مقايسه روش انتخاب ژنومي و كلاسيك در اصلاح نژاد طيور بومي ايران

Comparison of genomic and classic selection method in breeding of Iranian native chickens

زمينه مطالعاتي: در كشورهاي در حال توسعه مخصوصا" ايران سرمايه­ هاي بومي نقش مهمي در اقتصاد روستايي ايفا مي­ كنند. نژادهاي بومي در مقايسه با سويه­ هاي تجاري مي­ توانند سطوح بالاتري از عملكرد را در شرايط نامساعد محيطي حفظ ­كنند. هدف: اين مطالعه به منظورمقايسه راهكارهاي انتخاب ژنومي و انتخاب كلاسيك در طيور بومي ايران با استفاده از نرم ­افزار ZPLAN+ انجام شد. روش كار: يك سناريوي مرجع و يك سناريوي ژنومي با تعداد 3460 پرنده در هر دو سناريو شبيه­سازي شد. سناريوي مرجع بر پايه اطلاعات فنوتيپي و سناريوي ژنومي بر پايه تركيبي از اطلاعات فنوتيپي و ژنومي با دو جمعيت مرجع 500 و 1000 حيوان براي هر دو جنس شبيه ­سازي شد. اطلاعات ژنومي مربوط به 4000 مرغ و تعداد متغير خروس (800 تا 4000) بود. صفات مورد مطالعه شامل تعداد تخم­ مرغ، وزن بدن در هشت هفتگي، متوسط وزن تخم­ مرغ و سن بلوغ جنسي بود. براي شبيه ­سازي اين صفات از پارامترهاي انحراف ­معيار فنوتيپي، وراثت ­پذيري، همبستگي­ هاي ژنتيكي و فنوتيپي و ضرايب اقتصادي استفاده شد. نتايج: فاصله بين­نسلي در هر دو سناريو برابر 14/5 ماه بود. با افزودن اطلاعات ژنومي به سناريوي مرجع دقت برآوردها از 0/62 براي خروس­ها و 0/64 براي مرغ­ها به 0/77 براي هر دو جنس در سناريوي ژنومي افزايش يافت. رشد ژنتيكي صفات با افزايش تعداد خروس­هاي تعيين ژنوتيپ شده و همچنين با افزايش تعداد پرنده در جمعيت مرجع افزايش يافت. مقادير رشد ژنتيكي صفت تعداد تخم­مرغ، وزن بدن در هشت هفتگي، متوسط وزن تخم­مرغ و سن بلوغ جنسي به ترتيب از 0/22، 2/57، 0/09 و 0/23- در سناريوي مرجع به 0/30، 3/60، 0/11 و 0/27- درسناريوي ژنومي با جمعيت مرجع 1000 حيوان افزايش يافت. سود حاصل از برنامه اصلاحي تنها در سناريوي ژنومي با جمعيت مرجع 1000 پرنده نسبت به سناريوي مرجع بالاتر بود. نتيجه­گيري نهايي: استفاده از اطلاعات ژنومي باعث افزايش رشد ژنتيكي در تمام صفات شد. در اين تحقيق هزينه­ ها كاهش نيافتند اما اطلاعات ژنومي دقت انتخاب برنامه اصلاح نژادي را افزايش داد.

Introduction : The indigenous stocks play an important role in villager econom y in developing countries, especially in Iran . Indigenous breeds could maintain higher level of performance under i ncompatible environment compared to commercial strains. In classic breeding programs for poultry, selection of birds was based on phenotypic and pedigree information. The development of genomic selection prefers new strategies in animal breeding. Genomic selection has a major lim itation for implementation. This method need genotyping of large numbers of markers for implementation and the costs of genotyping for these markers is high, especially for developing countries. To overcome this problem, before applying genomic selection, different scenarios have to be compared using computer simulation. The objective of this study was comparison of results in genomic selection and classic selection method in Iranian native fowls by using ZPLAN+ software ( Täubert 2010) . ZPLAN+ software is a very useful tool to optimize conventional and genomic breeding programs this software allows modeling of all relevant breeding structures, while taking all relevant biological, technological and economic parameters for complex breedin g programs into account (Sitzenstock et al. 2013) . This software then generates results such as the annual genetic gain for the breeding objective using a pure deterministic approach (Dekkers 2007) . This program has been based on the discounted gene flow - m ethod ( Hazel 1943) and selection index theory ( Hazel and Lush 1942) . This software calculates genetic gain, discounted return, profit and costs within and over selection paths. The results of monetary in ZPLAN+ are standardized to an animal unit and are given per year (Sitzenstock et al. 2013) . Material and m ethods : A reference scenario and a genomic scenario were simulated on 3460 bird s in both sexes . Reference scenario was simulated base d o n phenotyp ic information and genomic scenario was simulated bas ed o n combination of phenotyp ic and genomic data with two reference populations of 500 and 1000 bird s . Genomic data was based on the information of 4000 hens and variable numbers of cocks (800 to 4000) . S tudied traits included egg number, body weight at 8 weeks, mean of egg weight and age at sexual maturity. In this simulation, genetic and phenotypic parameters were used (Table 1 ) . These parameters included: phenotypic standard deviation, heritability, genetic and phenotypic correlations and traits economic coefficients . Economic weights were based on the study of Kianimanesh et al. (2001) and the other parameters were extracted from the study of Yousefi 201 2 . The variable costs of rearing a cock or a hen were assumed to be 44 0000 Rial per animal (over a period of 20 weeks). During production, daily feeding costs resulted from a feed consumption of 0.11 kg per day at a price of 12000 Rial per kg. For each cock and hen, additional costs for the animal care (20000 Rial) were assu med. The costs of selection were assumed 40000 Rial per animal. The fixed costs were not considered in conventional scenario, because it was difficult to quantify them in breeding program. But these costs must reduce from profit. The interest rate was set to %7 for discounted costs and %2 for discounted returns (Sitzenstock et al. 2013) . Results and d iscussion : The generation interval for both scenarios was 14.5 months. By adding genomic information to reference scenario, accuracy of estimations increase d from 0.6 2 for chocks and 0.64 for hens in reference scenario to 0.77 for both sex in genomic scenario. Genetic development of traits increased with increas e in the number of genotyped bird s and the number of bird s of reference population. Genetic development for traits egg number, body weight at 8 weeks, mean of egg weight and age at sexual maturity increased from 0.22, 2.57, 0.09 and - 0.23 (Table 2) respectively in reference scenario to 0.3 0 , 3.6 0 , 0.11 and - 0.27 respectively in genomic selection with 1000 reference population. The profit of breeding program was higher than reference scenario only in genomic scenario with reference population with 1000 bird s (Figure 2) . The discounted return per animal unit in the conventional scenario was 2010240 0 Rial per year. The variable costs for conventional scenario were 1057200 Rial per animal unit. This resulted in a profit of 19044800 Rial per animal unit. The accuracy of the genomic information and the size of the reference population have a large impact on the benefits from genomic selection. Dekkers 2007 showed that with increasing of marker information increase d the benefits from genomic scenarios. C onc lusion : The use of genomic information caused increasing genetic development in all traits. Although i n this study costs were not reduced , but genomic information increased the accuracy of selection of breeding program. This study showed that genomic selection can increase the genetic improvement rate of native chickens. However, the costs of genomic scenarios were higher than conventional scenario, but genomic information increased accuracy of selection and genetic gain of breeding goals traits. To ov ercome this problem, use of low density SNP chips is suggested.