5/20/2014. Ideal for trait to have high heritability and observed before reproductive age. Molecular genetics alleviates some of these problems

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1 Marker assisted selection / genotypic assisted selection Marker assisted introgression Parentage نشانگرھای مولکولی در اصالح نژاد Analysis of genetic diversity new crossbreeds Genomic selection Other Tracing livestock domestication Traceability of animal products Several limitations due to: Phenotype is imperfect predictor of BV e.g. measured late in life, have few recordings, sex-limited, sacrificial traits Some negative associations between genes are caused by linkage and epitasis Ideal for trait to have high heritability and observed before reproductive age. Molecular genetics alleviates some of these problems Based on genetic parameters i.e. heritability, genetic variance, and correlation Uses statistical analysis of phenotypic data from pedigrees No knowledge of number of genes, their effects or location in genome is used Assume mean performance improved by accuracy of breeding values, selection intensity, generation interval and genetic variation QTL refers to genes with significant effects (major genes) large enough to be detected on the genome Knowledge of genes located at QTL can increase accuracy of estimating BV QTL can be targeted by use of genetic markers Genetic markers are landmarks at the genome chosen for their proximity to QTL 1

2 MAS and GAS MAS and truncation selevtion Marker assisted selection (MAS) انتخاب نشانگرھای مولکولی پيوسته به QTL مورد نظر => انتخاب غيرمستقيم نشانگرھا ممکن است در تعادل پيوستگی (LE) و يا عدم تعادل پيوستگی (LD) Animals with EBV s closest to the truncation point Pick up the animals most likely to change rank relative to the truncation point با QTL باشند Genotypic assisted selection (GAS) انتخاب مستقيم ژنھا مورد نظر( mutations (causative => انتخاب مستقيم EBV s before genotyping EBV s after genotyping 7 MAS to optimise breeding scheme The reasons to consider a detected QTL: more accurate evaluation in breeding scheme reduce the cost of progeny testing by pre-screening the potential young bulls Selection scheme each year for StartTime 12 mon. Calf is born MA-BLUP evaluation BLUP evaluation Realized the phenotypes and genetic evaluation Candidates are identified for genotyping Realized the phenotypes and genetic evaluation Final selection Mating Therefore, if selection program optimised, using MAS leads to increase genetic merit Population outline 6 mon. Selection stages Pre-selection (for genotyping) Selection Age of reproduction (yrs) Young bulls Proven bulls

3 MAS, markers in LE GAS Ram -2 Ram -2 Progeny +8 Marked gene from sire Other genes from sire Genes from dam Progeny +8 Marked gene from sire Other genes from sire Genes from dam -2-2 Progeny Progeny +8 Although if recombination between the marker and gene occurs.. نکاتی پيرامون MAS GAS MAS QTL ( ) Ram -2 Progeny -2 Marked gene from sire Other genes from sire Genes from dam LE MAS +8 QTL Progeny 3

4 برخی نکات GAS causative mutation (population wide) صفات و نشانگرھا نشانگرھا بسيار مفيد برای صفاتی ھستند که ازطريق روشھای معمول بھبود آنھا بسختی صورت ميگيرد ph GAS MAS markers in LD MAS markers in LE Accuracy of selection Ease of industry implementation Cost to detect markers طراحی برنامه به نژادی جھت بھره برداری از نشانگرھا برای مثال آزمون نتاج در گاوشيری: گاوھای نر جوان کانديد جھت progeny test تعيين ژنوتيپ ھای نشانگر(البته مرتبط با (QTL تنھا آنھايی آزمون ميشوند که ژنوتيپ ھای محتمل را دارند 4

5 Accommodating markers in breeding schemes مزيت نسبی MAS/GAS نسبت به روش انتخاب معمولی باالتر است اگر: وراثت پذيری صفت پايين QTL دارای اثر باال فراوانی آلل مساعد پايين امکان رديابی توارث QTL بوسيله نشانگرھا با دقت باال نوع اثر ژنی تمايل به غيرافزايشی داشته 5

6 اثرات کوتاه مدت و دراز مدت در MAS Accuracy of the predicted breeding values for young bulls (progeny testing) انتخاب بکمک نشانگر (MAS) انتخاب معمولی پاسخ انتخاب Short-terms benefits 2% to 60% سال 23 استفاده عملی در صنعت : Accuracy of the predicted total breeding values forproven bulls LE MAS LD MAS GAS 24 6

7 موارد مرتبط با کاربرد تجاری Frequency of favourable QTL allele در استفاده از MAS بوسيله نشانگرھای LD چه تعداد QTL چه تعداد نشانگردراطراف QTL 25 Inbreeding rate تعداد QTL QTL 10 QTL ( 50 ) 20 QTL ( ) QTL 26 7

8 تعداد نشانگربرای ھر QTL LD <1 2 5 استفاده در اھداف اصالح نژاد ( ) 8

9 Examples of tests on the market Name Trait Company GeneSTAR Marbling in beef Genetic Solutions (Aus) Igenity - L TM Marbling in beef Select Sires (USA) GeneSTAR Tenderness in beef Genetic Solutions (Aus) TenderGENE Tenderness in beef Select Sires (USA) Igenity-OptiYIELD TM Milk production in dairy Select Sires (USA) Igenity-ComponentMaker TM Milk composition in dairy Select Sires (USA) Introgression: Marker assisted introgression introgressallele from Breed A into Breed B A x B rounds of [identify animals with favourableallele and backcross to Breed B] 99% Breed B with favourableallele from Breed A In relation to MAI, markers can be used to Identify animals that have inherited the allele being introgressed quantify % of original breed Factors affecting livestock production may look like. آزمون انساب Parentage MAS/GAS Evaluation & selection Management Smallest gains Reproductive Breeding technologies program design با استفاده از تعدادی نشانگرھای مولکولی Typically markers More markers if population is inbred / markers are uninformative بصورت تجاری برای برخی از گونه ھای حيوانی انجام ميشود Largest gains Farming systems e.g. which species نرم افزار انساب CERVUS 9

10 انتخاب ژنوميکی SNP genotyping of 10,000+ markers Genomics has become a popular word in the dairy industry Allows for application of LD-MAS, however some level of pedigree recording will still be required The technology will likely play a significant role in helping dairymen breed a better Holstein cow Genomic Predictions Genomics is the sequencing of genetic material in cattle DNA using that information: to better understand how genes are Expressed Controlled what relationships they have with each other where they are physically located on the CHR Genomic Predictions 10

11 Holstein herds should consider to stay at the forefront of this technology Aims: Providing the most up-to-date genomic information Genomic Predictions Genomic Predictions Genomic Information A GTPIsignifies that genomic information was used in the calculation of the individual PTAs and overall index Genomic information will appear on pedigrees following an animal s genomic test Genomic Predictions Genomic Predictions 11

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