Objective: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic d...
Objective: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. Methods: In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. Results: The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations ($F_{IT}=0.237$), was partly due to the heterozygote deficiency within populations ($F_{IS}=0.114$) and moderate level of genetic differentiation among populations ($F_{ST}=0.137$). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. Conclusion: The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.
Objective: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. Methods: In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. Results: The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations ($F_{IT}=0.237$), was partly due to the heterozygote deficiency within populations ($F_{IS}=0.114$) and moderate level of genetic differentiation among populations ($F_{ST}=0.137$). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. Conclusion: The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.
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제안 방법
Neighbor-joining tree constructed using pairwise population matrix of FST values (A) and Nei’s genetic distances (B) of eight duck popullations.
The PCR was performed in a 20 μL volume containing 2 μL of 10 ng/μL of duck genomic DNA, 2× multi HS Prime Taq Premix (GeNet Bio, Daejeon, Korea), 8 pmol of each forward and reverse primer (Applied Biosystems, Foster City, CA, USA), and distilled water.
The genetic diversity among populations was determined by these indicators: number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) which were estimated using Cervus ver.3.0 program [17], and F-statistics, including inbreeding coefficient of an individual relative to the subpopulations (FIS), inbreeding coefficient of an individual relative to the total population (FIT), and genetic differentiation index between population (FST) which were calculated using GenAlex ver. 6.501 [18]. The software was also employed to determine genetic diversity within each population (Na, Ho, He, and FIS).
501 [18]. The software was also employed to determine genetic diversity within each population (Na, Ho, He, and FIS). For phylogenetic relationship analysis, GenAlex software was used to perform pairwise population matrices based on either FST or Nei’s genetic distance and to construct principal coordinates analysis (PcoA).
성능/효과
F-statistics were estimated in a fixation index as genetic differentiation (FST), global deficit among eight duck populations (FIT), and the heterozygote deficit within duck populations (FIS), with an average value of 0.137, 0.237, and 0.114, respectively (Table 1). The average value of FST indicated that about 13.
In conclusion, the results of this study demonstrate moderate level of genetic diversity and differentiation among populations, but low to moderate level of genetic diversity within populations. Preventing loss of further alleles with low genetic diversity in populations studied should be considered by implementing effective breeding strategies to reduce inbreeding and increase heterozygosity.
368). In contrast, RM and TR duck populations were highest for the mean number of alleles while MG duck population showed highest genetic diversity compared to the others (He = 0.545). Observed heterozygosity was lower than expected heterozygosity in all populations, except AL duck population.
Genetic diversity indicators are summarized in Table 1 and Table 2 for among and within duck populations studied, respectively. In total, 153 alleles were detected at these 22 loci in 240 individuals, with the number of alleles per locus ranging from 3 (CAUD128, AMU123, and CAUD009) to 22 (CAUD048), with an average value of 6.96 alleles per locus. Observed and expected heterozygosity values ranged from 0.
MG and MJ duck populations were consistently grouped in one cluster that was closer to the AL duck population compared to the remaining populations. One interesting result was that RM and TR duck populations (originated from Java island) also tended to join together and clustered with BY, PG, and PT duck populations (originated from Sumatera island) in both NJ trees. In the past, many migrants from Java island moved to Sumatera island and other larger islands in Indonesia to get more land for agriculture.
114, respectively (Table 1). The average value of FST indicated that about 13.70% of total genetic variation corresponded to differences between populations, while 86.30% was explained by differences between individuals.
In total, 240 animals representing eight local duck populations in Indonesia (30 animals per population) were sampled from six provinces (Figure 1). The eight duck populations were AL and MJ from Pelaihari, South Kalimantan; BY and PT from West Sumatera, MG from Central Java; PG from South Sumatera; RM from West Java; and TR from Special Region of Yogyakarta (DIY). The blood samples were obtained from the ulnar vein using vacutainer tubes with K2-ethylenediamine-tetraacetic acid anticoagulant.
A PcoA is also presented using allele frequencies of 22 loci to summarize population relationships (Figure 3). The first, second and third components accounted for 54.20%, 18.83%, and 9.83%, respectively to the total of genetic variability. AL and two populations (MG and MJ) were clearly separated into different single quadrate that differs from other populations (PcoA axis 1 and 2).
137). The results showed that genetic diversity maintained within duck populations was higher than the one preserved among duck populations. This genetic diversity could be a valuable tool for implementing future genetic improvement and conservation of duck populations in Indonesia.
Such phenomenon can be explained by various factors such as non-random mating, unamplified alleles (“null” alleles) and subdivision in populations studied (Wahlund’s effects). The studied populations revealed a moderate genetic differentiation among eight populations (FST = 0.137). The results showed that genetic diversity maintained within duck populations was higher than the one preserved among duck populations.
Therefore, it is possible for BY, PG, PT, RM, and TR duck populations to share common ancestors when the migrants brought the ducks with them to the new region. The study highlighted that geograhic distance is not always a predictor of phylogenetic relationship. However, to get better understanding of phylogenetic among populations, it is important to combine information on the basis of phenotypic and molecular genetic characterization, as well as geographic and historical information of the analyzed populations.
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