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Phenotypic characterization of local female duck populations in Indonesia
Journal of Asia-Pacific Biodiversity xxx (xxxx) xxx
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Original Article
Phenotypic characterization of local female duck populations in Indonesia Dyah Maharani a, *, Dwi N.H. Hariyono a, Daniel D.I. Putra a, Jun-Heon Lee b, Jafendi H.P. Sidadolog a a b
Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history: Received 12 November 2018 Received in revised form 17 March 2019 Accepted 3 July 2019 Available online xxx
Information on phenotypic traits is a prerequisite in animal genetic resource conservation and improvement. Phenotypic characteristics of 180 Indonesian female ducks collected from six populations (Alabio, Bayang, Magelang, Pegagan, Pitalah, and Rambon ducks) were studied. Data on qualitative traits were analyzed with descriptive statistics (percentages), while one-way analysis of variance was used to analyze the effect of populations on quantitative traits observed. The results revealed that the predominant plumage colors of the neck, breast, abdomen, back, secondary wings, primary wings, and thigh were brown (49.74%), brown (34.03%), brown (31.94%), brown (50.26%), dark brown (25.13%), light brown (35.08%), and brown (31.94%), respectively. The dominant bill and web color were black (77.49%) and dark brown (48.17), respectively. Variations were also found in quantitative morphological traits. The principal component analysis showed two to four principal components extracted from the factor analysis with varimax rotation, which accounted for 57.33%, 66.26%, 64.43%, 54.66%, and 77.44% of the total variance in the original variables for Alabio, Magelang, Pegagan, Pitalah, and Rambon ducks, respectively. Generally, the first factor in each population had high loadings on beak width. The observed phenotypic diversity in Indonesian local ducks could be useful in designing breeding programs and selection. Ó 2019 National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA), Publishing Services by Elsevier. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Local ducks Phenotypic characterization Qualitative traits Quantitative traits
Introduction In Indonesia, populations of a number of local ducks spread across the Indonesian archipelago are included as a part of animal genetic resources (AnGRs) (Hariyono et al 2019). They are mostly reared under traditional scavenging management system by villagers in various agroclimatic conditions. The duck only represents 2.34% of the total poultry population, and its current population is about 49.7 billion heads in 2017 (Ditjennak 2017). Despite the low contribution to the total poultry production, the duck in Indonesia has a vital role in either improving nutritional status and incomes or reducing hunger and food insecurity among households, especially in rural areas. Implementing appropriate strategies of the world’s AnGRs is an ever-greater challenge for the international community (FAO 2007). Current global AnGR status is mainly undergoing threats
* Corresponding author. Tel.: þ62 274 513363; fax: þ62 274 521578. E-mail address: [email protected] (D. Maharani). Peer review under responsibility of National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA).
because of the rapid transformation of the agricultural system, and by implication, decisions on its management should be appropriate. Appropriate utilization of a livestock species or breed is dependent on accurate understanding of its unique characteristics differentiating it from other breeds or species (Oguntunji and Ayorinde 2015). Breed characterization is a prerequisite in the urgent task of genetic resource conservation (Latshaw and Bishop 2001; FAO 2012). Breed characterization based on either phenotypic traits or genetic characteristics provides significant information on the sustainable management of the local breeds and a reasonable representation of genetic differences among breeds (Yakubu et al 2011). In addition, the current trend on the improvement of indigenous animals relies on the variations (within and between breeds) of certain traits, and such a variation is a great opportunity for selection and breeding programs. Phenotypic characterization has been used by researchers to describe and compare morphological characteristics of indigenous poultry species in different agroecological zones. For instance, phenotypic characterization was conducted on Indian ducks (Veeramani et al 2014), Ethiopian chickens (Moreda et al 2014),
https://doi.org/10.1016/j.japb.2019.07.004 pISSN2287-884X eISSN2287-9544/Ó 2019 National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA), Publishing Services by Elsevier. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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Nigerian chickens (Egena et al 2014; Rotimi et al 2016), and Nigerian ducks (Yakubu et al 2011; Ogah and Kabir 2014; Oguntuji and Ayorinde 2015). In general, all of these studies found a considerable phenotypic diversity, including body weight, body size, and plumage and skin color, which are useful for breed or population identification and classification. Limited studies regarding breed characterization of the local ducks in Indonesia have been carried out, either for phenotypic (Setioko et al 2005; Sopiyana et al 2006; Suryana and Hardjosworo 2011; Wulandari et al 2015) or for genetic characterization (Rahayu et al 2015; Maharani et al 2017; Hariyono et al 2019). Generally, the phenotypic diversity of Indonesian local duck populations is yet to be investigated in detail. Hence, the present work was carried out to characterize the local duck populations in Indonesia based on the phenotypic traits. Material and methods Location of the study and experimental animals
further tested by the use of Duncan’s multiple range test. The statistical model used was as follows: Yij ¼ mþGi þeij where Yij is the individual body measurement, m is the overall mean, Gi is the fixed effect of the genotype, and eij is the random error. Principal component analysis (PCA) representing a linear combination of the available variables into a factor or component was determined separately for each duck population. Kaiser-MeyerOlkin (KMO) measures of sampling adequacy and Bartlett’s test of sphericity were determined to test the validity of the factor analysis of each of the data sets. These indicators were used to test whether the partial correlations among quantitative traits were small. A KMO measure of 0.50 and more was considered adequate (Kaiser 1974). Therefore, the KMO values of the data set for each duck population with less than 0.50 were excluded for PCA. PCA is a method for transforming the variables in a multivariate data set X1, X2, .Xp into new uncorrelated variables Y1, Y2, .Yp, which account for decreasing proportions of the total variance of the original variables (Everitt et al 2001) defined as follows:
Data were obtained from 180 female ducks (12e18 months of age) randomly selected within six Indonesian local duck populations. These comprised 30 individuals each from Alabio, Bayang, Magelang, Pegagan, Pitalah, and Rambon duck populations. The sites of this study were in Pelaihari district (latitude 3 520 59.8800 S and longitude 114 520 0.1200 E) of South Borneo province (for Alabio duck), Magelang district (latitude 7 250 3900 S and longitude 110 90 42.8400 E) of Central Java (for Magelang duck), Cirebon district (latitude 6 450 50.7600 S and longitude 108 280 44.0400 E) of West Java (for Rambon duck), Ogan Ilir district (latitude 3101200 S and longitude 104 280 4800 E) of South Sumatra (for Pegagan duck), Pesisir Selatan district (latitude 1210000 S and longitude 100 3401.200 E) of West Sumatra (for Bayang duck), and Tanah Datar district (latitude 0 270 000 S and longitude 100 340 58.800 E) of West Sumatra (for Pitalah duck). All duck populations (except the Alabio duck) were kept under the traditional scavenging system by local farmers. For the Alabio duck, it was kept under a controlled breeding system by the Centre of Excellence for Livestock Breeding and Forages (BPTUHPT) Pelaihari, in which the selection program had been conducted for a particular trait. All the duck breeds investigated in the present study are included as national germplasm by the Indonesian Ministry of Agriculture.
with coefficients being chosen so that, y1, y2, ...yp account for decreasing proportions of the total variance of the original variables x1, x2, ... xp. The PCA was performed using SPSS (2001) version 16 (SPSS Inc., Chicago, IL, USA).
Traits measured
Bill color
All animals were characterized for the qualitative and quantitative traits following the descriptors by Cuesta (2008) and Francesch et al (2011). The qualitative traits observed were bill color, web color, and plumage color (i.e. neck, breast, abdomen, back, secondary wings, primary wings, and thigh). The quantitative traits recorded were beak width, beak length, neck length, neck diameter, shank length, toe length, foot width, and claw length. All quantitative traits were taken by measuring tape and slide calipers and measured in centimeters. We visually appraised and identified the qualitative traits. All measurements were taken by the same person to avoid individual variations.
The most predominant bill color across the investigated duck populations was black (77.49%). However, no variation in bill color was observed in the Alabio duck population, with yellow being the only bill color in this population. Similarly, the observed highest frequency of black bill in this study agrees with the report of Baghel (2007) on Muscovy ducks and Oguntunji and Ayorinde (2015) on Nigerian ducks. A previous study by Chia and Momoh (2012) observed three variants (all black, black-yellow, and black-pink) of bill color in North Central Nigerian Muscovy ducks.
Statistical analysis
Eight variants for neck color (white, brown, black, ash, ash brown, ash black, light brown, and dark brown) were observed across the duck populations. Brown neck had the highest frequency (49.74%), whereas white neck had the lowest frequency (1.05%). A published study by Suryana et al (2011) reported five variants (black, white-gray, black-gray, brown, and brown-gray) found for bill color in Alabio ducks (Suryana et al 2011), which was in contrast to the present study. Furthermore, pink-white is the most common
Data on qualitative traits were analyzed using descriptive statistics and compared as percentages. Coefficient of variation for the data on quantitative traits at various duck populations was performed. One-way analysis of variance was used to analyze the effect of the genotype of the duck populations on the quantitative traits, and significantly different means (P<0.05) among populations was
y1 ¼ a11x1 þ a12x2 þ .... þ a1pxp y2 ¼ a21x1 þ a22x2 þ ....þ a2pxp yp ¼ ap1x1 þ ap2x2 þ .... þ appxp
Results and discussion Variation in qualitative traits Descriptive statistics for qualitative traits such as bill color, web color, and plumage color (i.e. neck, breast, abdomen, back, secondary wings, primary wings, and thigh) among the six local duck populations in Indonesia are presented in Table 1.
Neck color
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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Table 1. Variation of qualitative traits among Indonesian local ducks. Trait
Color (%)
Alabio
Magelang
Rambon
Pegagan
Pitalah
Bayang
Overall
Bill color
Yellow Black Brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown Yellow Light Brown Dark brown
100.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00
2.44 70.73 0.00 4.88 63.41 4.88 0.00 0.00 0.00 0.00 0.00 2.44 65.85 4.88 0.00 0.00 0.00 0.00 0.00 12.20 60.98 0.00 0.00 0.00 0.00 0.00 0.00 2.44 70.73 0.00 0.00 0.00 0.00 0.00 0.00 2.44 0.00 12.20 0.00 0.00 0.00 0.00 58.54 9.76 0.00 0.00 0.00 0.00 0.00 63.41 0.00 17.07 53.66 2.44 0.00 0.00 0.00 0.00 0.00 2.44 63.41 7.32
0.00 73.17 0.00 0.00 70.73 2.44 0.00 0.00 0.00 0.00 0.00 2.44 0.00 2.44 0.00 0.00 0.00 34.15 34.15 7.32 63.41 2.44 0.00 0.00 0.00 0.00 0.00 2.44 68.29 2.44 0.00 0.00 0.00 0.00 0.00 2.44 0.00 2.44 0.00 0.00 0.00 34.15 34.15 0.00 0.00 2.44 0.00 0.00 0.00 51.22 19.51 2.44 0.00 2.44 0.00 0.00 0.00 12.20 56.10 4.88 0.00 68.29
0.00 70.73 2.44 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 29.27 43.90
0.00 73.17 0.00 0.00 24.39 48.78 0.00 0.00 0.00 0.00 0.00 2.44 19.51 51.22 0.00 0.00 0.00 0.00 0.00 0.00 24.39 48.78 0.00 0.00 0.00 0.00 0.00 0.00 21.95 51.22 0.00 0.00 0.00 0.00 0.00 0.00 21.95 51.22 0.00 0.00 0.00 0.00 0.00 0.00 26.83 46.34 0.00 0.00 0.00 0.00 0.00 0.00 21.95 51.22 0.00 0.00 0.00 0.00 0.00 19.51 21.95 31.71
0.00 73.17 0.00 0.00 73.17 0.00 0.00 0.00 0.00 43.90 29.27 0.00 0.00 0.00 0.00 0.00 0.00 43.90 29.27 2.44 0.00 0.00 0.00 0.00 0.00 46.34 24.39 0.00 0.00 0.00 0.00 0.00 0.00 43.90 29.27 0.00 0.00 0.00 0.00 0.00 0.00 48.78 24.39 0.00 0.00 0.00 0.00 0.00 0.00 48.78 24.39 2.44 0.00 0.00 0.00 0.00 0.00 43.90 26.83 0.00 0.00 73.17
16.23 77.49 0.52 1.05 49.74 12.04 21.47 5.76 4.19 9.42 6.28 1.57 34.03 12.57 5.76 5.76 4.19 16.75 13.61 20.42 31.94 10.99 5.76 5.76 4.19 9.95 5.24 1.05 50.26 11.52 5.76 5.76 4.19 9.42 6.28 1.05 4.71 14.14 21.47 5.76 4.19 17.80 25.13 2.09 5.76 10.47 21.47 5.76 4.19 35.08 9.42 4.71 31.94 12.04 5.76 5.76 4.19 12.04 17.80 21.47 24.61 48.17
Neck color
Breast color
Abdomen color
Back color
Secondary wings
Primary wings
Thigh color
Web color
bill color, whereas slate gray is the least common bill color in Muscovy ducks in Egypt (FAO 2009). Web color Dark brown was the most common web color, with 48.17%, followed by light brown with 24.61%; yellow was the least common web color, with 21.47%. However, yellow web has the highest proportion in the Alabio duck population, with 100%. Similarly, the highest frequency of yellow web was also reported by Oguntunji
and Ayorinde (2015) in Nigerian Muscovy ducks. Baghel (2007) reported four variants (black, yellow black with black spots, cream with greyish spots, and pale yellow with algae green spots) of web color in Muscovy ducks. Plumage color Figure 1 represents plumage color variation among Indonesian local duck populations. The predominant plumage color of each observed qualitative trait, that is, neck (brown, 49.74%), breast
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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Figure 1. The plumage color variation of Indonesian local duck populations: A, Alabio duck; B, Bayang duck; C, Magelang duck; D, Pegagan duck; E, Pitalah duck; F, Rambon duck.
(brown, 34.03%), abdomen (brown, 31.94%), back (brown, 50.26%), secondary wings (dark brown, 25.13%), primary wings (light brown, 35.08%), and thigh (brown, 31.94%), was found across the duck populations. The results are in agreement with the findings of the studies by Sopiyana et al (2006) and Setioko et al (2005) who reported that variation in plumage color was observed among Indonesian duck populations kept under the traditional scavenging system. In contrast, no variation for qualitative traits was detected in Alabio ducks, an investigated duck population kept under the controlled breeding system. As reported by Suryana et al (2011), low variation was also observed for the plumage color in the Alabio duck population, although the studied population was kept by traditional farmers in the semi-intensive breeding system. Interestingly, a specific attribute was observed in the Magelang duck population. It has a neck ring with white color, and this attribute is absent in other duck populations, suggesting that this characteristic is specific to Magelang ducks. Previously, Rahayu et al (2015) observed 11 kinds of plumage color pattern in Magelang ducks; those are Jarakan Polos, Bosokan, Kalung Ombo, Kalung Ciut, Gambiran, Jarakan Kalung, Jowo Polos, Klawu Borok, Cemani, Wiroko, and Putih Polos. The observed plumage color variation in Indonesian duck populations implies an opportunity for future selection in the breeding program of ducks. In general, the six Indonesian local duck populations can be classified into three agroecological conditions, that is, swamplands (Alabio and Pegagan), lowlands (Magelang, Rambon, and Bayang), and highlands (Pitalah). Based on the agroecological conditions, the duck population (Pitalah) that was reared in the highland area has predominantly black plumage color, whereas the duck populations
reared in the remaining agroecological conditions have relatively light brown plumage color. Interspecific variation in plumage color was also found among birds, indicating an adaptive response to variation in light environments across habitats (McNaught and Owens 2002). Habitats and climate differences in selective pressures may well be responsible for producing color variation in species with broad ecological niches, and both visual and physiological effects (functions) of color pigmentation might be involved (Gaelotti et al 2003). In addition, genetic factor affects plumage color variation, mediated by multiple loci (Evans and Sheldon 2012). In general, variation for qualitative traits was observed in Indonesian local duck populations, such as in Magelang, Rambon, Pegagan, Pitalah and Bayang duck populations, kept under the traditional scavenging system by many villagers, indicating the lack of selection directed toward the choice of plumage color. Variation in quantitative traits The mean, standard errors, and coefficients of variation of quantitative traits measured among Indonesian local ducks are summarized in Table 2. Variation was found for all quantitative traits measured, depicted by significant differences between means (P<0.05) among studied duck populations for each trait. The overall mean values for beak width, beak length, neck length, neck diameter, shank length, toe length, foot width, and claw length of the local duck populations in Indonesia were 2.770.01 cm, 5.920.03 cm, 16.040.10 cm, 1.600.01 cm, 6.450.03 cm, 6.310.05 cm, 7.000.04 cm, and 1.150.14 cm, respectively.
Table 2. Mean, standard errors (SEs), and coefficients of variation (CVs) of quantitative traits measured among Indonesian local duck populations. Trait
Beak width (cm) Beak length (cm) Neck length (cm) Neck diameter (cm) Shank length (cm) Toe length (cm) Foot width (cm) Claw length (cm) abcde
Alabio
Magelang
Rambon
Pegagan
Pitalah
Bayang
Overall mean
MeanSE
CV
MeanSE
CV
MeanSE
CV
MeanSE
CV
MeanSE
CV
MeanSE
CV
2.760.08c 5.920.05a 17.140.14a 1.530.09c 6.610.04b 6.140.05c 7.440.05a 1.440.02a
2.33 5.21 4.76 6.01 3.58 4.34 3.98 8.79
2.820.13ab 5.950.33d 14.831.21d 1.660.21a 6.270.47d 7.230.66a 6.560.53d 1.230.10b
4.43 5.58 8.15 12.38 7.54 9.12 8.05 7.74
2.650.09d 6.090.35c 15.451.24c 1.580.09bc 6.840.35a 6.140.40c 6.750.45cd 1.100.08c
3.46 5.81 8.02 5.89 5.09 6.54 6.67 7.46
2.820.14ab 6.010.29b 16.511.23a 1.700.10a 6.420.30cd 6.000.33cd 7.050.64b 1.090.08c
4.96 4.91 7.43 5.98 4.74 5.56 9.11 7.54
2.680.11d 5.600.64b 16.401.26ab 1.560.10bc 5.980.27e 5.830.35d 6.890.44bc 0.950.11d
3.97 11.50 7.65 6.65 4.53 5.98 6.35 11.97
2.860.12a 5.970.26bc 15.901.21bc 1.600.11b 6.520.29bc 6.540.33b 7.320.40a 1.090.10c
4.17 4.37 7.59 6.77 4.42 5.01 5.50 9.59
2.770.01 5.920.03 16.040.10 1.600.01 6.450.03 6.310.05 7.000.04 1.150.14
Mean in same rows with different superscripts are significantly different (P<0.05).
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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The highest mean for beak width (2.860.12 cm) was observed in Bayang ducks, while the lowest mean was observed in Rambon ducks (2.650.09 cm). For beak length, the values ranged between 5.600.64 cm (Pitalah ducks) and 6.090.35 cm (Pegagan ducks). For neck length, a mean value of 17.140.14 cm (Alabio ducks) was found to be the highest, while that of 14.831.21 (Magelang ducks) was found to be the lowest. For neck diameter, Pegagan ducks had the highest mean value (1.700.10 cm), whereas Alabio ducks had the lowest mean value (1.530.09). Mean values of shank length varied from 5.980.27 cm (Pitalah ducks) to 6.610.04 cm (Alabio ducks). For toe length, a range value from 5.830.35 cm (Pitalah ducks) to 7.230.66 cm (Magelang ducks) was observed. Mean values for foot width ranged between 6.560.53 cm (Magelang ducks) and 7.440.05 cm (Alabio ducks). The last predictor for quantitative traits was claw length, in which the highest mean value was observed in Alabio ducks (1.440.02 cm), whereas the lowest mean value was found in Pitalah ducks (0.950.11). The overall mean values for beak width and beak length observed in this study were higher than those reported by Setioko et al (2005) in Cirebon ducks (beak width ¼ 2.35 cm; beak length ¼ 5.55 cm). Wulandari et al (2015) observed a mean value of 7.830.41 for beak length in Magelang ducks, which was higher than that obtained in this study. The overall mean values for shank length and beak length were comparable with those reported by Setioko et al (2005) in Cirebon and Turi ducks. For neck length, the overall mean value of 16.040.10 cm obtained in this study was higher than that of 13.190.17 cm reported in Indian ducks (Veeramani et al 2014). Such variation provides an opportunity for future genetic improvement among and within duck populations. Quantitative traits such as body measurements are useful indicators that are used to describe a breed or population along with qualitative traits and agroecological conditions the breeds inhabited. Principal component analysis PCA allows assessment of overall variance and defines the variables with greater discriminatory power between groups. KMO measure of sampling adequacy computed for Alabio, Bayang, Magelang, Pegagan, Pitalah, and Rambon ducks was found to be 0.73, 0.44, 0.54, 0.63, 0.66, and 0.56, respectively. The significance of the correlation matrices tested with Bartlett’s test of sphericity for all quantitative traits in Alabio (c2 ¼68.42; P < 0.00), Magelang (c2 ¼60.36; P < 0.00), Pegagan (c2 ¼47.54; P < 0.01), Pitalah (c2 ¼57.34; P < 0.00), and Rambon (c2 ¼60.03; P < 0.00) ducks provided support for the validity of the factor analysis of the data sets. Nonsignificance of Bartlett’s test of sphericity for body measurements was only observed in Bayang (c2 ¼37.24; P < 0.11) ducks. Hence, we excluded Bayang ducks for PCA. The eigenvalues of the total variance, the rotated component matrix, and communalities for all quantitative traits in the investigated duck populations are presented in Table 3. The communalities representing estimates of the variance in each variable observed ranged between 0.291 and 0.709 in Alabio, 0.347 and 0.738 in Bayang, 0.413 and 0.896 in Magelang, 0.402 and 0.846 in Pegagan, 0.292 and 0.740 in Pitalah, and 0.633 and 0.846 in Rambon ducks. The PCA showed two to four principal components extracted from the factor analysis with varimax rotation. In Alabio ducks, the principal components by PCA which accounted for 40.192% (PC1) and 17.137% (PC2) of the total variance in the original variables measured, with eigenvalues of 3.125 and 1.371, respectively, were identified. PC1 had high loadings on beak length (0.778), neck diameter (0.758), and foot width (0.797), whereas PC2 had high loadings on neck length (0.836). In Magelang ducks, three principal components were extracted, which accounted for 66.26% of the
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Table 3. Eigenvalues, percentage of total variance, rotated component matrix, and communalities of quantitative traits observed in Indonesian local duck populations. Trait Alabio Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Magelang Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Pegagan Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Pitalah Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Rambon Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance
PC1
PC2
PC3
PC4
Communalities
0.733 0.778 0.102 0.758 0.532 0.666 0.797 0.354 3.125 40.192
0.200 0.321 0.836 0.230 0.497 0.217 0.130 0.407 1.371 17.137
e e e e e e e e e e
e e e e e e e e e e
0.578 0.708 0.709 0.628 0.530 0.490 0.651 0.291
0.776 0.731 0.730 0.245 0.267 0.484 0.783 0.344 2.766 34.571
0.154 0.345 0.021 0.533 0.511 0.727 0.192 0.344 1.372 17.153
0.288 0.005 0.130 0.405 0.284 0.148 0.369 0.812 1.163 14.536
e e e e e e e e e e
0.709 0.652 0.550 0.509 0.413 0.784 0.787 0.896
0.575 0.572 0.701 0.458 0.602 0.717 0.498 0.549 2.786 34.819
0.619 0.575 0.286 0.573 0.192 0.443 0.026 0.014 1.358 16.971
0.097 0.433 0.161 0.410 0.181 0.037 0.697 0.317 1.011 12.638
e e e e e e e e e e
0.723 0.846 0.598 0.706 0.432 0.712 0.735 0.402 e e
0.643 0.085 0.370 0.629 0.843 0.793 0.539 0.647 3.001 37.508
0.226 0.772 0.701 0.326 0.171 0.216 0.026 0.223 1.372 17.151
e e e e e e e e e e
e e e e e e e e e e
0.465 0.603 0.629 0.502 0.740 0.675 0.292 0.468
0.857 0.253 0.380 0.498 0.187 0.733 0.860 0.303 2.594 32.421
0.078 0.395 0.226 0.572 0.109 0.386 0.241 0.787 1.377 17.214
0.036 0.447 0.073 0.322 0.872 0.021 0.042 0.339 1.188 14.852
0.322 0.462 0.788 0.124 0.157 0.215 0.077 0.052 1.032 12.905
0.846 0.633 0.821 0.694 0.832 0.733 0.804 0.828
total variance in the original variables, with eigenvalues of 2.766, 1.372, and 1.163, respectively. PC1 had high loadings on beak width (0.776) and foot width (0.783) and negative loadings on claw length (-0.344). Negative loadings were observed for beak length (-0.345), neck diameter (-0.533), and shank length (-0.511) in PC2. PC3 had only high loadings on claw length (0.812). In Pegagan ducks, three principal components were extracted after varimax rotation, which accounted for 64.43% of the total variance in the original variables, with eigenvalues of 2.786 (PC1), 1.358 (PC2), and 1.011 (PC3), respectively. PC1 had high positive loadings on all traits measured, ranging from 0.458 for neck diameter to 0.717 for toe length. PC2 had high loadings on beak length (0.772), whereas PC3 had no high loadings on all traits measured. However, PC3 had negative loadings on beak length, neck length, neck diameter, and toe length. In
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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Pitalah ducks, two principal components were identified with eigenvalues of 3.001 (PC1) and 1.372 (PC2), respectively. The two factors accounted for 54.66% of the total variance present in original measurements. PC1 had high loadings on shank length (0.843) and toe length (0.793), whereas PC2 had high loadings on beak length (0.772). In Rambon ducks, four principal components were extracted, with eigenvalues of 2.594 (PC1), 1.377 (PC2), 1.188 (PC3), and 1.032 (PC4), respectively. The four factors combined accounted for 77.44% of the total variance present in the original variables measured. PC1 had high loadings on beak width (0.857) and foot width (0.860). PC2, PC3, and PC4 had high loadings on claw length (0.787), shank length (0.872), and neck length (0.788), respectively. The findings of this study are comparable with the reports on ducks (Yakubu et al 2011), chickens (Egena et al 2014; Dahloum et al 2016), and turkeys (Ogah 2011). The observed traits loaded in the same principal component were classified together in the same cluster, which may probably have common genomic sites for their genetic control. The results implied an important biological aspect underlying the relationship between the observed phenotypic traits. High communalities were observed in Nigerian chickens, ranging between 0.759 (neck length) and 0.974 (neck length) (Yakubu et al 2009). Udeh and Ogbu (2011) reported a wide range of communalities from 0.413 to 0.940 in broiler chickens. The lower communality observed for claw length in Alabio (0.291), Pegagan (0.402), and Pitalah (0.468) duck populations indicates that this trait was weak in explaining the total variation in the body measurements. In contrast, the medium to high communalities were observed in beak width, beak length, and neck length and diameter, indicating that these traits were able to explain the total variation in the body measurements. Yakubu et al (2009) reported that the first factor had high loadings on body size. The PC1 had also been reported by Mendes (2011) to have high loadings on several quantitative traits such as shank length, breast circumference, and body weight in broiler chickens. Furthermore, Ogah et al (2009) reported that PC1 had the largest variance on the duck’s body measurements, with high positive loadings on shank length, bill width, body length, body width, neck length, and head length. The three PCAs resulted in this study could be useful information for selection purposes of the animals and for genetic improvement of a particular trait. Conclusion This study revealed phenotypic diversity, both in qualitative and quantitative traits, among local duck populations in Indonesia. The PCA revealed medium to high communalities in beak width, beak length, and neck length and diameter, indicating that these traits were able to explain the total variation in the body measurements. Because of unpredictable agroecological conditions and market demands in future, variation observed among duck populations is useful sources for genetic improvement. But this phenotypic diversity could not ascertain the genetic structure of the populations, and the need for genetic characterization based on molecular techniques is ultimately needed. Both phenotyic and genetic diversity should be considered together for appropriate utilization of local ducks. Conflict of interest The authors declare that there is no conflict of interest. Acknowledgments This work represented an international research collaboration between Universitas Gadjah Mada, Yogyakarta, Indonesia, and Chungnam National University, Daejeon, South Korea, supported by
the Indonesian Ministry of Research, Technology and Higher Education (RISTEKDIKTI) with contract no. 1025/UN1eP.III/LT/DIT- LIT/ 2016. The authors also thank the Agricultural and Livestock Bureau of Cirebon, Magelang, Ogan Ilir, Pesisir Selatan, Tanah Datar, and the Centre of Excellence for Livestock Breeding and Forages (BPTUHPT) Pelaihari for assisting in data collection from breeding flocks.
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Original Article
Phenotypic characterization of local female duck populations in Indonesia Dyah Maharani a, *, Dwi N.H. Hariyono a, Daniel D.I. Putra a, Jun-Heon Lee b, Jafendi H.P. Sidadolog a a b
Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history: Received 12 November 2018 Received in revised form 17 March 2019 Accepted 3 July 2019 Available online xxx
Information on phenotypic traits is a prerequisite in animal genetic resource conservation and improvement. Phenotypic characteristics of 180 Indonesian female ducks collected from six populations (Alabio, Bayang, Magelang, Pegagan, Pitalah, and Rambon ducks) were studied. Data on qualitative traits were analyzed with descriptive statistics (percentages), while one-way analysis of variance was used to analyze the effect of populations on quantitative traits observed. The results revealed that the predominant plumage colors of the neck, breast, abdomen, back, secondary wings, primary wings, and thigh were brown (49.74%), brown (34.03%), brown (31.94%), brown (50.26%), dark brown (25.13%), light brown (35.08%), and brown (31.94%), respectively. The dominant bill and web color were black (77.49%) and dark brown (48.17), respectively. Variations were also found in quantitative morphological traits. The principal component analysis showed two to four principal components extracted from the factor analysis with varimax rotation, which accounted for 57.33%, 66.26%, 64.43%, 54.66%, and 77.44% of the total variance in the original variables for Alabio, Magelang, Pegagan, Pitalah, and Rambon ducks, respectively. Generally, the first factor in each population had high loadings on beak width. The observed phenotypic diversity in Indonesian local ducks could be useful in designing breeding programs and selection. Ó 2019 National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA), Publishing Services by Elsevier. This is an open access article under the CC BY-NC-ND license (http:// creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Local ducks Phenotypic characterization Qualitative traits Quantitative traits
Introduction In Indonesia, populations of a number of local ducks spread across the Indonesian archipelago are included as a part of animal genetic resources (AnGRs) (Hariyono et al 2019). They are mostly reared under traditional scavenging management system by villagers in various agroclimatic conditions. The duck only represents 2.34% of the total poultry population, and its current population is about 49.7 billion heads in 2017 (Ditjennak 2017). Despite the low contribution to the total poultry production, the duck in Indonesia has a vital role in either improving nutritional status and incomes or reducing hunger and food insecurity among households, especially in rural areas. Implementing appropriate strategies of the world’s AnGRs is an ever-greater challenge for the international community (FAO 2007). Current global AnGR status is mainly undergoing threats
* Corresponding author. Tel.: þ62 274 513363; fax: þ62 274 521578. E-mail address: [email protected] (D. Maharani). Peer review under responsibility of National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA).
because of the rapid transformation of the agricultural system, and by implication, decisions on its management should be appropriate. Appropriate utilization of a livestock species or breed is dependent on accurate understanding of its unique characteristics differentiating it from other breeds or species (Oguntunji and Ayorinde 2015). Breed characterization is a prerequisite in the urgent task of genetic resource conservation (Latshaw and Bishop 2001; FAO 2012). Breed characterization based on either phenotypic traits or genetic characteristics provides significant information on the sustainable management of the local breeds and a reasonable representation of genetic differences among breeds (Yakubu et al 2011). In addition, the current trend on the improvement of indigenous animals relies on the variations (within and between breeds) of certain traits, and such a variation is a great opportunity for selection and breeding programs. Phenotypic characterization has been used by researchers to describe and compare morphological characteristics of indigenous poultry species in different agroecological zones. For instance, phenotypic characterization was conducted on Indian ducks (Veeramani et al 2014), Ethiopian chickens (Moreda et al 2014),
https://doi.org/10.1016/j.japb.2019.07.004 pISSN2287-884X eISSN2287-9544/Ó 2019 National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA), Publishing Services by Elsevier. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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Nigerian chickens (Egena et al 2014; Rotimi et al 2016), and Nigerian ducks (Yakubu et al 2011; Ogah and Kabir 2014; Oguntuji and Ayorinde 2015). In general, all of these studies found a considerable phenotypic diversity, including body weight, body size, and plumage and skin color, which are useful for breed or population identification and classification. Limited studies regarding breed characterization of the local ducks in Indonesia have been carried out, either for phenotypic (Setioko et al 2005; Sopiyana et al 2006; Suryana and Hardjosworo 2011; Wulandari et al 2015) or for genetic characterization (Rahayu et al 2015; Maharani et al 2017; Hariyono et al 2019). Generally, the phenotypic diversity of Indonesian local duck populations is yet to be investigated in detail. Hence, the present work was carried out to characterize the local duck populations in Indonesia based on the phenotypic traits. Material and methods Location of the study and experimental animals
further tested by the use of Duncan’s multiple range test. The statistical model used was as follows: Yij ¼ mþGi þeij where Yij is the individual body measurement, m is the overall mean, Gi is the fixed effect of the genotype, and eij is the random error. Principal component analysis (PCA) representing a linear combination of the available variables into a factor or component was determined separately for each duck population. Kaiser-MeyerOlkin (KMO) measures of sampling adequacy and Bartlett’s test of sphericity were determined to test the validity of the factor analysis of each of the data sets. These indicators were used to test whether the partial correlations among quantitative traits were small. A KMO measure of 0.50 and more was considered adequate (Kaiser 1974). Therefore, the KMO values of the data set for each duck population with less than 0.50 were excluded for PCA. PCA is a method for transforming the variables in a multivariate data set X1, X2, .Xp into new uncorrelated variables Y1, Y2, .Yp, which account for decreasing proportions of the total variance of the original variables (Everitt et al 2001) defined as follows:
Data were obtained from 180 female ducks (12e18 months of age) randomly selected within six Indonesian local duck populations. These comprised 30 individuals each from Alabio, Bayang, Magelang, Pegagan, Pitalah, and Rambon duck populations. The sites of this study were in Pelaihari district (latitude 3 520 59.8800 S and longitude 114 520 0.1200 E) of South Borneo province (for Alabio duck), Magelang district (latitude 7 250 3900 S and longitude 110 90 42.8400 E) of Central Java (for Magelang duck), Cirebon district (latitude 6 450 50.7600 S and longitude 108 280 44.0400 E) of West Java (for Rambon duck), Ogan Ilir district (latitude 3101200 S and longitude 104 280 4800 E) of South Sumatra (for Pegagan duck), Pesisir Selatan district (latitude 1210000 S and longitude 100 3401.200 E) of West Sumatra (for Bayang duck), and Tanah Datar district (latitude 0 270 000 S and longitude 100 340 58.800 E) of West Sumatra (for Pitalah duck). All duck populations (except the Alabio duck) were kept under the traditional scavenging system by local farmers. For the Alabio duck, it was kept under a controlled breeding system by the Centre of Excellence for Livestock Breeding and Forages (BPTUHPT) Pelaihari, in which the selection program had been conducted for a particular trait. All the duck breeds investigated in the present study are included as national germplasm by the Indonesian Ministry of Agriculture.
with coefficients being chosen so that, y1, y2, ...yp account for decreasing proportions of the total variance of the original variables x1, x2, ... xp. The PCA was performed using SPSS (2001) version 16 (SPSS Inc., Chicago, IL, USA).
Traits measured
Bill color
All animals were characterized for the qualitative and quantitative traits following the descriptors by Cuesta (2008) and Francesch et al (2011). The qualitative traits observed were bill color, web color, and plumage color (i.e. neck, breast, abdomen, back, secondary wings, primary wings, and thigh). The quantitative traits recorded were beak width, beak length, neck length, neck diameter, shank length, toe length, foot width, and claw length. All quantitative traits were taken by measuring tape and slide calipers and measured in centimeters. We visually appraised and identified the qualitative traits. All measurements were taken by the same person to avoid individual variations.
The most predominant bill color across the investigated duck populations was black (77.49%). However, no variation in bill color was observed in the Alabio duck population, with yellow being the only bill color in this population. Similarly, the observed highest frequency of black bill in this study agrees with the report of Baghel (2007) on Muscovy ducks and Oguntunji and Ayorinde (2015) on Nigerian ducks. A previous study by Chia and Momoh (2012) observed three variants (all black, black-yellow, and black-pink) of bill color in North Central Nigerian Muscovy ducks.
Statistical analysis
Eight variants for neck color (white, brown, black, ash, ash brown, ash black, light brown, and dark brown) were observed across the duck populations. Brown neck had the highest frequency (49.74%), whereas white neck had the lowest frequency (1.05%). A published study by Suryana et al (2011) reported five variants (black, white-gray, black-gray, brown, and brown-gray) found for bill color in Alabio ducks (Suryana et al 2011), which was in contrast to the present study. Furthermore, pink-white is the most common
Data on qualitative traits were analyzed using descriptive statistics and compared as percentages. Coefficient of variation for the data on quantitative traits at various duck populations was performed. One-way analysis of variance was used to analyze the effect of the genotype of the duck populations on the quantitative traits, and significantly different means (P<0.05) among populations was
y1 ¼ a11x1 þ a12x2 þ .... þ a1pxp y2 ¼ a21x1 þ a22x2 þ ....þ a2pxp yp ¼ ap1x1 þ ap2x2 þ .... þ appxp
Results and discussion Variation in qualitative traits Descriptive statistics for qualitative traits such as bill color, web color, and plumage color (i.e. neck, breast, abdomen, back, secondary wings, primary wings, and thigh) among the six local duck populations in Indonesia are presented in Table 1.
Neck color
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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Table 1. Variation of qualitative traits among Indonesian local ducks. Trait
Color (%)
Alabio
Magelang
Rambon
Pegagan
Pitalah
Bayang
Overall
Bill color
Yellow Black Brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown White Brown Black Ash Ash brown Ash black Light brown Dark brown Yellow Light Brown Dark brown
100.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00 0.00 0.00 0.00 0.00 100.00 0.00 0.00
2.44 70.73 0.00 4.88 63.41 4.88 0.00 0.00 0.00 0.00 0.00 2.44 65.85 4.88 0.00 0.00 0.00 0.00 0.00 12.20 60.98 0.00 0.00 0.00 0.00 0.00 0.00 2.44 70.73 0.00 0.00 0.00 0.00 0.00 0.00 2.44 0.00 12.20 0.00 0.00 0.00 0.00 58.54 9.76 0.00 0.00 0.00 0.00 0.00 63.41 0.00 17.07 53.66 2.44 0.00 0.00 0.00 0.00 0.00 2.44 63.41 7.32
0.00 73.17 0.00 0.00 70.73 2.44 0.00 0.00 0.00 0.00 0.00 2.44 0.00 2.44 0.00 0.00 0.00 34.15 34.15 7.32 63.41 2.44 0.00 0.00 0.00 0.00 0.00 2.44 68.29 2.44 0.00 0.00 0.00 0.00 0.00 2.44 0.00 2.44 0.00 0.00 0.00 34.15 34.15 0.00 0.00 2.44 0.00 0.00 0.00 51.22 19.51 2.44 0.00 2.44 0.00 0.00 0.00 12.20 56.10 4.88 0.00 68.29
0.00 70.73 2.44 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 0.00 0.00 26.83 26.83 19.51 0.00 0.00 0.00 29.27 43.90
0.00 73.17 0.00 0.00 24.39 48.78 0.00 0.00 0.00 0.00 0.00 2.44 19.51 51.22 0.00 0.00 0.00 0.00 0.00 0.00 24.39 48.78 0.00 0.00 0.00 0.00 0.00 0.00 21.95 51.22 0.00 0.00 0.00 0.00 0.00 0.00 21.95 51.22 0.00 0.00 0.00 0.00 0.00 0.00 26.83 46.34 0.00 0.00 0.00 0.00 0.00 0.00 21.95 51.22 0.00 0.00 0.00 0.00 0.00 19.51 21.95 31.71
0.00 73.17 0.00 0.00 73.17 0.00 0.00 0.00 0.00 43.90 29.27 0.00 0.00 0.00 0.00 0.00 0.00 43.90 29.27 2.44 0.00 0.00 0.00 0.00 0.00 46.34 24.39 0.00 0.00 0.00 0.00 0.00 0.00 43.90 29.27 0.00 0.00 0.00 0.00 0.00 0.00 48.78 24.39 0.00 0.00 0.00 0.00 0.00 0.00 48.78 24.39 2.44 0.00 0.00 0.00 0.00 0.00 43.90 26.83 0.00 0.00 73.17
16.23 77.49 0.52 1.05 49.74 12.04 21.47 5.76 4.19 9.42 6.28 1.57 34.03 12.57 5.76 5.76 4.19 16.75 13.61 20.42 31.94 10.99 5.76 5.76 4.19 9.95 5.24 1.05 50.26 11.52 5.76 5.76 4.19 9.42 6.28 1.05 4.71 14.14 21.47 5.76 4.19 17.80 25.13 2.09 5.76 10.47 21.47 5.76 4.19 35.08 9.42 4.71 31.94 12.04 5.76 5.76 4.19 12.04 17.80 21.47 24.61 48.17
Neck color
Breast color
Abdomen color
Back color
Secondary wings
Primary wings
Thigh color
Web color
bill color, whereas slate gray is the least common bill color in Muscovy ducks in Egypt (FAO 2009). Web color Dark brown was the most common web color, with 48.17%, followed by light brown with 24.61%; yellow was the least common web color, with 21.47%. However, yellow web has the highest proportion in the Alabio duck population, with 100%. Similarly, the highest frequency of yellow web was also reported by Oguntunji
and Ayorinde (2015) in Nigerian Muscovy ducks. Baghel (2007) reported four variants (black, yellow black with black spots, cream with greyish spots, and pale yellow with algae green spots) of web color in Muscovy ducks. Plumage color Figure 1 represents plumage color variation among Indonesian local duck populations. The predominant plumage color of each observed qualitative trait, that is, neck (brown, 49.74%), breast
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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Figure 1. The plumage color variation of Indonesian local duck populations: A, Alabio duck; B, Bayang duck; C, Magelang duck; D, Pegagan duck; E, Pitalah duck; F, Rambon duck.
(brown, 34.03%), abdomen (brown, 31.94%), back (brown, 50.26%), secondary wings (dark brown, 25.13%), primary wings (light brown, 35.08%), and thigh (brown, 31.94%), was found across the duck populations. The results are in agreement with the findings of the studies by Sopiyana et al (2006) and Setioko et al (2005) who reported that variation in plumage color was observed among Indonesian duck populations kept under the traditional scavenging system. In contrast, no variation for qualitative traits was detected in Alabio ducks, an investigated duck population kept under the controlled breeding system. As reported by Suryana et al (2011), low variation was also observed for the plumage color in the Alabio duck population, although the studied population was kept by traditional farmers in the semi-intensive breeding system. Interestingly, a specific attribute was observed in the Magelang duck population. It has a neck ring with white color, and this attribute is absent in other duck populations, suggesting that this characteristic is specific to Magelang ducks. Previously, Rahayu et al (2015) observed 11 kinds of plumage color pattern in Magelang ducks; those are Jarakan Polos, Bosokan, Kalung Ombo, Kalung Ciut, Gambiran, Jarakan Kalung, Jowo Polos, Klawu Borok, Cemani, Wiroko, and Putih Polos. The observed plumage color variation in Indonesian duck populations implies an opportunity for future selection in the breeding program of ducks. In general, the six Indonesian local duck populations can be classified into three agroecological conditions, that is, swamplands (Alabio and Pegagan), lowlands (Magelang, Rambon, and Bayang), and highlands (Pitalah). Based on the agroecological conditions, the duck population (Pitalah) that was reared in the highland area has predominantly black plumage color, whereas the duck populations
reared in the remaining agroecological conditions have relatively light brown plumage color. Interspecific variation in plumage color was also found among birds, indicating an adaptive response to variation in light environments across habitats (McNaught and Owens 2002). Habitats and climate differences in selective pressures may well be responsible for producing color variation in species with broad ecological niches, and both visual and physiological effects (functions) of color pigmentation might be involved (Gaelotti et al 2003). In addition, genetic factor affects plumage color variation, mediated by multiple loci (Evans and Sheldon 2012). In general, variation for qualitative traits was observed in Indonesian local duck populations, such as in Magelang, Rambon, Pegagan, Pitalah and Bayang duck populations, kept under the traditional scavenging system by many villagers, indicating the lack of selection directed toward the choice of plumage color. Variation in quantitative traits The mean, standard errors, and coefficients of variation of quantitative traits measured among Indonesian local ducks are summarized in Table 2. Variation was found for all quantitative traits measured, depicted by significant differences between means (P<0.05) among studied duck populations for each trait. The overall mean values for beak width, beak length, neck length, neck diameter, shank length, toe length, foot width, and claw length of the local duck populations in Indonesia were 2.770.01 cm, 5.920.03 cm, 16.040.10 cm, 1.600.01 cm, 6.450.03 cm, 6.310.05 cm, 7.000.04 cm, and 1.150.14 cm, respectively.
Table 2. Mean, standard errors (SEs), and coefficients of variation (CVs) of quantitative traits measured among Indonesian local duck populations. Trait
Beak width (cm) Beak length (cm) Neck length (cm) Neck diameter (cm) Shank length (cm) Toe length (cm) Foot width (cm) Claw length (cm) abcde
Alabio
Magelang
Rambon
Pegagan
Pitalah
Bayang
Overall mean
MeanSE
CV
MeanSE
CV
MeanSE
CV
MeanSE
CV
MeanSE
CV
MeanSE
CV
2.760.08c 5.920.05a 17.140.14a 1.530.09c 6.610.04b 6.140.05c 7.440.05a 1.440.02a
2.33 5.21 4.76 6.01 3.58 4.34 3.98 8.79
2.820.13ab 5.950.33d 14.831.21d 1.660.21a 6.270.47d 7.230.66a 6.560.53d 1.230.10b
4.43 5.58 8.15 12.38 7.54 9.12 8.05 7.74
2.650.09d 6.090.35c 15.451.24c 1.580.09bc 6.840.35a 6.140.40c 6.750.45cd 1.100.08c
3.46 5.81 8.02 5.89 5.09 6.54 6.67 7.46
2.820.14ab 6.010.29b 16.511.23a 1.700.10a 6.420.30cd 6.000.33cd 7.050.64b 1.090.08c
4.96 4.91 7.43 5.98 4.74 5.56 9.11 7.54
2.680.11d 5.600.64b 16.401.26ab 1.560.10bc 5.980.27e 5.830.35d 6.890.44bc 0.950.11d
3.97 11.50 7.65 6.65 4.53 5.98 6.35 11.97
2.860.12a 5.970.26bc 15.901.21bc 1.600.11b 6.520.29bc 6.540.33b 7.320.40a 1.090.10c
4.17 4.37 7.59 6.77 4.42 5.01 5.50 9.59
2.770.01 5.920.03 16.040.10 1.600.01 6.450.03 6.310.05 7.000.04 1.150.14
Mean in same rows with different superscripts are significantly different (P<0.05).
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The highest mean for beak width (2.860.12 cm) was observed in Bayang ducks, while the lowest mean was observed in Rambon ducks (2.650.09 cm). For beak length, the values ranged between 5.600.64 cm (Pitalah ducks) and 6.090.35 cm (Pegagan ducks). For neck length, a mean value of 17.140.14 cm (Alabio ducks) was found to be the highest, while that of 14.831.21 (Magelang ducks) was found to be the lowest. For neck diameter, Pegagan ducks had the highest mean value (1.700.10 cm), whereas Alabio ducks had the lowest mean value (1.530.09). Mean values of shank length varied from 5.980.27 cm (Pitalah ducks) to 6.610.04 cm (Alabio ducks). For toe length, a range value from 5.830.35 cm (Pitalah ducks) to 7.230.66 cm (Magelang ducks) was observed. Mean values for foot width ranged between 6.560.53 cm (Magelang ducks) and 7.440.05 cm (Alabio ducks). The last predictor for quantitative traits was claw length, in which the highest mean value was observed in Alabio ducks (1.440.02 cm), whereas the lowest mean value was found in Pitalah ducks (0.950.11). The overall mean values for beak width and beak length observed in this study were higher than those reported by Setioko et al (2005) in Cirebon ducks (beak width ¼ 2.35 cm; beak length ¼ 5.55 cm). Wulandari et al (2015) observed a mean value of 7.830.41 for beak length in Magelang ducks, which was higher than that obtained in this study. The overall mean values for shank length and beak length were comparable with those reported by Setioko et al (2005) in Cirebon and Turi ducks. For neck length, the overall mean value of 16.040.10 cm obtained in this study was higher than that of 13.190.17 cm reported in Indian ducks (Veeramani et al 2014). Such variation provides an opportunity for future genetic improvement among and within duck populations. Quantitative traits such as body measurements are useful indicators that are used to describe a breed or population along with qualitative traits and agroecological conditions the breeds inhabited. Principal component analysis PCA allows assessment of overall variance and defines the variables with greater discriminatory power between groups. KMO measure of sampling adequacy computed for Alabio, Bayang, Magelang, Pegagan, Pitalah, and Rambon ducks was found to be 0.73, 0.44, 0.54, 0.63, 0.66, and 0.56, respectively. The significance of the correlation matrices tested with Bartlett’s test of sphericity for all quantitative traits in Alabio (c2 ¼68.42; P < 0.00), Magelang (c2 ¼60.36; P < 0.00), Pegagan (c2 ¼47.54; P < 0.01), Pitalah (c2 ¼57.34; P < 0.00), and Rambon (c2 ¼60.03; P < 0.00) ducks provided support for the validity of the factor analysis of the data sets. Nonsignificance of Bartlett’s test of sphericity for body measurements was only observed in Bayang (c2 ¼37.24; P < 0.11) ducks. Hence, we excluded Bayang ducks for PCA. The eigenvalues of the total variance, the rotated component matrix, and communalities for all quantitative traits in the investigated duck populations are presented in Table 3. The communalities representing estimates of the variance in each variable observed ranged between 0.291 and 0.709 in Alabio, 0.347 and 0.738 in Bayang, 0.413 and 0.896 in Magelang, 0.402 and 0.846 in Pegagan, 0.292 and 0.740 in Pitalah, and 0.633 and 0.846 in Rambon ducks. The PCA showed two to four principal components extracted from the factor analysis with varimax rotation. In Alabio ducks, the principal components by PCA which accounted for 40.192% (PC1) and 17.137% (PC2) of the total variance in the original variables measured, with eigenvalues of 3.125 and 1.371, respectively, were identified. PC1 had high loadings on beak length (0.778), neck diameter (0.758), and foot width (0.797), whereas PC2 had high loadings on neck length (0.836). In Magelang ducks, three principal components were extracted, which accounted for 66.26% of the
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Table 3. Eigenvalues, percentage of total variance, rotated component matrix, and communalities of quantitative traits observed in Indonesian local duck populations. Trait Alabio Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Magelang Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Pegagan Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Pitalah Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance Rambon Beak width Beak length Neck length Neck diameter Shank length Toe length Foot width Claw length Eigenvalues % of total variance
PC1
PC2
PC3
PC4
Communalities
0.733 0.778 0.102 0.758 0.532 0.666 0.797 0.354 3.125 40.192
0.200 0.321 0.836 0.230 0.497 0.217 0.130 0.407 1.371 17.137
e e e e e e e e e e
e e e e e e e e e e
0.578 0.708 0.709 0.628 0.530 0.490 0.651 0.291
0.776 0.731 0.730 0.245 0.267 0.484 0.783 0.344 2.766 34.571
0.154 0.345 0.021 0.533 0.511 0.727 0.192 0.344 1.372 17.153
0.288 0.005 0.130 0.405 0.284 0.148 0.369 0.812 1.163 14.536
e e e e e e e e e e
0.709 0.652 0.550 0.509 0.413 0.784 0.787 0.896
0.575 0.572 0.701 0.458 0.602 0.717 0.498 0.549 2.786 34.819
0.619 0.575 0.286 0.573 0.192 0.443 0.026 0.014 1.358 16.971
0.097 0.433 0.161 0.410 0.181 0.037 0.697 0.317 1.011 12.638
e e e e e e e e e e
0.723 0.846 0.598 0.706 0.432 0.712 0.735 0.402 e e
0.643 0.085 0.370 0.629 0.843 0.793 0.539 0.647 3.001 37.508
0.226 0.772 0.701 0.326 0.171 0.216 0.026 0.223 1.372 17.151
e e e e e e e e e e
e e e e e e e e e e
0.465 0.603 0.629 0.502 0.740 0.675 0.292 0.468
0.857 0.253 0.380 0.498 0.187 0.733 0.860 0.303 2.594 32.421
0.078 0.395 0.226 0.572 0.109 0.386 0.241 0.787 1.377 17.214
0.036 0.447 0.073 0.322 0.872 0.021 0.042 0.339 1.188 14.852
0.322 0.462 0.788 0.124 0.157 0.215 0.077 0.052 1.032 12.905
0.846 0.633 0.821 0.694 0.832 0.733 0.804 0.828
total variance in the original variables, with eigenvalues of 2.766, 1.372, and 1.163, respectively. PC1 had high loadings on beak width (0.776) and foot width (0.783) and negative loadings on claw length (-0.344). Negative loadings were observed for beak length (-0.345), neck diameter (-0.533), and shank length (-0.511) in PC2. PC3 had only high loadings on claw length (0.812). In Pegagan ducks, three principal components were extracted after varimax rotation, which accounted for 64.43% of the total variance in the original variables, with eigenvalues of 2.786 (PC1), 1.358 (PC2), and 1.011 (PC3), respectively. PC1 had high positive loadings on all traits measured, ranging from 0.458 for neck diameter to 0.717 for toe length. PC2 had high loadings on beak length (0.772), whereas PC3 had no high loadings on all traits measured. However, PC3 had negative loadings on beak length, neck length, neck diameter, and toe length. In
Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004
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D Maharani et al. / Journal of Asia-Pacific Biodiversity xxx (xxxx) xxx
Pitalah ducks, two principal components were identified with eigenvalues of 3.001 (PC1) and 1.372 (PC2), respectively. The two factors accounted for 54.66% of the total variance present in original measurements. PC1 had high loadings on shank length (0.843) and toe length (0.793), whereas PC2 had high loadings on beak length (0.772). In Rambon ducks, four principal components were extracted, with eigenvalues of 2.594 (PC1), 1.377 (PC2), 1.188 (PC3), and 1.032 (PC4), respectively. The four factors combined accounted for 77.44% of the total variance present in the original variables measured. PC1 had high loadings on beak width (0.857) and foot width (0.860). PC2, PC3, and PC4 had high loadings on claw length (0.787), shank length (0.872), and neck length (0.788), respectively. The findings of this study are comparable with the reports on ducks (Yakubu et al 2011), chickens (Egena et al 2014; Dahloum et al 2016), and turkeys (Ogah 2011). The observed traits loaded in the same principal component were classified together in the same cluster, which may probably have common genomic sites for their genetic control. The results implied an important biological aspect underlying the relationship between the observed phenotypic traits. High communalities were observed in Nigerian chickens, ranging between 0.759 (neck length) and 0.974 (neck length) (Yakubu et al 2009). Udeh and Ogbu (2011) reported a wide range of communalities from 0.413 to 0.940 in broiler chickens. The lower communality observed for claw length in Alabio (0.291), Pegagan (0.402), and Pitalah (0.468) duck populations indicates that this trait was weak in explaining the total variation in the body measurements. In contrast, the medium to high communalities were observed in beak width, beak length, and neck length and diameter, indicating that these traits were able to explain the total variation in the body measurements. Yakubu et al (2009) reported that the first factor had high loadings on body size. The PC1 had also been reported by Mendes (2011) to have high loadings on several quantitative traits such as shank length, breast circumference, and body weight in broiler chickens. Furthermore, Ogah et al (2009) reported that PC1 had the largest variance on the duck’s body measurements, with high positive loadings on shank length, bill width, body length, body width, neck length, and head length. The three PCAs resulted in this study could be useful information for selection purposes of the animals and for genetic improvement of a particular trait. Conclusion This study revealed phenotypic diversity, both in qualitative and quantitative traits, among local duck populations in Indonesia. The PCA revealed medium to high communalities in beak width, beak length, and neck length and diameter, indicating that these traits were able to explain the total variation in the body measurements. Because of unpredictable agroecological conditions and market demands in future, variation observed among duck populations is useful sources for genetic improvement. But this phenotypic diversity could not ascertain the genetic structure of the populations, and the need for genetic characterization based on molecular techniques is ultimately needed. Both phenotyic and genetic diversity should be considered together for appropriate utilization of local ducks. Conflict of interest The authors declare that there is no conflict of interest. Acknowledgments This work represented an international research collaboration between Universitas Gadjah Mada, Yogyakarta, Indonesia, and Chungnam National University, Daejeon, South Korea, supported by
the Indonesian Ministry of Research, Technology and Higher Education (RISTEKDIKTI) with contract no. 1025/UN1eP.III/LT/DIT- LIT/ 2016. The authors also thank the Agricultural and Livestock Bureau of Cirebon, Magelang, Ogan Ilir, Pesisir Selatan, Tanah Datar, and the Centre of Excellence for Livestock Breeding and Forages (BPTUHPT) Pelaihari for assisting in data collection from breeding flocks.
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Please cite this article as: Maharani D et al., Phenotypic characterization of local female duck populations in Indonesia, Journal of Asia-Pacific Biodiversity, https://doi.org/10.1016/j.japb.2019.07.004