• Animal Bioscience
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• v.35 no.6
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• pp.826-837
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• 2022

Objective: Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide. Methods: A Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds. Results: A total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries. Conclusion: Cambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.7
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• pp.911-921
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• 2015

At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2003.09a
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• pp.334-337
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• 2003

This study was carried out to investigate the effect of soil properties, such as soil organic matter(SOM) content and water content on die-off and regrowth of indigenous microbes due to in-situ ozonation. Four different soils were collected and the soil samples applied to different ozonation time(0-360 min) were incubated during 4 weeks. Population of the indigenous microbes was monitored during incubation period. The number of indigenous microbes in all samples dramatically decreased (more than 90%) within 30 minutes of ozone injection. With increased ozonation time by 360 minutes, the number of the indigenous microbes decreased by 99.99% in all samples. Die-off of the indigenous microbes due to ozone treatment was inversely proportional to SOM and water content. Especially, sample 3 and Sample 4 containing relatively high SOM content and water content showed high regrowth rate, and this resulted from the increase of water soluble and biodegradable organic fraction in soil water after ozone treatment. Soil sample ozonated for 360 minutes showed minor increase in microbial population during 4 weeks of incubation period.

• Animal Bioscience
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• v.34 no.7
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• pp.1123-1133
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• 2021

Objective: Shandong indigenous pig breeds are important Chinese pig resources. Their progressive population decline in recent decades has attracted attention towards their conservation. Conservation genetics of these indigenous breeds are essential for developing a conservation and utilization scheme. Methods: A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. Results: The results showed that Shandong indigenous pig breeds varied greatly in genetic diversity, effective population size, inbreeding level, and genetic distance with the Western commercial breeds. Specifically, Laiwu and Dapulian displayed low genetic diversity, and had a genetically distant relationship with the Western commercial breeds (average F statistics [F_ST] value of 0.3226 and 0.2666, respectively). Contrastingly, the other five breeds (Yantai, Licha, Yimeng, Wulain, and Heigai) displayed high genetic diversity within breed and had some extent of mixture pattern with the Western commercial breeds, especially Duroc and Landrace (F_ST values from 0.1043 to 0.2536). Furthermore, intensive gene flow was discovered among the seven Shandong indigenous breeds, particularly Wulian, Licha, and Heigai, as indicated by the large cluster formed in the principal component analysis scatterplot and small population differentiation (average of 0.1253) among them. Conclusion: Our study advances the understanding of genetic characteristics of Shandong indigenous breeds and provides essential information for developing an appropriate conservation and utilization scheme for these breeds.

• Journal of Microbiology and Biotechnology
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• v.17 no.10
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• pp.1704-1707
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• 2007

Monitoring of the phage-host system of Microlunatus phosphovorus indigenous in activated sludge was attempted. A laboratory-scale activated sludge process was operated for 5 weeks with synthetic wastewater. The phage-host system population in the process was monitored by plaque assay and FISH methods at every 3 days. During the process operation, the phage-host system populations were more or less steady, except for 1 week in the middle of the operation. In that period, initially M. phosphovorus decreased significantly and its lytic bacteriophages increased, and then M. phosphovorus increased back to its original level while its lytic bacteriophages decreased. This observation suggests that lytic bacteriophages should be considered as one of the biological factors affecting the bacterial population dynamics in activated sludge processes.

• Korean Journal of Soil Science and Fertilizer
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• v.19 no.1
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• pp.38-49
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• 1986

In order to improve effectiveness of rhizobia-legume symbiotic nitrogen fixation, ecological and physiological characteristics of indigenous rhizobia distributed in Korea soil, that is, the effects of soybean cultivation, physico-chemical properties and climate on the population of indigenous rhizobia and other soil microbes were investigated. The results were summarized as follows: The population of indigenous rhizobia were ranged from $5.1{\times}10^4$ cells to $196.8{\times}10^4$ cells per gram of soil in soybean cultivated soils but from $1.6{\times}10^4$ cells to $78.6{\times}10^4$ cells per gram of soil in soybean un-cultivated soils sampled from 9 different agro-climate zone. The highest population was observed in a soybean cultivated loamy soil from southern part of Korea. The content of available phosphate, exchangeable Ca, Mg, Cu, and B in soil were positively correlated but active Fe, exchangeable Al, Na, and $SO_4$ were inversely correlated to the population of indigenous rhizobia. The inverse relationship was observed between the number of indigenous rhizobia and actinomycetes.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.10
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• pp.1491-1500
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• 2019

Objective: European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods: Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results: The results showed that Thai pig populations had a high genetic diversity with mean total and effective ($N_e$) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity ($H_e$) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher $H_e$ compared to observed heterozygosity ($H_o$) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean $F_{ST}$ estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion: Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.7
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• pp.939-945
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• 2003

Seventeen Chinese indigenous pig breeds and three introduced pig breeds had been carried out by means of vertical polyacrylamide gel electrophoresis (PAGE). According to the results, eight serum protein loci were highly polymorphic except Pi-2 and Cp. The polymorphism information content (PIC) of Hpx was the highest (0.5268), while that of Cp was the lowest (0.0257). The population genetic variation index showed that about 84% genetic variation existed in the population, and the rest of 16% distributed between the populations. The genetic variation of Yimeng black pig and Duroc were the highest and the lowest, respectively. The genetic variation of Chinese indigenous pig breeds was much more than that of exotic groups. Genetic distance results showed that Chinese indigenous pig breeds were classified into four groups with the three introduced pig breeds clustered into another group. The results also supported the geographic distribution of Chinese indigenous pig breeds in certain extent.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.5
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• pp.726-732
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• 2004

In this manuscript, a review of the diversity of Chinese indigenous goat breeds according to data from body stature and appearance, chromosome group, blood proteins, DNA molecular markers (mitochondria DNA, random amplified polymorphic DNA, microsatellite DNA, major histocompatibility complex) has been introduced. All of these provide efficient tools for the diversity analysis of Chinese indigenous goat breeds and are very important for biodiversity conservation, restoration of declining goat breeds, the priority defining in Chinese indigenous goat breeds' protection and the selection of nature preservation zones. Many Chinese indigenous goat breeds with small population size in the isolated mountains or reservoir areas are verging the potential threat of extinction, effectively lost with the rapid destroying of ecological environment. On the other hand, as a result of the introduction of modern commercial goat breeds and shortage of effective conservation, some populations, such as Small-xiang goat and Tibetan goat decrease rapidly in number of sires. In the interests of the long-term future of the goat breeds in China, conservation of goat breeds' genetic resources should be considered urgently and some conservation measures should be adopted. In addition, the continuing development of molecular biology will further enhance conservation of diversity of Chinese indigenous goat breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.9
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• pp.1393-1400
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• 2018

Objective: This study was carried out to assess the haplotype diversity and population dynamics in cattle populations of Ethiopia. Methods: We sequenced the complete mitochondrial cytochrome b gene of 76 animals from five indigenous and one Holstein Friesian${\times}$Barka cross bred cattle populations. Results: In the sequence analysis, 18 haplotypes were generated from 18 segregating sites and the average haplotype and nucleotide diversities were $0.7540{\pm}0.043$ and $0.0010{\pm}0.000$, respectively. The population differentiation analysis shows a weak population structure (4.55%) among the populations studied. Majority of the variation (95.45%) is observed by within populations. The overall average pair-wise distance ($F_{ST}$) was 0.049539 with the highest ($F_{ST}=0.1245$) and the lowest ($F_{ST}=0.011$) $F_{ST}$ distances observed between Boran and Abigar, and Sheko and Abigar from the indigenous cattle, respectively. The phylogenetic network analysis revealed that all the haplotypes detected clustered together with the Bos taurus cattle and converged to a haplogroup. No haplotype in Ethiopian cattle was observed clustered with the reference Bos indicus group. The mismatch distribution analysis indicates a single population expansion event among the cattle populations. Conclusion: Overall, high haplotype variability was observed among Ethiopian cattle populations and they share a common ancestor with Bos taurus.