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Plumage colours Stability in Inbreed Pelung Chicken

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Hendry T.S.G. Saragih
Hendry T.S.G. Saragih
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Ayudha Bahana Ilham Perdamaian at Universitas Gadjah Mada
Ayudha Bahana Ilham Perdamaian
Sadiman
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Iwan Roosdianto
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Abstract and Figures

Pelung is one of the most importance local chicken in Indonesia. Genetic introgression and inbreeding depression were the major threat for local chicken gene pool. The objective of this research was to investigate the effect of serial inbreeding mating to plumage colours of Pelung chicken. Pure Pelung chicken which purchased from Cianjur sub-district was undergo full-sib mating through five generation. All offspring phenotypes was recorded. The results show gradual plumage phenotype change of inbreed Pelung chicken. Initially, adult male chicken had Black-red coloured as wildtype (WT) shifted to partridge and black-silver coloured in later generations. The current findings indicating that inbreeding made recessive traits to be expressed which some of them might had deleterious effect. Random mating should be maintained to preserve genetics stability of Pelung chicken
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Plumage colours Stability in Inbreed Pelung
Chicken
Hendry T.S.G. Saragih1*, Ayudha B.I. Perdamaian2, Sadiman3, Iwan Roosdianto2, Budi S.
Daryono2
1Laboratory of Animal Structure Development, Faculty of Biology, Universitas Gadjah Mada. Jl.
Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia
2Gama Chicken Research Team, Laboratory of Genetics and Breeding, Faculty of Biology,
Universitas Gadjah Mada. Jl. Teknika Selatan, Sekip Utara, Sleman 55281, Yogyakarta, Indonesia
3Pelung Chicken Farmer, Magetan, East Java, Indonesia
*Corresponding author: saragihendry@ugm.ac.id
Abstract. Pelung is one of the most importance local chicken in Indonesia.
Genetic introgression and inbreeding depression were the major threat for
local chicken gene pool. The objective of this research was to investigate the
effect of serial inbreeding mating to plumage colours of Pelung chicken.
Pure Pelung chicken which purchased from Cianjur sub-district was undergo
full-sib mating through five generation. All offspring phenotypes was
recorded. The results show gradual plumage phenotype change of inbreed
Pelung chicken. Initially, adult male chicken had Black-red coloured as
wildtype (WT) shifted to partridge and black-silver coloured in later
generations. The current findings indicating that inbreeding made recessive
traits to be expressed which some of them might had deleterious effect.
Random mating should be maintained to preserve genetics stability of
Pelung chicken
1 Introduction
Indonesia is among world’s largest chicken breeds biodiversity spot. Indonesia has 25 local
breeds where Cemani [1], Sumatra [2], Kedu [2], Bantam/Kate [3], Nunukan [4], and Pelung
[5–8] are the most studied breeds. In Indonesia, exotic chicken both commercial lines (broiler
and layer) and ornamental breeds are sold freely. These made both genetics introgression and
inbreeding depression are the major threads for native Indonesian chicken breeds.
Uncontrolled interbreeding threats the genetics identity of local breed. Whole genome
sequencing shows the lost genetics identity of Black Sumatra and Black Java chicken breeds
in US [2]. Introgression of broiler chicken into local chicken was found in China [9].
Crossbreeding of layer chicken to Bangkok chicken for derived meat-type chicken [10] is
massively practiced in Indonesia. Male layer chicken also sold as meat-type chicken. These
actions increase the possibility of stock leaks to rural areas and mating to pure breeds
ultimately decreasing population size of local breeds. Hybrid chicken might transmit
pathogen to local breed as well.
© The Authors, published by EDP Sciences. This is an open access article distributed under the terms of the Creative Commons
Attribution License 4.0 (http://creativecommons.org/licenses/by/4.0/).
BIO Web of Conferences 33, 01005 (2021)
ICAVESS 2021
https://doi.org/10.1051/bioconf/20213301005
On the other hand, small flock and intended inbreeding will increase inbreeding
Coefficient (IC) lead to vulnerability. To date, most stringent breeding programme for local
chicken was reported in Pelung breed and IC reach 0.57 at selected individual [11].
There are limited studies related to genetics and phenotypic marker of introgession and
inbreeding depression in Indonesian chicken. This study aims to investigate the effect of
inbreeding to the phenotypes of Pelung chicken.
2 Materials and Methods
2.1 Chicken and rearing
This research was conducted from 2007 to 2021 in Magetan, East Java, Indonesia. Adult
male and female Pelung chicken which purchased from Cianjur, West Java Province were
reared in pens. All chicken were given free access to feed (BR1, Japfa, Indonesia) and water
and natural photoperiodization. All eggs were naturally incubated by hen. Hatched Day olds
chick (DOC) were feed by commercially available starter feed (BR1, japfa, Indonesia).
2.2 Chicken mating scheme
Adult male and female Pelung chicken were naturally mated in pens. All offspring were
mated to their sibling (full-sib). Sibling mating were practiced through five generation
(Fig.1.).
Fig. 1. The full-sib breeding scheme of Pelung chicken through five generation. Black tetragonal
indicated male whereas black circle indicated female Pelung.
3 Result and Discussion
To date, this was the first attempt to conduct five generation inbreeding in Pelung chicken.
Inbreeding practice in this study led recessive traits related to plumage, beak and shank
colours to be expressed (Table 1.; Fig.2.). The first generation (G1) of Pelung possess black
beak, black shank, and black plumage combined with secondary red plumage. This trait stated
as wildtype (WT) because resemble of red jungle fowl (Gallus gallus) plumage. All second
generation (G2) of inbreed Pelung still expressed the wildtype plumage. In the third
generation (G3), flock began to show the variety of their plumage. Brown (eb) and birch (Er)
plumage were recorded. In the fourth generation (G4), the plumage distribution in the flock
2
BIO Web of Conferences 33, 01005 (2021)
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https://doi.org/10.1051/bioconf/20213301005
was brown (eb). In the fifth generation (G5), the majority of Pelung plumage was brown (eb)
similar to the fourth generation.
Fig. 2. The plumage phenotype of adult male and female Pelung chicken through five generation of
inbreeding.
In this research, five generation of inbreeding confirmed the theory of dominant-recessive
model of plumage colours. Wildtype (Black with red secondary plumage colours; e+) was
dominant over brown (eb; ebc) and birch (Er) [12,13]. Wildtype plumage colour was
eliminated at fifth generation (G5) aftermath inbreeding in small flock (Table 1.).
Table 1. The phenotype percentage of Pelung through five generation of inbreeding
Parameters
Phenotype
(Genotype)
Phenotype percentage (%)
G1
(n: 2)
G2
(n: 10)
G3
(n: 10)
G4
(n: 10)
G5
(n: 10)
Comb type
Single (WT; rrpp)
100
100
100
100
100
Beak Color
Black
Light yellow
Pale yellow
White
100
-
-
-
100
-
-
-
-
50
50
-
-
50
50
-
50
50
-
-
Eye color
Dark brown
100
100
100
100
100
Plumage
color
Black (WT; e+)
Birch (Er)
Brown (eb)
Light brown (ebc)
100
-
-
-
100
-
-
-
-
40
40
20
-
-
100
-
-
-
100
-
Secondary
plumage
color
Red (WT)
Light Red
Silver
Brown
100
-
-
-
100
-
-
-
-
25
50
25
-
50
-
50
-
-
-
100
Shank color
Yellow
Black (wwD-)
Green (WT; W-D-
)
White
-
100
-
-
-
100
-
-
-
50
50
-
25
25
50
-
-
-
100
-
3
BIO Web of Conferences 33, 01005 (2021)
ICAVESS 2021
https://doi.org/10.1051/bioconf/20213301005
In this research, the authors find abnormal pial formation in the adult male of fifth
generation (G5). The abnormal pial was similar to adult female Pelung indicate several gene
not working correctly. The normal type of inbreeded Pelung pial must be single (rprp). This
result should be investigated further with molecular approach to elucidate the molecular
background.
Figure 3. Adult male fifth generation (G5) of Pelung show different type of pial
Pelung is considered as specific local chicken which easily recognised by its long crowing
character [7,14,15]. Unlike Kedu and Sentul chicken breed which recognised by its standard
plumage colours, Pelung exist with many plumage colours types [16]. Blue colour in Sentul
plumage and Black or brown colours in Black Kedu and Brown Kedu chicken breeds
plumage [17]. Pelung had all types of plumage colours. However, wildtype plumage had
possibility to carries brown and birch plumage allels. Based on recent results, recessive
plumage traits is marker for chicken with high inbreeding experience.
Unlike its red jungle fowl predecessor, domestic chicken exhibit diverse types of plumage
colours. The plumage colour variety rise through the domestication process [18].
Local chicken suffered from admixture and decreasing population size and not only
occurred in Indonesia but also at other countries [19].
4 Conclusion
Based on recent results, Pelung chicken with wildtype plumage (black combined with red
secondary plumage) had possibility to carry recessive brown plumage colour traits.
Inbreeding might erase wildtype plumage traits in the flock. Recessive plumage traits are
marker for chicken with high inbreeding experience.
The authors acknowledge Ministry of research and higher education for providing INSINAS research
grant. The authors would like to thank the University Farm (Pusat Inovasi Agroteknologi; PIAT)
Universitas Gadjah Mada for providing breeding facility.
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5
BIO Web of Conferences 33, 01005 (2021)
ICAVESS 2021
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... Indonesia merupakan salah satu negara yang memiliki keanekaragaman ayam lokal terbesar di dunia (Saragih et al., 2021). Terdapat sekitar 31 jenis ayam lokal Indonesia yang tersebar di berbagai daerah (Hidayat & Asmarasari, 2015). ...
... Salah satu cara yang dilakukan adalah dengan menyilangkan antara jenis ayam lokal pilihan yang dapat menghasilkan keturunan dengan potensi pertumbuhan lebih cepat. Ayam lokal yang paling banyak dipelajari antara lain, ayam Cemani, Sumatera, Kedu, Banten/Kate, Nunukan, dan Pelung (Saragih et al., 2021). Berdasarkan penelitian Daryono et al. (2010) persilangan antara ayam jantan Pelung dengan ayam betina Cemani dapat menghasilkan anakan dengan rerata berat badan rata-rata pada minggu ke-7 sebesar 532 ± 39,294 g. ...
... Walaupun memiliki fenotipe yang bervariasi, tetapi anakan tersebut memiliki karakter seperti ayam lokal (Gambar 3; Gambar 4; Gambar 5). Menurut hasil penelitian Saragih et al. (2021) ayam Pelung memiliki warna bulu yang sangat variatif. Penelitian lebih lanjut diperlukan untuk menemukan karakter yang khas dari ayam Supel hasil perkawinan ayam betina Jawa super dengan ayam jantan Pelung. ...
Performa Anakan Ayam Supel (Super Pelung) Hasil Persilangan Indukan Ayam Betina Jawa Super dan Ayam Jantan Pelung [Gallus gallus gallus, (Linnaeus 1758)]
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  • May 2016
  • BMC GENOMICS
Background More than 2,500 breeds of chicken are reared throughout the world as a source of eggs or meat and as pets. The primary ancestor of the present domestic chicken is widely believed to be the red junglefowl, although genetic contributions from other junglefowls cannot be excluded entirely. The reference genome for chicken was obtained from a red junglefowl, the genetic purity of which has been debated. There is, at present, insufficient data to resolve these interesting issues. Results In this study, we performed whole-genome sequencing to compare various species and breeds of chicken, including wild red and green junglefowl, as well as the Indonesian native chickens Sumatera and Kedu Hitam and their respective descendants, the American Black Sumatra and Black Java. The data indicate that wild junglefowls have retained their genetic identity, but the Indonesian and American breeds have not. The Black Sumatra and Black Java are now closely related to each other, suggesting loss of genetic identity after export to the United States. In addition, the results indicate that the red junglefowl used as reference genome is more closely related to domestic chickens and apparently different from other wild red junglefowls. Conclusions This study illuminates the genetic and phylogenetic relationships among these species. It provides a framework for genetic studies in wild junglefowls and native and domestic chicken breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2652-z) contains supplementary material, which is available to authorized users.
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A deleted retroviral insertion at the ev21-K complex locus in Indonesian chickens
Article
Full-text available
  • Jun 1997
Very poor feather development has been observed in chickens of the Nunukan strain, originating from Indonesia. The wing of the newly hatched chick does not show any primary or covert feathers; this phenotype will be referred to as very-late feathering (VLF). As adults, chickens are feathered but tail feathers are short and fragile. An experimental population was set up at the National Institute of Agronomic Research (INRA), Jouy-en-Josas, from one Nunukan male and four Nunukan females. Preliminary observations did not support the hypothesis of a sex-linked dominant mode of inheritance for the VLF phenotype. A restriction fragment length polymorphism (RFLP) study using five restriction enzymes and two probes, RAV-2 and endogenous virus (ev) ev21-int specific for the endogenous viral locus ALVE21, showed the presence of the expected 3' junction fragments for the ev21 occupied site but failed to reveal the expected 5' junction fragments for ev21 in Nunukan chickens. The unoccupied site corresponded to the ev21 unoccupied repeat (UR) of type a (URa). A deletion in the 5' region of the provirus and of the insertion site was indicated by the RFLP analysis and confirmed by a PCR study. Primers were designed in order to amplify a 5' junction fragment specific to the modified ev21 found in the Nunukan chickens. The sequence of this amplified product showed that the deletion started 652 bp upstream of the insertion site of ev21 and ended within the pol gene of the viral genome. This deletion represents a new allele, OSD, at the ev21 insertion site (locus ALVE21), that appears insufficient to produce a complete virus. Current data do not show a clear causal relationship between OSD and the VLF phenotype. The presence of OSD may be required but is not in itself sufficient to obtain the VLF phenotype. The genetic relationships between OSD and the altered feathering phenotype of Nunukan chickens will be investigated further in families segregating for the VLF phenotype, using the locus-specific PCR test developed as part of this study.
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  • Jan 2017
  • PLOS ONE
  • 4
  • A B Dharmayanthi
  • Y Terai
  • S Sulandari
  • M S A Zein
  • T Akiyama
  • Y Satta
A.B. Dharmayanthi, Y. Terai, S. Sulandari, M.S.A. Zein, T. Akiyama, Y. Satta. PLoS One. 12, 4 (2017)
  • Jan 2016
  • BMC GENOMICS
  • 1
  • M Ulfah
  • R Kawahara-Miki
  • A Farajalllah
  • M Muladno
  • B Dorshorst
  • A Martin
M. Ulfah, R. Kawahara-Miki, A. Farajalllah, M. Muladno, B. Dorshorst, A. Martin. et al. BMC Genomics. 17, 1 (2016).
  • Jan 2017
  • MOL BIOL EVOL
  • M S Wang
  • N O Otecko
  • S Wang
  • D D Wu
  • M M Yang
  • Y L Xu
M.S. Wang, N.O. Otecko, S. Wang, D.D. Wu, M.M. Yang, Y.L. Xu, et al. Mol Biol Evol. 34 (2017).
  • Jan 1997
  • M Tixier-Boichard
  • A Boulliou-Robic
  • M Morisson
  • G Coquerelle
  • P Horst
  • B Benkel
M. Tixier-Boichard, A. Boulliou-Robic, M. Morisson, G. Coquerelle, P. Horst, B. Benkel B. Poult Sci. 76 (1997).