Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using Bayesian methods

ABSTRACT

1. Theoretically, haplotype blocks might be a more suitable alternative to SNP genotypes as they are usually better at capturing multi-allelic QTL effects, compared to individual SNP genotypes in genome-wide association studies. The objectives of this study were to identify genomic regions related to egg weight traits by Bayesian methods (BayesA, BayesB, and BayesN) that fit fixed-length haplotypes using GenSel software.

2. Genotypes at 294,705 SNPs, that were common on a 600K Affymetrix chip, were phased for an egg-laying hen population of 1,063 birds. Recorded traits included first egg weight (FEW) and average egg weight at 28, 36, 56, 66, 72 and 80 weeks of age.

2. Fitting 1Mb haplotypes from BayesB resulted in the highest proportion of genetic variance explained for the egg weight traits. Based on the trait, the genetic variance explained by each marker ranged from 27% to 76%.

3. Different haplotype windows associated with egg weight traits only explained a small percentage of the genetic variance.

4. The top one 1-Mb window on GGA1 explained approximately 4.05% of total genetic variance for the FEW. Candidate genes, including PRKAR2B, HMGA2, LEMD3, GRIP1, EHBP1, MAP3K7, and MYH were identified for egg weight traits.

5. Several genomic regions, potentially associated with egg weight traits, were identified, some of which overlapped with known genes and previously reported QTL regions for egg production traits.     

Investigation of meteorological drought characteristics in Fars province,Iran

Drought is a lack of moisture in nature, consistent or unnatural. The term consistent refers to a state of shortage, and unnatural refers to the deviation from an index of the regional natural condition. The objective of this research was to examine and forecast the intensity, duration, frequency and extent of droughts in Fars province. For this purpose, and in order to survey droughts in the province, a standard precipitation index (SPI) was determined as a selective index, considering its capacity to facilitate accurate positional analysis between various regions of the drought extent. For this, precipitation data within the same statistical period of 32 years (1968 to 1999) in 5 time scales of 3, 6, 12, 24 and 48 months from some 26 stations located within and out of the province were used, and the trends were assessed by using a time series analysis. At the next stage, RUN theory and Markov Chain were combined, on this basis to create transition probability and a steady matrix, and then the conditions of long term droughts in the province in terms of number and duration were forecast for the subsequent 10 years. The characteristics of the extent of drought were determined by using the Geographic Information System (GIS) with the help of geo-statistical methods. The results of the drought station surveys for the mentioned characteristics showed that the highest drought intensity (in terms of % deviation from normal) was at the Gozoon station and the longest duration of drought in months was at the Polkhan station; droughts both of long duration and with the highest frequency during the statistical period were observed at the Jahrom and Darshahy stations. The map of the extent of droughts showed higher intensity in the south and central regions of the province, while northern parts of the province were less sensitive to the effects of droughts. Also, the results of the maps of drought duration in various periods showed that droughts in the south of the province were of higher intensity and longer duration than elsewhere.     

Direct somatic embryogenesis in Epipactis veratrifolia,a temperate terrestrial orchid

Most temperate terrestrial orchids are endangered species. Attempts to produce plantlets from plants of the genus Epipactis by asexual methods have totally failed. This study was conducted using somatic embryogenesis as a rapid vegetative propagation technique for conservation of E. veratrifolia. For these purposes, effects of different types of plant growth regulators (PGRs), different types of explants, light and dark conditions, and the effect of gibberellic acid (GA₃) and Paclobutrazol (PBZ) were investigated on somatic embryogenesis induction. Abscisic acid (ABA) pre-treatment effectiveness on inducting somatic embryogenesis and increasing the number of embryos per explant were investigated. Subsequently, 16 media were tested to find the best medium for plant regeneration and shoot and root proliferation. BA (3 mg L^?1) resulted in a better response than the other PGRs by supporting the development of 17 embryos per protocorm. PBZ, which resulted in 11 embryos per explant, was better than GA₃. FAST medium supplemented with organic substances was recognized as the best medium for plant regeneration and shoot and root proliferation. ABA pre-treatment had positive effect on somatic embryogenesis initiation. This study, for the first time, succeeded in finding a rapid and suitable protocol for propagation and genetic resource conservation of E. veratrifolia.     

Spatial variability of water retention parameters and saturated hydraulic conductivity in a calcareous Inceptisols (Khuzestan province of Iran) under sugarcane cropping

The objective of this study was to quantify inherent spatial variability and spatial cross-correlation of the van Genuchten retention parameters and saturated hydraulic conductivity (K_s) of surface and subsurface layers in a calcareous Inceptisols (Khuzestan province, Iran) under sugarcane cropping. Measurements were performed on 100-cm³ undisturbed soil cores collected at 94 locations along a 30-m-long transect with horizontal sampling distance intervals of 0.3 and 1 m at soil depths of 0–40 and 40–80 cm, respectively. Spatial variability was investigated using conventional statistics and geostatistical techniques. Coefficient of variation (CV) varied from 8.2% (for shape parameter, n at 40–80 cm depth) to 256.7% (for K_s at 0–40 cm depth). The n parameter and saturated water content, θ_s, showed a small-scale spatial heterogeneity with a maximum CV of 11.3% for the first depth and 9.2% for the second depth. Most of the hydraulic parameters at both depths showed a spatial structure and convex experimental semivariograms with dominant spherical models with the influence range of 3.2–41 m. In most cases, the extent of spatial correlation scales of cross-semivariograms for pairs of cross-correlated hydraulic variables was found to be different with reference to those relating to the direct semivariograms of correlated variables.     

Brenneria spp. and Rahnella victoriana associated with acute oak decline symptoms on oak and hornbeam in Iran

Decline diseases of forest trees are complex syndromes not attributable to single causal factors. In Iran, symptoms of decline disease have been observed in a number of native forest species including Quercus castaneifolia (chestnut‐leaved oak), Q. brantii (Persian oak) and Carpinus betulus (hornbeam). The symptoms are prevalent in the northern forests and the Zagros mountain forests. There are parallels between the disease in Iran and acute oak decline (AOD) reported in the UK, specifically the presence of weeping cankers, which have been attributed to a polybacterial complex wherein Brenneria goodwinii is considered a key necrogen. Based on the AOD symptomatology, and as a first step towards discovering potential causal agents of the stem weeping symptoms of affected trees in Iran, necrotic tissues were tested primarily for the presence of B. goodwinii. Symptomatic Q. castaneifolia and C. betulus from the Mazandaran Province and symptomatic Q. brantii from Kohgiluyeh and Boyerahmad Province were sampled. Isolation and culture on a selective medium yielded uniform bacterial colonies. Isolates were characterized using phenotypic and genotypic (DNA sequencing) tests. The isolates were phenotypically identical to members of Pectobacteriaceae and Yersiniaceae, specifically Brenneria and Rahnella spp. The nucleotide sequences of the 16S rRNA and housekeeping genes gyrB, infB and atpD (MLSA) amplified via PCR demonstrated that the isolates from the trees in Iran were indeed B. goodwinii, B. roseae subsp. roseae, Rahnella victoriana and an unknown species of Brenneria. Most bacteria isolated from non‐symptomatic trees were Gram‐positive, and Pseudomonas spp. were dominant, but bacterial species isolated from the diseased trees were not detected in healthy trees. Hypersensitivity response tests were positive, but inoculation on saplings was more variable with internal necrosis developing only once in the test period. Therefore, further testing is required. This is the first report of the incidence of B. goodwinii, B. roseae subsp. roseae, R. victoriana and Brenneria sp. associated with acute oak decline‐like symptoms on Q. castaneifolia, Q. brantii and C. betulus across the western forests of Iran and in the world.     

First report of leaf spot caused by <Emphasis Type="Italic">Alternaria alternata</Emphasis> on <Emphasis Type="Italic">Drimia maritima</Emphasis>

Drimia maritima (squill) is a historically important medicinal plant. During the spring of 2016, small, yellow leaf spots, which became brown and finally necrotic, were observed on squill plants in Kohgiluyeh and Boyer-Ahmad Provinces in Iran. A fungus was consistently isolated from infected leaves and identified as Alternaria alternata based on morphological and phylogenetic analyses. Pathogenicity tests confirmed A. alternata to be the causal agent of the newly observed leaf spot disease. This is the first report of leaf spot on D. maritima caused by A. alternata in the world.     

Drought tolerance in four-day-old seedlings of a drought-sensitive cultivar of wheat

Four-day-old seedlings of spring wheat (Triticum aestivum L. cv. Marvdasht) can tolerate severe dehydration and recover after re-watering. In order to clarify tolerance mechanism, in a completely randomized design, the seedlings were exposed to drought by complete water cessation for 10 and 20 days, followed by re-watering for 3 and 7 days. Upon dehydration, the activity of α-amylase increased whereas growth parameters; photosynthetic pigments; and the activities of lipoxygenase, indole acetic acid (IAA) oxidase, and ascorbate peroxidase (APX) decreased. The activity of APX and the expression of its gene, however, increased after re-watering. Prolonged dehydration was also accompanied by increase in sucrose, soluble proteins, fructans, and certain amino acids, e.g. proline, glutamine, and valine. The results indicated that during dehydration, 4-day-old wheat seedlings shifted their energy expenditure from basal metabolism to withstand water deficiency via lowering the activity of membrane-damaging enzymes and enhancing the production of osmoprotectants.     

Recovery of sperms bearing X chromosomes with different concentrations of magnetic nanoparticles in ram

Pre-conceptual sex selection is still a highly debatable process whereby X and Y chromosome bearing spermatozoa are isolated before oocyte fertilization. Recently, magnetic nanoparticles (MNP) have been used to determine X and Y chromosomes bearing spermatozoa as a result of searching for a cheap, highly efficient method using non-toxic materials. This study aimed to recover the sperm bearing X chromosomes in ram with different concentrations of MNP and then evaluate the success of this method using polymerase chain reaction (PCR). Ram sperms were divided into four groups, treated with 0 (control), 50, 100 and 200 μg/ml MNP, respectively. MNP was used to restore sperm cells bearing X chromosomes. Upon recovery, the PCR was performed to identify the X and Y sperms, Methyl ThiazoleTetrazolium (MTT), to assess MNP toxicity and sperm viability and acridine orange (AO) to evaluate sperm DNA integrity. The results of PCR revealed that the treatment of spermatozoa- bearing X chromosomes with 50 μg/ml MNP had the highest effects on the recovery of X sperm rather than the other concentrations of MNP. However, the concentrations of MNP did not have any toxic effects on spermatozoa, sperm viability and, DNA integrity, but the high concentration of MNP (200 μg/ml) significantly reduced DNA integrity. According to MTT and AO results, the concentrations of MNP used in this study had no toxic effects on spermatozoa and did not reduce the sperm viability and DNA integrity, except that 200 μg/ml MNP significantly reduced DNA integrity.     

Relationship between calving difficulty and fertility traits in first‐parity Iranian Holsteins under standard and recursive models

The main objective of this study was to estimate the genetic and phenotypic relationships between calving difficulty (CD) and fertility traits, including success at first service (SF), number of inseminations to conception (INS), interval from calving to first service (CTFS), interval between first and last service (IFL) and days open (DO), in first‐parity Iranian Holsteins under standard (SMMs) and recursive (RMMs) mixed models. The data analysed in this paper included 29 950 records on CD and fertility traits, collected in the time period from 1995 to 2014 by the Animal Breeding and Improvement Center of Iran. Under all observed SMMs and RMMs, five bivariate sire‐maternal grandsire models (ten bivariate analyses in total) were used for the analyses. Recursive models were applied with a view to consider that CD influences the fertility traits in the subsequent reproductive cycle and the genetic determination of CD and fertility traits by fitting CD as covariate for any of the fertility traits studied. The existence of such cause‐and‐effect is considered in RMMs but not in SMMs. Our results implied a statistically non‐zero magnitude of the causal relationships between CD and all the fertility traits studied, with the former influencing the latter. The causal effects of CD on SF (on the observed scale, %), INS, CTFS, IFL and DO were ?2.23%, 0.10 services, 1.93 days, 3.76 days and 5.61 days, respectively. Direct genetic correlations between CD and the fertility traits under both models were not statistically different from zero (95% HPD interval included zero), except for the correlation between CD and CTFS, which were 0.197 and 0.134 under SMM and RMM, respectively, indicating that genes associated with difficult births also increase intervals between calving and the first insemination afterwards. Comparison of both models by the deviance information criterion (DIC) demonstrated the plausibility of RMMs over SMMs.     

Improvement of trivalent leptospira vaccine by removal of anaphylactic agents

The anaphylactic reactions in cattle following leptospira vaccination mostly booster dose in different parts of Iran have been reported. The serum proteins as allergic substances are components of liquid phase of the vaccine. Therefore, the vaccine was modified by washing the whole cultures by centrifugations. The modified vaccine was safe in laboratory animals and cattle as well as under field conditions. Microagglutination test revealed a similar pattern of antibody response to the three Leptospira interrogans serovars (Canicola, Grippotyphosa, and Sejro hardjo) in all vaccinated cattle groups while was higher than the response of control animals. The results of the present investigation revealed that we can minimize postvaccination shock in vaccinated cattle populations with removing the shock proteins.