Run of Homozygosity a Procedure to Detecting Inbreeding in Farm Animals
محورهای موضوعی : Camel
م. نصرتی
1
(
Department of Agriculture, Payame Noor University, Tehran, Iran
)
کلید واژه: inbreeding, autozygosity, farm animal, run of homozygosity,
چکیده مقاله :
Inbreeding depression is a harmful phenomenon in livestock which is outcome of inbreeding. Inbreeding is consequence mating between two individuals who are more related to each other than average relatedness in population, which results in reducing in fitness of progenies and genetic variability in populations. Development of high-density genome-wide single nucleotide polymorphism (SNP) array facilitated inbreeding measurement as molecular data through calculating autozygosity region in individual genome. Autozygosity refer to chromosomal fragments that are identical-by-descent (IBD) and can be measured using runs of homozygosity (ROH). ROH is therefore defined as contiguous homozygous regions of the genome where two haplotypes inherited from the parents are IBD. The length and frequency of ROH may describe the history and recent bottlenecks in population and also revealed signatures of positive selection in population. Inbreeding coefficient can be derived from ROH (FROH), which is defined as total lengths of all ROH divided by the total autosomal genome length. A lot of studies calculated inbreeding level as FROH in human, cattle, pig, sheep, chicken and other farm animals through SNP array. In most of them, accuracy and preciseness of FROH were confirmed in comparing to FPED, Some of them calculated inbreeding depression by using FROH and some other evaluated the relationship between ROH location with gene and quantitative trait locus (QTL) position on genome. These studies indicated that inbreeding levels in bovine and porcine populations are much higher than those in human populations. Even though most of researches concluded that FROHcan precisely calculated Inbreeding and it can be useful for estimating inbreeding coefficient in absent of pedigree, but some concern were exist in about of panel density, genotyping errors and undetected heterozygosity within continuous ROH which complicated identifying and quantifying ROH. In this review, run of homozygosity is defined and discussed in detail in human and livestock.
افت ناشی از همخونی، پدیده‌ای مضر در حیوانات اهلی است که ناشی از پرورش خویشاوندی است. پرورش خویشاوندی تلاقی‌های متوالی بین دو فرد است که رابطه خویشی آنها بیش از میانگین جامعه است و منجر به کاهش شایستگی فرزندان و تنوع ژنتیکی در جامعه می‌شود. گسترش آرایه‌های جهش تک نوکلئوتیدی متراکم اندازه‌گیری همخونی را با داده‌های مولکولی از طریق محاسبه اتوزایگوسیتی در ژنوم افراد آسان ساخته است. اتوزایگوسیتی به قطعه کروموزمی اتلاق می‌شود که یکسان اجدادی باشد و می‌تواند از طریق رشته‌های هموزیگوت اندازه‌گیری شود. بنابراین ROH مناطق هموزایگوت بهم پیوسته‌ای است که دو هاپلوتیپ به ارث رسیده از والدین در آن محل یکسان اجدادی‌اند. طول و فراوانی ROH می‌تواند تاریخچه، گلوگاه ژنتیکی و نشانه‌های انتخاب را در جامعه تعیین کند. ضریب خویشاوندی نیز می‌تواند از طریق ROH تعیین شود (FROH)، که در قالب کل طول ROH به طول ژنوم تعریف می‌شود. مطالعات زیادی سطح همخونی را از طریق FROH در گاو، خوک، گوسفند، مرغ و سایر حیوانات مزرعه‌ای از طرق آرایه‌های جهش تک نوکلئوتیدی بدست آورده‌اند. در بیشتر این مطالعات صحت و دقت FROH در مقایسه با FPED تأیید شده است. برخی افت ناشی از همخونی را با FROH برآورد کرده‌اند و برخی ارتباط بین محل ROH را با موقعیت QTLها و ژنها ارزیابی کرده‌اند. این مطالعات نشان دادند که سطح همخونی در جمعیت‌های خوکی و گاوی بسیار بیشتر از انسان است. اگر‌چه بیشتر تحقیقات نتیجه گرفتند که FROH می‌تواند همخونی را به دقت اندازه‌گیری کند و در هنگام عدم دسترسی به شجره مفید باشد. اما نگرانی‌های در رابطه با تراکم پانل‌ها، خطای تعیین ژنوتیپ و عدم شناسایی هتروزیگوسیتی در درون ROH بهم پیوسته که تعیین و تشخیص ROH را دشوار می‌کند وجود دارد. این مقاله به تعریف ROH و بحث در مورد جزئیات آن در انسان و حیوانات اهلی می‌پردازد.
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