فهرست مطالب

فصلنامه تحقیقات تولیدات دامی
سال یازدهم شماره 3 (پاییز 1401)

  • تاریخ انتشار: 1401/09/01
  • تعداد عناوین: 7
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  • فاطمه ربیعی، رامین عبدلی*، فرجاد رفیعی، نوید قوی حسین زاده صفحات 1-13
    در مطالعه حاضر، توالی های کامل ژنوم میتوکندریایی همراه با توالی های جداگانه 13 ژن رمزگر پروتیین به ازای هر ژنوم از شش گونه گوسفند وحشی شامل Asian Mouflon (Ovis orientalis)، Bighorn (Ovis canadensis)، Argali (Ovis ammon)، Urial (Ovis vignei)، Snow (Ovis nivicola)، Dall (Ovis dalli) و گونه گوسفند اهلی (Ovis aries) از بانک اطلاعاتی NCBI استخراج و با یکدیگر مقایسه شدند. نتایج حاصل از تجزیه و تحلیل فاصله توالی ها نشان دهنده بیشترین شباهت ژنتیکی (8/99 درصد) بین گوسفند وحشی Ovis orientalis و گوسفند اهلی (Ovis aries) بود. کمترین شباهت ژنتیکی (95 درصد) بین گوسفند اهلی (Ovis aries) و گوسفند وحشی Ovis dalli مشاهده شد. در تجزیه و تحلیل تبارشناختی، دو خوشه اصلی، هر کدام با زیرخوشه های متفاوت شناسایی شدند. گوسفند گونه اهلی (Ovis aries) همراه با گوسفندان وحشی Ovies orientalis، Ovis vignei و Ovis ammon خوشه های متمایزی تشکیل دادند و گوسفندان گونه وحشی Ovis nivicola، Ovis dalli و Ovis canadensis در یک خوشه مشابه قرار گرفتند. نتایج حاصل از تمامی 13 ژن رمزگر پروتیین با نتایج حاصل از توالی های کامل ژنوم های میتوکندریایی، مشابه بودند. بر اساس نتایج حاصل از مطالعه حاضر، توالی های ژنوم میتوکندریایی می توانند برای تجزیه و تحلیل تبارشناختی دقیق و خوشه بندی گونه های متفاوت گوسفند مورد استفاده قرار گیرند.
    کلیدواژگان: درخت تبارشناسی، شباهت ژنتیکی، گوسفند، میتوژنوم
  • محسن قلی زاده*، سید مهدی اسماعیلی فرد صفحات 15-26
    چندقلوزایی یکی از مهمترین صفات اقتصادی در گوسفند با تنوع داخل و بین نژادی است. این مطالعه به منظور شناسایی مکان های ژنومی موثر بر چندقلوزایی در گوسفند با رویکرد مگاآنالیز مطالعه ارتباط ژنومی و با استفاده از داده های ژنوتیپی و فنوتیپی شش نژاد گوسفند از پایگاه داده انجام شد. کنترل کیفیت با استفاده از نرم افزار Plink و ایمپیوتیشن با روش LD-kNNi انجام شد. مگاآنالیز با استفاده از مدل خطی مختلط در نرم افزار TASSEL  با در نظر گرفتن خویشاوندی و ساختار جمعیت انجام شد. پس از پایان کنترل کیفیت، تعداد 305 حیوان و 351615 نشانگر SNP با متوسط MAF  برابر با 33/0 برای ادامه تجزیه مورد استفاده قرار گرفتند. نتایج مگاآنالیز، یک SNP را روی کروموزوم 21 در سطح ژنوم و 10 SNP در سطح کروموزومی روی کروموزوم های 1، 2، 3، 14، 17 و 22 شناسایی کرد که به طور معنی داری با چندقلوزایی در گوسفند در ارتباط بودند. ژن های OPCML، GULP1، RBP4، MMP2 و LPCAT2 شناسایی شده در این تحقیق، نقش موثری در باروری و موفقیت آبستنی دارند. نتایج این تحقیق می تواند در درک ساز و کار ژنتیکی کنترل کننده چندقلوزایی در گوسفند مورد استفاده قرار گیرد.
    کلیدواژگان: چندقلوزایی، گوسفند، مطالعه ارتباط ژنومی، مگاآنالیز، نشانگر
  • علی جوانروح*، صلاح الدین خدامرادی صفحات 27-40
    در این تحقیق جهت مطالعه ساختار ژنتیکی جمعیت گوسفند شین بش، تعداد 75 نمونه خون از محل پراکنش این حیوانات جمع آوری شد. استخراج DNA با روش بهینه یافته Salting-Out انجام گرفت. تعداد 10 جایگاه ریزماهواره و یک ناحیه کنترلی D-Loop مربوط به DNA میتوکندریایی (mtDNA) مورد مطالعه قرار گرفت. برای تکثیر جایگاه های ریزماهواره از یک PCR چندگانه استفاده شد. آغازگرهای انتخابی نشان دار شده و  با استفاده از دستگاه Genetic Analyser تعیین ژنوتیپ افراد انجام گرفت. در مجموع، 84 آلل در جمعیت مورد مطالعه شناسایی شد، لذا متوسط تعداد آلل به ازای هر نشانگر برابر با 4/8 بود. میانگین هتروزیگوسیتی مورد انتظار و هتروزیگوسیتی مشاهده شده در این جمعیت به ترتیب برابر با 042/0±724/0 و 058/0±80/0 بود. مقدار FIS در این جمعیت برابر با  108/0-  بود که نشان دهنده غیرهمخون بودن و وجود تنوع قابل توجه در این جمعیت است. نتایج حاصل از ناحیه کنترلی mtDNA نشان داد که میزان تنوع هاپلوتیپی و درصد جایگاه های چندشکل در این جمعیت به ترتیب 039/0±938/0 و 59/4 است. از مجموع 24 نمونه تعیین توالی شده در ناحیه کنترلی mtDNA، تعداد 17 هاپلوتیپ در جمعیت مورد مطالعه مشخص شد. میزان تنوع نوکلیوتیدی در جمعیت شین بش، 0013/0±0131/0 به ازای هر جایگاه به دست آمد. نتایج این تحقیق نشان داد که 50 درصد از افراد جمعیت شین بش دارای هاپلوگروه A، 2/29 درصد افراد دارای هاپلوگروه B و 8/20 درصد افراد دارای هاپلوگروه C هستند.
    کلیدواژگان: خصوصیات ژنتیکی، گوسفند شین بش، نشانگر ریزماهواره، DNA میتوکندریایی
  • امیر حسین خلت آبادی فراهانی*، حسین محمدی، محمد حسین مرادی، حسینعلی قاسمی، ایمان حاج خدادادی صفحات 41-53
    تحقیق حاضر با هدف شناسایی مناطق ژنومی و ژن های کاندیدای مرتبط با صفات وزن تخم مرغ، بر اساس پویش ژنومی با استفاده از تراشه پربرون داد Affymetrix 600K chip در 1078 پرنده نسل یازدهم مرغ نژاد رد آیلند رد انجام شد. برای هر پرنده، هفت صفت شامل وزن تخم مرغ در اولین تخم گذاری، و وزن تخم مرغ در سنین 28، 36، 56، 66، 72 و 80 هفتگی جمع آوری شده بود. ارتباط بین هر یک از نشانگرهای چندشکل تک نوکلیوتیدی (SNP) و صفات مختلف با استفاده از روش های بیز A و B در نرم افزار GenSel نسخه 90/4 بررسی شد. در مجموع، نتایج این تحقیق نشان داد روش بیز A از نظر میزان واریانس ژنتیکی افزایشی توجیه شده در مقایسه با روش بیز B دارای عملکرد بهتری بود. تعداد نه نشانگر حاصل از روش بیزA  با بیشترین میزان واریانس ژنتیکی روی کروموزوم های شماره 1، 3، 5 و 20 قرار داشتند. SNP های شناسایی شده در نزدیکی 35 ژن قرار گرفته بودند که از این میان، ژن های کاندیدای BPIFB2، OCX36، CPT1A، TCF15، CECR2، SIAH3، FADS1، FADS2 و SGK1 عملکردهای مهمی را در فرآیند تولید تخم مرغ از راه تشکیل پروتیین آلبومین، سوخت و ساز اسیدهای چرب و تشکیل پوسته تخم مرغ داشتند. نتایج تحقیق حاضر نشان می دهد هنگامی که معماری صفات بررسی شده از مدل تعداد زیاد جایگاه ژنی پیروی کند، معمولا روش بیز A بر روش بیز B برتری دارد. علاوه بر این، با توجه به شناسایی مناطق ژنومی جدید و نقش کلیدی ژن های ذکر شده در ایجاد وزن تخم مرغ، می توان کارآیی روش بیز A برای پویش ژنومی در صفات وزن تخم مرغ را تایید کرد.
    کلیدواژگان: پویش ژنومی، روش بیزی، ژن کاندیدا، وزن تخم مرغ
  • مهدی خجسته کی، ابوالحسن صادقی پناه، نادر اسدزاده، علیرضا آقاشاهی، مرتضی کیخا صابر، مرتضی بیطرف ثانی*، سعید اسماعیل خانیان صفحات 55-66
    از آنجا که استفاده از روش های جایگزین، از جمله روش های مبتنی بر استفاده از هوش مصنوعی، می توانند فرآیند وزن کشی دام ها را تسهیل کند، مطالعه حاضر با هدف پیش بینی وزن گاوهای سیستانی با استفاده از فناوری بینایی رایانه ای انجام شد. بدین منظور، گاوهای سیستانی موجود در ایستگاه زهک برای یک دوره یک ساله وزن کشی شده و به طور هم زمان از نمای جانبی هر دام، تصاویر دیجیتال تهیه شد. تصاویر دیجیتال ابتدا با استفاده از نرم افزار Matlab مورد پیش پردازش قرار گرفت و سپس برخی خصوصیات شکل شناسی از هر یک از آنها استخراج شد. برای پیش بینی وزن گاوها، خصوصیات استخراج شده از تصاویر به عنوان ورودی و وزن هر دام به عنوان خروجی جهت آموزش به شبکه عصبی مصنوعی معرفی شد. مدلی که دارای بالاترین دقت و کمترین خطا بود به عنوان مدل نهایی جهت پیش بینی وزن دام ها انتخاب شد. بر اساس نتایج، قطر معادل، طول محور اصلی، طول محور فرعی، جعبه محاطی، مساحت قسمت محدب، مساحت ناحیه پر شده، محیط تصویر، مساحت تصویر و تعداد نقاط سفید تصویر دارای همبستگی بالاتری با وزن گاوهای سیستانی بود (01/0P<). مدل شبکه عصبی مصنوعی توانست با دقت 4/97 درصد، وزن گاوهای سیستانی را از روی خصوصیات تصاویر دیجیتال آن ها پیش بینی کند. نتایج مطالعه حاضر نشان داد، فناوری بینایی رایانه ای، قابلیت مناسبی برای پیش بینی وزن گاوهای سیستانی داشته و می تواند جایگزین روش های متداول کنونی شود.
    کلیدواژگان: بینایی رایانه ای، پیش بینی وزن، گاو سیستانی، هوش مصنوعی
  • رضا کنعانی، روح الله کیان فر*، حسین جانمحمدی، وو کیون کیم، مجید علیایی صفحات 67-81
    آزمایشی به منظور بررسی تاثیر ویتامین D3 و اسید لاکتیک بر عملکرد، کیفیت تخم مرغ و جوجه درآوری در مرغان مادر گوشتی انجام شد. تعداد 240 قطعه مرغ و 24 قطعه خروس مادر گوشتی سویه راس 308 به مدت 12 هفته (از سن 49 تا 61 هفتگی) در قالب طرح کاملا تصادفی با آرایش فاکتوریل 2×2 شامل دو سطح ویتامین D3 (3500 و 5500 واحد بین المللی) و دو سطح اسید لاکتیک (صفر و 500 میلی گرم در کیلوگرم) در چهار تیمار، شش تکرار و 10 قطعه مرغ و یک قطعه خروس به ازای هر تکرار استفاده شد. در طول دوره آزمایش، صفات عملکرد تولید و جوجه درآوری ثبت، و هر 28 روز یک بار، تعداد چهار عدد تخم مرغ از هر تکرار برای بررسی کیفیت داخلی و خارجی مورد ارزیابی قرار گرفت. نتایج نشان داد که اثر اصلی ویتامین D3 در سطوح بالاتر، وزن تخم مرغ را تحت تاثیر قرار داد و باعث کاهش وزن تخم مرغ  شد (05/0>P). اثر اصلی ویتامین D3 در سطوح بالاتر سبب افزایش pH سفیده و کاهش pH زرده شد و درصد پوسته، ضخامت پوسته و وزن مخصوص تخم مرغ را افزایش داد (05/0>P). افزودن اسید لاکتیک باعث بهبود عملکرد شد  (05/0>P). همچنین اسید لاکتیک، جوجه درآوری و ضخامت پوسته را افزایش و تعداد تخم مرغ های شکسته را کاهش  داد (05/0>P)، اما اثر آن بر سایر صفات، معنی دار نبود. اثر متقابل ویتامین D3 و اسید لاکتیک بر فراسنجه های عملکردی، اندازه تخم مرغ و کیفیت پوسته، معنی دار بود (05/0>P)،  به طوری که در سطوح پایین ویتامین D3، افزودن اسید لاکتیک باعث بهبود عملکرد و ضخامت پوسته شد و درصد شکستگی پوسته را کاهش داد (05/0>P). بنابراین استفاده از اسید لاکتیک و ویتامین D3 سبب افزایش درصد تولید، ضخامت پوسته، کاهش شکستگی تخم مرغ، بهبود ضریب تبدیل غذایی و همچنین افزایش تعداد جوجه تولیدی به ازای هر مرغ در اواخر دوره تولید مرغان مادر گوشتی شد.
    کلیدواژگان: اسید لاکتیک، پوسته تخم مرغ، تخم مرغ قابل جوجه کشی، مرغ مادر گوشتی، ویتامین D3
  • مجتبی افشین*، نظر افضلی، جواد حسینی واشان، علی حاجی بابائی صفحات 83-92
    اثر جایگزینی جیره ای یونجه با برگ زرشک بر عملکرد و برخی فراسنجه های خونی شترمرغ های پرواری با استفاده از 20  قطعه جوجه شترمرغ پرواری (از سن دو تا هفت ماهگی) در قالب یک طرح کاملا تصادفی با پنج تیمار و چهار تکرار بررسی شد. تیمارهای آزمایشی شامل: 1) شاهد (بدون برگ زرشک)، 2) جایگزینی 25 درصد یونجه با برگ زرشک، 3) جایگزینی 50 درصد یونجه با برگ زرشک، 4) جایگزینی 75 درصد یونجه با برگ زرشک، و 5) جایگزینی 100 درصد یونجه با برگ زرشک، بودند. نتایج نشان داد، با افزایش درصد جایگزینی برگ زرشک در جیره، ماده خشک مصرفی افزایش یافت (05/0P<). جایگزینی 50 درصد یونجه با برگ زرشک سبب افزایش وزن روزانه در مقایسه با تیمار شاهد شد (05/0P<). در کل دوره، ضریب تبدیل خوراک شترمرغ ها در جیره با نسبت جایگزینی 50 درصد، کمتر از جیره با نسبت جایگزینی 100 درصد برگ زرشک بود (05/0P<). بالاترین غلظت گلوکز در 90 و 210 روزگی به ترتیب 33/191 و 30/ 193 میلی گرم در دسی لیتر در جیره شاهد مشاهده شد (05/0P<). جایگزینی 50، 75 و 100 درصد یونجه با برگ زرشک سبب کاهش معنی دار غلظت آلانین آمینوترانسفراز پلاسما در مقایسه با تیمار شاهد شد (05/0P<). نتایج به دست آمده از این پژوهش نشان می دهد جایگزینی 50 درصدی یونجه با برگ زرشک در جیره شترمرغ های پرواری قابل توصیه است.
    کلیدواژگان: برگ زرشک، عملکرد، شاخص های خونی، شترمرغ، یونجه
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  • F. Rabiei, R. Abdoli *, F. Rafeie, N. Ghavi Hossein-Zadeh Pages 1-13
    Introduction
    Mitochondrial DNA (mitogenome) is a small and extra-chromosomal DNA, located in the cytoplasm and presents an ideal model to study evolution and genetic similarity. Classical phylogenetics is based on the morphological characteristics of the organisms, while in modern approaches, the phylogenetic distance and its related comparative methods are estimated based on observed genetic diversity in the studied genetic sequences. The aim of the present study was to investigate the divergence and percentage of genetic similarity along with the phylogenetic analysis of the seven main known species of wild and domestic sheep based on the complete sequence of the mitochondrial genome and the separate sequences of 13 protein-coding genes for each genome.
    Materials and methods
    In the present study, complete mitochondrial genome sequences along with separate sequences of 13 protein-coding genes (including NADH ubiquinone oxidoreductase (ND1, ND2, ND3, ND4, ND5, and ND6), cytochrome c oxidase (COX1, COX2, and COX3), ATP synthase (ATP6 and ATP8), NADH dehydrogenase 4 L (ND4L), and cytochrome b (CYTB))  per each genome from six wild species of sheep including Asian Mouflon (Ovis orientalis), Bighorn (Ovis canadensis), Argali (Ovis ammon), Urial (Ovis vignei), Snow (Ovis nivicola), Dall (Ovis dalli), and domesticated species of sheep (Ovis aries) were retrieved from NCBI database and compared to each other. Mitochondrial genomes and genes’ alignment were accomplished by the MegAlign module of DNASTAR software and compared by the Clustal W method. The Sequence Distances sub-section of the MegAlign module of DNASTAR also was used for the analysis of complete genome and gene sequences divergence and similarity percentage. For phylogenetic analysis, complete mitochondrial genomes and protein-coding genes’ sequences were aligned using MEGA7 software. Based on the alignment, phylogenetic tree was constructed using the maximum likelihood method. The percentage of replicate trees of 1000 replicates of bootstrap test was used to represent the evolutionary history for the studied sheep species.
    Results and discussion
    The results obtained from sequence distance analysis showed high genetic similarity (99.8 %) between Ovis orientalis and Ovis aries. Also, the lowest similarity (95 %) was observed between Ovis aries and Ovis dalli. In phylogenetic analysis, two main clusters, each with different sub-clusters were identified. Domesticated species of sheep (Ovis aries) along with Ovis orientalis, Ovis vignei, and Ovis ammon wild species of sheep formed distinct cluster, and Ovis nivicola, Ovis dalli, and Ovis Canadensis fell in a same cluster. In terms of all 13 protein-coding genes (including NADH ubiquinone oxidoreductase (ND1, ND2, ND3, ND4, ND5, and ND6), cytochrome c oxidase (COX1, COX2, and COX3), ATP synthase (ATP6 and ATP8), NADH dehydrogenase 4 L (ND4L) and cytochrome b (CYTB)), the results obtained from sequence distance similarity analysis and phylogenetic trees were similar to the sequences of the complete mitochondrial genomes. More than 99% of the genetic similarity for ND1, ND2, ND5, ND6, COX1, COX2, COX3, and ATP6 genes and 100% of the genetic similarity for ND3, ND4, ND4L, ATP8, and CYTB genes between domestic sheep (Ovis aries) and Mouflon (Ovis orientalis) sheep species were found. Also, similar to the results obtained from the comparison of the complete mitochondrial genome, the domestic sheep species (Ovis aries) showed the least genetic similarity with the Dall (Ovis dalli) and Bighorn (Ovis canadensis) wild sheep species in all 13 protein-coding genes. Similar to the results of phylogenetic analysis of complete mitochondrial genomes, domestic sheep species (Ovis aries) together with Ovies orientalis wild sheep were placed in the same sub-cluster and Ovis vignei and Ovis ammon species were placed in other distinct sub-clusters. In addition, the Ovis nivicola, Ovis dalli, and Ovis canadensis wild species fell in another main cluster, and in this cluster, Ovis dalli and Ovis canadensis were placed in a similar sub-cluster and Ovis nivicola in another distinct sub-cluster.
    Conclusions
    In previous studies, small parts of the mitochondrial genome (such as a part of the control region or cytochrome b gene) have been considered to show the genetic differences and phylogenetic relationships between different species and breeds of sheep. In the present study, the complete sequences of the mitochondrial genome along with the complete sequences of 13 protein-encoding genes per each genome in seven main species of wild and domestic sheep have been considered for examining genetic similarity and divergence and phylogenetic analysis for the first time. Based on the results obtained from the present study, mitochondrial genome sequences could be used for accurate phylogenetic analysis and clustering of different species of sheep.
    Keywords: Phylogenetic tree, Genetic similarity, Sheep, mitogenome
  • M. Gholizadeh *, S. M. Esmaeili-Fard Pages 15-26
    Introduction
    Reproduction is one of the most important economic traits in sheep with within and between-breeds variation. Reproductive traits normally show low to medium heritability and therefore response to conventional selection methods is not satisfactory for these traits. Considering the genetic information of the genetic variants underlying reproduction variability could efficiently increase the selection efficacy. Genome-wide association studies (GWAS) have been used to identify associations between genotypes and phenotypes as well as candidate genes for economically important traits. Statistical power in GWAS is mostly affected by sample size. The low sample size is hence a main obstacle in GWAS. Combining multiple data sets of different studies for joint (mega) GWAS provides an opportunity to increase the sample size required for GWAS. This study was performed to identify genomic regions affecting litter size in sheep using the mega-analysis of GWAS.
    Materials and methods
    Multi-population joint GWAS was performed using genotypic and phenotypic data of six sheep breeds retrieved from the database. Quality control was performed using the Plink software. The markers or individuals were removed from the further study based on the following criteria: (1) unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. Before analysis, imputation of missing genotypes for combined data set was implemented by LD-kNNi method. Mega-analysis was performed using a mixed linear model in TASSEL software considering kinship and population structure (top five components of principal component analysis (PCA)) as confounding effects. The quantile–quantile (Q–Q) plot was visualized by plotting the distribution of obtained vs. expected log10 (P-value). The association results along the genome and the significant SNPs were visualized in the Manhattan plot. To account for multiple test problem and identify the genome-wide and chromosome-wide significance level, Bonferroni test was used based on the number of independent SNPs obtained from pairwise linkage disequilibrium analysis. After GWAS analysis, the 300 bp sequence upstream and downstream of the significant SNP was explored to identify the adjacent candidate genes using Ovis aries_v4.0 (UCSC).
    Results and discussion
    In the present study, we implemented a mega GWAS using six different sheep breed data to identify the genetic mechanisms responsible for litter size in sheep. After quality control, 305 animals and 351,615 SNP markers with a mean MAF of 0.33 were kept for further analysis. The results of the mega-analysis identified one marker on chromosome 21 at the genome-wide level and 10 markers at the chromosome-wide level on chromosomes 1, 2, 3, 14, 17, and 22. The quantile–quantile plot that features the total distribution of the observed P-values (−log10 P-values) of quality passed SNPs vs. the expected values, showed the effective control for confounding effects. Many of the significant SNPs identified in this study were located in or very adjacent to known genes (OPCML, GULP1, RBP4, MMP2, and LPCAT2) that have been already reported for their contribution to fertility and pregnancy success. It has been reported that OPCML is more consistently expressed in cells lining the uterus, oviduct, and rete ovarii. OPCML has been reported as a tumor suppressor protein that is frequently inactivated in epithelial ovarian cancer. It has been reported that the RBP4 gene is expressed during the period of fast elongation of the pig blastocyst which is a crucial period for the survival of the embryos. Also, it has been suggested that RBP4 has the main contribution in uterine and conceptus physiology during the establishment of pregnancy and therefore can be considered as a candidate gene for litter size. MMP2 has an essential function during ovulation and pregnancy through extracellular matrix (ECM) components degradation and therefore enabling cell migration and angiogenesis.
    Conclusions
    Comparison of the results of this study with previous reports showed that the mega-analysis of GWAS, compared to the meta-analysis already reported for GWAS results, had comparable power in identifying genomic regions influencing litter size in sheep but identified fewer genomic regions than individual GWAS for each breed. No previously reported major genes controlling litter size in sheep were identified using our mega GWAS. The results of our research are suggested for further investigations in identifying causal genetic variants or genomic regions underlying the litter size variation in sheep and can be used to understand the genetic mechanism controlling this trait.
    Keywords: Prolificacy, Sheep, Genome-wide association study, Mega-analysis, Marker
  • A. Javanrouh *, S. Khodamoradi Pages 27-40
    Introduction
    West Azerbaijan province is the second most populous sheep province in Iran. In this province, different breeds of sheep such as Makui, Herki, Ghezel, Afshar, and Shin Bash are bred. Shin Bash sheep are bred in the south of West Azerbaijan province, especially in the cities of Mahabad and Piranshahr, and its population is about 200,000. Nowadays, the management of genetic resources and the study of the risk of genetic diversity of populations has become very important. The need to preserve the genetic resources of native livestock and use these genetic resources in the future determines the genetic structure of populations, and the study of the genetic diversity within each population can help manage genetic resources and provide good information for breeding programs. With the development of molecular techniques and the use of molecular markers as a tool to assess genetic diversity, useful information has been provided at various levels such as population structure, gene flow rate, phylogenetic relationships, and genealogy tests. Identification of livestock using various molecular techniques is highly accurate and the results of studies can be used in breeding and management programs. The purpose of this study was to study the genetic structure of Shin Bash sheep using microsatellite markers on the nuclear genome and SNP markers on mitochondrial DNA (mtDNA) and to introduce a lesser-known population.
    Materials and methods
    To study the genetic structure of the Shin Bash sheep population, 75 blood samples were collected from their geographic regions. Genomic DNA was extracted by using a modified Salting-Out method. Ten microsatellite markers and a control region (CR) of D-Loop belonging to mitochondrial DNA (mtDNA) were studied. Microsatellite loci were amplified in a multiplex PCR. Selected primers were labeled and genotyping was conducted using the Genetic Analyzer system. To analyze the data obtained from microsatellite markers, population parameters include: the Hardy-Weinberg equilibrium test, number of alleles per site, number of effective alleles, observed and expected heterozygosity, Shannon index, and F-statistic were calculated using POPGENE software version 3.1 and GENALEX version 6.5. In this research, Chromas ver. 2.33 (http://www.technelysium.com.au/chromas.html) was used to sort the sequencing data. Thus, the nucleotide sequence of each individual in this software was called and saved after sorting in the FASTA format. Also, to ensure the correct reading of the nucleotides, all sequences were examined using Blast online software at the NCBI site, indicating that this sequence is related to sheep mtDNA. To analyze the data obtained from sequencing in the control region of sheep mtDNA, MEGA version 7.0 and DnaSP version 6.12 were used.
     
    Results and discussion
      A Total of 84 alleles were identified; thus, the mean number of alleles per locus was 8.4. A total of 10 microsatellite loci were studied, seven were at Hardy-Weinberg equilibrium and three had significant deviations from Hardy-Weinberg equilibrium. Hardy-Weinberg disequilibrium can be caused by an increase in homozygotes vs. heterozygotes or, conversely, a high mutation rate, the formation of new alleles, and the presence of null alleles. The mean expected heterozygosity and observed heterozygosity in this population were 0.724 ± 0.042 and 0.80 ± 0.058, respectively. The FIS value for this population was -0.108 which showed low inbreeding and considerable diversity in the studied population. The results of the control region (CR) of mtDNA showed that haplotype diversity and percentage of the polymorphic site were 0.938 ± 0.039 and 4.59, respectively. A total of 24 sequenced individuals of the control region (CR) of mtDNA and 17 haplotypes were identified in the studied population. The amount of nucleotide diversity in the Shin Bash population was 0.0131 ±0.0013 per site. The results of this study showed that 50% of the Shin Bash population has haplogroup A, 29.2% haplogroup B, and 20.8% haplogroup C.
    Conclusions
    The results of this study, using microsatellite markers, showed that the population of Shin Bash sheep has significant genetic diversity. The negative FIS index indicates the observed heterozygosity superiority over the expected heterozygosity and thus indicates non-inbreeding and the existence of acceptable diversity within the Shin Bash sheep population. The results of mtDNA control region sequencing also showed the presence of haplotypic diversity and higher nucleotide diversity in the Shin Bash sheep population. On the other hand, the results of determining haplotype groups showed that this population has all three types of haplotype groups A, B, and C.
    Keywords: Genetic characterizations, Shin Bash sheep, Microsatellite marker, mitochondrial DNA (mtDNA)
  • A. H. Khaltabadi Farahani *, H. Mohammadi, M. H. Moradi, H. A. Ghasemi, I. Hajkhodadadi Pages 41-53
    Introduction
    The goal of genome-wide association (GWA) studies of quantitative traits is to identify genomic regions that explain a substantial proportion of the genetic variation for the trait, with the ultimate goal to identify causal mutations underlying the genetic basis of the trait. The standard GWA approach is to genotype a population that has been phenotyped for the trait(s) of interest and genotyped for many genetic markers across the genome and to analyze these data by estimating and testing the effects of marker genotypes on phenotypes using a regression-type of analysis for each single nucleotide polymorphism (SNP), one at a time. Bayesian methods such as Bayes A and Bayes B assume a heavy tail prior distribution for SNP effects and use Markov Chain Monte Carlo (MCMC) to sample from the posterior distribution. Although the objective of these methods was to predict the breeding value of selection candidates (genomic breeding values), they do that by estimating the effects of all SNPs. The estimated SNP effect, the proportion of variance explained by a SNP, or the number of times the SNP fits in the model with non–zero effect can be used as criteria to identify locations or genomic regions that affect the trait of interest. Results have shown that these Bayesian methods can effectively detect QTL in simulated and real data. Recently, a new methodology has been developed to address this limitation and allow for a better understanding of the genetic architecture of complex traits through a gene network analysis. For this purpose, to identify genomic regions and candidate genes associated with egg weight (EW), a genome-wide association study (GWAS) was performed in the present study using Affymetrix 600 K high density SNP array in 1,078 hens of 11th generation of Rhode Island Red.
    Materials and methods
    Data available for 1,078 pedigree-recorded hens were used to collect phenotypic EW-related data. Seven traits, including egg weight at the first laying of hens, and egg weight at 28, 36, 56, 66, 72, and 80 weeks of age were collected for each bird.  The analyses were performed using GenSel v4.73R, by fitting covariates for haplotype alleles in BayesA and BayesB models. A single Markov chain Monte Carlo (MCMC) chain of length 41,000, including burn-in of 1,000 first iterations, was computed for each analysis to obtain posterior estimates of covariate effects. These were used to obtain a direct genetic variance for animals. The primary analysis showed that correlations and regression coefficients had converged at this chain length. Annotation terms and pathway analyses were conducted using protein analysis through evolutionary relationships of PANTHER software version 10.0.
    Results and discussion
    The results showed that the BayesA method performed better in explaining additive genetic variance compared to BayesB method. Nine markers obtained from BayesA with the highest additive genetic variance were located on chromosomes 1, 3, 5, and 20. Genes that overlap in regions of interest were identified with the Ensembl BioMart data mining (http://www.ensembl.org/biomart/) based on the Galgal6 assembly and the Ensembl Genes 96 database. The detected SNPs were located close to 35 genes, among which, the candidate genes of BPIFB2, OCX36, CPT1A, TCF15, CECR2, SIAH3, FADS1, FADS2, and SGK1 play important functions in the egg production process through the albumen protein formation, fatty acids metabolism, and eggshell formation. It is noteworthy that the present study has detected an association in regions different from that reported by previous studies. This can be because of flock particularities, such as the extent of linkage disequilibrium, allelic frequencies, and statistical approaches.
    Conclusions
    The results of the present study showed that when the genetic architecture of studied traits follows infinitesimal model assumptions, the BayesA method usually performs better than BayesB. Moreover, considering the identification of new genome regions and the key role of the mentioned genes on the development of egg weight, the efficiency of the BayesA method can be confirmed for GWAS in egg weight traits.
    Keywords: Genome-wide association, Bayesian method, Candidate gene, Egg weight
  • M. Khojastehkey, A. Sadeghipanah, N. Asadzadeh, A. Aghashahi, M. Keikhah Saber, M. Bitaraf Sani *, S. Esmaeilkhanian Pages 55-66
    Introduction
    Sistani cows are generally restless animals; therefore, controlling, treating, and weighing them is difficult. On the other hand, recording the weight of domestic animals, including Sistani cows, is inevitable, because it provides a good scale for management decisions in the herd such as balancing the diet, changing environmental conditions, or determining the time of slaughter of fattening animals. In addition to scales, various methods are commonly used to measure the body weight of large animals. Some of these methods include the use of weight-meters, appraisal assessments, and the use of mathematical models. One of the new methods for predicting livestock weight is artificial intelligence. Because some reports are indicating that artificial intelligence could facilitate the weighing process of animals, this study was performed to predict the body weight of Sistani cows using computer vision technology.
    Materials and methods
    The data required for this study were recorded in the Zahak breeding station located in Sistan and Baluchestan province of Iran. The recording operation involved the weighing and biometric measurement of about 190 Sistani cattle, including calves, heifers, and male and female animals, every three months during a year. At the time of weighing, images of the lateral view of each animal were taken and recorded using the CANON SX150IS digital camera. During this period, a total of 358 weight records of Sistani cows at different ages were recorded. The digital images were initially preprocessed using MATLAB software, and then some morphological features were extracted from each image. For predicting the weight of Sistani cows via the Artificial Neural Network (ANN), the extracted features of images were introduced to the ANN model as input and the weight of cows as output. The "feed-forward neural network", which was trained by the "error propagation" algorithm, was used to predict the weight of cows. The function used in the hidden layer of the ANN model was sigmoidal and in the output layer was linear. An ANN model which had the highest precision and lowest error was selected as the final model for predicting the animal weights. The criteria for selecting the best model were the highest determination coefficient (R2) and the lowest mean square error (MSE) compared to other available models.
    Results and discussion
    Out of 22 features extracted from each image, only 15 of them, which had a higher correlation with the body weight of cows at different ages, were selected as effective features. As result, equivalent diameter, major axis length, minor axis length, bounding box, convex area, filled area, area, perimeter, and the number of non-zero pixels of the image (NNZ) had the highest correlation with the cattle weights (P<0.01) and used as effective features to train the ANN model. The final ANN model had 15 neurons in the input layer including selected image features, 11 neurons in the hidden layer, and one neuron in the output layer including the weight of the cows. The precisions of the artificial neural network in the training, validation, and test phase were 0.974, 0.970, and 0.981, respectively. The results showed that the final ANN model had acceptable precision in all light, medium, and heavy-weight cows, and the size and the age of animals did not have a significant effect on the precision of the artificial neural network model. A correlation between the actual weight of Sistani cows and the weights predicted by the ANN model was 98.3%. The average error of the model in predicting the weight of cows was 1.11%. In the practical test, a 2.32 kg deviation was observed between the predictions of the ANN model and actual weights in Sistani cows. The accuracy of the ANN model for predicting the weight of Sistani cows in the present study is acceptable and within the range of the other reports.
    Conclusions
    The proposed method based on image processing and ANN, had acceptable results in predicting the weight of Sistani cows. Given the difficulties of weighing Sistani cows as heavy livestock and sometimes the time-consuming process, it seems that the use of new technologies such as computer vision methods can be a good alternative to conventional weighing methods and facilitate and reduce recording costs of Sistani cows.
    Keywords: Computer vision, weight prediction, Sistani cattle, Artificial intelligence
  • R. Kanaani, R. Kianfar *, H. Janmohammadi, W. Kyun Kim, M. Olyaee Pages 67-81
    Introduction
    Vitamin D3 is one of the important vitamins in calcium metabolism, which is significantly involved in the absorption of calcium from the intestine. The main role of 1, 25-hydroxyvitamin D3 in vertebrates is to regulate calcium homeostasis, as 1, 25-hydroxyvitamin D3 has a direct effect on the gut, kidney, and bones by inhibiting the production of parathyroid hormone in the parathyroid glands. The synthesis of 1, 25-dihydroxycholecalciferol is tightly controlled, and the main stimulus for its synthesis is the reduction in plasma calcium. This is a feedback stimulus for the release of parathyroid hormone from the parathyroid gland. This hormone in turn stimulates the 1-hydroxylase enzyme complex in the kidney and causes the conversion of 25-hydroxycholecalciferol through the synthesis of calcium-binding protein in the duodenum, thereby increasing dietary calcium absorption and ultimately plasma calcium. Another powerful factor in calcium absorption is organic acids. By lowering the pH of the digestive tract, organic acids (lactic acid) prevent the formation of an insoluble complex of phytic acid with minerals, making phytate more sensitive to the action of endogenous phytase and preventing it from interfering with the absorption of minerals. Therefore, the purpose of this research was to study the effect of vitamin D3 and lactic acid on performance, egg quality, and hatchability in broiler breeders.
    Materials and methods
    A total of 240 broiler breeder hens and 24 roosters of Ross 308 strain were used in a completely randomized design with a 2×2 factorial arrangement including two levels of vitamin D (3500 and 5500 IU) and two levels of organic acid (zero and 500 mg/kg) in four treatments, six replications, and 10 hens and one rooster per replication. During the experiment, the percentage of hatchability, the number, and weight of eggs produced by each pen were recorded and using the common formulas of egg mass (as the percentage of laying multiplied by the average egg weight), the percentage of egg production as chicken-day and the feed conversion factor (as grams of feed consumed per gram of egg), the amount of feed used to produce each number of eggs and each piece of chicken, as well as the number of chickens produced per chicken was also calculated. Egg characteristics (egg weight and shape index) and egg shell quality (egg specific weight, eggshell weight compared to total egg weight and eggshell thickness), albumen and yolk pH, yolk index, Haugh unit, yolk color, percentage albumen and yolk percentage of four eggs from each replicate were measured every 28 days. The specific weight of the eggs was determined using the flotation method. The egg shape index was determined by measuring the width and length of the egg with a caliper to calculate the ratio of width to length. To determine eggshell parameters, eggs were identified and broken individually. Eggshells were washed under running water and dried at 35 °C for 72 hours. Then the eggshells were weighed and their relative weight was calculated. A digital micrometer (Series 500, Mitoyota, Tokyo, Japan) was used to measure the shell thickness.
    Results and discussion
    Results showed that the main effect of vitamin D3 at higher concentrations was affecting egg weight and reducing egg weight (P<0.05). The main effect of vitamin D3 at higher concentrations caused an increase in albumen pH, shell percentage, shell thickness, and specific gravity of the egg, and a decrease in yolk pH (P<0.05). Probably, with the increase in vitamin D3, the concentration of 1,25-cholecalciferol and the amount of calcium absorption increase, and since most of the shell is related to calcium carbonate, this leads to an increase in the thickness of the eggshell. The main effect of lactic acid showed a significant effect on performance parameters, and the addition of lactic acid improved performance (P<0.05). Lactic acid also significantly increased hatchability and shell thickness and reduced the number of broken eggs (P<0.05). It appears that organic acids increase the solubility of wheat phytates during germination. Therefore, acidification of the diet provides a better environment for phytase to reduce the amount of phytate present in digestion and flowing into the small intestine, thereby largely preventing the formation of insoluble mineral-phytate complexes and increasing the quality of the eggshell. Also, the main effect of lactic acid showed no significant influence on the internal quality of the eggs. The low levels of vitamin D3 and the addition of lactic acid improved shell thickness and reduced the percentage of shell breakage (P<0.05).
    Conclusions
    In general, according to the results of the present experiment, the use of lactic acid at the rate of 500 mg/kg along with 3500 IU of vitamin D3 can increase the percentage of production, shell thickness, reduce the number of broken eggs, improve the feed conversion ratio, increase chicken production and reduce feed consumption per egg and chicken at the end of the production period of broiler breeder hens.
    Keywords: Lactic acid, Eggshell, Settable eggs, Broiler breeder, Vitamin D3
  • M. Afshin *, N. Afzali, S. J. Hosseini-Vashan, A. Hajibabaei Pages 83-92
    Introduction
    The term “Livestock Revolution” was coined to describe the projected increase in demand for animal products due to population growth, increased income, and urbanization in developing countries. In this context, a decision to rear well-adapted livestock species, like the ostrich, could be effective in meeting present and future demands for animal products in a sustainable manner. On the other hand, most of the ostrich production costs are associated with the feeding price similar to broiler chickens. Due to the high ability of ostrich regarding fiber consumption, it is expected that ostriches can benefit from cheaper native foods such as barberry leaves. Ostrich digestive system has a great ability to use fiber diets due to having a long rectum (about eight meters). Furthermore, the microbial population of the cecum and colon in ostrich is similar to the rumen. The total area of barberry cultivation in Iran was reported to be 16007 hectares in 2017 and more than 14700 hectares of that were placed in South Khorasan. The amount of foliage of each barberry shrub is between three to five kg dry mater which remains almost unused after fruit harvesting. Hence, large amounts of branches and leaves from barberry harvesting could be considered agricultural residues for usage in animal feeding, annually. This study aimed to study the effect of replacing dietary alfalfa with barberry leaf on growth performance and blood indices in ostrich.
    Materials and methods
    The effects of replacing dietary alfalfa with barberry leaf on ostrich growth performance and some blood parameters were investigated using 20 ostriches (two to seven months of age) in a completely randomized design with five treatments (four replicates each). Barberry leaves and alfalfa used in this study were prepared manually from South Khorasan farms. Then samples were separately pooled and grounded in a hammer mill and were transferred to the laboratory to determine the amount of crude energy, dry matter, crude fat, crude protein, ash, neutral detergent fiber, and acid detergent fiber (all in three replications). The experimental diets were prepared by replacing alfalfa at 0, 25, 50, 75, and 100% with barberry leaf. Diets contain the same metabolizable energy and crude protein. Ostriches had free access to feed and water during the trial. Feed intake and body weight gain of each experimental unit were measured at 60, 120, and 210 days of age, and the feed conversation ratio (FCR) was calculated. At 90 and 210 days of age, blood samples were harvested from the wing vein of ostrich using tubes containing Li-heparin as an anticoagulant, then the blood samples were centrifuged at 3000 × g, 15 min at room temperature, and stored at −20 ◦C temperature for later analysis. The plasma concentrations of glucose, cholesterol, triglycerides, high-density lipoprotein (HDL), protein, and albumin as well as the activity of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were determined by auto-analyzer spectrophotometry according to the procedures of the manufacturers.
    Results and discussion
    The results revealed that dry matter intake (DMI) was enhanced with increasing dietary levels of barberry leaf (P<0.05). These findings showed the favorable effects of barberry leaves on feed intake. One of the main reasons associated with the reduction of dry matter consumption following the inclusion of agricultural by-products is the high amount of phenolic compounds, especially the tannins of these products. Barberry leaves have a low concentration of phenolic compounds (especially tannins) compared to other by-products such as pistachio peel, pomegranate pulp, Elaeagnus angustifolia leaves, etc. Substitution of alfalfa hay with barberry leaf at 50% of the diet significantly increased daily weight gain compared to the control group (P<0.05). In the whole experimental period, FCR was lower in the diet containing 50% of barberry leaf than in the diet with 100% replacement of alfalfa with barberry leaf (P<0.05). Increasing the FCR in the diet by replacing more than 50% of barberry leaves can be related to the reduction of the digestibility of the diet due to a decrease in the particle size of barberry leaves as well as its nature after milling compared to alfalfa and the reduction of the supply of amino acid profile due to synergy of two sources of alfalfa and barberry leaves. The highest concentration of plasma glucose at 90 and 210 days of age (191.33 and 193.3, respectively) were observed in the control diet. Numerous studies have reported the hypoglycemic effects of barberry. Replacement of 50, 75, and 100% of alfalfa with barberry leaf decreased significantly the plasma activity of ALT as compared to the control group (P<0.05). Although there are no reports of the use of barberry leaves or its active ingredient (berberine) in ostrich, previous reports have shown that the use of barberry fruit extract reduced liver enzyme concentrations.
    Conclusions
    Overall, the results of the current study showed that alfalfa hay could be replaced partially or completely with barberry leaves in the diet of ostriches without severe deleterious effects on performance. Replacement of 50% of alfalfa with barberry leaf would recommend for use in ostrich diets.
    Keywords: Barberry leaf, Performance, blood parameters, Ostrich, Alfalfa