavior, adaptation, etc.,), which provides new opportunities to better understand the mechanisms regulating animals' actual performance. The cost of omics technology and expertise of several fields like biology, bioinformatics, statistics, and computational biology make these technology impediments to its use in some cases. The population size and accurate phenotypic data recordings are other significant constraints for appropriate selection and breeding strategies. Nevertheless, omics technologies can estimate more accurate breeding values (BVs) and increase the genetic gain by assisting the section of genetically superior, disease-free animals at an early stage of life for enhancing animal productivity and profitability. This manuscript provides an overview of various omics technologies and their limitations for animal genetic selection and breeding decisions.