Characterization, Evaluation and Conservation of Indigenous Animal
Genetic Resources in the Sultanate of Oman
Project Code:
Funds:
Funding Source:
Start Date:
Duration:
Researchers
Prof. Osman Mahgoub (P.I.)
Prof. Isam Tawfik Kadim
Dr. Waleed Saeed Al-Marzooqi
Dr. Yasmin Elhag Eltahir
Dr. Hamza Ali Babiker
Dr. Aisha Al-Khayat Al-Shihi
Mr. Mohamed Ali Al-Abri
Eng. Eid Salim Al-Shukaili
Eng. Rashid Saud Al-Habsi
Mr. Musab Hilal Al-Busaidi
Ms.Kaadia Khalaf Al-Kharousi
Mr. Sadeq Mohamed Al-Lawati
Mrs.Samera Q. Khalaf
Dr Mushtaq A. Memon
Dr Albano Beji Pereira
(SR/AGR/ANVS/08/01)
80,000 OMR
His Majesty’s Trust Fund
02 May 2008
3.5 years
Research Assistants
Graduate Students
Mr. Mohamed Nasser Al-Kindi
Ms.Salwa Mohamed Hassan
Ms. Zainab Salam Suliman Al-Hashmi
Mr. Nasser Ali Al-Araimi
Mr. Badr Ali Al-Qamshoui
Ms. Karima Rashid Al-Sinani
Washington State University, USA
University of Porto, Portugal
Consultant
Consultant
Executive Summary
Objectives
The project aimed at examining the genetic makeup of indigenous Omani livestock breeds using molecular
markers to provide information on genetic variation within native cattle, sheep and chicken. The project also
aimed at testing the reproductive efficiency of Omani male animals. In addition, the project envisaged training
of Omani personnel, including biomedical scientists, undergraduate and postgraduate students as well as
establishment of molecular genetic facilities in the college of Agriculture and Marine Sciences and at SQU.
Methods
The genetic analysis used in the project was based on state-of-the-art approach for genotyping of microsatellites, which is the most informative and powerful genetic markers for both linkage analysis and
population based studies. Microsatellites analysis was carried out on cattle, goats and chicken of local breeds
from different regions of Oman.
For goats, a total of 202 samples from five native Omani breeds (Batina, Musandam, Dhofari, Al Jabal Al
Akhdar and Sharqiyah.) and two commercial goats (Iranian and Somali goat breed) were analyzed. Blood
sample were collected and the genomic DNA for these animals was extracted. PCR amplified with 10
microsatellite markers. In addition, we collected 100 samples of Omani cattle, 36 of these samples were
genotyped using 11 microsatellites and compared with Libyan, Indian and Portuguese cattle to throw light on
the origin of Omani cattle. Similarly, we analyzed samples from 158 Omani native chickens from six Agroecological zones: Batina, Dhofar, North Hajar, East Hajar, Musandam, and East Coast. Following DNA
extraction, electrophoregram processing and allele-size scoring was performed with the RFLP SCAN
software package (Scanalytics). Microsatellite toolkit was used to estimate total number of alleles, allele
frequencies, and average number of alleles per locus.
Breeding Soundness Examination (BSE) was carried out on Omani native bulls and bucks to test their
breeding efficiency utilizing established international standards. Each animal was examined for body
condition score, musculoskeletal problems, and overall physical condition. Testes and epididymides were
tested and accessory glands of the bulls were examined per rectum. Semen from bulls and bucks was
collected with electroejculator and was evaluated for sperm mass activity, motility, concentration and sperm
morphology using standard methods.
The project investigated the possibility of long-term cryo-preservation of semen collected from male bucks
and bulls. Semen samples were evaluated then stored frozen in liquid nitrogen for future genetic studies and
for artificial insemination of females.
Results
A high degree of genetic diversity was observed among Omani goats. The observed number of alleles for
unlinked 10 microsatellite locus ranged from 36 (OarFCB020) to 96 (HSC) across seven breeds. The mean
number of alleles of Omani breeds was 9.02 with a range between 7.7 (Batina and Sharqiyah goat) and 11.6
(Musandam goat) whereas the mean number was found in Iranian and Somali breeds were lower than Omani
goat breeds 8 and 6.6 respectively. Genetic distance was least (0.130) between Sharqiyah and Jabal Akhdar
and highest between Jabal Akhdar and Somali breeds (0.478). In the cattle study, all loci were polymorphic
and the number of alleles per loci varied between 8 and 17 with no considerable differences between breeds
expected heterozygosities. The analyses of molecular variance (AMOVA) showed that 80% of the variation
occurs within populations and only 20% of dataset variance is justified by differences among populations. The
PCo admixture analysis revealed that Omani cattle is a mixture of Indian zebu with African and Near East
taurine cattle with Indian zebu cattle playing a key role in the genesis of the Omani local breed. The study on
Omani chicken revealed a total of 217 alleles observed across all populations. The average number of alleles
per locus was 5.3±2.43. The mean number of alleles reflected high level of genetic variability in the
investigated populations. The overall expected heterozygosity was 0.62±0.03 while the observed
heterozygosity was 0.54±0.02. The overall value of Fis was 0.130±0.024 with a range of 0.193 (Dhofar) and
0.056 (North Hajar). The largest Nei’s unbiased genetic distance was found between the Batina and Dhofari
populations and the smallest between the Batina and North Hajar populations. The Dhofari population was
found to be the most genetically distant among all populations studied.
Native Omani breeding bulls and bucks BSE parameters (scrotal circumference, semen mass activity, sperm
morphology, etc.) were established and compared to Zebu/Zebu-cross bulls; and bucks in the tropics. The
mean volume of semen and the sperm concentration obtained by electro ejaculation in Omani bulls was 9±1
ml (range of 5 to 14 ml) and 285±25 million/ml, respectively. There was no significant variation during the
present study between the extenders as far as post thaw evaluation of the percent intact acrosome,
percentage of spermatozoa that reacted to HOST and sperm abnormalities.
Semen samples were successfully collected and evaluated from Omani bulls and bucks then stored in liquid
nitrogen in straws. These samples will be regularly tested to study the effect of long storage on semen quality.
They may be used for breeding Omani native cows and does using AI in the future. This part of the project
would provide optimum methods for genetic material conservation to assist conserving national animal
bioresources for future use in future genetic improvement programs. Omani personnel has been trained using
workshops and in the University of Porto, Portugal.
Conclusions
The Omani populations of goats, cattle and chicken were found to have high level of genetic diversity. The
genetic diversity observed in Omani cattle is an indicative of gene flow from other regions that perhaps still is
ongoing with the Indian zebu cattle played a major role in the genesis of the Omani population. Breeding
soundness of Omani male goats and cattle has been tested and semen was successfully preserved in liquid
nitrogen ready for breeding females. The conservation strategies of these local breed should be considered in
near future. These results can be used to establish national conservation and breed improvement strategies
for economic traits. Omani technical staff and postgraduate students have been trained within the project.
Rejuvenating Lime Production in Oman: Resolving Current Challenges
Project Code:
Funds:
Funding Source:
Start Date:
Duration:
Team Members:
(SR/AGR/CROP/08/01)
114,000 OMR
His Majesty’s Trust Fund
02 May 2008
3.5 years
Researchers
Dr. Rashid Abdullah Al-Yahyai (PI)
Dr. Fahad Al-Julanda Al Said
Prof. Michael Deadman
Prof. Iqrar Khan
Dr. Abdullah Mohammed Al-Sadi
Dr. Ali Khalfan Al-Wahaibi
Dr. Said salim Al-Ismaily
Dr. Malik Mohammed Al-Wardy
Dr. Ali Hussain Al-Lawati
Dr. Abdullah Dawood Al-Zidjali
Eng. Abdul-Rahman Mohamed Al-Matrooshi
Research Assistants
Graduate Students
Mr. Issa Hashil Al-Mahmooli
Ms. Shamsa Abdullah Al-Hilali
Ms. Zakiya Hilal Al-Kalbani
Ms. Hanan Salim Al-Moqbali
Mr. Yahya Khalfan Al-Maamari
Ms. Zakariya Said Al-Nabhani
Ms. Aisha Ghareeb Al-Ghaithi
Ms. Mariyam Khamis Al-Hashmi
Ms. Laila Nasser Al-Jahwari
Mr. Aqeel Yousef Al-Bulushi
Mr. Shihab Hamed Al-Rubaei
Executive Summary
Objectives:
This research aimed at providing short-term integrated management strategies for sustainable
production from lime trees infected with Witches’ Broom Disease of Lime (WBDL) associated with
Candidatus Phytoplasma aurantifolia. Another objective is the development of long-term solutions
through detailed investigation of the causal agent, victors, and hosts of WBDL. Furthermore, the
project aimed at investigating the major biotic and abiotic factors that influence infection and spread of
the WBDL. The project ultimately provided information that is critical for continued production from
infected trees while long-term resistance is sought.
Methods:
The project implementation was divided into several sub-projects that investigated the followings: A
field survey to determine the extent of the spread of the disease throughout Oman, the biological
diversity of lime trees, and the associated diseases to WBDL; molecular analysis of the collected
samples using Polymerase Chain Reaction (PCR) techniques; entomological studies of the disease
vectors and hosts in selected regions of Oman; physiological studies using infra-red gas exchange
measurements; soil and water status as determined by capacitance probes; yield and fruit quality of
infected trees using standard fruit quality analytical methods; and tree phenological cycles by
associating tree phenological cycles observed visually with weather data.
Results:
Survey of limes was conducted in all Governorates of Oman and found that WBDL incidence was
found in 97% of the farms visited including new areas in Al-Wusta and Dhofar. The survey also found
that old non-symptomatic trees were found in limited numbers, indicating potential for disease
resistance. A serious viral disease called Citrus Tresteza Virus (CTV) was detected in over 85% of the
surveyed wilayats. A moderate to high levels of infection with CTV in lime were detected in the
Northern part of Oman (15-47%) compared to the South (0-12%). CTV was found to be introduced
into Oman via infected citrus seedlings imported from Syria, Lebanon, India, Pakistan and Egypt,
where 45% of the seedlings were found to be infected with the virus. CTV was detected for the first
time in sweet lime, sweet lemon, citron, mandarin and sweet orange in Oman. Low genetic diversity of
Omani lime with similarity index of > 95% indicated that Omani limes are genetically identical thus little
resistance to WBDL was present. Furthermore, gene flow indicated that limes were exchanged among
farms which may have helped spread the diseases in new regions. Asymptomatic limes that are
infected with the disease were biochemically different from symptomatic with high percentages of
Citral (45%), Limonene (7%), and Cineole (7%), that may play a role in the development of the
symptoms in infected trees. However, little variations in physiological indicators were detected among
the lime trees. Results from infected trees showed that an economical yield and good fruit quality can
be obtained from WBDL-infected lime trees. PCR analysis of periwinkle (Vinca rosa) grown in Oman
as an ornamental plants with symptoms of stunted growth, yellowing and little leaf showed that
periwinkle is infected with phytoplasma. This phytoplasma is identical to the one infecting lime trees
and can be transmitted by a seed thus contributing to the spread of Withces’ Broom disease. Forty
two morphospecies of hoppers (leafhoppers, planthoppers, and pysllids), were found on lime/citrus
and other host plants at SQU Agricultural Experimental Station in AlKhodh, Muscat Gov. Two species
(Hishimonus phycitus, Diaphorina citri) were commonly found on citrus. Hishimonus phycitus, the
hopper species most suspected as a vector of WBDL was collected also from different sites in
Musandam (Daba and Madha), Al-Jabal Al-Akhdhar, and Salalah. Yield and fruit quality of Omani lime
is superior to that of imported lime and that fruiting can extend beyond ten years when proper cultural
management is implemented in lime orchards.
Conclusions:
Results from this project indicated that lime biodiversity is low, thus further work on enhancing the
genetic base of Omani lime is needed. This can be achieved by introduction of resistant citrus cultivars
for field evaluation. Limit the spread of the disease by limiting the distribution of infected materials is
important and the eradication of alternative hosts, such as Vinca rosa is vital. Immediate actions to
limit the spread of CTV are urgently needed and the introduction of resistant rootstocks that are
adapted to the Oman’s edaphic and climatic conditions. Mechanism of disease transmission and the
role of infected seeds and the insect vectors needs further investigation. Practices such as irrigation,
fertilizer and nutrient management, and pruning of symptomatic shoots are essential for prolonged
production of economic yield and good quality fruit from infected trees.
Stock Assessment of Kingfish
Project code:
Funds:
Funding Source:
Starting Date:
Duration:
(SR/AGR/FISH/08/01)
80,000 OMR
His Majesty’s Trust Fund
02 May 2008
4 years
Team Members:
Researchers
Dr Anesh Govender (PI)
Dr Aaron Henderson
Dr Hemesiri Kotagama
Dr Lubna Hamoud Al-Kharusi
Research Assistants
Mr Salim Juma Al-Kusaibi
Mr Suliaman Salim A-Sheilli
Graduate students
Ms Baderia Yousuf
Siyabi
Mr Abdullah Helal
Balushi
AlAl-
Ms Aisha Ahmed Ambuali
Mr Nasr Khalfan Al-Jardani
Executive Summary
Objectives
To evaluate the effectiveness of the implementation of a closed fishing season on the re-building
of kingfish Scomberomorus commerson in Oman. Unfortunately a closed season was not
implemented and the research had to focus on other aspects that contributed, overall, to the
management of kingfish in Oman. Four objective foci were identified and researched: (1) the
optimal sampling of age data from kingfish to estimate statistically robust growth parameters (2) a
comparison of reading whole otoliths between age readers as well as a comparison between
reading whole and sectioned otoliths. This comparison would lead to a more cost-effective means
of determining the age from kingfish otoliths (3) a drafting of a “dummy” fisheries management
plan for kingfish harvested in Oman and to determine if the plan agrees with the expectations of
both fisheries managers and fishermen alike (4) to train and supervise two students to the level of
a Masters degree.
Methods
Kingfish harvested throughout the coast of Oman were sampled mainly from landing sites. This
was carried out on a monthly basis from September 2008 until January 2011. Basic biological
data such as fish length, fish weight, sex, date of landing, gonad weight and maturity stage and
otoliths were collected. Also recorded was the price of kingfish paid for the samples. To
determine the age of the fish, otoliths were either read whole or embedded in a clear resin and
then sectioned and read. To determine the optimal sampling of kingfish a simulation study was
undertaken and a computer programme written to undertake this task. A questionnaire was
prepared to determine the reaction of fisheries managers and fishermen to our proposed fisheries
management plan for kingfish in Oman. Fisheries managers filled in these questions while faceto-to face interviews (as a group) were undertaken for the fishermen.
Results
In recent years the price of kingfish has been increasing indicating a dwindling resource: the
average sizes of both male and female kingfish decreased dramatically and the majority of the
catch consists of immature individuals. Females dominate all age classes i.e. more females than
males are harvested. The optimal sample of kingfish to sample annually for growth estimates is
approximately 400 kingfish of both sexes. Sectioned otoliths produce higher age estimates than
whole otoliths; however, whole otoliths do provide reasonable age estimates for stock
assessment purposes. Both fisheries managers and fishermen agree that the kingfish resource in
Oman is overfished. Fishermen, in particular believe that drastic government intervention is
required if kingfish is to be a sustainable one.
Conclusions
Too many immature kingfish are being harvested in Oman (in particular females) which may lead
to a total collapse of the fishery. Urgent measures need to be implemented to save a valuable
resource.
Microbial Enhanced Oil Recovery (MEOR)
Project Code:
Funds:
Funding Source:
Start Date:
Duration:
Team Members:
(SR/SCI/BIOL/08/01)
104,600 OMR
His Majesty’s Trust Fund
02 May 2008
4 years
Researchers
Research Assistants
Graduate Students
Dr. Abdulkader Elshafie (P.I.)
Dr. Saif Naseer Al-Bahry (Co-P.I.)
Dr. Yahya Mansour Al-Wahaibi
Ms. Wafa Juma Al-Alawi
Ms. Ratiba Ali Al-Maaini
Dr. Sanket Janakray Joshi
Mr. Musallam Nasser Al-Mandhari
Dr. Zaid Khamis Al-Siyabi
Ms. Hanaa Salim Al-Sulaimani
Ms. Rayah Rashid Al-Hattali
Ms. Balqees Saud Al-Hinai
Ms. Asma Khamis Al-Bahry
Ms. Hind Said Al-Makhmari
Ms. Aida Tagi Bagir Al-Lawatia
Ms. Muna Mohamed Al-Habsi
Ms. Muna Mabrook Al-Jabri
Executive Summary
Objectives:
Our aim was to study the microflora of Omani oil fields and their abilities to produce biosurfactants,
gases and biopolymers in different media. Their abilities to grow and form byproducts in core-floods
were studied. The ‘MEOR lab of excellence’ was established to serve the Sultanate of Oman and the
Region by capacity building of research scientists and by training technicians and students on MEOR
biotechnology.
Methods:
In Oman, due to the complexity of the reservoir rock and its fluid properties, crude oil recovery is very
low compared to other countries worldwide. As a result, operating oil companies in Oman have
considered several EOR/IOR methods (thermal, polymer & gas injection) to increase oil recovery. So
far, no systematic screenings were carried out in this field, MEOR is thus proposed as a potential and
cost effective technique that can be considered as an alternative for enhancing oil recovery. In this
study, we initiated microbiological screening of Omani oil wells over a period of 3 years.
Results:
We researched for both In-situ and Ex-situ MEOR. For in-situ MEOR, we've isolated and identified
indigenous microbial consortia from Wafra oil wells and Suwaihat gathering station, which are capable
of growing under strict anaerobic and halotolerant conditions. A total of 33 microbial genera and 58
microbial species were identified, all of which are first records for Oman. Caminicella sporogenes is
the second world record and first world record from an oil field. For ex-situ MEOR we have isolated
several aerobic spore-forming bacterial isolates from diverse habitats, for biosurfactant and
biopolymer production and identified using DNA sequencing and fingerprinting. Bacillus subtilis W19
was found to be the best isolate for the production of biosurfactant that reduced the ST and IFT
significantly (~3.3mN/m). The biosurfactant was observed to be stable under harsh reservoir
conditions. The effect of biosurfactant on wettability alteration of rock surfaces were studied using the
Amott index and atomic force microscopy (AFM). Adsorption to rock surfaces was also studied, which
was comparable to reported values of chemical surfactants.
The crude biosurfactant was partially identified using FTIR, GC-MS/MS and ESI – MS/MS and MALDI
TOF – MS/MS. It showed functional groups similar to the highly potent lipopeptide biosurfactant Surfactin. Core flood experiments showed the potential to recover extra 9.7%oil by using crude
biosurfactant and 13% by using concentrated biosurfactant. To evaluate the economic potential of
biosurfactant in enhancing oil recovery, different combinations of biosurfactant and chemical
surfactants were used for core flood experiments. It was observed that 50:50 mixture of biosurfactantchemical surfactant gave more oil recovery, as compared to either alone. The practical significance of
the result obtained in this basic scientific study in MEOR biotechnology could be utilized in field
application.
Conclusions:
This is the first national screening programme for potential microorganisms to be used in MEOR
biotechnology in Oman. MEOR biotechnology could be applied in some Omani oil fields, where it
can increase oil recovery. MEOR technology is simple, inexpensive and environmentally friendly.
A state of the art MEOR laboratory has been established at SQU, where well trained Omani
researchers and technicians can take this research further into field application.
Investigating the Applications of Wastewater Effluents and Sludge:
Environmental Risk or Potential Water and Energy Source
Project Code:
Funds:
Funding Source:
Start Date:
Duration:
Team Members:
(SR/ENG/CIVL/08/01)
90,000 OMR
His Majesty’s Trust Fund
02 May 2008
3 years
Researchers
Dr. Mahad Said Baawain (P.I.)
Dr. Ahmed Mohammed Al-Futaisi
Dr. Ibrahim Ashour
Dr. Mansoor Hamod Al-Harthi
Dr. Abdelaziz Ali Al-Mashikhi
Dr. Salim Said Al-Wahaibi
Dr. Abdulaziz Yahya Al-Kindi
Dr. Tabisam Khan
Dr. Mushtaque Ahmed
Mr. Sulaiman Nasser Al-Akhzami
Research Assistants
Mr. Fouzul Ameer Marikar
Mr. Salim Abdullah Al-Shuaili
Mr. Said Salim Al-Jahaffi
Mr. Said Zahir Al-Busaidi
Mr. Abdulrahim Ali Al-Omairi
Mr. Mohsin Sulaiman Al-Jabri
Mr. Mohammed Abdullah Al-Khaburi
Mr. Haitham Mohammed Al-Aghbari
Mr. Sufyan Abdullah Al-Mamari
Ms.Sumaiya Salim Al-Manthari
Graduate Students
Mr. Abdulrahim Ali Al-Omairi
Mr. Mohsin Sulaiman Al-Jabri
Executive Summary
Objectives:
This project aims at providing decision makers with the complete picture about the current situation of
wastewater treatment effluents and sludge in Muscat, Sohar and Salalah areas and any potential
effects on the environment and public health. Also, it should provide a reliable database that can be
used to quantify the amount of sludge that can be used to assess the possibility of producing energy
from such end products. Specific objectives were: to identify major sources of wastewater and sludge,
to investigate the current applications of the effluent wastewater and sludge, to identify the
characteristics of wastewater and sludge related to each source, to estimate the risk associated with
the application of the effluent wastewater and sludge, to propose quality control plan of such effluents
through identifying the required treatment technologies, to quantify the resultant sludge from the new
treatment methods, and to estimate the biogas production rate.
Methods:
Field samples of wastewater and sludge from wastewater treatment plants in Muscat, Sohar and
Salalah were collected using grab method technique which is very common for such research
compared to composite sampling method which requires huge resources due to the large number of
samples, treatment plants and locations. The choice of a sampling procedure is related to the
sampling objective, in our case measuring treatment plants efficiency. The reliability of measurement
and analysis carried out from a grab sample is thus limited to the composition of wastewater for a
given control point at one moment. Nevertheless, grab sampling is extensively used for water and
wastewater quality monitoring, and can be very useful. The sampling process included 4 sewage
treatment plants (STPs) in Muscat, 2 STPs in Sohar, and 3 STPs in Salalah. For each treatment plant,
6 to 8 samples were collected from the different treatment stages. Additional water and wastewater
samples were collected from 8 locations in Sohar industrial port and 22 wells around the recharge line
in Salalah. All samples were collected in special cool boxes and transported directly to SQU
laboratories within 4 to 8 hours of collection time to analyze them directly. The analysis methods for
physical, chemical, and biological parameters (more than 25 tests per sample!) were conducted
according to Standard Methods for water and wastewater samples which are adopted internationally
by the vast majority of research institutions. The collection and analysis of the wastewater samples
were carried over a period of 2 years.
Results:
During this study, the total number of samples exceeded 1500 samples and the number of conducted
tests exceeded 35000 tests ranged between physical, chemical and biological parameters. All
obtained results for water, wastewater and sludge samples showed high variation. However, the
produced treated effluents have met most of regulatory limits stated by Omani Standards except some
parameters such Nitrate, E coli and TSS in certain plants. The average obtained values of the heavy
metals in sludge samples were within the Omani standards for agricultural application except for Cd in
Rusail Industrial Estate STP and Zn in Sohar STP. Due to high volatile content, an anaerobic digester
3
followed by a composting system for an STP with a wastewater capacity of 20000 m /d can produce
35 MWh of energy and around 15 ton/d of compost which can be used for agricultural applications.
The groundwater along Salalah coastal strip was found not suitable for drinking purposes without
proper treatment. However, it was found suitable for agricultural and livestock requirements. Results
from Sohar industrial port showed possible microbial contamination of discharge effluents which could
be attributed to possible discharge of sewage water to the channel which was designed to convey
cooling water to the sea.
Conclusions:
This study obtained a comprehensive picture about the current situation of wastewater and sludge in
Muscat, Sohar and Salalah areas. Modifications to STPs were suggested to improve treated effluents
and utilize the resultant sludge through proper treatment techniques for production of energy and
compost. Moreover, a dynamic treatment system for STPs was recommended for better optimization
of resources and treatment levels. Finally, a quality control plan was developed to ensure proper
treatment and monitoring of wastewater and sludge in Oman.