بررسی تنوع تعداد کپی در ژنوم گوسفندان بلوچی با استفاده از تجزیه مقایسهای الگوریتم های PennCNV و QuantiSNP

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی دکتری، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه کشاورزی و منابع طبیعی ساری

2 استادیار، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه کشاورزی و منابع طبیعی ساری

3 استادیار، گروه علوم دامی، دانشکده علوم دامی، دانشگاه اراک

4 استاد، گروه علوم دامی، دانشکده علوم دامی و شیلات، دانشگاه کشاورزی و منابع طبیعی ساری

چکیده

تنوع تعداد کپی (CNV)، از مهمترین تغییرات ساختاری ژنوم، به عنوان منبع مهم تنوع ژنتیکی و فنوتیپی شناخته شده است. هدف از این مطالعه بررسی مقایسه‌ای CNV در گوسفندان نژاد بلوچی با استفاده از الگوریتم‌های PennCNV و QuantiSNP بود. تجزیه داده‌ها با استفاده از آرایه تعیین ژنوتیپ SNP50K گوسفندی روی 96 گوسفند بلوچی انجام شد. پس از تشخیص CNVها، مناطق تنوع تعداد کپی (CNVRs) با استفاده از برنامه CNVRuler تعیین شدند. در مجموع تعداد 201 و 916 CNV به ترتیب با الگوریتم­های PennCNV و QuantiSNP شناسایی شد. همچنین 91 CNVR (به طول 75/18 تا 7/511 کیلو جفت ‌باز) با الگوریتم PennCNV و 316 CNVR (به طول 7/5 تا 1280 کیلو جفت ‌باز) با الگوریتم QuantiSNP شناسایی شد که به ترتیب در بر‌گیرنده 46/0 و 33/1 درصد از کل ژنوم گوسفند بود. تعداد CNVهای نوع حذف در الگوریتم QuantiSNP حدود پنج برابر و در الگوریتم PennCNV حدود سه برابر بیشتر از تعداد اضافه‌ها بود. همچنین تعداد CNV‌های شناسایی شده با الگوریتم QuantiSNP حدود چهار برابر بیشتر بود. میزان 6/86 درصد (174 CNV با متوسط طول 67/122 کیلو جفت ‌باز) از CNVهای شناسایی شده به وسیله الگوریتم PennCNV با CNVهای شناسایی شده در الگوریتم QuantiSNP مطابقت داشتند. در مجموع، نتایج این تحقیق نشان داد که استفاده از چندین الگوریتم می‌تواند تغییرات ساختاری ژنوم را با دقت بیشتری تشخیص دهد و منجر به درک بهتری از ژنوم گوسفند ‌شود.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Investigation of copy number variation in Baluchi sheep genome using comparative analysis of PennCNV and QuantiSNP algorithms

نویسندگان [English]

  • K. Taghizadeh 1
  • M. Gholizadeh 2
  • M. H. Moradi 3
  • GH. Rahimi Mianji 4
1 Ph.D Student, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
2 Assistant Professor, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
3 Assistant Professor, Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
4 Professor, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
چکیده [English]

Copy number variation (CNV), one of the most important structural changes in the genome, has been known as an important source of genetic and phenotypic variations. The purpose of this study was to compare the two different algorithms in CNV detection consisting PennCNV and QuantiSNP in Baluchi sheep.Data analysis was performed using the Illumina OvineSNP50k BeadChip on 96 Baluchi sheep.After CNV calling, the copy number variation regions (CNVRs) were determined using the CNVRuler program.91 CNVRs with a length range of 18.75 up to 511.7 kbp were identified by the PennCNV algorithm, covering 0.46% of whole sheep genome.Also, 316 CNVRs with the length range of 7.5 up to 1280 kbp were obtained using QuantiSNP algorithm, covering 1.33% of whole sheep genome. The number of loss events was about five and three times more than the number of gain events for QuantiSNP and PennCNV algorithms, respectively.Also, the number of CNVs detected by QuantiSNP was about four times higherthan PennCNV.Also, 86.6% of total CNVs (174 CNVs with average length of 12.62 kb) identified by PennCNV were common with CNVs detected by QuantiSNP. In general, the results showed that the use of several algorithms could improve the accuracy for detecting the structural variation in the genome and led to a better understanding of the sheep genome. 

کلیدواژه‌ها [English]

  • Genotyping array
  • PennCNV and QuantiSNP algorithms
  • Structural variation
  • Copy number variation

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تحقیقات تولیدات دامی
دوره 9، شماره 1
خرداد 1399
صفحه 29-44

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