Simulated Comparison Between Different Scenarios of Modular Chicken Breeding Program using MoBPSweb v.1.6.62 | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Simulated Comparison Between Different Scenarios of Modular Chicken Breeding Program using MoBPSweb v.1.6.62 I Wayan Swarautama Mahardhika, Fitriana Nur Laissya Hida, Bambang Retnoaji, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1289983/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Background: An optimal selective breeding program must balance ethical risks and operational costs without necessarily compromising its effectiveness and aims. For this purpose, a modular breeding simulator was used. Modular simulation acts as a preliminary evaluation instrument to predict the entire likelihood of outputs from a complex selective breeding program. Methods: A web-based modular stochastic simulator (MoBPSweb) facilitates the design-test-analysis workflow of the meat-type Pelung chicken selective breeding program with the nickname Gama Ayam Kambro. Several specific selective parameters were formulated and tested against the actual breeding scheme according to Gama Ayam Kambro's research. Three selection scenarios applied to Gama Ayam Kambro's breeding scheme, constructed based on three technical principles of crossings. These scenarios were compared based on accuracy, F coefficient, kinship, and observed phenotypes. An available feature on MoBPSweb also allowed the projections of specific economic parameters. Results: Crossing techniques, selection model scenarios, and breeding schemes determine the accuracy, F coefficient, kinship, and observed phenotypes. The selection accuracy of male 5 th Kambro and Pelung could be optimized using the design of genomic selection scenario_1 and outbreeding crossing techniques, both for Broiler and Pelung selection index. The selection model scenario and similar crossing technique are also quite effective in controlling the F coefficient. However, the outbreeding crossing technique is less effective in increasing the achievements of AFE, BW49D, EN, and FCR, contrarily for FEML, TL, and BW56D. Therefore, for AFE and FEML, the selection of 5 th Kambro dan Pelung males could be more optimal by using scenario_2 (BV) and scenario_3 (PHEN), respectively. Meanwhile, for BW49D and EN, the reciprocal applies. Therefore, the selection of 5 th Kambro and Pelung males for FCR and BW56D would be more optimal if scenario_1 (GEN) and scenario_3 (PHEN) were used, respectively. Meanwhile, for TL, it would be more optimal if scenario_3 with a phenotype selection design was used for both. The projection of economic parameters indicates that the total operational cost per year is required around ±500 million rupiahs for these three selection model scenarios using Gama Ayam Kambro breeding scheme with 100 intensive rearing enclosure units and 50 breeding generations. In addition, the projected operational cost must consider the inflation and interest rate of rupiah per year. Conclusions: Digitalization of selective breeding program using MoBPSweb stochastic simulator allows the design-test-analysis (DTA) procedure in Gama Ayam breeding scheme and its parameters and scenarios to be executed immediately and the results evaluated in real-time. However, there are at least two things to consider about this research. Firstly, genomic parameters that are specific cause a niche of reference, which means that this research is difficult to compare with other relevant studies. Therefore, the only solution is to do directly testing in the field. Implicitly, it is projected that there will be an exponential increase in the amount of data that must be accommodated by greater computing power to maintain and increase the simulation sensitivity. Therefore, these computational requirements may need to be considered one of the operational cost components, especially for the digital integrated poultry industry. Computational Biology Agricultural Engineering Food Science & Technology chicken breeding selection scenarios modular program stochastic simulation MoBPSweb Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Full Text Supplementary Files tbv08AFE.tif tbv08BW49D.tif tbv08BW56D.tif tbv08EN.tif tbv08FCR.tif tbv08FEML.tif tbv08TL.tif SupplementalFileSIM08.pdf swarautamacosts.tif Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-1289983","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":78859418,"identity":"a94e3ae5-c92f-4d2a-ab36-68a5dd05be21","order_by":0,"name":"I Wayan Swarautama Mahardhika","email":"","orcid":"https://orcid.org/0000-0002-3489-3156","institution":"Universitas Gadjah Mada","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"I","middleName":"Wayan Swarautama","lastName":"Mahardhika","suffix":""},{"id":78859419,"identity":"abf727c1-28dd-44f5-96dc-72b01da3e92a","order_by":1,"name":"Fitriana Nur Laissya Hida","email":"","orcid":"https://orcid.org/0000-0003-2008-1162","institution":"Universitas Gadjah Mada","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Fitriana","middleName":"Nur Laissya","lastName":"Hida","suffix":""},{"id":78859420,"identity":"b206b6b1-1b60-41be-84f4-9e88bf360d1c","order_by":2,"name":"Bambang Retnoaji","email":"","orcid":"https://orcid.org/0000-0002-0290-9723","institution":"Universitas Gadjah Mada","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Bambang","middleName":"","lastName":"Retnoaji","suffix":""},{"id":78859421,"identity":"1f1d9bb2-7d1d-4410-b5a1-fb5901f67dc6","order_by":3,"name":"Slamet Widiyanto","email":"","orcid":"https://orcid.org/0000-0002-5877-9112","institution":"Universitas Gadjah Mada","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Slamet","middleName":"","lastName":"Widiyanto","suffix":""},{"id":78859422,"identity":"3a950672-a696-40a8-9e3e-7caef1bf3552","order_by":4,"name":"Torsten Pook","email":"","orcid":"https://orcid.org/0000-0001-7874-8500","institution":"Georg-August-Universität Göttingen","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Torsten","middleName":"","lastName":"Pook","suffix":""},{"id":78859423,"identity":"8d0e5014-c440-4aa2-8555-3370bc058713","order_by":5,"name":"Budi Setiadi Daryono","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABB0lEQVRIiWNgGAWjYBACAyCWgDCZDwC5FnAZHoYDBLWwJQC5EiRp4UFigwEOLeb8Bxhv/NxzWM6cvefrhh8FEgwG51cnMPyoYZDhw6HFckYCs2XPs8PGlj1nt93sATrM4MbbDYw9xxh4JHE57AYDmwTPgcOJG27kbrvBA9ZydgMDbwPQnbi0nD/AJvkHrCXn2c0/UC2Mf/FpOZDAJg2xJYftNtiW870bmPHZAvKLtcyBdGODM8fMbssYSPBI3uDdcFjmmAROv4BC7OabA9ZyBsebn91888dGju/82Y0P39TY2OMKMQYG/g9AohnO5WGQSADFiAQu9TBQh2wGTtNHwSgYBaNghAIAKdxgwuxX4XoAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0002-0703-2123","institution":"Universitas Gadjah Mada","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Budi","middleName":"Setiadi","lastName":"Daryono","suffix":""}],"badges":[],"createdAt":"2022-01-24 03:17:09","currentVersionCode":2,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":true,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false,"coiExplicitlySet":false},"doi":"10.21203/rs.3.rs-1289983/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-1289983/v2","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":17629365,"identity":"bbc5d8c6-d65d-42af-88e8-04d4278ebefe","added_by":"auto","created_at":"2022-01-25 12:06:05","extension":"tif","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":652466,"visible":true,"origin":"","legend":"\u003cp\u003eGama Ayam Kambro breeding scheme. 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MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"accuracy08.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/756cdda5c65d93c7aaeff19b.tif"},{"id":17629451,"identity":"01caa457-0081-4ddb-93f0-3f20795fb247","added_by":"auto","created_at":"2022-01-25 12:12:06","extension":"tif","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":2730636,"visible":true,"origin":"","legend":"\u003cp\u003eThe F coefficient and weekly kinship of the Gama Ayam Kambro three selection model scenario. MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"inbreedingrelationshipscohortsweeks08.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/f84fb3b1e0da5a4407ddc378.tif"},{"id":17629364,"identity":"2deaa6f3-7481-4616-b74a-bdec2300707b","added_by":"auto","created_at":"2022-01-25 12:06:05","extension":"tif","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1903411,"visible":true,"origin":"","legend":"\u003cp\u003eThe observed phenotype of AFE from the Gama Ayam Kambro three selection model scenarios. MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"phen08AFE.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/5de202669d4a8371db34bc10.tif"},{"id":17629373,"identity":"93e7ef3b-ef71-4497-b15d-18165c2fffb4","added_by":"auto","created_at":"2022-01-25 12:06:06","extension":"tif","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":2759783,"visible":true,"origin":"","legend":"\u003cp\u003eThe observed phenotype of BW49D from the Gama Ayam Kambro three selection model scenarios. MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"phen08BW49D.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/bc79ab51825ecf622eaaa21f.tif"},{"id":17629363,"identity":"1ea0626f-0020-4047-aef1-1cebce767e4e","added_by":"auto","created_at":"2022-01-25 12:06:05","extension":"tif","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":2020939,"visible":true,"origin":"","legend":"\u003cp\u003eThe observed phenotype of BW56D from the Gama Ayam Kambro three selection model scenarios. MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"phen08BW56D.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/2d51417aff41a7a2139a442b.tif"},{"id":17629368,"identity":"a160eab0-53e9-4d95-969b-e8b379dc6720","added_by":"auto","created_at":"2022-01-25 12:06:06","extension":"tif","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":2245117,"visible":true,"origin":"","legend":"\u003cp\u003eThe observed phenotype of EN from the Gama Ayam Kambro three selection model scenarios. MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"phen08EN.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/aa4bb531d44e24dfed7e2c81.tif"},{"id":17629391,"identity":"226da1db-56f5-41c0-be34-ed1c49abdf5e","added_by":"auto","created_at":"2022-01-25 12:09:06","extension":"tif","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":1571624,"visible":true,"origin":"","legend":"\u003cp\u003eThe observed phenotype of FCR from the Gama Ayam Kambro three selection model scenarios. MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"phen08FCR.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/44a08bf6856fb9edb31810b0.tif"},{"id":17629378,"identity":"dc754106-aa91-4704-97a5-65bd3f1d5702","added_by":"auto","created_at":"2022-01-25 12:06:06","extension":"tif","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":1814225,"visible":true,"origin":"","legend":"\u003cp\u003eThe observed phenotype of FEML from the Gama Ayam Kambro three selection model scenarios. MoBPSweb (2021).\u003c/p\u003e","description":"","filename":"phen08FEML.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/694f76c2c91b836a126f7099.tif"},{"id":17629390,"identity":"902d4387-4265-4145-a20e-c3dec18117bb","added_by":"auto","created_at":"2022-01-25 12:09:06","extension":"tif","order_by":10,"title":"Figure 10","display":"","copyAsset":false,"role":"figure","size":1736389,"visible":true,"origin":"","legend":"\u003cp\u003eThe observed phenotype of TL from the Gama Ayam Kambro three selection model scenarios. 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12:06:06","extension":"tif","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":13954912,"visible":true,"origin":"","legend":"","description":"","filename":"tbv08TL.tif","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/cfe9f63f35af6d6cf514ba34.tif"},{"id":17629535,"identity":"b0a02d11-9cc6-425c-987e-4616a7921d25","added_by":"auto","created_at":"2022-01-25 12:15:06","extension":"pdf","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":1477340,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementalFileSIM08.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1289983/v2/8557acf21ec849b7f470ba08.pdf"},{"id":17629382,"identity":"b83b7a73-98a1-4758-9e51-ce5aa96b913e","added_by":"auto","created_at":"2022-01-25 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Mada","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"
[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"chicken breeding, selection scenarios, modular program, stochastic simulation, MoBPSweb","lastPublishedDoi":"10.21203/rs.3.rs-1289983/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1289983/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e An optimal selective breeding program must balance ethical risks and operational costs without necessarily compromising its effectiveness and aims. For this purpose, a modular breeding simulator was used. Modular simulation acts as a preliminary evaluation instrument to predict the entire likelihood of outputs from a complex selective breeding program.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eMethods: \u003c/strong\u003eA web-based modular stochastic simulator (MoBPSweb) facilitates the design-test-analysis workflow of the meat-type Pelung chicken selective breeding program with the nickname Gama Ayam Kambro. Several specific selective parameters were formulated and tested against the actual breeding scheme according to Gama Ayam Kambro's research. Three selection scenarios applied to Gama Ayam Kambro's breeding scheme, constructed based on three technical principles of crossings. These scenarios were compared based on accuracy,\u0026nbsp;\u003cem\u003eF\u003c/em\u003e coefficient, kinship, and observed phenotypes. An available feature on MoBPSweb also allowed the projections of specific economic parameters.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults: \u003c/strong\u003eCrossing techniques, selection model scenarios, and breeding schemes determine the accuracy, \u003cem\u003eF \u003c/em\u003ecoefficient, kinship, and observed phenotypes. The selection accuracy of male 5\u003csup\u003eth\u003c/sup\u003e Kambro and Pelung could be optimized using the design of genomic selection scenario_1 and outbreeding crossing techniques, both for Broiler and Pelung selection index. The selection model scenario and similar crossing technique are also quite effective in controlling the\u0026nbsp;\u003cem\u003eF\u003c/em\u003e\u0026nbsp;coefficient. However, the outbreeding crossing technique is less effective in increasing the achievements of AFE, BW49D, EN, and FCR, contrarily for FEML, TL, and BW56D. Therefore, for AFE and FEML, the selection of 5\u003csup\u003eth\u003c/sup\u003e Kambro dan Pelung males could be more optimal by using scenario_2 (BV) and scenario_3 (PHEN), respectively. Meanwhile, for BW49D and EN, the reciprocal applies. Therefore, the selection of 5\u003csup\u003eth\u003c/sup\u003e Kambro and Pelung males for FCR and BW56D would be more optimal if scenario_1 (GEN) and scenario_3 (PHEN) were used, respectively. Meanwhile, for TL, it would be more optimal if scenario_3 with a phenotype selection design was used for both. The projection of economic parameters indicates that the total operational cost per year is required around ±500 million rupiahs for these three selection model scenarios using Gama Ayam Kambro breeding scheme with 100 intensive rearing enclosure units and 50 breeding generations. In addition, the projected operational cost must consider the inflation and interest rate of rupiah per year.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusions:\u003c/strong\u003e Digitalization of selective breeding program using MoBPSweb stochastic simulator allows the design-test-analysis (DTA) procedure in Gama Ayam breeding scheme and its parameters and scenarios to be executed immediately and the results evaluated in real-time. However, there are at least two things to consider about this research. Firstly, genomic parameters that are specific cause a niche of reference, which means that this research is difficult to compare with other relevant studies. Therefore, the only solution is to do directly testing in the field. Implicitly, it is projected that there will be an exponential increase in the amount of data that must be accommodated by greater computing power to maintain and increase the simulation sensitivity. Therefore, these computational requirements may need to be considered one of the operational cost components, especially for the digital integrated poultry industry.\u003c/p\u003e","manuscriptTitle":"Simulated Comparison Between Different Scenarios of Modular Chicken Breeding Program using MoBPSweb v.1.6.62","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2022-01-25 12:06:03","doi":"10.21203/rs.3.rs-1289983/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"
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