بررسی بیوانفورماتیکی داده‌های توالی‌یابی کل ژنوم در اردک پیکین به‌منظور تخمین میزان ضریب هم‌خونی ژنومی و شناسایی جزایر الگوهای هموزیگوسیتی

در گله های اردک همچون سایر گونه‌‌های دامی، شناسایی مناطق ژنومی موثر بر صفات مهم اقتصادی امری ضروری محسوب می شود. در این راستا، هدف از پژوهش حاضر، برآورد میزان ضریب هم‌خونی ژنومی و تجزیه و تحلیل عملکردی مناطق ژنومی کاندیدای مرتبط با تعداد تخم در اردک می باشد. در مجموع، از اطلاعات انفرادی ژنومی 630 اردک که به‌وسیله پلتفرم dnbseq t7 توالی یابی شده بودند، استفاده گردید. تخمین ضریب هم‌خونی، از طریق الگوی هموزیگوت ژنومی با برنامه plink محاسبه شد. به‌عنوان پیش‌فرض، یک درصد از نشانگرهای snp با بالاترین فراوانی در قطعات هموزیگوت به‌عنوان جزایر roh در نظر گرفته شدند. در نهایت، آنالیز غنی سازی مجموعه های ژنی با استفاده از برنامه آنلاین david انجام شد. نتایج این مطالعه نشان داد که میزان ضریب هم‌خونی محاسبه‌شده با الگوی هموزیگوسیتی 0.204 در اردک‌های پیکین می‌باشد. میانگین تعداد و طول roh محاسبه‌شده در اردک‌ها برابر با 141 و 1.52 مگاجفت‌باز نوکلئوتیدی در هر پرنده بود. همچنین، مجموع 91 جزیره roh با طول 1.60 تا 13 مگاباز شناسایی شد. توزیع جزایر roh در سرتاسر ژنوم یکنواخت نبود، به‌طوری‌که بیشترین و کمترین تعداد جزایر roh به‌ترتیب روی کروموزوم های شماره 1 و 31 مشاهده شدند. در تفسیر مجموعه های ژنی، تعداد 10 مسیر هستی‌شناسی ژنی و بیوشیمیایی شناسایی شد. بررسی ژن های گزارش‌شده در این مناطق نشان داد که ژن های col1a2، fchsd2،dazap1 و nsg1 عملکرد‌های مهمی را در ارتباط با فرآیند تخمک اندازی، تشکیل پوسته تخم و فسفریله کردن گلیکوپروتئین ها بر عهده دارند. ژن های متعددی که در نواحی شناسایی‌شده براساس عملکرد می توانند به‌عنوان کاندیداهای تحت انتخاب مطرح باشند. به هر حال، بررسی بیشتر ژن های مرتبط با مناطق ژنومی به‌دست‌آمده از مطالعات جستجوی پویش کل ژنومی ضروری است. استفاده از یافته های این تحقیق می تواند در درک ساز‌و‌کار ژنتیکی کنترل‌کننده صفت تعداد تخم تولیدی مورد استفاده قرار گیرد، به‌طوری‌که در انتخاب ژنتیکی اردک از طریق پرندگان برتر، باعث تسریع در پیشرفت ژنتیکی برنامه های اصلاح نژادی شود.

bioinformatics analysis of whole genome sequencing data to estimation of genomic inbreeding coefficient and identification of runs of homozygosity islands in pekin duck

introduction: ducks are more resilient to unfavorable environmental conditions than other poultry, making them less susceptible to disease. they are easy to raise and exhibit rapid growth. to meet the needs of industrial duck production, it is essential to develop meat, egg, and dual purpose strains. this will help determine breeding costs and ensure the productivity required by the industry. high weight gain, a lower food conversion ratio, more eggs, and high egg fertility are the four main ways that the breeding population and herds should be taken into consideration, in accordance with the significance of the economic coefficients of breeding and the relative selection of the product. designing breeding programs for ducks requires first identifying the genomic region linked to economic traits in duck populations. the management and breeding sciences should pay attention to the negative correlation coefficient with the egg production trait because a rise in one trait will result in a fall in the values of another trait. molecular biology and biotechnology have made significant strides in recent years, giving researchers a potent tool for studying animal genetics. decoding the genome information of this species has been made possible by powerful tools like next generation sequencing technology. following one another is known as a run of homozygosity (roh). in light of this research, the current study sought to use whole genome sequencing data to identify the loci linked to the duck’s egg production trait by performing an inbreeding coefficient, identifying the roh islands, and performing a functional analysis based on gene set enrichment analysis.materials and methods: there were 581 purebred peking ducks used in this study. the animals hatched from the same batch and are of the same strain. pronase was used to extract genomic dna. a wavelength of 260 nm was used to measure the amount and concentration of dna, and a wavelength ratio of 260/280 was used to assess the purity and quality of the extracted dna. all of this information was obtained using a spectrophotometer. on the dnbseq t7 platform, this dna sample was subjected to whole genome resequencing using a 150 bp paired end read strategy and an average sequencing depth of 2.06×. to conduct additional analysis, the acquired reads were compared to the reference genome of the mallard duck. using vcftools ( min alleles 2, max alleles 2) and plink ( geno 0.05 maf 0.01 mind 0.05), we implemented quality control to guarantee data quality. 581 individuals and 1,111,649 snps were retained for additional analysis following quality control. run of homozygosity (froh) was used to compute the inbreeding coefficient using the plink 1.9 program. a roh island was defined as one percent of the snps with the highest frequency in roh. assigning snps to genes, assigning genes to functional categories, and then analyzing the relationships between each functional category and the desired phenotype comprise the three main steps of gene set analysis analysis. to assign the genes to functions, a gene enrichment analysis was finally carried out using the kobas software.results and discussion: based on froh, the average pekin duck inbreeding coefficient was 0.204. there were 82,253 roh segments found in all, with an average of 141 point 50 segments per person. roh that consisted primarily of shorter segments (1–2 mb) made up roughly 77–85% of all roh. the larger roh (>2 mb) class, on the other hand, only made up 22–15% of all roh segments. chromosome 1 exhibited the highest roh (runs of homozygosity) value, while chromosome 31 showed the lowest. the 91 identified roh islands covered less than 1% of the sheep genome, with lengths ranging from 1.60 to 13 mb. these roh islands were located across nine genomic regions on chromosomes 1, 2, 3, 4, 5, 8, 13, 29, and 35. in this study, we discovered several sets of candidate genes associated with the duck egg production trait: col1a2, fchsd2, dazap1, and nsg1. pathway analysis revealed that the egg production trait was linked to ten biological and gene ontology pathways. certain genes were discovered to be involved in biological pathways linked to skeletal muscle growth and development, positive regulation of skeletal muscle fiber development, negative regulation of negative chemotaxis, release of sequestered calcium ions into the cytosol, and cellular response to hormone stimulus. these findings are in line with some earlier research. taking into account that the economic coefficient of duck egg production is very significant and more significant than the weight increase of breeding ducks and economic activity.conclusion: the findings of this study showed that the pekin duck breed’s selection processes for economic traits over a number of years have resulted in the formation of numerous roh islands in the duck genome. as a result, scanning these regions at the genome level may be an alternate method of identifying genes and related loci with economic traits. additionally, our findings aid in the design and implementation of breeding and conservation strategies for study ducks, as well as the understanding of genetic diversity and population demography.