Animal and Plant Genomics

Diversity in Haemonchus contortus: A case study from Sudan

Title: Diversity in Haemonchus contortus: A case study from Sudan


Khalid Mohammedsalih1,2,3, Amna Khalafalla2, Ahmed Bashar1, Jürgen Krücken3, Georg von Samson-Himmelstjerna3

1Faculty of Veterinary Science, University of Nyala, P.O. Box 155, Nyala, Sudan

2Faculty of Veterinary Medicine, University of Khartoum, P.O. Box 32, Khartoum North, Sudan

3Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany

Corresponds to Khalid Mohammedsalih, Faculty of Veterinary Science, University of Nyala, P.O. Box 155, Nyala, Sudan. Email:, Tel: +249115948886.


Haemonchus contortus is a major parasitic gastrointestinal nematode species affecting small ruminants health and results in great economic losses worldwide. The control of haemonchosis has mainly depended on the use of anthelmintics (e.g. benzimidazoles), but the excessive and the prolonged use of these drugs has resulted in the development of resistance. Development of benzimidazoles resistance is confirmed when a single nucleotide polymorphism (SNP) occurred in each of codon F167Y (TTC/TAC), E198A (GAA/GCA) or F200Y (TTC/TAC) of β-tubulin isotype 1 gene of H. contortus. Basically, our goal here was to detect the presence of each of the three mentioned mutations in Haemonchus from goats isolated from four different South Darfur (Sudan) study areas using PCR, gene sequencing and pyrosequencing assays. All the tested samples (n=34) confirmed as H. contortus when species-specific PCR performed. The allele frequencies were 3% and 7% at codon F167Y and F200Y, respectively. These values were below the threshold for resistance development (>10%). Quantification of alleles using pyrosequencing assays at the position of codon E198A was failed in all tested samples, and sequence mismatches were detected when Sanger sequencer adopted. The findings of this first study of SNPs in the β-tubulin isotype 1 gene of H. contortus populations from Sudan suggest that mutations were not occurred at codon F167Y and F200Y, and both codons were excluded as a cause of benzimidazole resistance in South Darfur. With codon E198A, the study recommends the establishment of a new molecular protocol for allele frequency measurement.


Haemonchus contortus, benzimidazole resistance, sequence mismatches, goat, Sudan





Sumaya Kambal1, Amna Alnazir2, Bashir Salim3


1Faculty of Animal Production Science & Technology, Sudan University of Science & Technology, 2Faculty of Veterinary Medicine, University of Khartoum, 3Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum




Background: Western Baggara cattle breed is naturally inhabiting the western regions of the Sudan, primarily raised by nomadic pastoralists in Darfur and Kurdofan states and ranked the best beef producing cattle breed in the country. This breed had structured phenotypically into three populations, Nyalawi, Rezaigi and Messairi. Decades to date, western Baggara cattle breed-Nyalawi population (WBCB-NP) is the most reputable beef cattle among the other types by its large size that contribute significantly to local meat consumption as well as to the export revenue.


Aims: This study was undertaken to investigate the maternal genetic diversity and the demography dynamic by addressing whether this population had undergone demographic expansion, decline or equilibrium.


Method: Genomic DNA was extracted from blood of 30 animals selected WBCB-NP and subjected to PCR targeting the entire mitochondrial DNA D-loop region and subsequently to DNA sequencing.

Results: This resulted in 43 polymorphic sites that defined 28 haplotypes of which 4 signatures of breed specific transition were detected when compared to bovine reference sequence. Genetic diversity indices revealed high level of haplotype diversity (1.000 ± 0.0091) and low level of nucleotide diversity (0.005 ± 0.0028) between these haplotypes that agreed with the Median Joining and Minimum Spanning networks’ pattern, and the Neighbor Joining phylogenetic tree. The revealed unimodal pattern of the mismatch distribution among the haplotypes was in a good accordance with both the negative values of Tajima’s D (-2.259; P= 0.000) and Fu’s Fs (-25.671; P= 0.000) results that are significantly deviated from the neutral model, suggesting population demographic expansion event.


Conclusion: It is concluded that WBCB-NP is highly divers and had experienced a demographic growth. This study has raised important queries about the nature and the factors of this demographic expansion that can be compared with other populations of cattle for historical dynamics tracing purpose.



The presenter: Sumaya Yousof Yassin Kambal

Teaching Assistant

Faculty of Animal Production Science and Technology, Sudan University of Science and Technology


Genome diversity and adaptations of indigenous Sudanese livestock Breeds

Genome diversity and adaptations of indigenous Sudanese livestock Breeds

Hassan H. Musa1, 2*, Taha H. Musa2, Abdelkareem A. Ahmed2, Jaafar S. Fedail2, Ibrahim H. Musa2

1Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan

2BRI, Darfur University College, Nyala, Sudan




The geography of Sudan offers diversified ecological conditions and climate types that had influenced notably the distribution of today’s existence Sudanese livestock breeds. In this study, we carried out whole genome resequencing for Sudanese indigenous cattle comprising of three dairy breeds (Kenana, Butana and Aryshai) and three beef breeds (Baggara, Gash and Fulani). Eleven Sheep breeds comprising Sudan Desert ecotype (Kabbashi, Hammari,
Meidobe, Dubasi, Ashgar, Watish, Beja and Riverine wool), Arid land ecotype (Zaghawi), West African Fulani ecotype (Fallata or Um bororo) and Sudanese fused ecotype (Garage). Three goat breeds (Nubain, Desert and Tiggar). In addition, five camel breeds comprising three packing camel (Arabian Kenani, Lahawi) and two riding (racing) camel (Bishari and Anafi) were genotyped using the pair-end GBS technology.

The aim was to investigate their genome diversity, population structure and signature of positive selection. Genomic DNA was extracted from whole blood using Qiagen DNeasy extraction kit (Qiagen, Valencia, CA, USA). Whole genome re-sequencing and GBS were performed on the Illumina HiSeq 2000 platform by Novogene (Novogene Co., Ltd, Tianjin, China).

Genomic diversity and population structure were assessed among the Sudanese livestock breeds compared with other African and non-African livestock breeds. Genomic signatures of positive selection were assessed using pooled heterozygosity (Hp) approach for within breed analysis and genetic differentiated (Fst) test between the dairy and beef breeds and/or between backing and riding camels. The common candidate selected genes are related to growth and conformation traits, skeletal muscles development and functionality, immunity, residual feed intake, heat stress response and tick resistance. This study for the first time report the valuable genetic resources for Sudanese indigenous animal breeds and provide insights into their genomic features. The variants discovered will pave way for further research into the genetic basis of economically important traits.


Keywords: Genomic diversity, genomic signatures, livestock breeds, Sudan


The Epidemic of Rinderpest in the 19th century Ethiopia: In search of Genomic signatures 

The Epidemic of Rinderpest in the 19th century Ethiopia: In search of Genomic signatures” 

Fikirte Adugna



Rinderpest is one of the oldest animal diseases in the world. It has originated from the Asian subcontinent. The disease has also been wide spread to the medieval Europe and Middle East in the early 17th century, through livestock imports and military invasion.

Rinderpest had appeared in Ethiopia in 1884 via cattle imports. At the end of 19th c the Italian government has occupied Massawa. At that time Italian imported cattle from Asia the continent where Rinderpest originated, thus introducing Rinderpest to Ethiopia. The disease had wide spread all over the country and became a cause for the death of more than 90 percent of the cattle. It also affected the agricultural production since the farmers’ had used the cattle to plow their farmland. Consequently, the Ethiopian great famine ensued in 1888 accounting for the death of more than one million people from hunger within four years. The epidemic is an example of a historic event that may have had far-reaching consequences on the genomes of animals and humans. There are avenues where genomics can look at such impacts by detecting population “bottlenecks”, signatures of selection and other genomic manifestations.


Sunday Aina poster


Aina Faith Sunday1 and Gloria Adewale2

1: Phytoremediation Unit, department of Agriculture, Lagos State Polytechnic

2: Environmental Health Department, Olabisi Onabanjo Univeristy, Nigeria

Lead is rated second of all harzardous substances and has become persistent in the soil and environment due to anthrpogenic activities such as mining, fuel combustion, synthetic fertilizers and from lead-acid batteries. Lead can be retained in the environment for up to 5000 years without degrading. Lead is toxic to living organisms even at low concentration. Attempts have been made to remove lead accumulation from our environment using plant species such as Arabdiosis, Helianthus, Oryza sativa and Lantana camara; a process known as Phytoremediation. However, the effectiveness of clean up haave been very low compared to amount deposited in our environment. This study documents genetic enhancement utilized for a better phytoremediation of lead from  our society. Phytochelatin synthase gene from wheat plant inserted into Nicotiana glauca, the use of Agrobacterium, methallothionein, metal chelator, metal transporter genes transfereered into plants for better lead uptake from the soil have been developed. This genetic engineering technique has not only proved succesful but also increase the hope of getting better molecular techniques which will eventually be used to effectively reduce the accumulation of toxic metals from our environment.



Arwa Elsamany poster


Arwa Alsammany1 , Sumaia M.A. Abukashawa1

1Faculty of Science, University of Khartoum

Background: The importance of reproduction traits in dairy cattle breeding programs has dramatically increased recently. Leptin gene is one of the candidate genes, which located at chromosome 4 and is consisted from 3 exons and 2 introns. Identification of single nucleotide polymorphisms (SNP) opened new vistas in animal breeding and several polymorphic studies on the bovine leptin gene have been reported, SNP LEP/Sau3AI is situated in the second intron. Objective: The objective of this research was to evaluate the frequency of leptin gene polymorphism among Bos indicus and Bos Taurus crossbred cattle in Sudan. Materials and Methods:  This study was cross sectional study. During 2016 blood was collected from Holstein Friesian x Kenana crossbreed into EDTA sterile tubes, AA, AB, BB genotypes were detected using PCRRFLP technique. Data analysis was done by using SPSS software. Finding:  Genotype AA was found to be frequent in LEP/Sau3AI SNP. Conclusion:  Genotype AA is more frequent in LEP/Sau3AI SNP, suggesting that it can be used as a good genetic marker in selection and breeding of dairy cattle.



Adetunji Nigeria



Adetunji Charles Oluwaseuna,b, Paomipem Phazangb, Adetunji Juliana Bunmic,  Neera Bhalla Sarinb,

aEdo University, Department of Microbiology, Applied Microbiology, Biotechnology and Nanotechnology Laboratory, Iyamho, Edo State. Nigeria.

bJawaharlal Nehru University, School of Life Sciences, Laboratory of Genetic Manipulation for Stress Alleviation and Value Addition in Plants, New Delhi-110067. INDIA

c Osun State University, Nutritional and toxicological Research Laboratory, Department of Biochemistry, Osogbo Nigeria.



This study utilized secondary metabolites produced from the wild Brassica juncea callus (PMWC) modulated with gamma TMT gene for the production of ecofriendly biopesticides with high tolerance to abiotic and biotic stress in a tomato plant. The phytotoxic metabolites from the transgenic callus (PMTC) were produced from the Agrobacterium-mediated transformation of the wild callus of Brassica juncea.


Pest and pathogens have been highlighted as a major constrains affecting the increase in agricultural productivity globally. The persistent use of pesticides has led not only to pest and disease resistance but also, bioaccumulation, biomagnification which subsequently affect human health and consequently result to environmental pollution.

The in-vitro biological control efficacy of these phytotoxic metabolites was evaluated in a greenhouse in comparison with synthetic fungicide. The physiochemical and antioxidant properties were evaluated on the harvested tomato fruits while the in-vivo biochemical assessment of the harvested tomato fruits was carried-out using an albino rat.
The greenhouse evaluations showed a significant increase (p>0.05) in biological control efficacy, growth and yield components of the tomato plant treated with PMTC followed by PMWC when compared with the synthetic fungicide. The harvested tomato fruits showed a reduction in weight loss, ascorbic acid value, soluble solids content, enhanced firmness, higher lycopene content, increase in the activity of catalase, peroxidase, superoxide dismutase and prevented the release of superoxide free radicals in the following order PMTC > PMWC > synthetic fungicide. The histopathological and biochemical analysis on albino-rat fed with harvested tomato fruits shows mild toxicity with PMTC followed by PMWC when compared to a synthetic fungicide.


Finally, considering the broad-spectrum antifungal activity, plant growth-supporting characteristic, antioxidant promoting qualities, and human health friendliness, make these biopesticides particularly attractive for efficient agricultural applications in plant disease management.