Abstract: A DNA microarray technology is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. It is handled by clustering which reveals the natural structures and identifying the interesting patterns in the underlying data. In this paper, gene based clustering in gene expression data is proposed using Cuckoo Search with Differential Evolution (CS-DE). The experiment results are analyzed with gene expression benchmark datasets. The results show that CS-DE outperforms CS in benchmark datasets. To find the validation of the clustering results, this work is tested with one internal and one external cluster validation indexes.
Abstract: The paper presents the results of the molecular
genetics analysis in sports research, with special emphasis to use
genetic information in diagnosing of motoric predispositions in Roma
boys from East Slovakia. The ability and move are the basic
characteristics of all living organisms. The phenotypes are influenced
by a combination of genetic and environmental factors. Genetic tests
differ in principle from the traditional motoric tests, because
the DNA of an individual does not change during life. The aim of
the presented study was to examine motion abilities and to determine
the frequency of ACTN3 (R577X) gene in Roma children. Genotype
data were obtained from 138 Roma and 155 Slovak boys from 7 to 15
years old. Children were investigated on physical performance level
in association with their genotype. Biological material for genetic
analyses comprised samples of buccal swabs. Genotypes were
determined using Real Time High resolution melting PCR method
(Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The
software allows creating reports of any analysis, where information
of the specific analysis, normalized and differential graphs and many
information of the samples are shown. Roma children of analyzed
group legged to non-Romany children at the same age in all the
compared tests. The % distribution of R and X alleles in Roma
children was different from controls. The frequency of XX genotype
was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX
genotype was 9.26% which is comparable to a frequency of an Indian
population. Data were analyzed with the ANOVA test.
Abstract: The safflower seed contains about 25-40% solvent extract and 20-33% fiber. It is well known that dietary phospholipids lower serum cholesterol levels effectively. The nutrient composition of safflower seed changes depending on region, soil and genotypes. This research was made by using of six natural selected (A22, A29, A30, C12, E1, F4, G8, G12, J27) and three commercial (Remzibey, Dincer, Black Sun1) varieties of safflower genotypes. The research was conducted on field conditions for two years (2009 and 2010) in randomized complete block design with three replications in Konya-Turkey ecological conditions. Oil contents, mineral contents and their correlations were determined in the research. According to the results, oil content was ranged from 22.38% to 34.26%, while the minerals were in between the following values: 1469, 04-2068.07 mg kg-1 for Ca, 7.24-11.71 mg kg-1 for B, 13.29-17.41 mg kg-1 for Cu, 51.00-79.35 mg kg-1 for Fe, 3988-6638.34 mg kg-1 for K, 1418.61-2306.06 mg kg-1 for Mg, 11.37-17.76 mg kg-1 for Mn, 4172.33-7059.58 mg kg-1 for P and 32.60-59.00 mg kg-1 for Zn. Correlation analysis that was made separately for the commercial varieties and wild lines showed that high level of oil content was negatively affected by all the investigated minerals except for K and Zn in the commercial varieties.
Abstract: In order to study the Mutual effect of genotype ×
environment for the percent of oil index in sunflower items, an
experiment was accomplished form complete random block designs
in four iteration and was four diverse researching station comprising
Esfahan, Birjand, Sari, and Karaj. Complex variance analysis showed
that there is an important diversity between the items under
investigation. The results relevant the coefficient variation of items
Azargol and Vidoc has respectively allocated the minimum
coefficient of variations. According to the results extrapolated from
Shokla stability variance, the Items Brocar, Allison and Fabiola, are
among the stable genotypes for oil percent respectively. In the biplot
GGE, the location under investigations divided in two superenvironments,
first one comprised of locations naming Esfahan,
Karaj, and Birjand, and second one were such a location as Sari. By
this point of view, in the first super-environment, the Item Fabiola
and in the second Almanzor item was among the best items and
crops.
Abstract: Gastric Cancer (GC) has high morbidity and fatality
rate in various countries. It is still one of the most frequent and
deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes
are highly expressed in the normal stomach epithelium and play
important roles in maintaining the integrity and homeostasis of
stomach mucosal epithelial cells. In this study, 47 paired samples that
were grouped according to the types of gastric cancer and the clinical
characteristics of the patients, including gender and average of age.
They were investigated with gene expression analysis and mutation
screening by monitoring RT-PCR, SSCP and nucleotide sequencing
techniques. Both GKN1 and GKN2 genes were observed significantly
reduced found by (Wilcoxon signed rank test; p
Abstract: Evolution strategy (ES) is a well-known instance of evolutionary algorithms, and there have been many studies on ES. In this paper, the author proposes an extended ES for solving fuzzy-valued optimization problems. In the proposed ES, genotype values are not real numbers but fuzzy numbers. Evolutionary processes in the ES are extended so that it can handle genotype instances with fuzzy numbers. In this study, the proposed method is experimentally applied to the evolution of neural networks with fuzzy weights and biases. Results reveal that fuzzy neural networks evolved using the proposed ES with fuzzy genotype values can model hidden target fuzzy functions even though no training data are explicitly provided. Next, the proposed method is evaluated in terms of variations in specifying fuzzy numbers as genotype values. One of the mostly adopted fuzzy numbers is a symmetric triangular one that can be specified by its lower and upper bounds (LU) or its center and width (CW). Experimental results revealed that the LU model contributed better to the fuzzy ES than the CW model, which indicates that the LU model should be adopted in future applications of the proposed method.
Abstract: Determination of genetic variation is useful for plant
breeding and hence production of more efficient plant species under
different conditions, like drought stress. In this study a sample of 28
recombinant inbred lines (RILs) of wheat developed from the cross of
Norstar and Zagross varieties, together with their parents, were
evaluated for two years (2010-2012) under normal and water stress
conditions using split plot design with three replications. Main plots
included two irrigation treatments of 70 and 140 mm evaporation
from Class A pan and sub-plots consisted of 30 genotypes. The effect
of genotypes and interaction of genotypes with years and water
regimes were significant for all characters. Significant genotypic
effect implies the existence of genetic variation among the lines
under study. Heritability estimates were high for 1000 grain weight
(0.87). Biomass and grain yield showed the lowest heritability values
(0.42 and 0.50, respectively). Highest genotypic and phenotypic
coefficients of variation (GCV and PCV) belonged to harvest index.
Moderate genetic advance for most of the traits suggested the
feasibility of selection among the RILs under investigation. Some
RILs were higher yielding than either parent at both environments.
Abstract: Crops diversity and maintaining and enhancing the
fertility of agricultural lands are basic principles of organic farming.
With a wider range of crops in agroecosystem can improve the ability
to control weeds, pests and diseases, and the performance of crops
rotation and food safety. In this sense, the main objective of the
research was to study the productivity and chemical composition of
some alternative crops and their adaptability to soil and climatic
conditions of the agricultural area in Southern Romania and to
cultivation in the organic farming system. The alternative crops were:
lentil (7 genotypes); five species of grain legumes (5 genotypes); four
species of oil crops (5 genotypes). The seed production was, on
average: 1343 kg/ha of lentil; 2500 kg/ha of field beans; 2400 kg/ha
of chick peas and blackeyed peas; more than 2000 kg/ha of atzuki
beans, over 1250 kg/ha of fenugreek; 2200 kg/ha of safflower; 570
kg/ha of oil pumpkin; 2150 kg/ha of oil flax; 1518 kg/ha of camelina.
Regarding chemical composition, lentil seeds contained: 22.18%
proteins, 3.03% lipids, 33.29% glucides, 4.00% minerals, and 259.97
kcal energy values. For field beans: 21.50% proteins, 4.40% lipids,
63.90% glucides, 5.85% minerals, 395.36 kcal energetic value. For
chick peas: 21.23% proteins, 4.55% lipids, 53.00% glucides, 3.67%
minerals, 348.22 kcal energetic value. For blackeyed peas: 23.30%
proteins, 2.10% lipids, 68.10% glucides, 3.93% minerals, 350.14 kcal
energetic value. For adzuki beans: 21.90% proteins, 2.60% lipids,
69.30% glucides, 4.10% minerals, 402.48 kcal energetic value. For
fenugreek: 21.30% proteins, 4.65% lipids, 63.83% glucides, 5.69%
minerals, 396.54 kcal energetic value. For safflower: 12.60%
proteins, 28.37% lipids, 46.41% glucides, 3.60% minerals, 505.78
kcal energetic value. For camelina: 20.29% proteins, 31.68% lipids,
36.28% glucides, 4.29% minerals, 526.63 kcal energetic value. For
oil pumpkin: 29.50% proteins, 36.92% lipids, 18.50% glucides,
5.41% minerals, 540.15 kcal energetic value. For oil flax: 22.56%
proteins, 34.10% lipids, 27.73% glucides, 5.25% minerals, 558.45
kcal energetic value.
Abstract: Durian is the flagship fruit of Mindanao and there is
an abundance of several cultivars with many confusing identities/
names.
The project was conducted to develop procedure for reliable and
rapid detection and sorting of durian planting materials. Moreover, it
is also aimed to establish specific genetic or DNA markers for routine
testing and authentication of durian cultivars in question.
The project developed molecular procedures for routine testing.
SSR primers were also screened and identified for their utility in
discriminating durian cultivars collected.
Results of the study showed the following accomplishments:
1. Twenty (29) SSR primers were selected and identified based on
their ability to discriminate durian cultivars,
2. Optimized and established standard procedure for identification
and authentication of Durian cultivars
3. Genetic profile of durian is now available at Biotech Unit
Our results demonstrate the relevance of using molecular
techniques in evaluating and identifying durian clones. The most
polymorphic primers tested in this study could be useful tools for
detecting variation even at the early stage of the plant especially for
commercial purposes. The process developed combines the efficiency
of the microsatellites development process with the optimization of
non-radioactive detection process resulting in a user-friendly protocol
that can be performed in two (2) weeks and easily incorporated into
laboratories about to start microsatellite development projects. This
can be of great importance to extend microsatellite analyses to other
crop species where minimal genetic information is currently
available. With this, the University can now be a service laboratory
for routine testing and authentication of durian clones.
Abstract: The grain quality of chickpea in Iran is low and
instable, which may be attributed to the evolution of cultivars with a
narrow genetic base making them vulnerable to biotic stresses. Four
chickpea varieties from diverse geographic origins were chosen and
arranged in a randomized complete block design. Mesorhizobium sp.
cicer strain SW7 was added to all the chickpea seeds. Chickpea seeds
were planted on October 9, 2013. Each genotype was sown 5 m in
length, with 35 cm inter-row spacing, in 3 rows. Weeds were
removed manually in all plots. Results showed that Analysis of
variance on the studied traits showed significant differences among
genotypes for N, P, K and Fe contents of chickpea, but there is not a
significant difference among Ca, Zn and Mg continents of chickpea.
The experimental coefficient of variation (CV) varied from 7.3 to
15.8. In general, the CV value lower than 20% is considered to be
good, indicating the accuracy of conducted experiments. The highest
grain N was observed in Hashem and Jam cultivars. The highest grain
P was observed in Jam cultivar. Phosphorus content (mg/100g)
ranged from 142.3 to 302.3 with a mean value of 221.3. The negative
correlation (-0.126) was observed between the N and P of chickpea
cultivars. The highest K and Fe contents were observed in Jam
cultivar.
Abstract: Phelipanche ramosa is the most damaging obligate
flowering parasitic weed on wide species of cultivated plants. The
semi-arid regions of the world are considered the main centers of this
parasitic plant that causes heavy infestation. This is due to its
production of high numbers of seeds (up to 200,000) that remain
viable for extended periods (up to 20 years). In this study, 13
treatments for the control of Phelipanche were carried out, which
included agronomic, chemical, and biological treatments and the use
of resistant plant methods. In 2014, a trial was performed at the
Department of Agriculture, Food and Environment, University of
Foggia (southern Italy), on processing tomato (cv ‘Docet’) grown in
pots filled with soil taken from a field that was heavily infested by P.
ramosa). The tomato seedlings were transplanted on May 8, 2014,
into a sandy-clay soil (USDA). A randomized block design with 3
replicates (pots) was adopted. During the growing cycle of the
tomato, at 70, 75, 81 and 88 days after transplantation, the number of
P. ramosa shoots emerged in each pot was determined. The tomato
fruit were harvested on August 8, 2014, and the quantitative and
qualitative parameters were determined. All of the data were
subjected to analysis of variance (ANOVA) using the JMP software
(SAS Institute Inc. Cary, NC, USA), and for comparisons of means
(Tukey's tests). The data show that each treatment studied did not
provide complete control against P. ramosa. However, the virulence
of the attacks was mitigated by some of the treatments tried: radicon
biostimulant, compost activated with Fusarium, mineral fertilizer
nitrogen, sulfur, enzone, and the resistant tomato genotype. It is
assumed that these effects can be improved by combining some of
these treatments with each other, especially for a gradual and
continuing reduction of the “seed bank” of the parasite in the soil.
Abstract: To study the effect of the cross direction in bead
wheat, three hybrid combinations (Babyle 113, Iratome), (Sawa,
Tamose2) and (Al Hashymya, Al Iraq) were tested for plant height,
spike and awn length, number of grains per spike, 1000-grain weight,
number of tillers/m and grain yield. The results revealed that the
direction of the crosses significantly effect on the number of
grains/spike, number of tillers/m and grain yields. Grain yield was
positively and significantly correlated with 1000-grain weight,
number of grains per spike and tillers. Depend on the results of
heritability and genetic advance it was suggested that 1000-grain
weight, number of grains per spike and tillers should be given
emphasis for future wheat yield improvement programs.
Abstract: A collection of thirty cultivars/clones of a red pitaya
was used to investigate flowering response to lighting
supplementation in the winter season of 2013-2014 in southern
Taiwan. The night-breaking treatment was conducted during the
period of 10 Oct. 2013 to 5 Mar. 2014 with 4-continuous hours
(22.00 – 02.00 hrs) of additional lighting daily using incandescent
bulbs (100W). Among cultivars and clones tested, twenty-three
genotypes, most belonging to the red-magenta flesh type, were found
to have positively flowering response to the lighting treatment. The
duration of night-breaking treatment for successful flowering
initiation varied from 33- 48 days. The lighting-sensitive genotypes
bore 1-2 flowering flushes. Floral and fruiting stages took 21-26 and
46-59 days, respectively. Among sixteen fruiting genotypes, the
highest fruit set rates were found in Damao 9, D4, D13, Chaozou
large, Chaozhou 5, Small Nick and F22. Five cultivars and clones
(Orejona, D4, Chaozhou large, Chaozhou 5 and Small Nick) produced
fruits with an average weight of more than 300 g per fruit which were
higher than those of the fruits formed in the summer of 2013. Fruits
produced during off-season containing total soluble solids (TSS)
from 17.5 to 20.7oBrix, which were higher than those produced inseason.
Abstract: The tomato is a very important crop, whose
cultivation in the Mediterranean basin is severely affected by the
phytoparasitic weed Phelipanche ramosa. The semiarid regions of
the world are considered the main areas where this parasitic weed is
established causing heavy infestation as it is able to produce high
numbers of seeds (up to 500,000 per plant), which remain viable for
extended period (more than 20 years). In this paper the results
obtained from eleven treatments in order to control this parasitic
weed including chemical, agronomic, biological and biotechnological
methods compared with the untreated test under two plowing depths
(30 and 50 cm) are reported. The split-plot design with 3 replicates
was adopted. In 2014 a trial was performed in Foggia province
(southern Italy) on processing tomato (cv Docet) grown in the field
infested by Phelipanche ramosa. Tomato seedlings were transplant
on May 5, on a clay-loam soil. During the growing cycle of the
tomato crop, at 56-78 and 92 days after transplantation, the number
of parasitic shoots emerged in each plot was detected. At tomato
harvesting, on August 18, the major quantity-quality yield parameters
were determined (marketable yield, mean weight, dry matter, pH,
soluble solids and color of fruits). All data were subjected to analysis
of variance (ANOVA) and the means were compared by Tukey's test.
Each treatment studied did not provide complete control against
Phelipanche ramosa. However, among the different methods tested,
some of them which Fusarium, gliphosate, radicon biostimulant and
Red Setter tomato cv (improved genotypes obtained by Tilling
technology) under deeper plowing (50 cm depth) proved to mitigate
the virulence of the Phelipanche ramose attacks. It is assumed that
these effects can be improved combining some of these treatments
each other, especially for a gradual and continuing reduction of the
“seed bank” of the parasite in the soil.
Abstract: Domestic goats (Capra hircus) are extremely diverse
species and principal animal genetic resource of the developing
world. These facilitate a persistent supply of meat, milk, fibre, and
skin and are considered as important revenue generators in small
pastoral environments. This study aimed to fingerprint β-LG gene at
PCR-RFLP level in native Saudi goat breeds (Ardi, Habsi and Harri)
in an attempt to have a preliminary image of β-LG genotypic patterns
in Saudi breeds as compared to other foreign breeds such as Indian
and Egyptian. Also, the Phylogenetic analysis was done to investigate
evolutionary trends and similarities among the caprine β-LG gene
with that of the other domestic specie, viz. cow, buffalo and sheep.
Blood samples were collected from 300 animals (100 for each breed)
and genomic DNA was extracted. A fragment of the β-LG gene
(427bp) was amplified using specific primers. Subsequent digestion
with Sac II restriction endonuclease revealed two alleles (A and B)
and three different banding patterns or genotypes i.e. AA, AB and
BB. The statistical analysis showed a general trend that β-LG AA
genotype had higher milk yield than β-LG AB and β-LG BB
genotypes. Nucleotide sequencing of the selected β-LG fragments
was done and submitted to GenBank NCBI (Accession No.
KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and
KJ874959). Phylogenetic analysis on the basis of nucleotide
sequences of native Saudi goats indicated evolutional similarity with
the GenBank reference sequences of goat, Bubalus bubalis and Bos
taurus. However, the origin of sheep which is the most closely
related from the evolutionary point of view, was located some
distance away.
Abstract: The present study involved analysis of certain
characteristics of the perennial ryegrass (Lolium perenne L.)
genotypes collected from the natural flora of Ankara, and explores a
correlation among them. In order to evaluate the plants for breeding
purpose as per Turkey's environmental conditions, the perennial
ryegrass plants were collected from natural pasture of Ankara in 2004
and were utilized for the study. Seeds of the collected plants were
sown in pots and seedlings were prepared in a greenhouse. In 2005,
the seedlings were transplanted at 50 × 50 cm2 intervals in
Randomized Complete Blocks Design in an experimental field. In
2007 and 2008, data were recorded from the observations and
measurements of 568 perennial ryegrasses. The plant characteristics,
which were investigated, included re-growth time in spring, color,
density, growth habit, tendency to form inflorescence, time of
inflorescence, plant height, length of upper internode, spike length,
leaf length, leaf width, leaf area, leaf shape, number of spikelets per
spike, seed yield per spike and 1000 grain weight and the correlation
analyses were made using this data. Correlation coefficients were
estimated between all paired combinations of the studied traits. The
yield components exhibited varying trends of association among
themselves. Seed yield per spike showed significant and positive
association with the number of spikelets per spike, 1000 grain weight,
plant height, length of upper internode, spike length, leaf length, leaf
width, leaf area and color, but significant and negative association
with the growth habit and re-growth time in spring.
Abstract: Osteoporosis is a common multifactorial disease with
a strong genetic component characterized by reduced bone mass and
increased risk of fractures. Genetic factors play an important role in
the pathogenesis of osteoporosis. The aim of our study was to
identify the genotype and allele distribution of T245G polymorphism
in OPG gene in Slovak postmenopausal women. A total of 200
unrelated Slovak postmenopausal women with diagnosed
osteoporosis and 200 normal controls were genotyped for T245G
(rs3134069) polymorphism of OPG gene. Genotyping was performed
using the Custom Taqman®SNP Genotyping assays. Genotypes and
alleles frequencies showed no significant differences (p=0.5551;
p=0.6022). The results of the present study confirm the importance of
T245G polymorphism in OPG gene in the pathogenesis of
osteoporosis.
Abstract: In the present study, RAPD-PCR was used to assess genetic diversity of the rye including landrances and new rye cultivars coming from Central Europe and the Union of Soviet Socialist Republics (SUN). Five arbitrary random primers were used to determine RAPD polymorphism in the set of 38 rye genotypes. These primers amplified altogether 43 different DNA fragments with an average number of 8.6 fragments per genotypes. The number of fragments ranged from 7 (RLZ 8, RLZ 9 and RLZ 10) to 12 (RLZ 6). DI and PIC values of all RAPD markers were higher than 0.8 that generally means high level of polymorphism detected between rye genotypes. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The cultivars were grouped into two main clusters. In this experiment, RAPD proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.
Abstract: Several yield-based stress indices have been developed that may be more applicable to work on drought tolerance. In this study, we investigate possibility of using stress susceptibility index (SSI), tolerance index (TOL), yield stability index (YSI), yield index (YI), stress tolerance index (STI), geometric mean productivity (GMP), harmonic mean (HARM), mean productivity (MP) to identify genotypic performance of some maize cultivars under normal and stressed condition. The results indicate that it was possible to identify superior genotypes for drought tolerance based on their stress indices and generally SSI indices which showed the lowest negative correlation with dry matter yield can be used as the best index for maize breeding programs to introduce drought tolerant hybrids. It was found that SC 647 showed the best behavior under drought stress condition based on TOL and SSI. A higher STI, GMP, and HARM values were attained for ko6. It can be suggested that ko6 should be cultivated in moderate stressful environment of Iran.
Abstract: The effect of exogenous application; seed priming or foliar spraying of salicylic acid (SA) on Yecora Rojo and Paragon wheat cv. under NaCl-salinity. Gas exchange parameters, growth parameters, yield and yield components were reduced in both cultivars under salinity stress with foliar spray and soaking seeds. Exogenous application of SA through foliar spraying or seed soaking showed a slight increases or decreases with the application method or between cultivars. SA foliar spraying exhibited a slight improvement over SA seed soaking in most parameters, particularly in Paragon. Although, seed soaking was less effective than foliar spraying, it was a slightly better with Yecora Rojo in some parameters. However, the low SA concentration; 0.5mM tended to improve most parameters in both cultivars. From data of the experiment, it has been concluded that the effect of SA depends on cultivar genotype and SA concentration.