Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study.

Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the farmgtex project results as a complete bovine database for mastitis and milk production. The results of colocalization and TWAS approaches were used for the detection of functional associated candidate genes with milk production and mastitis traits on multiple tissue-based transcriptome records. Also, we used the david database for gene ontology to identify significant terms and associated genes. For the identification of interaction networks, the genemania and string databases were used. Also, the available z-scores in TWAS results were used for the calculation of the correlation between tissues. Therefore, the present results confirm that LYNX1, DGAT1, C14H8orf33, and LY6E were identified as significant genes associated with milk production in eight, six, five, and five tissues, respectively. Also, FBXL6 was detected as a significant gene associated with mastitis trait. CLN3 and ZNF34 genes emerged via both the colocalization and TWAS approaches as significant genes for milk production trait. It is expected that TWAS and colocalization can improve our perception of the potential health status control mechanism in high-yielding dairy cows.

Construction of a circRNA- lincRNA-lncRNA-miRNA-mRNA ceRNA regulatory network identifies genes and pathways linked to goat fertility.

Background: There is growing interest in the genetic improvement of fertility traits in female goats. With high-throughput genotyping, single-cell RNA sequencing (scRNA-seq) is a powerful tool for measuring gene expression profiles. The primary objective was to investigate comparative transcriptome profiling of granulosa cells (GCs) of high- and low-fertility goats, using scRNA-seq. Methods: Thirty samples from Ji'ning Gray goats (n = 15 for high fertility and n = 15 for low fertility) were retrieved from publicly available scRNA-seq data. Functional enrichment analysis and a literature mining approach were applied to explore modules and hub genes related to fertility. Then, interactions between types of RNAs identified were predicted, and the ceRNA regulatory network was constructed by integrating these interactions with other gene regulatory networks (GRNs). Results and discussion: Comparative transcriptomics-related analyses identified 150 differentially expressed genes (DEGs) between high- and low-fertility groups, based on the fold change (≥5 and ≤-5) and false discovery rate (FDR <0.05). Among these genes, 80 were upregulated and 70 were downregulated. In addition, 81 mRNAs, 58 circRNAs, 8 lincRNAs, 19 lncRNAs, and 55 miRNAs were identified by literature mining. Furthermore, we identified 18 hub genes (SMAD1, SMAD2, SMAD3, SMAD4, TIMP1, ERBB2, BMP15, TGFB1, MAPK3, CTNNB1, BMPR2, AMHR2, TGFBR2, BMP4, ESR1, BMPR1B, AR, and TGFB2) involved in goat fertility. Identified biological networks and modules were mainly associated with ovary signature pathways. In addition, KEGG enrichment analysis identified regulating pluripotency of stem cells, cytokine-cytokine receptor interactions, ovarian steroidogenesis, oocyte meiosis, progesterone-mediated oocyte maturation, parathyroid and growth hormone synthesis, cortisol synthesis and secretion, and signaling pathways for prolactin, TGF-beta, Hippo, MAPK, PI3K-Akt, and FoxO. Functional annotation of identified DEGs implicated important biological pathways. These findings provided insights into the genetic basis of fertility in female goats and are an impetus to elucidate molecular ceRNA regulatory networks and functions of DEGs underlying ovarian follicular development.

A genome-wide association study of morphometric traits in dromedaries.

BACKGROUND: Investigating genomic regions associated with morphometric traits in camels is valuable, because it allows a better understanding of adaptive and productive features to implement a sustainable management and a customised breeding program for dromedaries. OBJECTIVES: With a genome-wide association study (GWAS) including 96 Iranian dromedaries phenotyped for 12 morphometric traits and genotyped-by-sequencing (GBS) with 14,522 SNPs, we aimed at identifying associated candidate genes. METHODS: The association between SNPs and morphometric traits was investigated using a linear mixed model with principal component analysis (PCA) and kinship matrix. RESULTS: With this approach, we detected 59 SNPs located in 37 candidate genes potentially associated to morphometric traits in dromedaries. The top associated SNPs were related to pin width, whither to pin length, height at whither, muzzle girth, and tail length. Interestingly, the results highlight the association between whither height, muzzle circumference, tail length, whither to pin length. The identified candidate genes were associated with growth, body size, and immune system in other species. CONCLUSIONS: We identified three key hub genes in the gene network analysis including ACTB, SOCS1 and ARFGEF1. In the central position of gene network, ACTB was detected as the most important gene related to muscle function. With this initial GWAS using GBS on dromedary camels for morphometric traits, we show that this SNP panel can be effective for genetic evaluation of growth in dromedaries. However, we suggest a higher-density SNP array may greatly improve the reliability of the results.

Selective genotyping to implement genomic selection in beef cattle breeding.

Genomic selection (GS) plays an essential role in livestock genetic improvement programs. In dairy cattle, the method is already a recognized tool to estimate the breeding values of young animals and reduce generation intervals. Due to the different breeding structures of beef cattle, the implementation of GS is still a challenge and has been adopted to a much lesser extent than dairy cattle. This study aimed to evaluate genotyping strategies in terms of prediction accuracy as the first step in the implementation of GS in beef while some restrictions were assumed for the availability of phenotypic and genomic information. For this purpose, a multi-breed population of beef cattle was simulated by imitating the practical system of beef cattle genetic evaluation. Four genotyping scenarios were compared to traditional pedigree-based evaluation. Results showed an improvement in prediction accuracy, albeit a limited number of animals being genotyped (i.e., 3% of total animals in genetic evaluation). The comparison of genotyping scenarios revealed that selective genotyping should be on animals from both ancestral and younger generations. In addition, as genetic evaluation in practice covers traits that are expressed in either sex, it is recommended that genotyping covers animals from both sexes.

A critical review of the recent concept of artificial mechanical uterus design in relation to the maternal microbiome: An Update to past researches.

The microbiome in the female reproductive tract plays an essential role in immune modulation and reproductive health. However, various microbes become established during pregnancy, the balance of which plays a crucial role in embryonic development and healthy births. The contribution of disturbances in the microbiome profile to embryo health is poorly understood. A better understanding of the relationship between reproductive outcomes and the vaginal microbiota is needed to optimize the chances of healthy births. In this regards, microbiome dysbiosis refers to conditions in which the pathways of communication and balance within the normal microbiome are imbalanced due to the intrusion of pathogenic microorganisms into the reproductive system. This review summarizes the current state of knowledge on the natural human microbiome, with a focus on the natural uterine microbiome, mother-to-child transmission, dysbiosis, and the pattern of microbial change in pregnancy and parturition, and reviews the effects of artificial uterus probiotics during pregnancy. These effects can be studied in the sterile environment of an artificial uterus, and microbes with potential probiotic activity can be studied as a possible therapeutic approach. The artificial uterus is a technological device or biobag used as an incubator, allowing extracorporeal pregnancy. Establishing beneficial microbial communities within the artificial womb using probiotic species could modulate the immune system of both the fetus and the mother. The artificial womb could be used to select the best strains of probiotic species to fight infection with specific pathogens. Questions about the interactions and stability of the most appropriate probiotics, as well as dosage and duration of treatment, need to be answered before probiotics can be a clinical treatment in human pregnancy.

Changes in the gene expression profile of the mammary gland lipogenic enzymes in Saanen goats in response to dietary fats.

BACKGROUND: The second half of the first pregnancy is a critical period in the growth and development of the mammary gland. The use of functional compounds during this period may positively impact livestock performance. OBJECTIVES: In this study, changes in lipogenic enzyme gene expression in the mammary gland of Saanen goats in response to different dietary fat sources were analysed. METHODS: Goats from four groups (10 each) received these diets from the last two months of pregnancy through four months of lactation: C-, no added fat (negative control group), C+, with saturated palm oil (positive control group), SB, with roasted soybeans (omega-6 group) and FS, with extruded flaxseed (omega-3 group). The fat content was about 4% of dry matter. Milk yield, milk fatty acid profile, milk health index (HI) and gene expression of four lipogenic enzymes in mammary tissue were measured. RESULTS: The FS group had significantly higher milk production with lower omega-6 to omega-3, monounsaturated to polyunsaturated, and total saturated fatty acids compared to other groups. The shorter and longer than16-carbon chain of total milk fatty acid indicates significantly higher values for the C- and C+ groups, respectively. The milk HI for the SB group was significantly higher. The gene expression profile for acetyl-coenzyme A carboxylase was higher in the C- group than other experimental groups. CONCLUSIONS: The results show that manipulation of the diet with unsaturated fat supplements improved milk production, synthesis of milk fat and molecular expression of lipogenic enzymes in mammary tissue in primiparous Saanen goats.

Supplementation of broiler chicken diets with bovine lactoferrin improves growth performance, histological parameters of jejunum and immune-related gene expression.

The aim of this study was to investigate the influence of dietary supplementation of bovine lactoferrin (bLF) on growth performance, carcass traits, histomorphology of jejunum, immune function and hepatic and splenic gene expression of interferon-gamma (IFN-γ) and interleukine-2 (IL-2) in broiler chickens. A total of 240 one-day-old Ross 308 male broiler chickens were randomly allotted into six dietary treatments with four replicate pens (10 chicks per pen) and fed experimental diet in 3 feeding phases (starter: d 0-10, grower: d 11-24 and finisher: d 25-42). The experimental treatments were (1) corn-soya bean meal-based basal diet (control), (2-5) basal diet supplemented with 200, 400, 600, 800 mg/kg bLF, respectively, and (6) basal diet supplemented with 200 mg/kg oxytetracycline (OTC). The average body weight gain (ABWG) of broilers fed 800 mg/kg bLF was 8.48% higher than those fed a corn-soybean meal-based diet during the starter period (d 0-10) (linear effect, p = 0.002; quadratic effect, p = 0.24). Average daily feed intake (ADFI) and the feed conversion ratio (FCR) were not affected (p>0.05) by bLF supplementation. At 42 days of age, the breast meat percentage and carcass yield of broilers fed 800 mg/kg bLF compared with the control group significantly increased by 9.51% and 6.03% respectively (p < 0.05). Compared with the chicks fed the control diet, the chicks fed diets supplemented with bLF had higher villus height, muscle thickness and villus surface area (p > 0.05). Dietary bLF inclusion increased the total immunoglobulin (IgT) titre against sheep red blood cells (SRBCs) antigen (linear effect, p = 0.031; quadratic effect, p = 0.035) and improved the phytohaemagglutinin-P (PHA-P)-skin test of broilers. Compared with the control, bLF enhanced the gene expression of IFN-γ in spleen (p = 0.048, linear effect, p = 0.009; quadratic effect, p = 0.093) and liver (p = 0.012, linear effect, p = 0.008; quadratic effect, p = 0.01) and IL-2 expression in spleen (p = 0.021, linear effect, p = 0.026; quadratic effect, p = 0.103). The bLF supplementation had no effect on IL-2 gene expression in liver (p > 0.05, linear effect, p = 0.213; quadratic effect, p = 0.159). In conclusion, we found that supplementation of broiler diets with 800 mg/kg bLF can improve the growth performance, carcass yield, cell-mediated and antibody-mediated immune responses and enhance the IL-2 and IFN-γ gene expression of broilers.

Variation and frequency of supernumerary teats, litter size, histological features and the fibroblast growth factor 2 (FGF-2) gene expression pattern in goats.

Historically, female domestic goats carrying multiple kids are mostly unable to express sufficient nursing ability due to a limited number of functional teats. Therefore, the functional teat is an important component in prolific goat breeding, and plays a key role in the future health of their kids. With this motivation, we wanted to investigate the phenotypic features, litter size, histology of adult female mammary glands, and the gene expression profile of the fibroblast growth factor 2 (FGF-2) gene in goats. To illustrate this, the initial dataset of the current study consists of an electronic questionnaire that includes 697 individuals (548 does and 149 bucks) of five endemic and three exotic goats from 2015 to 2020 in different geographic areas of Iran, from 59 Markhoz (MARG), 50 Azari (AZAR), 73 Busheri (BUSH), 69 Sarbisheh (SARB), 165 Mahabadi (MOHA) indigenous goats and also exotic breeds, including 183 Saanen (SANN), 39 Alpine (ALPN), and 59 Boer (BORE) goats. The results of this study confirmed that MOHA goats (4.16%), BORE (4.43%) and SANN goat breeds (5.75%) have larger litter sizes. Interestingly, the evidence gathering when SNTs occurred showed that both the BUSH and BORE goat breeds had the highest frequency of SNTs. Moreover, under the same physiological and lactation conditions, there was no statistically significant difference in histological features between the three compared does class consist of the two teats, SNTs, and four functional teats. In addition, the results of the gene expression profile significantly highlight the FGF-2 gene pattern in two teat groups compared to other SNT groups (P < 0.01). In summary, this scenario can be used to generate further research and facts on responsible candidate genes, the variations in teat numbers in goats, examining both the incidence of SNT and litter size.

The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations.

Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds.

BACKGROUND: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. RESULTS: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). CONCLUSIONS: We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.

Three dimensional metal/N-doped nanoplate carbon catalysts for oxygen reduction, the reason for using a layered nanoreactor.

A layered nanoreactor (zinc hydroxide gallate/nitrate nanohybrid) has been designed as a nano-vessel to confine the gallate/nitrate reaction inside zinc hydroxide layers for production of metal/nitrogen-doped carbon catalysts. Metals (Fe2+, Co2+ and Ni2+) doped and bare zinc hydroxide nitrates (ZHN) were synthesized as the α-phase hydroxide hosts. By an incomplete ion-exchange process, nitrate anions between the layers of the hosts were then partially replaced by the gallate anions to produce the layered nanoreactors. Under heat-treatment, the reaction between the remaining un-exchanged nitrate anions and the organic moiety inside the basal spacing of each nanohybrid plate resulted in obtaining highly porous 3D metal/nitrogen-doped carbon nanosheets. These catalysts were then used as extremely efficient electrocatalysts for catalyzing oxygen reduction reaction (ORR). This study is intended to show the way to get maximum electrocatalytic activity of the metal/N-doped carbon catalysts toward the ORR. This exceptionally high ORR performance originates from the increased available surface, the best pore size range and the uniform distribution of the active sites in the produced catalysts, all provided by the use of new idea of the layered nanoreactor.

Morpho-molecular analysis as a prognostic model for repulsive feedback of the medicinal plant "Andrographis paniculata" to allogamy.

Andrographis paniculata Nees. (AP) is a self-pollinated medicinal herb with a wide range of pharmaceutical properties, facing a low diversity in Malaysia. Cross-pollination of AP accessions leads to considerable rates of heterosis in the agro-morphological characteristics and anticancer phytochemicals of this eminent medicinal herb. However, the poor crossability of the plant at the interpopulation or intraspecific levels is an obstacle from the evolutionary and breeding points of view as an average of 4.56% crossability was recorded for AP in this study. Hence, this research aimed to elicit the impact of parental genetic distances (GDs) on the rate of crossability of AP using seven accessions in 21 possible cross combinations. To this end, a set of 55 randomly amplified polymorphic DNA (RAPD) primers and a total of 13 agro-morphological markers were employed to test the hypothesis. Twenty-two out of the 55 RAPD primers amplified a total of 257 bands of which 107 bands were found to be polymorphic. The principal component analysis (PCA) based on the RAPD markers revealed that the studied AP accessions were distributed to three distinct groups. Furthermore, it was noticed that even a minor increase in GD between two parents can cause a decline in their crossability. Unlike, the morphological-based GDs acted neutrally to crossability. This finding suggests that, despite the low genetic diversity among the Malaysian APs, a population prescreening using RAPD markers would be useful to enhance the rate of fruit set through selecting the genetically adjacent parents.

Microsatellite-based evidences of genetic bottlenecks in the cryptic species "Andrographis paniculata Nees": a potential anticancer agent.

Andrographis paniculata (AP) is a medicinal plant species introduced into Malaysia. To address the genetic structure and evolutionary connectedness of the Malaysian AP with the Indian AP, a DNA sequence analysis was conducted based on 24 microsatellite markers. Out of the 24 primer sets, seven novel microsatellite primers were designed and amplified intra-specifically according to the available Indian AP sequences at the National Centre for Biotechnology Information (NCBI), where 17 of them were amplified using the cross-species strategy by employing the primers belonging to Acanthus ilicifolius Linn (Acanthaceae) and Lumnitzera racemosa Wild (Combretaceae). The primers were then applied on the Malaysian AP accessions. Sixteen of the new microsatellite loci were amplified successfully. Analysis of these microsatellite sequences, revealed some significant differences between the Indian and Malaysian AP accessions in terms of the size and type of the repeat motifs. These findings depicted the cryptic feature of this species. Despite identifying several heterozygous alleles no polymorphism was observed in the detected loci of the selected accessions. This situation was in concordance with the presence of "fixed heterozygosity" phenomenon in the mentioned loci. Accordingly, this was fully consistent with the occurrence of the genetic bottleneck and founder effect within Malaysian AP population. Apart from the amplification of new microsatellites in this species, our observations could be in agreement with the risk of genetic depletion and consequently extinction of this precious herb in Malaysia. This issue should be taken into consideration in the future studies.

Random amplified polymorphic markers as indicator for genetic conservation program in Iranian pheasant (Phasianus colchicus).

The objective of present study was identification of genetic similarity between wild Iran and captive Azerbaijan Pheasant using PCR-RAPD markers. For this purpose, in overall, 28 birds were taken for DNA extraction and subsequently 15 arbitrary primers were applied for PCR-RAPD technique. After electrophoresis, five primers exhibited sufficient variability which yielded overall 65 distinct bands, 59 polymorphic bands, for detalis, range of number of bands per primer was 10 to 14, and produced size varied between 200 to 1500 bp. Highest and lowest polymorphic primers were OPC5, OPC16 (100%) and OPC15 (81%), respectively. Result of genetic variation between two groups was accounted as nonsignificant (8.12%) of the overall variation. According to our expectation the wild Iranian birds showed higher genetic diversity value than the Azerbaijan captive birds. As general conclusion, two pheasant populations have almost same genetic origin and probably are subpopulations of one population. The data reported herein could open the opportunity to search for suitable conservation strategy to improve richness of Iran biodiversity and present study here was the first report that might have significant impact on the breeding and conservation program of Iranian pheasant gene pool. Analyses using more regions, more birds, and more DNA markers will be useful to confirm or to reject these findings.

Mutations in bone morphogenetic protein 15 and growth differentiation factor 9 genes are associated with increased litter size in fat-tailed sheep breeds.

The objective of this study was to investigate association between GDF9 and BMP15 gene polymorphism and litter size in fat-tailed sheep, a total of 97 mature ewes from four breeds (Afshari=19; Baluchi=18; Makui=30 and Mehraban=30) were genotyped for the BMP15 HinfI and GDF9 HhaI polymorphisms by PCR-RFLP technique. The highest and lowest mutant allele frequencies were found in Makui (0.27) and Afshari (0.10) sheep for the BMP15 gene and in Afshari (0.24) and Mehraban (0.18) sheep for the GDF9 gene, respectively. Litter size was significantly influenced by genotype of the ewe for two genes (P < 0.01). Heterozygous genotypes for both loci showed higher litter size than homozygous genotypes (P < 0.01). None of the individuals carried homozygous genotype for both of the GDF9 and BMP15 variants in these breeds. The individuals carrying the mutant allele for one of the investigated candidate gene still showed fertile phenotype. Thus, existence of homozygosity at one of the BMP15 and GDF9 variant is not probably able to block normal hormonal pathway of reproduction in fat-tailed sheep.

Genetic variation of ten microsatellite loci in Makui sheep of Iran.

The native breeds, because of their natural selection against harsh environment and adaptation to regional conditions are important to resource-poor farmers and pastoralists. The molecular characterization of genetic variation is a fundamental step to manage and conserve indigenous breeds. The aim of this study was to determine the genetic variation of Makui sheep. Totally, 100 sheep (60 ewes, 10 ram and 30 lambs) were used in this study. Polymerase Chain Reaction (PCR) was performed using microsatellite primers BM1329, OarAE101, OarFCB11, OarFCB128, OarFCB129, OarFCB20, OarFCB304, OarFCB5, OarHH35 and OarHH55 in a standard 25 microl reaction. All microsatellite loci were amplified and produced minimum 2 and maximum 14 alleles ranging from 90 to 185 bp in size. The mean number of alleles for each locus was 6.8. Loci OarFCB128 and OarAE101 produced the highest (8.5288) and the lowest (1.0304) effective number of alleles, respectively. The mean expected heterozygosity for all loci was 0.6893 (range 0.0295-0.8837). The highest (2.12) and the lowest (0.07) Shanon Index was observed in OarFCB11 and OarAE101, respectively. Only two (OarFCB5 and OarAE101) out of ten loci were in Hardy-Weinberg equilibrium. The present study was able to demonstrate a reasonable genetic variation and polymorphism across all microsatellite loci studied in the Makui sheep.