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- Banabazi, Mohammad Hossein
(författare)
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Identification of genome diversity in different breeds of Iranian native sheep using the whole genome sequencing data
- 2023
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Ingår i: Journal of agricultural biotechnology. - 2228-6705 .- 2228-6500. ; 15, s. 145-160
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Tidskriftsartikel (refereegranskat)abstract
- Objective Iran is considered to be one of the oldest centers of domestication and breeding of livestock and poultry species in the world. Currently, different ecotypes of indigenous sheep are kept in different geographical regions of the country, which have obvious differences from each other in terms of appearance and production characteristics. So far, there has not been a comprehensive study on the whole genome level to identify the genetic diversity of native Iranian sheep. Therefore, the aim of this study is to identify the genomic characteristics of these native reserves in order to organize appropriate programs for their exploitation and protection Materials and methods In this study, the whole genome sequences of 29 native Iranian sheep were downloaded from the NCBI database and analyzed. Whole genome sequencing of the studied data has been done by Hiseq2000 and Hiseq X Ten sequencer devices. Quality control of raw data sequences was done by FastQC program. To align the sequence data with the sheep reference genome (Oar v.4.0, https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.2), the BWA-MEM algorithm used in the BWA software package was used. Picard program was used to remove PCR duplicates from mapping outputs. The alignment outputs with the reference genome were processed in two stages, including re-alignment of deletions and small insertions and recalibration of the base quality score using the GATK program. The average coverage depth and alignment percentage for alignment output with the reference genome were calculated using depth and flagstat commands used in samtools software. Single nucleotide polymorphisms (SNPs) were identified by the UnifiedGenotyper tool used in the GATK program. Nucleotide diversity values and genomic inbreeding coefficient were calculated based on homozygous SNPs for each individual using the het command used in the VCFtools program. Results The average coverage depth of the used data in this study was 18.39 X. The average percentage of alignment of short sequences with the sheep reference genome was 99.89%. The values of genomic inbreeding coefficient in Iranian native sheep breeds ranged from 0.01 to 0.12. The lowest value of genomic inbreeding coefficient was observed in the genome of Mughani sheep (0.01) and the highest value of inbreeding coefficient was observed in the genome of Afshari sheep (0.12). Also, the average values of observed and expected percentage of heterozygosity calculated for single nucleotide polymorphisms in the genome of Iranian native sheep ecotypes ranged from 20.67 to 23.06 and 32.415 to 32.421. Conclusions The results obtained from this research can be used in the design of conservation and breeding programs for Iran's native sheep, especially in situations where information such as animal pedigrees, levels of genetic differences within and between populations, and the degree of their purity or admixture are not available.
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| 2. |
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| 3. |
- Naddafi, Rahmat
(författare)
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Application of stable isotopes of carbon (13δC) and nitrogen (15δN) in assessment of Gorgan Bay fish dynamic in Golestan province
- 2021
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Ingår i: Journal of Applied Ichthyological Research. - 2423-6349. ; 8, s. 46-53
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Gorgan Bay and the southeastern coasts of the Caspian Sea in the Golestan Province are important biological and fisheries areas, while in recent years, they have been heavily contaminated. In present study, the dynamic of fishes, using stable nitrogen and carbon isotopes was evaluated to determine the diet and its trophic status, which can accurately chart the ecosystem's biological conditions. Accordingly, in September-October 2015 at 5 ecological stations, sampling of prephytones, macrophytes, macro invertebrates and fish, were taken and dominant species were subjected to isotope analyzes using the EA-IRMS device. The results of the nitrogen15 and carbon-13 isotopes indicate an imbalance in ecosystem conditions that alters the diet of the organisms and reduces the efficiency of the food web. The main factors of pressure on the ecosystem, the closure of the main channels of the sea to the bay, the entry of various pollutants into the ecosystem and weak physiography of Gorgan Bay, were determined.
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| 4. |
- Ramezani, Habib
(författare)
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Assessing the Optimum Cluster Sampling Plan for Estimating the Quantitative Characteristics of Zagros Forests (Case study: watershed Olad Ghobad forests)
- 2022
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Ingår i: Iranian journal of forest. - 2008-6113 .- 2423-4435. ; 14, s. 37-48
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Tidskriftsartikel (refereegranskat)abstract
- Protection and conservation of forests require access to information and awareness of structural features such as number per hectare and canopy cover of trees. This study aimed to select the optimal cluster sampling design in estimating the quantitative characteristics of the forest according to the three measures including accuracy, precision, and time required for the sampling. For this purpose, 30 hectares of watershed Olad Ghobad forests in the west of Lorestan province were selected. The Cartesian coordinates of all the trees in them were determined. In Matlab2014 software environment, the position of all trees was simulated. Then different cluster sampling designs (triangular, square, star 1, linear, L-shaped, star 2) were defined in the research by taking into account the number of samples (30, 60, and 90) and three distances (10, 20, and 30 meters). These processes repeated 10,000 times. The results showed that there was no significant difference between the estimated mean of different designs of cluster sampling methods of the study area. Based on the number of samples and the distance studied, it was found that sampling error for linear design has the highest accuracy compared to other designs. The results of estimating the E%2× T index for the characteristic number of trees per hectare and canopy cover showed the lowest values for the square (770.99) and linear (2347) designs, respectively. The results of accuracy estimation for both mentioned characteristics of Star 2 Design showed the lowest values (18.83) and (-5.54), respectively. The results of accuracy estimation for both mentioned characteristics of Star 2 Design showed the lowest values (18.83) and (-5.54), respectively.
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| 5. |
- Varshoee, Ali, et al.
(författare)
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The Effect of Coupling Agent on Water Absorption Property of Natural Fiber-Cement Nanocomposites
- 2011
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Ingår i: Iranian Journal of Sciences and Techniques in Natural Resources. ; 6:2, s. 127-137
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Tidskriftsartikel (refereegranskat)abstract
- این تحقیق به منظور بررسی تاٌثیر ماده جفت کننده بر خصوصیات میکروسکوپی و جذب آب در نانو کامپوزیتهاي ساخته شده از الیاف دورریز خمیر کاغذ سولفیت و سیمان انجام گرفته است. در این پژوهش هشت تیمار شامل تاٌثیر دو سطح ماده جفتکننده بر پایه آمینو سیلان (0 و6 درصد وزنی الیاف) و چهار سطح نانو سیلیس (0 ،5/0 ،1 و 3 درصد جایگزینی وزنی سیمان) به عنوان عوامل متغیر و میزان الیاف و آب به ترتیب در سطح 10 درصد و نسبت یک به یک وزنی سیمان ثابت، بر خصوصیت جذب آب نمونه هاي ساخته شده مورد بررسی قرار گرفت. کلیه نمونه ها مطابق با استاندارد Part: 1881 BS 5 1983-122 در سه مرحله جامد، مایع و اختلاط نهایی ساخته و مورد آزمایش قرار گرفتند. تصاویر میکروسکوپی SEM جهت بررسی خواص ریز ساختاري کامپوزیتها از نمونه ها تهیه شد. نتایج به دست آمده نشان داد که با افزایش مقدار نانو ذرات سیلیس، جذب آب در مقایسه با نمونه شاهد کاهش یافت، همچنین افزودن ماده جفت کننده موجب افزایش جذب آب گردید. از طرفی اثر متقابل نانوذرات سیلیس و ماده جفت کننده در مقایسه با نمونههاي شاهد که حاوي مقدار 10 درصد الیاف آزبست بودهاند، نشان دهنده کاهش میزان جذب آب بوده است. نمونههاي حاوي 3 درصد نانو ذرات سیلیس و 6 درصد ماده جفتکننده داراي کمترین میزان جذب آب بوده اند. همچنین تصاویر SEM حاکی از بهبود ریزساختاري نانوکامپوزیتها با افزودن ماده جفت کننده بود.
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