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.     

Evaluation of Assouline–Or Adjusted Model to Express Soil Drainage Curve

Eurasian Soil Science - The objectives of this research are prediction of soil drainage curve using Assouline and Or (2014) adjusted soil drainage model and comparison of the predicted results with...     

Comparative evaluation of therapeutic efficacy of sulfadiazine-trimethoprim,oxytetracycline, enrofloxacin and florfenicol on Staphylococcus aureus–induced arthritis in broilers

1. Staphylococcus aureus is an important human and veterinary pathogen that causes economic loss in the poultry industry. This study aimed to compare therapeutic efficacy of 4 commonly used antibiotics in poultry on S. aureus–induced arthritis in broilers.

2. Sixty broilers, 8 weeks of age, were assigned at random into 7 groups as follows: (1) negative control (n = 5); (2) vehicle control (n = 5); (3) sulfadiazine-trimethoprim, 250 ml/1000 l drinking water (n = 10); (4) oxytetracycline 20%, 1 mg/l drinking water (n = 10); (5) florfenicol 10%, 1/1000 v/v in drinking water (n = 10); (6) enrofloxacin 10%, 1/1000 v/v in drinking water (n = 10) and (7) positive control (n = 10).

3. Birds in group 2 were injected with 1 ml of sterile TSB medium into the right tibiotarsal joint on d 0 while other birds (except group 1) were challenged with 1 ml of 1.2 × 10¹⁰ CFU/ml suspension of S. aureus bacteria.

4. Antibiotic therapy was started from d 4 post challenge and continued for 5 d. At the end, birds were weighed and clinical severity of arthritis was determined. After blood collection, birds were slaughtered and tibiotarsal and hip joints were evaluated grossly. The content of inflammatory exudates of tibiotarsal joint and the degree of femoral head necrosis were recorded. Mucin clot test and histopathological evaluation were performed on right tibiotarsal joint. Serum interleukin 6 was also assayed.

5. Sulfadiazine-trimethoprim had higher therapeutic efficiency with regard to most of the assayed criteria, whereas none of the antibiotics significantly affected femoral head necrosis and body weight. These data will help clinicians to have better antibiotic choice in field conditions.

     

Effect of dietary probiotic,prebiotic and synbiotic supplementation on performance,immune responses,intestinal morphology and bacterial populations in broilers

This study was conducted to investigate the effects of probiotic (Primalac), prebiotic (TechnoMos) and synbiotic (Primalac + TechnoMos) supplementation on performance, immune responses, intestinal morphology and bacterial populations of ileum in broilers. A total of 240 one‐day‐old broiler chicks were randomly divided into four treatment groups which included 60 birds. Control group did not receive any treatment. The chicks in the second, third and fourth groups were fed probiotic (0.9 g/kg), prebiotic (0.9 g/kg) and probiotic (0.9 g/kg) plus probiotic (0.9 g/kg; synbiotic), respectively, at entire period. Daily feed intake, daily weight gain and feed conversion ratio were evaluated. The birds were immunized by sheep red blood cell (SRBC) on days 12 and 29 of age and serum antibody titres were measured on days 28, 35 and 42. Newcastle vaccines administered on days 9, 18 and 27 to chicks and blood samples were collected on day 42. Intestinal morphometric assessment and enumeration of intestinal bacterial populations were performed on day 42. The results indicated that consumption of probiotic, prebiotic and synbiotic had no significant effect on daily feed intake, daily body weight gain, feed conversion ratio, carcass traits, intestinal morphology and bacterial populations of ileum (p > 0.05). Consumption of prebiotic increased total and IgM anti‐SRBC titres on days 28 and 42 and antibody titre against Newcastle virus disease on day 42 (p < 0.05). Synbiotic increased only total anti‐SRBC on day 28 (p < 0.05). It is concluded that consumption of prebiotic increased humoral immunity in broilers. Therefore, supplementation of diet with prebiotic for improvement of humoral immune responses is superior to synbiotic supplementation.     

Effects of thermo‐resistant non‐starch polysaccharide degrading multi‐enzyme on growth performance,meat quality,relative weights of body organs and blood profile in broiler chickens

This research was conducted to study the performance and carcass parameters of broiler chickens fed diets supplemented with heat‐treated non‐starch polysaccharide degrading enzyme. A total of 432 one‐day old Ross 308 broiler chickens were allocated to five treatments: (i) CON (basal diet), (ii) E1: CON + 0.05% multi‐enzyme, (iii) E2: CON + 0.1% multi‐enzyme, (iv) E3: CON + 0.05% thermo‐resistant multi‐enzyme and (v) E4: CON + 0.1% thermo‐resistant multi‐enzyme, each treatment consisted of six replications and 12 chickens in each replication. The chickens were housed in three floor battery cages during 28‐day experimental period. On days 1–7, gain in body weight (BWG) improved by feeding the diets supplemented with thermo‐resistant multi‐enzyme. On days 7–21 and 1–28, chickens fed the diets containing thermo‐resistant multi‐enzyme showed improved (p < 0.05) BWG and feed conversion ratio (FCR) compared to CON group. Supplementing the diets with multi‐enzyme or thermo‐resistant multi‐enzyme affected the percentage of drip loss on d 1 (p < 0.05). Drip loss percentage on days 3 and 5 and also meat colour were not affected significantly. Supplementing the diets with multi‐enzyme or thermo‐resistant multi‐enzyme did not affect the relative weights of organs but compared to CON group, relative weight of breast muscle increased and abdominal fat decreased (p < 0.05). Among measured blood constituents, chickens fed supplemented diets with thermo‐resistant multi‐enzyme showed higher (p < 0.05) IgG. Counts of red and white blood cells and lymphocyte percentage were not affected. In conclusion, the results demonstrated that supplementing pelleted diets with thermo‐resistant multi‐enzyme improved performance of broiler chickens.     

Microsatellite markers based assessment of genetic diversity in Iranian olive (Olea europaea L.) collections

To study the genetic variation in Iranian olive collections and some foreign olive cultivars, 47 accessions of 18 local cultivars from 6 olive collections of Iran (Roudbar, Zanjan, Ahvaz, Dezful, Kazeroon and Shiraz), were analyzed along with 30 imported cultivars using 16 microsatellite primer pairs. All the used microsatellite loci revealed polymorphism in the studied genotypes, except GAPU14 and GAPU113 markers. Fourteen microsatellite primers amplified 126 polymorphic alleles in the 87 selected olive accessions. The average number of alleles per locus was 9, ranging from 3 to 14. Polymorphic information content (PIC) was 0.85. The genetic similarity based on Jaccard coefficient ranged from 0.15 to 1. The genetic relationships among accessions were investigated using cluster analysis and principal component analysis (PCA). Most of the accessions with the same name were grouped together; some exceptions were also observed. As expected, close relationship was observed among accessions within same cultivar. Most of the Iranian olive accessions were clustered to a main distinct group. Two-dimensional scatter plot of principal component analysis revealed a clear separation of most of the Iranian olives from Syrian and other introduced cultivars. These suggest that Iranian cultivars have different origin related to West Mediterranean basin cultivars and have evolved independently from the others. Between and within Iranian and foreign cultivars (cultivars including three or more accessions) genetic diversity was analyzed using analysis of molecular variance (AMOVA). AMOVA revealed higher within cultivar genetic variation (62.76%) as compare to that between cultivar variations (37.24%). The intra- and inter-cultivar variance tested by permutation test showed significant genetic variation at both levels. The high level within cultivar genetic variance could be due to mislabeling and presence of homonyms in cultivars produced by vegetative propagation from original plants.     

Molecular characterization and genetic relationship among almond cultivars assessed by RAPD and SSR markers

RAPDs and SSRs were used to study the genetic diversity of Iranian almond cultivars and their relationship to important foreign cultivars and three related species. Eight unidentified almond Shahrodi cultivars and three wild almonds (Prunus communis, Prunus orientalis and Prunus scoparia) were also included. Of the primers tested, 42 (out of 80) RAPD and 18 (out of 26) SSR primers were selected for their reproducibility and high polymorphism. A total of 664 polymorphic RAPD bands were detected out of 729 bands. The number of presumed alleles revealed by the SSR analysis ranged from 3 to 10 alleles per locus with a mean value of 6.64 alleles per locus. Both techniques discriminated the genotypes very effectively, but only RAPDs were able to discriminate the cultivars Monagha and Sefied. Results demonstrated an extensive genetic variability within the tested cultivars as well as the value of SSR markers developed in peach for characterization of almond and related species of Prunus. Dice similarity coefficient was calculated for all pair wise comparisons and was used to construct a UPGMA dendrogram. For both markers a high similarity in dendrogram topologies was obtained although some differences were observed. All dendrograms, including that obtained by the combined use of both the marker data, depicted the phenetic relationships among the cultivars and species, depending upon their geographic region and/or pedigree information. Almond cultivars clustered with accession of P. communis showing their close relationship. P. orientalis and P. scoparia were clustered out of the rest of P. dulcis.     

Surface wildfire in conifer broad-leaved forests of the Hyrcanian region of Iran: short-term effect on regeneration and damage to trees

Wildfires in recent years have resulted in degradation and damage to the Hyrcanian forest ecosystems in Northern Iran.This study was carried out to investigate fire damage to trees and changes in regeneration in early-season growth after wildfires in the Golestan Province.For this purpose,a random sampling plan was used,with 60 circular plots(each plot is 1000 m2) for each stand and 240 circular(25 m2) plots for regeneration within the burned and unburned areas,respectively.In each plot,habitat factors were recorded,including crown canopy percentage,forest stratum,herb-layer cover percentage,species,diameter at breast height,tree and regeneration quality,and quantity of seedlings and saplings.Our results showed that bark is an important factor for fire resistance in Hyrcanian forests.The Persian ironwood and European yew has the highest and lowest fire resistance;as broad leave species are more resistant than needle leaf species.Density of regeneration in unburned area was higher than burned area,and statistical analysis showed significant differences for all species between two areas.Fire effects on sapling were different among species which indicates sapling has different resistance to fire.Forest floor fuel,season,stand composition and microclimate have more effects on fire severity while environmental factors,regeneration and management practices shaping future composition stands.     

Identification of QTLs for phenolic compounds in oilseed rape (<Emphasis Type="Italic">Brassica napus L.</Emphasis>) by association mapping using SSR markers

Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. In this study, association mapping was performed to detect QTL-linked and genome wide SSR markers linked to phenolic compounds of extraction meal in a population of 49 genetically diverse oilseed rape cultivars of dark-seeded, winter-type oilseed rape accessions. Correction for population structure was performed using 559 genome wide SSR markers. Results showed that seed colour is an important contributor to seed meal quality. Totally, 52 SSR markers linked to phenolic compounds were detected, five of them being QTL linked markers. Some of these markers were already mapped on Brassica napus chromosomes that contain known QTL controlling oilseed rape meal quality traits. Our results demonstrate that association mapping is a useful approach to complement and enhance previous QTL information for marker-assisted selection.     

Advanced lentil lines screened for resistance to <Emphasis Type="BoldItalic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="BoldItalic">lentis</Emphasis> under greenhouse and field conditions

Fusarium oxysporum f. sp. lentis is the most important pathogen of lentil plants, and most areas under lentil cultivation are reported to have a fusarium wilt disease background. The plants are infected in the seedling stage and later stages of their development. Fusarium wilt disease, which has appeared at high incidence rates during recent years, has caused sharp drops in the yield, especially in Moghan, in the northwest of Iran. Forty-five isolates of the pathogen were collected from different regions of the country with two isolates from ICARDA in the summer of 2008 and identified using Nelson’s key. The pathogenicity of the collected isolates was studied on a sensitive line (ILL 4605) under greenhouse conditions and significant differences in pathogenicity were found among them. The most pathogenic isolates from three provinces, East Azerbaijan (EA 30), Ardebil (Ar 3) and Khorasan (Kh 45), were selected and used in screening of 55 developed lines under greenhouse and field conditions. In the greenhouse, test plants were inoculated by immersing root tips in spore suspension and sowing seeds in pre-infested pot soil. Field tests were carried out in a naturally highly infested farm. At all stages, the plant response to the disease was based on the percentage of dead plants. Cluster analyses of the greenhouse and field data led to the selection of three lines (81S15, FLIP2007-42 L and FLIP2009-18 L) that were resistant under greenhouse and field conditions.