Simulated Comparison Between Different Scenarios of Modular Chicken Breeding Program using MoBPSweb v.1.6.62

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 5th 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 5th 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 5th 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.

Full text

Simulated Comparison Between Different Scenarios
of Modular Chicken Breeding Program using
MoBPSweb v.1.6.62
I Wayan Swarautama Mahardhika
Universitas Gadjah Mada https://orcid.org/0000-0002-3489-3156
Fitriana Nur Laissya Hida
Universitas Gadjah Mada https://orcid.org/0000-0003-2008-1162
Bambang Retnoaji
Universitas Gadjah Mada https://orcid.org/0000-0002-0290-9723
Slamet Widiyanto
Universitas Gadjah Mada https://orcid.org/0000-0002-5877-9112
Torsten Pook
Georg-August-Universität Göttingen https://orcid.org/0000-0001-7874-8500
Budi Setiadi Daryono (  bs_daryono@mail.ugm.ac.id )
Universitas Gadjah Mada https://orcid.org/0000-0002-0703-2123
Research Article
Keywords: chicken breeding, selection scenarios, modular program, stochastic simulation, MoBPSweb
Posted Date: January 25th, 2022
DOI: https://doi.org/10.21203/rs.3.rs-1289983/v2
License:   This work is licensed under a Creative Commons Attribution 4.0 International License. 
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Advanced Breeding Program 1
Simulated Comparison Between Different Scenarios of Modular Chicken Breeding Program 2
using MoBPSweb v.1.6.62 3
I Wayan Swarautama Mahardhika1, Fitriana Nur Laissya Hida1, Bambang Retnoaji2, Slamet Widiyanto3, 4
Torsten Pook4, and Budi Setiadi Daryono1,* 5
1Gama Ayam Research Team, Laboratory of Genetics and Breeding, Faculty of Postgraduate Biology, 6
Universitas Gadjah Mada, 55281 Daerah Istimewa Yogyakarta (DIY), Indonesia 7
2Animal Structure and Development Laboratory, Faculty of Postgraduate Biology, Universitas Gadjah Mada, 8
55281 Daerah Istimewa Yogyakarta (DIY), Indonesia 9
3Animal Physiology Laboratory, Faculty of Postgraduate Biology, Universitas Gadjah Mada, 55281 Daerah 10
Istimewa Yogyakarta (DIY), Indonesia 11
4Department of Animal Sciences, Animal Breeding and Genetics Group, Center for Integrated Breeding 12
Research, Georg-August-Universität Göttingen, 37075 Göttingen, Germany 13
ORCID ID: 0000-0002-3489-3156 (I. W. S. M.) 14
0000-0003-2008-1162 (F. N. L. H.) 15
0000-0002-0290-9723 (B. R.) 16
0000-0002-5877-9112 (S. W.) 17
0000-0001-7874-8500 (T. P.) 18
0000-0002-0703-2123 (B. S. D.) 19
*correspondence: +62 896-9690-0775 20
e-mail: bs_daryono@mail.ugm.ac.id 21
(to be submitted 30, 01, 2022) 22
ABSTRACT 23
Background: An optimal selective breeding program must balance ethical risks and operational costs without 24
necessarily compromising its effectiveness and aims. For this purpose, a modular breeding simulator was 25
used. Modular simulation acts as a preliminary evaluation instrument to predict the entire likelihood of 26
outputs from a complex selective breeding program. 27
Methods: A web-based modular stochastic simulator (MoBPSweb) facilitates the design-test-analysis 28
workflow of the meat-type Pelung chicken selective breeding program with the nickname Gama Ayam 29
Kambro. Several specific selective parameters were formulated and tested against the actual breeding scheme 30
according to Gama Ayam Kambro's research. Three selection scenarios applied to Gama Ayam Kambro's 31
breeding scheme, constructed based on three technical principles of crossings. These scenarios were 32
compared based on accuracy, F coefficient, kinship, and observed phenotypes. An available feature on 33
MoBPSweb also allowed the projections of specific economic parameters. 34
Results: Crossing techniques, selection model scenarios, and breeding schemes determine the 35
accuracy, F coefficient, kinship, and observed phenotypes. The selection accuracy of male 5th Kambro and 36
Pelung could be optimized using the design of genomic selection scenario_1 and outbreeding crossing 37
techniques, both for Broiler and Pelung selection index. The selection model scenario and similar crossing 38
technique are also quite effective in controlling the F coefficient. However, the outbreeding crossing 39
technique is less effective in increasing the achievements of AFE, BW49D, EN, and FCR, contrarily for 40
FEML, TL, and BW56D. Therefore, for AFE and FEML, the selection of 5th Kambro dan Pelung males could 41
be more optimal by using scenario_2 (BV) and scenario_3 (PHEN), respectively. Meanwhile, for BW49D 42
and EN, the reciprocal applies. Therefore, the selection of 5th Kambro and Pelung males for FCR and BW56D 43
would be more optimal if scenario_1 (GEN) and scenario_3 (PHEN) were used, respectively. Meanwhile, for 44
TL, it would be more optimal if scenario_3 with a phenotype selection design was used for both. The 45
projection of economic parameters indicates that the total operational cost per year is required around ±500 46
million rupiahs for these three selection model scenarios using Gama Ayam Kambro breeding scheme with 47
100 intensive rearing enclosure units and 50 breeding generations. In addition, the projected operational cost 48
must consider the inflation and interest rate of rupiah per year. 49
Conclusions: Digitalization of selective breeding program using MoBPSweb stochastic simulator allows the 50
design-test-analysis (DTA) procedure in Gama Ayam breeding scheme and its parameters and scenarios to be 51
executed immediately and the results evaluated in real-time. However, there are at least two things to 52
consider about this research. Firstly, genomic parameters that are specific cause a niche of reference, which 53
means that this research is difficult to compare with other relevant studies. Therefore, the only solution is to 54
do directly testing in the field. Implicitly, it is projected that there will be an exponential increase in the 55
amount of data that must be accommodated by greater computing power to maintain and increase the 56

simulation sensitivity. Therefore, these computational requirements may need to be considered one of the 57
operational cost components, especially for the digital integrated poultry industry. 58
Keywords: chicken breeding; selection scenarios; modular program; stochastic simulation; MoBPSweb 59
BACKGROUND 60
The domestic needs for poultry-based protein sources such as eggs and meats rely heavily on the 61
outsourced products, despite being facilitated locally (Ferlito and Respatiadi 2018). This high dependency 62
may jeopardize domestic and global food security, as Hodson (2017) described. Few may realize that global 63
food security has its limits and can no longer be sustained by conventional means or methods. On the other 64
hand, a growing concern about constant threats from environmental crises and the ever-increasing human 65
population adds to the problem. Although it may seem insignificant, this might mark the beginning of global 66
food security collapse. Gama Ayam Research Team creates a pathway to solving poultry problems in 67
Indonesia. A conceived solution was to tap into the vast biodiversity of Indonesian indigenous chicken 68
breeds. An extensive repertoire of Indonesian indigenous chicken breeds (Nataamijaya 2010; Henuk and 69
Bakti 2018; Mahardhika et al. 2021) provides a unique and promising opportunity to be developed. 70
Developing Indonesian indigenous chicken breeds would help secure food sources domestically, therefore 71
hindering any external interventions or collateral effects caused by the global food crisis. 72
For years, studies about one Indonesian indigenous chicken breed, Pelung chicken, have been undergone 73
since its conception as the potential candidate of Indonesia-owned meat-type chicken breed by Daryono et al. 74
(2010). During those years, a wide array of research involving selective breeding programs has developed 75
significant key findings regarding its phenotypes and molecular characteristics (Retnoaji et al. 2016; 76
Perdamaian et al. 2017; Utama et al. 2018; Mahardhika and Daryono 2019; Saragih et al. 2019; Mahardhika 77
et al. 2020; Mahardhika et al. 2021; Kurnia et al. 2021; Daryono et al. 2021; Saragih et al. 2021). In 78
conclusion, it was evident that the breed can be further developed to serve as a more sustainable and long-79
term solution for supporting the local poultry sector. For most of the years, the study mainly revolves around 80
three fundamental aspects: effectiveness, reliability, and minimum ethical cost (Mahardhika et al. 2021). 81
However, the complexity of the selective breeding program could not be handled so easily. The reason was 82
the breeding scheme or genetic architecture and the requisite necessity to create a balance between 83
operational cost, ethical costs, and breeding gains. Thus, it requires a direct experimental or field study and 84
an analytical study, which mainly focuses on predicting the program's outcome. 85
Collecting data from either internal or other relevant studies outside the Gama Ayam Research Team can 86
be utilized as selective parameters. This library of the selective parameter could serve as a pre-emptive 87
measure to avoid unnecessary chicken sacrifice, unethical rearing, cost requirement, and error probability 88
(Mahardhika et al. 2021). An advanced selective breeding program could be achieved using algorithms to 89
compute these selective parameters into a modular design of a chicken breeding scheme with different 90
scenarios and selections. A preliminary evaluation could be produced without strict parameters and the 91
flexibility to modulate or alternate the breeding scheme or scenarios. This digitalized state would provide an 92
instrument to evaluate, compensate or anticipate any outcome of the selective breeding program with reliable 93
precision and accuracy. The Modular Breeding Program Simulator web version (MoBPSweb) written and 94
constructed by Pook and the team was used to facilitate this purpose. Categorized as stochastic simulation, 95
MoBPS used the R language and was created based on the flaws of its predecessors (Pook et al. 2020; Pook 96
et al. 2021). This study investigated the candidate for meat-type Pelung chicken breed produced from the 97
actual selective breeding program Gama Ayam Kambro (Kampong-Broiler). Different selection scenarios 98
were compared and analyzed using MoBPSweb v.1.6.62. Specific selective parameters were formulated and 99
tested against the breeding scheme according to Gama Ayam Kambro's research. This study also explores the 100
feature provided by MoBPSweb to perform specific economic projections. 101
METHODS 102
Settings and parameters 103
The hardware used in this research is an ASUS X450JF-x64 notebook with core processor Intel® Core™ 104
i7-4700HQ CPU @ 2,4GHz, 2401Mhz, 4 Core(s), 8 Logical Processor(s), and 8 GB RAM capacity. The 105
operating system is Microsoft Windows 10 Education v.10.0.19043.1348 © Microsoft Corporation. The 106
observation focuses on the overview Gama Ayam Kambro selective breeding program under three different 107
selection model scenarios. Gama Ayam Kambro's breeding scheme and three selection model scenarios were 108
designed, tested, and analyzed by MoBPSweb v.1.6.62 simulator. The breeding scheme consists of four 109
crossbred generations purebred chicken nucleus as an elder (founder) with the level of crossbreed reaching 110
5th Filial or 5th Kambro (Figure 1.). Several crossing techniques are used, such as crossbreeding, inbreeding, 111
and outbreeding. The parameter used is constructed based on QTL information from the seven prioritized 112
phenotypic characters in the selection, residual-genetic correlation, selection index, phenotype class, the 113

average of phenotype performance, and economic parameters (Supp. File 1, Table 1-4). The seven QTLs 114
were obtained from the ChickenQTLdb chicken QTL database and relevant primer publications. There are 115
seven phenotypic characters, specifically BW49D, BW56D, FEML, AFE, EN, FCR, and TL. Breeding cycle 116
repetition and phenotypic information record (phenotyping) as much as 50 times (generations). Broiler-117
Pelung selection index and residual genetic correlation are applied. The designed selection model scenario 118
consist of scenario_1 (Genomic_SD), scenario_2 (Breeding Value_SD), and scenario_3 (Phenotypic_SD). 119
Each one of the selection model scenarios is tested toward the Gama Ayam Kambro breeding scheme. 120
Genomic parameters were constructed using the Ensembl Map Affymetrix Chicken 600K SNPs Array 121
genomic database. The marker density used is 300K SNPs, with the time unit simulation is set to per week. 122
Additional settings like miraculix and parallel computational are activated. In the genomic selection, the 123
SIM_08 procedure used five core processor with a maximum memory capacity of 30 GB and max the 124
maximum duration of the computational process is 48 hours. The effects of three selection model scenarios 125
on the Gama Ayam Kambro selective breeding program are known according to their output in each chicken 126
nucleus, from the elders to their tillers. The output consists of accuracy, F coefficient, kinship, observed 127
phenotypes, and economic parameter projections related to Gama Ayam Kambro selective breeding program. 128
Simulation 129
130
Fig 1. Gama Ayam Kambro breeding scheme. MoBPSweb (2021). 131
The breeding scheme was designed using nodes (nucleus or cohort) and edges (breeding action) 132
represented by color-coded boxes and arrows in sequence (Figure 1). Boxes of pink represent the chicken 133
group for the hen nucleus (♀) and light blue for the rooster nucleus (♂). Breeding action is represented by 134
red arrows (repeat), green arrows (selection), and orange arrows (reproduction). The repeat code sets the 135
breeding cycles repetition number, selection for selection model scenarios, and reproduction to execute 136
crossbreeding. Gama Ayam Kambro breeding scheme arranged by 200 chicken from BC500 hen nucleus ad 137
100 chicken from selected and crossed PBH rooster nucleus until it reaches 5th Kambro chicken nucleus. 138
There are three selection model scenarios selected through selection breeding action. Four purebred chicken 139
nuclei arrange Gama Ayam Kambro selective breeding as an elder (founder) with the stage of litters nucleus 140
(progeny) until it reaches the 5th Filial (F5) or 5th Kambro (Figure 1). The purebred elders chicken nucleus 141
comprises one hen nucleus, two PBH roosters nucleus, and one BC500 hen nucleus. Each individual will be 142
selected and crossed via reproduction breeding action. The total of generations or breeding cycles repetition 143
is determined by repeat breeding action. Selection model scenarios in the Gama Ayam Kambro scheme are 144
constructed based on scenario_1 (Genomic_SD), scenario_2 (Breeding Value_SD), and scenario_3 145
(Phenotypic_SD). 146

Scenario_1 (Genomic_SD) 147
Step 1. ♀ BC500 nucleus as [200 chickens], type of genotype generation [whole homozygote], phenotype class
[whole phenotyped], and operational cost [chicken feed, vaccine, and supplement]. Selected nucleus of ♀ BC500 [50
chickens], duration [52 weeks], selection type [BVE], BVE methods [DMM], selection index [Broiler], selection
proportion [0.25], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two prevous repetitive].
Step 2. ♂ PBH nucleus [100 chickens], type of genotype generation [random sample], phenotype class [whole
phenotyped], and operational cost [chicken feed, vaccine, and supplement]. Selected nucleus of ♂ PBH [25
chickens], duration [52 weeks], selection type [PHEN], selection index [Pelung], and selection proportion [0.25].
Step 3. The selected nucleus of ♀ BC500 is crossed with the nucleus of selected ♂ PBH with [50 times] breeding
cycles. That crossbreed produces ♀ 1st Kambro and ♂ 1st Kambro nucleus.
Step 4. The nucleus of ♀ 1st Kambro [200 chickens], phenotype class [whole phenotyped], and operational cost
[chicken feed, vaccine, and supplement]. Selected nucleus of 1st Kambro [100 chickens], ], duration [52 weeks],
selection type [BVE], BVE methods [REML-(G)BLUP], selection index [Broiler], selection proportion [0.5], kinship
matrix [VanRaden], and nucleus for BVE [manual selection of two prevous repetitive].
Step 5. The nucleus of ♂ 1st Kambro [100 chickens], phenotype class [whole phenotyped], and operational cost
[chicken feed, vaccine, and supplement]. Selected nucleus of ♂ 1st Kambro [50 chickens], duration [52 weeks],
selection type [BVE], BVE methods [REML-(G)BLUP], index selection [Pelung], proportion index [0.5], kinship
matrix [VanRaden], and nucleus for BVE [manual selection of two prevous repetitive].
Step 6. The nucleus of ♀ 1st Kambro is crossed with selected ♂ 1st Kambro [50 times] breeding cycles. Those
crossbreeding produce the nucleus of 2nd Kambro and ♂ 2nd Kambro.
Step 7. The nucleus of ♀ 2nd Kambro [200 chickens], phenotype class [whole phenotyped], and operational cost
[chicken feed, vaccine, and supplement]. Selected nucleus of ♀ 2nd Kambro [100 chickens], duration [52 weeks],
selection type [BVE], BVE method [REML-(G)BLUP], selection index [Broiler], selection proportion [0.5], kinship
matrix [VanRaden], and nucleus for BVE [manual selection of two prevous repetitive].
Step 8. The nucleus of ♂ 2nd Kambro [100 chickens], phenotype class [whole phenotyped], and operational cost
[chicken feed, vaccine, and supplement]. Selected nucleus of 2nd Kambro [50 chickens], duration [52 week],
selection type [BVE], BVE method [REML-(G)BLUP], selection index [Pelung], selection proportion [0.5], kinship
matrix [VanRaden], and nucleus for BVE [manual selection of two previous repetitive].
Step 9. The selected nucleus of ♀ 2nd Kambro is crossed with the nucleus of selected ♂ 2nd Kambro with a [50 times]
breeding cycle. The crossing breed produces a nucleus of ♀ 3rd Kambro and ♂ 3rd Kambro chickens.
Step 10. The nucleus of ♀ 3rd Kambro as much as [200 chickens], phenotype class [whole phenotype], and
operational costs [chicken feed, vaccines, and supplements]. Nucleus of selected ♀ 3rd Kambro as much as [100
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Broiler],
selection proportion [1], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 11. The nucleus of ♂ 3rd Kambro as much as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 3rd Kambro as much [50
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Pelung],
selection proportion [1], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 12. The nucleus of selected ♀ 3rd Kambro is crossed with the selected nucleus of ♂ 3rd Kambro with a breeding
cycle of [50 times]. That crossbreed produces the nucleus of ♀ 4th Kambro dan ♂ 4th Kambro.
Step 13. The nucleus of ♀ 4th Kambro as much as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 4th Kambro as much as [100
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Broiler],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 14. The nucleus of ♂ 4th Kambro as much as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 4th Kambro [50 chickens],
duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Pelung], selection
proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous replications].
Step 15. The selected nucleus of ♂ PBH as much as [100 chickens], genotype generation type [fully A allele],
phenotype class [whole phenotype], and operational costs [chicken feed, vaccines, and supplements]. The selected
nucleus of ♀ 4th Kambro is crossed with the nucleus of ♂ PBH with a breeding cycle of [50 times]. The crossbreed
produces a nucleus of ♀ 5th Kambro chickens.
Step 16. The nucleus of ♀ PBH as much as [100 chickens], genotype generation type [fully A allele], phenotype
class [whole phenotype], and operational costs [chicken feed, vaccines, and supplements]. The selected nucleus of ♂
4th Kambro is crossed with the nucleus of ♀ PBH with a breeding cycle of [50 times]. The crossbreed produces a
nucleus of ♂ 5th Kambro chickens.
Scenario_2 (Breeding Value_SD) 148
Step 1. The nucleus of ♀ BC500 as much as [200 chickens], genotype generation type [whole homozygote],
phenotype class [whole phenotyped], and operational costs [chicken feed, vaccines, and supplements]. Selected
nucleus of ♀ BC500 as much as [50 chickens], duration [52 weeks], selection type [BVE], BVE method [DMM],

selection index [Broiler], selection proportion [0.25], kinship matrix [VanRaden], and nucleus for BVE [manual
selection of two previous replications].
Step 2. The nucleus of ♂ PBH as many as [100 chickens], genotype generation type [full heterozygotes], phenotype
class [whole phenotyped], and operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂
PBH as many as [25 chickens], duration [52 weeks], selection type [BVE], BVE method [DMM], selection index
[Pelung], selection proportion [0.25], kinship matrix [pedigree], pedigree depth [7 levels], and nucleus for BVE
[manual selection of two previous tests].
Step 3. The selected nucleus of ♀ BC500 is crossed breeding with a selected nucleus of ♂ PBH with a breeding
cycle [50 times]. The crossbreed produces the nucleus of ♀ 1st Kambro and ♂ 1st Kambro chickens.
Step 4. The nucleus of ♀ 1st Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 1st Kambro as many as [100
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Broiler],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 5. The nucleus of ♂ 1st Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 1st Kambro as many as [50
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Pelung],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 6. The selected nucleus of ♀ 1st Kambro is crossed breeding with a selected nucleus of ♂ 1st Kambro with
breeding cycle [50 times]. The crossbreed produces the nucleus of ♀ 2nd Kambro and ♂ 2nd Kambro chickens.
Step 7. The nucleus of ♀ 2nd Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 2nd Kambro as many as [100
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Broiler],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 8. The nucleus of ♂ 2nd Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 2nd Kambro as many as [50
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Pelung],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 9. The selected nucleus ♀ 2nd Kambro is crossed breeding with a selected nucleus of ♂ 2nd Kambro with a
breeding cycle [50 times]. The crossbreed produces the nucleus of ♀ 3rd Kambro and ♂ 3rd Kambro chickens.
Step 10. The nucleus of ♀ 3rd Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 3rd Kambro as many as [100
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Broiler],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 11. The nucleus of ♂ 3rd Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 3rd Kambro as many as [50
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Pelung],
selection proportion [1], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 12. The selected nucleus ♀ 3rd Kambro is crossed breeding with a selected nucleus of ♂ 3rd Kambro with a
breeding cycle [50 times]. The crossbreed produces the nucleus of ♀ 4th Kambro and ♂ 4th Kambro chickens.
Step 13. The nucleus of ♀ 4th Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 4th Kambro as many as [100
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Broiler],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 14. The nucleus of ♂ 4th Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 4th Kambro as many as [50
chickens], duration [52 weeks], selection type [BVE], BVE method [REML-(G)BLUP], selection index [Pelung],
selection proportion [0.5], kinship matrix [VanRaden], and nucleus for BVE [manual selection of two previous
replications].
Step 15. The nucleus of ♂ PBH as many as [100 chickens], generation genotype type [random sample], phenotype
class [whole phenotyped], and operational costs [chicken feed, vaccines, and supplements]. Selected nucleus ♀ 4th
Kambro is a crossbreed with the nucleus of ♂ PBH with a breeding cycle [50 times]. That crossed breed produces the
nucleus of ♀ 5th Kambro as many as [200].
Step 16. The nucleus of ♀ PBH as many as [100 chickens], genotype generation type [random sample], phenotype
class [whole phenotyped class], and operational costs [chicken feed, vaccines, and supplements]. The selected
nucleus of ♂ 4th Kambro is a crossbreed with the nucleus of ♀ PBH with a breeding cycle as [50 times]. That crossed
breed produces a nucleus of ♂ 5th Kambro as many as [100].
Scenario_3 (Phenotypic_SD) 149

Step 1. The nucleus of ♀ BC500 as many as [200 chickens], genotype generation type [fully A allele], phenotype
class [whole phenotyped], and operational costs [chicken feed, vaccines, and supplements].
Selected nucleus of ♀ BC500 as many as [50 chickens], duration [52 weeks], selection type [BVE], BVE method
[DMM], selection index [Broiler], selection proportion [0.25], kinship matrix [pedigree], and nucleus for BVE
[manual selection of two previous replications].
Step 2. The nucleus of ♂ PBH as many as [100 chickens], genotype generation type [random sample], phenotype
class [whole phenotyped], and operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂
PBH as many as [25 chickens], duration [52 weeks], selection type [PHEN], selection index [Pelung], and selection
proportion [0.25].
Step 3. The selected nucleus of ♀ BC500 is crossed breeding with a selected nucleus of ♂ PBH with a breeding
cycle [50 times]. That crossbreed produces the nucleus of ♀ 1st Kambro and ♂ 1st Kambro chickens.
Step 4. The nucleus of ♀ 1st Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 1st Kambro as many as [100
chickens], duration [52 weeks], selection type [PHEN], selection index [Broiler], and selection proportion [0.5].
Step 5. The nucleus of ♂ 1st Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 1st Kambro as many as [50
chickens], duration [52 weeks], selection type [PHEN], selection index [Pelung], and selection proportion [0.5].
Step 6. The selected nucleus of ♀ 1st Kambro is crossed breeding with a selected nucleus of ♂ 1st Kambro with
breeding cycle [50 times]. The crossbreed produces the nucleus of ♀ 2nd Kambro and ♂ 2nd Kambro chickens.
Step 7. The nucleus of ♀ 2nd Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 2nd Kambro as many as [100
chickens], duration [52 weeks], selection type [PHEN], selection index [Broiler], and selection proportion [0.5].
Step 8. The nucleus of ♂ 2nd Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 2nd Kambro as many as [50
chickens], duration [52 weeks], selection type [PHEN], selection index [Pelung], and selection proportion [0.5].
Step 9. The selected nucleus ♀ 2nd Kambro is crossed breeding with a selected nucleus of ♂ 2nd Kambro with a
breeding cycle [50 times]. The crossbreed produces the nucleus of ♀ 3rd Kambro and ♂ 3rd Kambro chickens.
Step 10. The nucleus of ♀ 3rd Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 3rd Kambro as many as [100
chickens], duration [52 weeks], selection type [PHEN], selection index [Broiler], and selection proportion [0.5].
Step 11. The nucleus of ♂ 3rd Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 3rd Kambro as many as [50
chickens], duration [52 weeks], selection type [PHEN], selection index [Pelung], and selection proportion [1].
Step 12. The selected nucleus ♀ 3rd Kambro is crossed breeding with a selected nucleus of ♂ 3rd Kambro with a
breeding cycle [50 times]. The crossbreed produces the nucleus of ♀ 4th Kambro and ♂ 4th Kambro chickens.
Step 13. The nucleus of ♀ 4th Kambro as many as [200 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♀ 4th Kambro as many as [100
chickens], duration [52 weeks], selection type [PHEN], selection index [Broiler], and selection proportion [0.5].
Step 14. The nucleus of ♂ 4th Kambro as many as [100 chickens], phenotype class [whole phenotyped], and
operational costs [chicken feed, vaccines, and supplements]. Selected nucleus of ♂ 4th Kambro as many as [50
chickens], duration [52 weeks], selection type [PHEN], selection index [Pelung], and selection proportion [0.5].
Step 15. The nucleus of ♂ PBH as many as [100 chickens], generation genotype type [random sample], phenotype
class [whole phenotyped], and operational costs [chicken feed, vaccines, and supplements]. Selected nucleus ♀ 4th
Kambro is a crossbreed with the nucleus of ♂ PBH with a breeding cycle [50 times]. That crossed breed produces the
nucleus of ♀ 5th Kambro.
Step 16. The nucleus of ♀ PBH as many as [100 chickens], genotype generation type [random sample], phenotype
class [whole phenotyped class], and operational costs [chicken feed, vaccines, and supplements]. The selected
nucleus of ♂ 4th Kambro is a crossbreed with the nucleus of ♀ PBH with a breeding cycle as [50 times]. That crossed
breed produces a nucleus of ♂ 5th Kambro.
RESULTS & DISCUSSION 150
A review of accuracy from three selection model scenarios in the Gama Ayam Kambro selective 151
breeding program with 50 generations are elaborated per chicken nucleus for each selection index, from the 152
elders to their litters (Figure 2). For the Broiler selection index, in the nucleus of selected ♀ BC500 and ♂ 153
PBH elderly chicken, the three selection model scenarios have the upper and lower accuracy limit of 95% 154
and 60%, respectively, with the upper and lower limit of accuracy extreme fluctuations in each generation. In 155
the ♀/♂ 1st and 2nd Kambro chicken nucleus, there is still fluctuation followed by an increase in the 156
accuracy’s lower limit to 70%. Then, stability begins to be achieved in the ♀/♂ 3rd and 4th Kambro chicken 157
nucleus, followed by a decrease in the accuracy’s upper limit to 80%. In the ♀/♂ 3rd and 4th Kambro chicken 158
nucleus, an extreme lower limit of accuracy by -20% and 0%, respectively. When the elder ♀/♂ PBH 159
chicken nucleus been reintroducing into breeding, it was observed in the ♀/♂ 5th Kambro chicken nucleus 160
there is fluctuation followed by an increase in upper and lower limits of accuracy to 95% and 75%, 161
respectively. It can be concluded that for the Broiler selection index, there is an increase in the lower limit of 162

accuracy by 15% in the 5th Kambro chicken nucleus against the nucleus of selected elders chicken, which 163
indicates a decrease in the range of accuracy fluctuations by 15 points. According to this discovery, it is 164
pretty practical to use an outbreeding technique in increasing the accuracy of genomic prediction of the three 165
selection model scenarios was known. Implicitly, these three selection model scenarios reveal the fluctuation 166
patterns uniformity from the accuracy result. The accuracy result (r50) over 50 generations shows that 167
scenario_1 is the most suitable for selecting ♂ 5th Kambro chicken and ♂ Pelung elders chickens using 168
the Broiler selection index (Figure 2). 169
For the Pelung selection index, in the nucleus of the ♀ BC500 and ♂ PBH selected elder chickens, three 170
selection model scenarios have an accuracy limitation in upper and lower by 95% and 50%, in order with an 171
extreme fluctuation in each generation. In the ♀/♂ 1st and 2nd Kambro chicken nucleus, the fluctuation is still 172
happened, followed by the increase of accuracy’s lower limit to 65% and 70%, respectively. In the ♀/♂ 3rd 173
and 4th Kambro chicken nucleus begin to achieve stability, followed by a decrease in the upper accuracy limit 174
to 80%. In addition, extreme lower accuracy limits of -20% and 0% were detected, respectively. When the 175
♀/♂ PBH elders chicken nucleus being reintroduced in the breeding, it is observed that ♀/♂ 5th Kambro 176
chicken nucleus fluctuations occur followed by an increase in the upper and lower limit of accuracy to 90% 177
and 70%, respectively. 178
To conclude, for the Pelung selection index, the upper limit of 5th Kambro nucleus accuracy decreased 179
by 5% against the nucleus of selected elders chicken meanwhile, there is a 20% increase for the lower limit. 180
The fluctuation of the upper-and lower limit indicates a derivation in the range of accuracy by 25 points. 181
According to this discovery, using an outbreeding technique to increase genomic prediction accuracy from 182
the three selection model scenarios is pretty practical. In the entire perspective, these three selection model 183
scenarios show a uniformity of fluctuation pattern from obtaining accuracy. According to the acquisition of 184
accuracy (r50) of 50 generations, it is showing that scenario_1 is the most suitable for selecting ♂ 5th Kambro 185
chicken and ♂ Pelung elders chickens using the Pelung selection index (Figure 2). 186
The decrease in the accuracy fluctuating range from the three selection model scenarios in the Pelung 187
selection index is more significant than Broiler. However, the lower and upper limits of the 5th Kambro 188
chicken nucleus accuracy for the Pelung selection index are lessened than Broiler. On the other hand, in the 189
lower limit of elders, chicken nucleus accuracy for Broiler index selection are higher than Pelung. The 190
conclusion is that the use of the Broiler selection index is adequate than Pelung. The Pelung selection index 191
assigns a higher value to the FEML (5) and TL (5) phenotype characters, while the Broiler selection index to 192
FCR (5), BW49D (4), and BW56D (4). According to this discovery, weighting affects the accuracy of the 193
Gama Ayam Kambro three selection model scenario. Through the contrast of upper and lower accuracy limit 194
between the elders chicken nucleus and 5th Kambro, also known as the use/utilization of outbreeding 195
techniques, in general, are pretty effective in increasing the accuracy of genomic predictions of the three 196
selection model scenarios for the two selection index. The selection index of the three selection model 197
scenario shows the uniformity of fluctuation pattern from the accuracy result. According to the acquisition of 198
accuracy (r50) of 50 generations, it is showing that scenario_1 with genomic selection design is the most 199
applicable for selecting ♂ 5th Kambro and elder ♂ Pelung chickens, either using the Broiler or Pelung 200
selection index, under the Gama Ayam Kambro breeding scheme. 201

202
Fig 2. Accuracy of 𝑟(𝑆𝑘𝑒𝑛𝑎𝑟𝑖𝑜 , 𝑇𝐵𝑉) from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 203
(2021). 204
An overview regarding the F coefficient and weekly kinship of the three selection model scenarios in the 205
Gama Ayam Kambro selective breeding program is described in each chicken nucleus, starting from the 206
elders to the litters (Figure 3). For the F coefficient, in the nucleus of selected ♀ BC500 and ♂ PBH elders, it 207
is known that three selection scenarios have upper and lower limits of 0.3 and 0, respectively, with a linear 208
increase pattern per week. In the ♀/♂ 1st Kambro nucleus, an increasing linear pattern is still detected, 209
followed by a decrease in the upper limit of the F coefficient to 0.25. Meanwhile, the ♀/♂ 2nd Kambro, an 210
increased linear pattern followed by an increase in the upper and lower limits to 0.42 and 0.26, respectively. 211
In the ♀/♂ 3rd and 4th Kambro nucleus, there is an F coefficient of scenario_1 with scenario_2 and 212
scenario_3. As a result, scenario_1 has a higher increasing pattern of the F coefficient than scenario_2 and 213

scenario_3. In the 3rd Kambro nucleus, an increase in upper and lower limits of the F coefficient was detected 214
to 0.52 and 0.4, respectively. Meanwhile, an increase in the 4th Kambro nucleus was detected to 0.58 and 0.5, 215
respectively. As the ♀/♂ PBH elders nucleus was reintroduced to breeding, it was observed that the ♀/♂ 5th 216
Kambro nucleus fluctuated and followed by a decrease in the upper and lower limits of the F coefficient to 217
0.035 and 0.005, respectively (Figure 3). 218
According to upper and lower limits, there is a weekly increase in the F coefficient from the 2nd 219
Kambro to the 4th Kambro nucleus. In summary, there is a decrease in the upper limit of the 5th Kambro 220
nucleus F coefficient by 0.265 points against the nucleus of the selected elders, while for the lower limit, 221
there is an increase of 0.005 points. In addition, this also indicates a fluctuating range decrease in 222
the F coefficient by 0.04 points. According to these findings, using the outbreeding technique effectively 223
reduces the F coefficient of the three selection model scenarios. There is a separation of the F coefficient of 224
scenario_1 with scenario_2 and scenario_3 in the 3rd and 4th Kambro chicken nucleus. At least three factors 225
most likely underlie this occurrence: the choice of broodstock, crossing techniques, and the selected design. 226
It has been recognized that the F coefficient of the 2nd Kambro's nucleus has reached the relatively high 227
relative limit to the nucleus of the elders or 1st Kambro chicken. It is suspected to amplify the homozygotic 228
allele fraction when the selected 2nd Kambro is crossed with each other based on the common inbreeding 229
technique to form ♀/♂ 3rd Kambro nucleus. A similar procedure was also applied in forming the nucleus of 230
♀/♂ 4th Kambro. The selection model scenario factor is might play a passive role due to the accumulation of 231
the two previous factors. According to F coefficient (F5000) for 5000 weeks, it was found that scenario_1 with 232
the most practical selection design for selecting ♂ 5th Kambro and elder ♂ Pelung chicken under the Gama 233
Ayam Kambro breeding scheme (Figure 3). 234

235
Fig 3. The F coefficient and weekly kinship of the Gama Ayam Kambro three selection model scenario. MoBPSweb 236
(2021). 237
In terms of kinship, in the nucleus of the selected ♀ BC500 ♂ PBH and elders, it has known that the 238
three selection model scenarios have upper and lower limits of 0.5 and 0, respectively, with a linear increase 239
pattern per week. In the ♀/♂ 1st Kambro nucleus, the increasing linear pattern is still detected without 240
changing the kinship's upper and lower limits. In ♀/♂ 2nd Kambro nucleus, a linear pattern was improved, 241
followed by an increase in the upper and lower to 0.8 and 0.55, respectively. In the ♀/♂ 3rd and 4th Kambro 242
nucleus, there is a separation of kinship between scenario_1 with scenario_2 and scenario_3. Scenario_1 has 243
a higher increasing kinship pattern than scenario_2 and scenario_3. In the 3rd Kambro nucleus, there is an 244
uplift in the upper and lower limits of kinship to 1 and 0.8, respectively. 245

Meanwhile, an increase in the 4th Kambro nucleus was detected to 1.15 and 1, respectively. When the 246
♀/♂ PBH elders being reintroduced into breeding, it observed there is a fluctuation occurred and followed by 247
a decrease in the upper and lower limits of kinship to 0.3 and 0 in the ♀/♂ 5th Kambro nucleus, respectively 248
(Figure 3). According to upper and lower limits, there is an increase in the weekly kinship starting from the 249
2nd Kambro nucleus to the 4th Kambro. Therefore, it can be assumed that there is a decrease in the 5th Kambro 250
kinship's upper limit by 0.2 points to the chosen elders chicken's nucleus. According to this discovery, using 251
outbreeding techniques is quite effective in reducing the homozygotic allele fraction of the three selection 252
model scenarios. The kinship strengthens the factors of broodstock and crossing technique as 253
the F coefficient separation of in the 3rd and 4th Kambro. In addition, it also proves the amplification of the 254
homozygotic allele fraction, which leads to an increase in the F coefficient. It is concluded that the cohort's 255
close kinship increases the F coefficient. According to the kinship (R5000) over 5000 weeks, it was found that 256
scenario_1 with the genomic selection design is the most applicable for selecting ♂ 5th Kambro and elders of 257
♂ Pelung chicken, under the Gama Ayam Kambro chicken breeding scheme (Figure 3). 258
259
Fig 4. The observed phenotype of AFE from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 260
(2021). 261
An overview of the observed phenotypes of AFE from the three selection model scenarios in the Gama 262
Ayam Kambro selective breeding program with 50 generations was described per nucleus, from the elders to 263
litters (Figure 4). In the nucleus of selected ♀ BC500 elders and ♂ PBH, the three selection model scenarios 264
have upper and lower limits of AFE by 169 and 161 days, in order with a linear increase pattern per 265
generation. The lowest AFE was detected in the same nucleus at scenario_2, while the highest is in 266
scenario_3, followed by scenario_1. In the ♀/♂ 1st Kambro nucleus, linear increases pattern was still 267
detected, followed by a decrease in the upper limit of AFE to 168 days. While in the ♀/♂ 2nd Kambro 268
nucleus, a linear increases pattern followed by an increase in the upper and lower limits to 171 and 166 days, 269
respectively. The ♀/♂ 3rd Kambro nucleus, an increase in the upper and lower limits of AFE was detecter to 270
174 and 169 days, respectively. While in the ♀/♂ 4th Kambro nucleus, an increase was detected to 175 and 271
171 days, respectively. When the elders ♀/♂ PBH nucleus being reintroduced to breeding, it was observed in 272
the ♀/♂ 5th Kambro nucleus there are a decrease in the upper and lower limits of AFE to 174 and 160days, 273
respectively (Figure 4). According to upper and lower limits, there is an increase in AFE starting from the 274
nucleus of 2nd Kambro to 4th Kambro. There is an increase in the upper limit of AFE 5th Kambro nucleus by 5 275
points to the nucleus of the selected elders, while the lower limit decreased by 1 point. Moreover, that 276
indicates an increase in AFE fluctuating range by 6 points. According to these findings, using the 277
outbreeding technique reduces AFE from the three selection model scenarios. Based on AFE (AFE50) 278

throughout 50 generations, it is discovered that scenario_2 (BV) dan scenario_3 (PHEN) is the most 279
applicable for selecting the ♂ 5th Kambro and elder ♂ Pelung, respectively under the Gama Ayam Kambro 280
breeding scheme (Figure 4). 281
282
Fig 5. The observed phenotype of BW49D from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 283
(2021). 284
An overview of an observed phenotype of BW49D from the three selection model scenarios in the Gama 285
Ayam Kambro selective breeding program with 50 generations was described per nucleus, starting from the 286
elders to their litters (Figure 5). In the nucleus of selected elders ♀ BC500 and ♂ PBH, it has known that the 287
three selection model scenarios have upper and lower limits of BW49D of 780 and 710 grams, in order with 288
fluctuations per generation. In the same chicken nucleus, the lowest BW49D was detected in scenario_3, 289
while the highest was in scenario_2 and followed by scenario_1. The fluctuation in the nucleus of ♀/♂ 1st 290
Kambro still happens, followed by a decrease in the upper limit and an increase in the BW49D’s lower limit 291
to 770 and 720 grams, respectively. Meanwhile, in the ♀/♂ 2nd Kambro nucleus, an increase in the linear 292
pattern was detected attenuation of fluctuations without changes in the upper and lower limits of BW49D 293
relatively to the 1st Kambro nucleus. Finally, in the ♀/♂ 3rd Kambro nucleus, it is indicated that there is an 294
increase in the upper limit and a decreased lower limit of BW49D to 780 and 710 grams, respectively. 295
Meanwhile, in the ♀/♂ 4th Kambro nucleus, a decrease in the upper limit to 770 grams was detected. As 296
the nucleus of ♀/♂ PBH elders has been reintroducing into breeding, it has detected there was no change in 297
the upper and lower limits of BW49D in the nucleus of ♀/♂ 5th Kambro. In the nucleus of ♀/♂ 5th Kambro, 298
fluctuations, and convergence of the upper and lower limits of BW49D were detected from the three 299
selection model scenarios (Figure 5). According to upper and lower limits, there are no changes in the 300
BW49D from the 1st Kambro nucleus to the 4th Kambro. It summarizes a decrease in the BW49D upper limit 301
of the 5th Kambro nucleus by 10 points to the nucleus selected elders, while there was no change for the 302
lower limit. Otherwise, it indicates a decrease in the fluctuating range of BW49D by 10 points. In the 5th 303
Kambro nucleus, there was a convergence of upper and lower limits in the range of 750 and 710 grams, 304
respectively. According to these findings, outbreeding techniques are less effective in increasing BW49D 305
from the three selection model scenarios. Based on BW49D (BW49D50) over 50 generations, found that 306
scenario_3 (PHEN) and scenario_2 (BV) are the most suitable for selecting ♂ 5th Kambro chickens and ♂ 307
Pelung elder chickens, respectively under the Gama Ayam Kambro breeding scheme (Figure 5). 308

309
Fig 6. The observed phenotype of BW56D from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 310
(2021). 311
An overview of an observed phenotype of BW56D from the three selection model scenarios in the Gama 312
Ayam Kambro selective breeding program with 50 generations was described per nucleus, from the elders to 313
litters (Figure 6). In the nucleus of selected ♀ BC500 and ♂ PBH elders, the three selection model scenarios 314
have upper and lower limits of BW56D by 1500 and 900 grams, in order with increasing linear pattern. In the 315
nucleus of ♀/♂ 1st Kambro, an increasing linear pattern is detected without changes in the upper and lower 316
limits of BW56D. In the nucleus of ♀/♂ 2nd Kambro, an increasing linear pattern has been detected, followed 317
by an increase in upper and lower limits of BW56D to 1850 and 1450 grams, respectively. In the nucleus of 318
♀/♂ 3rd Kambro, a detected increase of upper and lower limits of BW56D to 2100 and 1750 grams, 319
respectively. In the nucleus of ♀/♂ 4th Kambro, an increase is detected in the upper and lower limits to 2250 320
and 1950 grams, respectively. The lowest of BW56D in the same nucleus is in scenario_3, whereas the 321
highest is in scenario_1 and then scenario_2. When the nucleus of ♀/♂ PBH elders reintroduced into the 322
breeding, it was observed that there is a decrease in upper and lower limits of BW56D to 2200 and 900 323
grams in the ♀/♂ 5th Kambro nucleus, respectively (Figure 6). Based on upper and lower limits, there is an 324
increase of BW56D starting from the nucleus of 2nd Kambro to 4th Kambro. The conclusion is an increase in 325
the upper limit of BW56D in the 5th Kambro nucleus by 700 points towards the elder’s nucleus, whereas, for 326
the lower limit, there was a decrease of 100 points. Moreover, that indicates there is a decrease fluctuating 327
range by 200 points. According to these findings, the outbreeding technique effectively increases BW56D 328
from the three selection model scenarios. Based on BW56D (BW56D50) over 50 generations, scenario_1 329
(GEN) and scenario_3) are the most applicable for selecting ♂ 5th Kambro chickens and ♂ Pelung chickens, 330
respectively under the Gama Ayam Kambro breeding scheme (Figure 6). 331

332
Fig 7. The observed phenotype of EN from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 333
(2021). 334
An overview of an observed phenotype of EN from the three selection model scenarios of the Gama 335
Ayam Kambro selective breeding program with 50 generations was described per nucleus, from the elders to 336
their litters (Figure 7). In the nucleus of selected ♀ BC500 and ♂ PBH elders, the three selection model 337
scenarios have an upper and lower limit of EN by 130 and 70 items/day, with fluctuations in each generation. 338
In the same nucleus, the lowest EN was detected in scenario_1, while the highest is in scenario_2, followed 339
by scenario_3. In the nucleus of ♀/♂ 1st Kambro, still detect a fluctuation, followed by the upper limit of EN 340
decreasing to 120 items/day. Meanwhile, in the nucleus of ♀/♂ 2nd Kambro, an increasing linear pattern with 341
a weakening fluctuation in the lower limit of EN to 60 items/day is detected. In the nucleus of ♀/♂ 3rd dan 4th 342
Kambro, an increasing linear pattern without any change on upper and lower limits of EN relatively to the 343
nucleus ♀/♂ 2nd Kambro is detected. When the nucleus of ♀/♂ PBH elders reintroduced into the breeding, it 344
observed that in the nucleus of ♀/♂ 5th Kambro, there is any change in upper and lower limits of EN (Figure 345
7). Based on upper and lower limits, there is no change in EN from the nucleus of 1st Kambro to 4th Kambro. 346
It summarizes a decreasing upper and lowers limits of the EN nucleus of 5th Kambro by 10 points towards 347
the nucleus of selected elders. In addition, it also indicates a stable range of EN fluctuations. According to 348
these findings, using the outbreeding technique is less effective in increasing EN from the three selection 349
scenarios. Based on EN (EN50) over 50 generations, scenario_3 (PHEN) and scenario_2 (BV) are suitable for 350
selecting ♂ 5th Kambro chickens and ♂ Pelung elder chickens, respectively under the Gama Ayam Kambro 351
breeding scheme (Figure 7). 352

353
Fig 8. The observed phenotype of FCR from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 354
(2021). 355
An overview of an observed phenotype of FCR from the three selection model scenarios of the Gama 356
Ayam Kambro selective breeding program with 50 generations was described per nucleus, from the elders to 357
their litter (Figure 8). In the nucleus of selected ♀ BC500 and ♂ PBH elders, the three selection model 358
scenarios have upper and lower limits of FCR by 4 and 2kg/kg, in order with fluctuations in each generation. 359
In the same nucleus, the lowest FCR was detected in scenario_3, while the highest is in scenario_2, followed 360
by scenario_1. The nucleus of ♀/♂ 1st Kambro has still detected fluctuation without any changes in the upper 361
and lower limits of FCR. Meanwhile, in the nucleus of ♀/♂ 2nd Kambro, an increasing linear pattern with a 362
weakening fluctuation followed by an increase in the upper limit of FCR to 4,5 and 2,5kg/kg, respectively. In 363
the nucleus of ♀/♂ 3rd dan 4th Kambro, an increasing linear pattern is detected, followed by an increase of 364
upper and lower limits of FCR to 5 and 3kg/kg, respectively. When reintroduced the nucleus of ♀/♂ PBH 365
elders into the breeding, it observed that in the nucleus of ♀/♂ 5th Kambro, there is a decrease in the lower 366
limit of FCR to 2kg/kg (Figure 8). Based on upper and lower limits, there is an increase in FCR that started 367
from the nucleus of 2nd Kambro to 4th Kambro. It can be concluded that there is an increase in the FCR upper 368
limit in the nucleus of 5th Kambro by 1 point towards the nucleus of the elders, while there is no change for 369
the lower limit. In addition, it also indicates an increased fluctuating range of FCR by 1 point. According to 370
these findings, using the outbreeding technique is less effective in lowering the FCR of the three selection 371
model scenarios. Based on FCR (FCR50) over 50 generations, scenario_1 (GEN) and scenario_3 (PHEN) are 372
the most suitable for selecting ♂ 5th Kambro chickens and ♂ Pelung elder chickens, respectively under the 373
Gama Ayam Kambro breeding scheme (Figure 8). 374

375
Fig 9. The observed phenotype of FEML from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 376
(2021). 377
An overview of an observed phenotype of FEML from the three selection model scenarios of the Gama 378
Ayam Kambro selective breeding program with 50 generations was described per nucleus, from the elders to 379
their litters (Figure 9). In the nucleus of selected ♀ BC500 and ♂ PBH elders, the three selection model 380
scenarios have upper and lower limits of FEML by 20 and 12 cm, respectively, with the increasing linear in 381
each generation. The lowest FEML is detected in the same nucleus at scenario_2, while the highest is at 382
scenario_3 and followed by scenario_1. The nucleus of ♀/♂ 1st Kambro an increasing linear pattern still 383
detected without any changes in the upper and lower limits of FEML. Meanwhile, in the nucleus of ♀/♂ 2nd 384
Kambro, an increasing linear pattern followed by increasing the upper and lower limits of FEML to 23 and 385
18 cm is detected, respectively. In the nucleus of ♀/♂ 3rd Kambro, an increasing linear pattern was detected, 386
followed by increasing the upper and lower limits of FEML to 27 and 23 cm, respectively. Meanwhile, in the 387
nucleus of ♀/♂ 4th Kambro, followed by increasing upper and lower limits of FEML by 28 and 25 cm, 388
respectively. When the nucleus of ♀/♂ PBH elders being reintroduced into the breeding, it observed a 389
decrease in the lower limits of FEML to 10 cm in the nucleus of ♀/♂ 5th Kambro (Figure 9). Based on upper 390
and lower limits, an increasing FEML started from the nucleus 2nd Kambro to 4th Kambro. It summarizes an 391
increase in the upper limit of FEML in the nucleus of 5th Kambro to 8 points towards the nucleus of elders, 392
which is a decrease by 2 points for the lower limit. In addition, it indicates an increase in the fluctuating 393
range of FEML by 10 points. Based on these findings, the outbreeding technique effectively increases the 394
FEML from the three selection model scenario. Based on FEML (FEML50) over 50 generations, scenario_2 395
(BV) and scenario_3 (PHEN) are the most suitable for selecting ♂ 5th Kambro chickens and ♂ Pelung elder 396
chickens, respectively under the Gama Ayam Kambro breeding scheme (Figure 9). 397

398
Fig 10. The observed phenotype of TL from the Gama Ayam Kambro three selection model scenarios. MoBPSweb 399
(2021). 400
An overview about an observed phenotype of TL from the three selection breeding scenarios of the 401
Gama Ayam selective breeding program with 50 generations was described per nucleus, starting from the 402
elders to their litters (Figure 10). In the nucleus of selected ♀ BC500 and ♂ PBH elders, the three selection 403
model scenarios have upper and lower limits of TL by 24 and 17 cm, in order with an increasing linear 404
pattern in each generation. It is detected that the lowest TL is in the same nucleus at scenario_2, the highest is 405
at scenario_3, followed by scenario_1. The nucleus of ♀/♂ 1st Kambro still detected an increasing linear 406
pattern, followed by a decrease in the lower TL limit by 16 cm. Meanwhile, in the nucleus of ♀/♂ 2nd 407
Kambro, an increasing linear pattern is detected, followed by an increase of TL's upper and lower limits to 28 408
and 23 cm, respectively. In the nucleus of ♀/♂ 3rd Kambro, an increase of TL's upper and lower limits to 23 409
and 26.5 cm is detected, respectively. In the nucleus of ♀/♂ 4th Kambro, TL's upper and lower limits 410
increased to 32.5 and 28.5 cm, respectively. When the nucleus of ♀/♂ PBH elders being reintroduced into 411
the breeding, it was observed in the nucleus of ♀/♂ 5th Kambro there is a decrease in upper and lower limits 412
of TL to 32 and 16 cm, respectively (Figure 10). Based on upper and lower limits, there is an increase in TL 413
starting from the nucleus of 2nd Kambro to 4th Kambro. It summarizes an increasing upper limit of TL in the 414
nucleus of 5th Kambro by 8 points towards the nucleus of the elders, while there is a decrease to 1 point for 415
the lower limit. 416
Meanwhile, it indicates an increased fluctuating range of TL by 9 points. According to these findings, the 417
outbreeding technique effectively increases TL from the three selection model scenarios. Therefore, based on 418
TL (TL50) over 50 generations, scenario_3 with phenotype design selection is most suitable for selecting the 419
♂ 5th Kambro chickens and ♂ Pelung elder chickens, under the breeding scheme of Gama Ayam Kambro 420
(Figure 10). 421
The economic parameters are designed based on the field operational cost in the Gama Ayam Kambro 422
selective breeding program with an interest rate of 2.5% and a EUR/Rp exchange rate of Rp 16.897 per 27 423
August 2021 (see Table 32, Appendix 16). The economic parameters were tested against the three selection 424
model scenarios and analyzed internally by the MoBPSweb simulator. The economic parameters are 425
projected for 50 breeding generations with operational cages in 100 units, and each will implement intensive 426
maintenance management. For ten years, the projection economic parameters produced a total of 113.975 427
chickens which accumulated from each nucleus, from the elders to their litters. The total required operational 428
cost is around ±4.79 billion rupiahs. The cost of operation is accumulated from three components which are 429
genotyping, phenotyping, and housing. The total genotyping cost required is ±1.89 billion rupiahs, while the 430

phenotyping and housing cost are around ±1.89 and ±0.995 billion rupiah, respectively (see 431
Supp.File_SIM08). Counting the inflation rate and interest rate of rupiah each year requires an operational 432
cost of around ±500 million rupiahs for applying the breeding scheme and selection procedure of Gama 433
Ayam Kambro. These findings summarized that the crossing technique, selection model scenario, and 434
breeding scheme affect the achievements of the Gama Ayam Kambro selective breeding program. From the 435
aspects of accuracy, it concluded that the selection of Pelung and 5th Kambro males would be more optimal 436
when using scenario_1 with the genomic selection design for both Broiler and Pelung selection index. The 437
same conclusion also applies to the F coefficient and kinship. Generally, the outbreeding technique is quite 438
effective in increasing the accusation and controlling the F coefficient. 439
However, different things concluded regarding the phenotype characters of AFE, BW49D, EN, and FCR. 440
Meanwhile, for the phenotype characters of FEML, TL, and BW56D, the conclusion is that the outbreeding 441
technique is quite effective for increasing those three achievements. Different results were obtained for each 442
phenotype character related to the selection model scenario. The phenotype characters of AFE and FEML 443
concluded that the selection of 5th Kambro and Pelung males would be more optimal when using scenario_2 444
(BV) and scenario_3 (PHEN), respectively. Meanwhile, for the BW49D and EN phenotype characters, 445
precocity applies. Different things concluded regarding the selection of 5th Kambro and Pelung males for the 446
phenotype characters of FCR and BW56D, which will be more optimal if using the scenario_1 (GEN) and 447
scenario_3 (PHEN), respectively. However, the male selection will be more optimal for the TL phenotype 448
character if using scenario_3 with phenotype design selection. 449
CONCLUSIONS 450
As well as accuracy, F coefficient, kinship, and observed phenotype are determined by crossing 451
technique, selection model scenario, and breeding scheme. The selection rate of 5th Kambro and Pelung males 452
can be optimized using the scenario_1 genomic selection design and outbreeding technique, both 453
for Broiler and Pelung selection index. The selection model scenario and similar crossing technique are also 454
quite effective in controlling the F coefficient. However, the outbreeding technique is less effective for 455
increasing the achievements of AFE, BW49D, EN, and FCR phenotype characters, otherwise for the 456
phenotype characters of FEML, TL, and BW56D. For the phenotype characters of AFE and FEML, the 457
selection of 5th Kambro and Pelung males can be optimized by using scenario_2 (BV) and scenario_3 458
(PHEN), respectively. 459
Meanwhile, for the phenotype characters of BW49D and EN, reciprocal applies. The selection of 5th 460
Kambro and Pelung males for the phenotype characters of FCR and BW56D will be more optimal if using the 461
scenario_1 (GEN) and scenario_3 (PHEN), respectively. Meanwhile, the phenotype characters of TL will be 462
more optimal if scenario_3 with phenotype design selection is used for both. The projections of economics 463
parameters show that the total operating costs required per year are around ±500 million rupiahs for the three 464
selection model scenarios using Gama Ayam Kambro breeding scheme with 100 units of intensive 465
maintenance management cages 50 breeding generations. Naturally, the projected operational costs must 466
count the inflation rates and interest rates in rupiah per year. Technically, computation has many 467
shortcomings; the number repetition, projections of economic parameters, outcome visualization, and analysis 468
options are still limited. Aside from that, several selection procedures need to be improved, especially for 469
marker density and particular kinship matrix for the ss(G)BLUP procedure. Nonetheless, the integration of 470
MoBPSweb provides highly unique and unprecedented opportunities to forecast for the first time the possible 471
outcome of a selective breeding program. In itself, this would help to breach further and handle both the 472
complexity and limitations of the breeding program without necessarily having to comprise the gains, ethical 473
risk, and operation costs. 474
Acknowledgments: Authors acknowledge the Gama Ayam Research Team for ensuring the completion of 475
this project. Pusat Inovasi Agroteknologi and Faculty of Biology Universitas Gadjah Mada Daerah Istimewa 476
Yogyakarta, Indonesia for facilitating the research. Pook, T. as a MoBPS conceptor and developer, and 477
Animal Breeding and Genetics Group, Center for Integrated Breeding Research for allowing us to privately 478
using the simulator in web version. 479
Authors’ contributions: Mahardhika, I.W.S. and Hida, F.N.L. contribute by performing the research, 480
analyzing the results, and preparing the manuscript for publication. Retnoaji, B., Widiyanto, S., Pook, T., and 481
Daryono, B.S. contribute by conceiving the idea, supervising, and advising throughout the research. Pook, T., 482
and Animal Breeding and Genetics Group, Center for Integrated Breeding Research contribute by cencepting 483
and constructing the simulator. 484
Funding: The author received no specific funding for this work. 485

Competing interests: The author has declared no competing interests exist. 486
Availability of data and materials: The selective parameters used in this study are included in this article 487
[Supplemental File 1]. 488
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Supplemental File 1. Parameters of MoBPSweb v.1.6.62
Table 2. Residual and genetic correlation.
BW49D
AFE
BW56D
EN
FCR
FEML
TL
BW49D
1
-0.75
-0.5
0.25
0.5
-0.9
-0.9
AFE
-0.5
1
0.75
0.14
0.9
0.2
0.2
BW56D
-0.8
0.3
1
0.13
0.9
0.4
0.4
EN
0.8
-0.2
-0.4
1
0.6
-0.4
-0.43
FCR
0.95
0.85
0.95
0.6
1
0.1
0.2
FEML
-0.5
0.2
0.32
-0.21
0.54
1
0.6
TL
-0.25
0.4
0.43
-0.34
0.56
0.71
1
Below the diagonal is genetic correlation; above the diagonal is residual correlation; values are generated via MoBPSweb serv er.
Table 3. Selection indexes and phenotyping classes.
Selection indexes
Standardization
BW49D
AFE
BW56D
EN
FCR
FEML
TL
Broiler
Genomic SD1, Breeding Value SD2, Phenotypic SD3
4
2
4
2
5
2
2
Pelung
Genomic SD1, Breeding Value SD2, Phenotypic SD3
2
3
2
3
2
5
5
Phenotyping classes
Phenotyping cost
BW49D
AFE
BW56D
EN
FCR
FEML
TL
Fully phenotyped
50
50
50
50
50
50
50
50
1Scenario_1; 2Scenario_2; 3Scenario_3; SD: Standard Deviation; AFE: Age at First Egg; BW49D: Body Weight 49 Days; BW56D: Body Weight 56 Days; EN: Egg Number; FCR: Feed
Conversion Ratio; FEML: Femur Length; TL: Tibia Length.
Table 4. General economy parameters.
Fixed cost (€-Rp)
Interest rate (%)
Genotyping cost per repeat (€)
Number of Housing (€)
Chicken feeds, vaccines, and supplements (€)
€ 50.729/Rp 857167.91
2.5
€ 50/Rp 844850
€ 100/Rp 1689700
€ 22.07/Rp 372916.79
1 € = Rp 16897 (August 27th, 2021).
Table 1. Phenotypes and major QTLs.
Traits
CHR
QTL peak/scan
QTL position
p
PHENO. μ (±SD)
Effect
Allele
frequency
Polygenic
loci
r
h2 (±SE)
Maternal
Paternal
Value
(€)
Gene/SNP
AA
AB
BB
AFEa
1
207 cM/205-215 cM
3MCW0007/4MCW0018
<0.05
159.95 d (1.1)
1.74
0.87
0.39
A(0.53)/B(0.47)
1000
0.6
0.51 (0.09)
0.065
11.98
1.3
MTNR1B/JQ249894:g.63C>T
BW49Db
1
205/205-241 cM
MCW0018/MCW0058
0.0061
728.66 gr (16.3)
42.66
-8.66
-34.66
A(0.57)/B(0.43)
1000
0.6
0.413 (0.01)
10
0
2
cGH/G+1705A
BW56Dc
1
444/0-100 cM
Unidentified
<0.01
858.84 gr (158.84)
-23.8
58
11.41
A(0.43)/B(0.57)
1000
0.3
0.25
0.42
0
1
ATGL/c.782G>A
ENd
1
145/122-205 cM
3ADL0019/4ADL0150
<0.05
84.58 count/d (6.07)
-14.22
40.34
30.56
A(0.41)/B(0.59)
1000
0.3
0.24 (0.07)
0
0
1.5
rs14878430
FCRe
1
50/98-128 cM
3MCW0011/4ADL0307
<0.01
1.82 kg/kg (0.31)
0.01
0.11
1.64
A(0.95)/B(0.05)
1000
0.1
0.07 (0.01)
0.52
0
2.3
USP44
FEMLf
1
72.6/72-94 cM
2MCW0010/5MCW0106
-
10.64 cm (0.84)
0.1
0.3
0.6
A(0.24)/B(0.76)
1000
0.95
0.92
0
1
1.05
LRCH1
TLg
1
98/0-100 cM
1MCW0011
<0.05
15.21 cm (0.84)
0.11
0.53
1.9
A(0.23)/B(0.77)
1000
0.6
0.59
0
1
1.04
LCORL/rs314487178
1Peak/2Upper.suggest/3Upper.sig/4Lower.sig/5Lower.suggest; AFE: Age at First Egg; BW49D: Body Weight 49 Days; BW56D: Body Weight 56 Days; EN: Egg Number; FCR: Feed Conversion Ratio; FEML: Femur Length; TL: Tibia Length.
a Tuiskula-Haavisto et al. (2004), Goto et al. (2011), dan Xu et al. (2011); b Jennen et al. (2005) dan Nie et al. (2005); c Zhou et al. (2006), Nie et al. (2010), dan Wang et al. (2021); d Hansen et al. (2005), Li et al. (2013), dan Yuan et al. (2015);
e De Koning et al. (2004) dan Wang et al. (2019); f Zhang et al. (2010); g Zhou et al. (2007).

Figures
Figure 1
Gama Ayam Kambro breeding scheme. MoBPSweb (2021).

Figure 2
Accuracy of ฀(฀฀฀฀฀฀฀฀, ฀฀฀) from the Gama Ayam Kambro three selection model scenarios. MoBPSweb
(2021).

Figure 3
The F coecient and weekly kinship of the Gama Ayam Kambro three selection model scenario.
MoBPSweb (2021).

Figure 4
The observed phenotype of AFE from the Gama Ayam Kambro three selection model scenarios.
MoBPSweb (2021).

Figure 5
The observed phenotype of BW49D from the Gama Ayam Kambro three selection model scenarios.
MoBPSweb (2021).

Figure 6
The observed phenotype of BW56D from the Gama Ayam Kambro three selection model scenarios.
MoBPSweb (2021).

Figure 7
The observed phenotype of EN from the Gama Ayam Kambro three selection model scenarios.
MoBPSweb (2021).

Figure 8
The observed phenotype of FCR from the Gama Ayam Kambro three selection model scenarios.
MoBPSweb (2021).

Figure 9
The observed phenotype of FEML from the Gama Ayam Kambro three selection model scenarios.
MoBPSweb (2021).

Figure 10
The observed phenotype of TL from the Gama Ayam Kambro three selection model scenarios.
MoBPSweb (2021).
Supplementary Files
This is a list of supplementary les associated with this preprint. Click to download.
tbv08AFE.tif
tbv08BW49D.tif
tbv08BW56D.tif
tbv08EN.tif

tbv08FCR.tif
tbv08FEML.tif
tbv08TL.tif
SupplementalFileSIM08.pdf
swarautamacosts.tif