اثر سطوح مختلف دام‌های تعیین ژنوتیپ شده در ارزیابی ssGBLUP بر صحت و پاسخ به انتخاب: یک مطالعه شبیه‌سازی

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه علوم دامی، دانشکده کشاورزی، دانشگاه تهران، کرج، ایران.

2 گروه علوم دامی، پردیس کشاورزی و منابع طبیعی، دانشگاه تهران، کرج، ایران.

چکیده

هدف پژوهش حاضر، بررسی اثر سطوح مختلف دام­های تعیین ژنوتیپ شده در ارزیابی ssGBLUP همراه با سطوح مختلف خطای شجره و وراثت­پذیری­ صفت از طریق شبیه­سازی بود. برای انجام تحقیق، صفت میانگین وزن شیرگیری بره­ها در طی پنج نسل شبیه سازی شد. از صحت انتخاب و پاسخ به انتخاب صفت مذکور برای مقایسه اثر سناریوهای مختلف استفاده شد. سناریوها شامل پنج سطح از دام­های تعیین ژنوتیپ شده و دو عامل خطای شجره و وراثت­پذیری، هرکدام با سه سطح بود. از نرم افزار R برای انجام این شبیه­سازی استفاده شد. با افزایش درصد دام­های تعیین ژنوتیپ شده در ارزیابی ssGBLUP، صحت انتخاب افزایش یافت ولی مقادیر عددی صحت انتخاب در سطوح مختلف وراثت­پذیری اختلاف کمتری نشان داد. میانگین صحت در سناریوی دام­های فاقد اطلاعات ژنوتیپی، و سطوح مختلف خطای شجره و وراثت­پذیری، 5/0 بود، و برای سناریوی با 100 درصد از دام­های تعیین ژنوتیپ شده، معادل 79/0 بود. در سناریوی دام­های فاقد اطلاعات ژنوتایپینگ، سطوح خطای شجره­ ارتباط معکوسی با صحت ارزیابی­های ssGBLUP داشت. با افزایش درصد دام­های تعیین ژنوتیپ شده، ارتباط خطای شجره با صحت ارزیابی­های ssGBLUP کمتر شد. با افزایش درصد دام­های تعیین ژنوتیپ شده، میانگین پاسخ به انتخاب نیز افزایش یافت. خطای شجره در سناریویی که تمام دام­های فاقد اطلاعات ژنوتیپی بودند اثر معنی داری را نشان داد. با افزایش درصد دام­های دارای اطلاعات ژنوتیپی، اثر خطای شجره­­تصحیح شده و اثر آن بر میزان پاسخ به انتخاب کمتر شد. با توجه به نتایج حاصله از تحقیق حاضر، می­توان گفت ssGBLUP گزینه بسیار مناسبی برای تحلیل ژنتیکی جمعیت­های دامی کوچک است.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

The effect of different levels of genotyped animals in ssGBLUP evaluation on accuracy and response to selection: A simulation study

نویسندگان [English]

  • mehdi Imani 1
  • Hossein Moradi Shahrbabak 2
  • Mohammad Moradi shahrebabak 2
1 Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
2 Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
چکیده [English]

The objective of this study was to investigate single step genomic BLUP (ssGBLUP) evaluation in different scenarios with different numbers of genotyped animals, pedigree errors and heritability using simulated data for weening weight of lambs. Different scenarios were simulated based on heritability and pedigree error, each of them with three levels, and genotyped animals based on five levels. Accuracy and response to selection were studied to compare different scenarios. The R environment was used to perform the simulation steps. With the increase in the percentage of genotyped animals in the ssGBLUP evaluation, the accuracy of selection increased and at different levels of heritability selection accuracy showed less difference. The mean accuracy in the scenario of non-genotyped animals with different levels of pedigree error and heritability was 0.5, and for the scenario with 100% of genotyped animals it was equal to 0.79. In the scenario with non-genotyped animals, pedigree error levels had an inverse relationship with the accuracy of the ssGBLUP evaluations. By increasing the percentage of genotyped animals, the effect of pedigree error with the accuracy of ssGBLUP evaluations becomes less. Also, with the increasing number of genotyped animals, response to selection mean increased. Pedigree error showed a significant effect in a scenario with non-genotyped animals. When the number of genotyped animals added the effect of pedigree error was adjusted and its effect on the response to selection rate decreased. According to obtained results, ssGBLUP evaluation is a suitable choice for genetic analysis of small animal populations.

کلیدواژه‌ها [English]

  • ssGBLUP
  • Pedigree error
  • Accuracy
  • Simulation

Extended Abstract

Introduction

Genomic information could help animal breeders to generate more accurate breeding values, if a dense assay that covers the entire genome becomes available. Single-step genomic BLUP procedure (ssGBLUP) combines the pedigree-based relationship matrix with the genomic relationship matrix into a single matrix (H) to predict the genomic estimated breeding value (GEBV). Therefore, the incorporation of data on genotyped and non-genotyped animals in this method is straightforward. Several studies have reported that the ssGBLUP is computationally efficient and accurate for genomic evaluation purposes. In addition, when the pedigree information is accurate better estimates of genetic evaluations are obtained. Pedigree information presents the degree of resemblance between relatives due to genetic factors. Unfortunately, pedigree errors are common in animal breeding populations. The presence of such errors can lead to incorrect estimates of genetic parameters, causing a decrease in the BLUP-BV based predictions accuracy.  The objective of this study was to investigate ssGBLUP evaluation in different scenarios of different numbers of genotyped animals, pedigree errors and heritability using simulated data for weening weight of lambs.

 

Materials and Methods

The R environment was used to perform the simulation steps.  The simulated genome had a total length of 1 cM, 342 markers and 38 QTLs randomly distributed over the 26 sheep autosomes. A simulated population consisted of base population that was created from 2500 males and 2500 females and five generations with 5000 observation in each generation. A total of 45 scenarios were tested with five repeat to each scenario (to correct sampling error). Different scenarios were simulated based on the three levels of heritability (0.10, 0.20, and 0.30) and pedigree error (0, 0.15, and 0.30) and genotyped animals based on five levels (0, 25, 50, 75, and 100%). The mean of the weening weight of lambs in generation zero 30 kg with additive genetic variance of 1.44 were simulated. Accuracy and response to selection were studied to compare different scenarios. In the BLUP model, a traditional genetic evaluation was performed using pedigree and phenotypic information. In ssBLUP, the inverse of the numerator relationship matrix (A-1) was replaced by H-1 that combines pedigree and genomic information.

 

Results and discussion

With the increase in the percentage of genotyped animals in the ssGBLUP evaluation, the accuracy of selection increased and at different levels of heritability selection accuracy showed less difference. The mean accuracy in the scenario of non-genotyped animals with different levels of pedigree error and heritability was 0.5, and for the scenario with 100% of genotyped animals it was equal to 0.79. In the scenario with non-genotyped animals, pedigree error levels had an inverse relationship with the accuracy of the ssGBLUP evaluations. By increasing the percentage of genotyped animals, the effect of pedigree error on the accuracy of ssGBLUP evaluations becomes less and disordered. Therefore, genomic information can moderate negative effect of pedigree error on selection accuracy. In all scenarios, heritability showed a positive relationship with the rate of response to selection. Also, with the increasing number of genotyped animals, the mean of response to selection increased. For example, in the scenario of non-genotyped animals, response to selection mean was 2.3 kg and response to selection increased with increasing genotyped animals. In the scenario with 100% of genotyped animals, response to selection mean was the highest (3.4 kg). In addition, in the scenario of non-genotyped animals with heritability of 0.10 and pedigree error 0.30% response to selection was obtained 1.70 kg. Also, in the scenario of 100% genotyped animals with heritability of 0.20 and pedigree error of 0.30% response to selection was 3.65 kg. Pedigree error showed a significant effect in a scenario with non-genotyped animals. When the number of genotyped animals added the effect of pedigree error was adjusted and its effect on the rate of response to selection decreased.

 

Conclusion

The ssGBLUP model is a common procedure to genetic evaluations by combining genotyped and non-genotyped animals.  In a situation where animals are non-genotyped, pedigree error levels significantly affect the results and inversely related to accuracy of ssGBLUP evaluation. In addition, as the percentage of genotyped animals increased, response to selection mean also increased. According to obtained results, ssGBLUP evaluation is a suitable choice for genetic analysis of small animal populations.

Data Availability Statement

This article contains all the data that were created or evaluated during the resear

Acknowledgements

    The authors would like to sincerely thank the members of the Faculty of Animal Sciences, Isfahan University of Technology Research Council for the approval and support of this research.

Conflict of interest

The author declares no conflict of interest.

 

مراجع

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علوم دامی ایران
دوره 57، شماره 1
فروردین 1405
صفحه 101-112

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  • تاریخ دریافت: 10 خرداد 1404
  • تاریخ بازنگری: 31 تیر 1404
  • تاریخ پذیرش: 07 مرداد 1404

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