Japanese Farms Research Articles

Genetic structure and origin of emu populations in Japanese farms inferred from large-scale SNP genotyping based on double-digest RAD-seq

The emu is a novel poultry species in Japan. However, Japanese farmed emu populations have reduced genetic diversity owing to inbreeding. We have previously suggested that there are genetic resources in the Tohoku Safari Park (TSP) and Fuji/Kakegawa Kachoen Garden Park (FGP/KGP) to extend the genetic diversity of commercial emu farms based on microsatellite (SSR) and mitochondrial DNA. However, those markers provide relatively poor information. Thus, we investigated the genetic structure of farmed Japanese populations based on a large-scale genotyping system using RAD-seq and verified the usefulness of TSP and FGP/KGP as genetic resources for expanding genetic diversity. Admixture, phylogenetic, and principal component analyses based on 28,676 SNPs showed that TSP individuals were ancestors in the Okhotsk Emu Farm (OEF). FGP/KGP individuals showed a unique genetic component that differed from that of the others. We have previously reported that the mitochondrial haplotypes of FGP/KGP were shared with an isolated wild population in eastern Australia. These results suggest that FGP/KGP individuals originated from an eastern Australia isolated population different from other populations including ancestral of OEF/TSP. Our results would provide information for the development of Japanese emu farms and industry and for the conservation of genetic resources in the Australian wild emu.

Transferable linezolid resistance genes (optrA and poxtA) in enterococci derived from livestock compost at Japanese farms

ObjectivesLinezolid is a last-resort antimicrobial in human clinical settings to treat multidrug-resistant Gram-positive bacterial infections. Mobile linezolid resistance genes (optrA, poxtA, and cfr) have been detected in various sources worldwide. However, the presence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in Japan remains uncertain. Therefore, we clarified the existence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in farm environments in Japan. MethodsEnterococci isolates from faeces compost collected from 10 pig and 11 cattle farms in Japan in 2021 were tested for antimicrobial susceptibility and possession of mobile linezolid resistance genes. Whole-genome sequencing of optrA and/or poxtA genes positive-enterococci was performed. ResultsOf 103 enterococci isolates, 12 from pig farm compost were not-susceptible (2 resistant and 10 intermediate) to linezolid. These 12 isolates carried mobile linezolid resistance genes on plasmids or chromosomes (5 optrA-positive Enterococcus faecalis, 6 poxtA-positive E. hirae or E. thailandicus, and 1 optrA- and poxtA-positive E. faecium). The genetic structures of optrA- and poxA-carrying plasmids were almost identical to those reported in other countries. These plasmids were capable of transferring among E. faecium and E. faecalis strains. The optrA- and poxtA-positive E. faecium belonged to ST324 (clade A2), a high-risk multidrug-resistant clone. The E. faecalis carrying optrA gene on its chromosome was identified as ST593. ConclusionsAlthough linezolid is not used in livestock, linezolid-not-susceptible enterococci could be indirectly selected by frequently used antimicrobials, such as phenicols. Moreover, various enterococci species derived from livestock compost may serve as reservoirs of linezolid resistance genes carried on globally disseminated plasmids and multidrug-resistant high-risk clones.

The association between farm-level antimicrobial usage and resistance of Staphylococcus spp., as the major genus isolated from aerosol samples, in Japanese piggeries.

Bacteria are the dominant particulate matter in livestock houses and can threaten animal and public health. Antimicrobial resistance (AMR) is a crucial concern worldwide, and nationwide measures established based on the One Health approach are being implemented in many countries. This requires multidisciplinary perspectives and collaboration among the human, animal, and environmental sectors. However, information on the AMR risk in livestock house aerosol is limited, especially its association with antimicrobial usage (AMU). Therefore, this study was conducted to reveal the AMR profile of Staphylococcus, the major bacterial genus in the aerosol of the piggeries of Japanese farms, and the association between farm-level AMU and AMR. The investigation at 10 farrow-to-finish pig farms revealed that regardless of the sampling season and the piggery group, the resistance rate of isolated staphylococci for oxacillin, erythromycin, and lincomycin was more than 40% of the median and tended to be higher than that for other antimicrobials. The AMU adjusted by the defined daily dose (DDD-adjusted AMU) in the fattening piggery group was significantly higher than that in the sow piggery group (p < 0.05). Finally, for the fattening piggery group, the generalized linear mixed model revealed that the AMR rate for oxacillin, erythromycin, tetracycline, and chloramphenicol was positively associated with the corresponding class-based DDD-adjusted AMU of penicillins (odds ratio (OR) = 2.63, p = 0.03), macrolides (OR = 6.89, p = 0.0001), tetracyclines (OR = 2.48, p = 0.04), and amphenicols (OR = 3.22, p = 0.03), respectively. These significant positive associations observed in this study imply that the resistance rate for these antimicrobials may decrease by reducing the corresponding antimicrobials' use. In addition, the resistance rates for erythromycin and chloramphenicol also displayed a positive association with the AMU of antimicrobial classes other than macrolides and amphenicols, respectively. The mechanism underlying these phenomena is unclear; therefore, further evaluation will be needed. As limited studies have reported staphylococci in piggery aerosol and its AMR with quantitative AMU, these results based on on-farm investigations are expected to aid in establishing countermeasures for AMR of aerosol bacteria in pig farms.

A review of smart agriculture and production practices in Japanese large-scale rice farming.

Japanese farms currently occur on a small but expanding average physical scale and annual sales, in a decreasing and aging labor force, increasingly abandoned farmland and massive access of corporations powerful in capital and management. The government has proposed to accelerate agricultural growth through adopting high-level smart technologies in large-scale farms, with a series of favorite policies and measures. This paper reviews the connotations, characteristics and technologies of smart agriculture in the views of Japanese scholars, the practice of smart agriculture in Japan, followed by a case study on the smart rice production model 'NoshoNavi1000'. The results show that Japanese scholars have conducted in-depth and massive studies in smart agriculture, with regional characteristics in the orientations on labor-saving, precise management, disaster reduction and inheriting traditional farming skills. The government's ambitious objective is supported by its all-round policy package, including project demonstration, supporting services, environmental improvement, education and training, and overseas outreaching. Closely combined with the planting structure of Japanese agriculture, rice production is an important sector for the R&D and application of smart farming in the form of either individual technologies or models. The policies and technologies have achieved benefits in saving labor and production costs, and improving the profit margin. Through years of on-farm application, 'NoshoNavi1000' has been developed to involve the major technological components of smart agriculture. It has contributed to improving rice yield, production efficiency and profitability of large-scale farms, through real-time data collection, comprehensive and professional data mining, and specific and practical feedbacks. © 2022 Society of Chemical Industry.

Milk Yield of Hyper-Prolific Sows, and Growth of Piglets in Japanese Farms

Milk Yield of Hyper-Prolific Sows, and Growth of Piglets in Japanese Farms

Exploring the characteristics of smart agricultural development in Japan: Analysis using a smart agricultural kaizen level technology map

This study aims to clarify the Japanese characteristics of the spread of smart agriculture utilizing digital technology, which is expected to spread worldwide, and to provide policy implications for further dissemination of the technology. We conducted a questionnaire survey on actual conditions related to smart agriculture on Japanese farms. We have also proposed creation of a Smart Agricultural Kaizen Level (SAKL) technology map by applying the evaluation method used in management technology theory for the manufacturing industry. Using the results of the questionnaire survey and the proposed SAKL technology map, we analyzed the current pattern of expansion of smart agricultural technologies in Japan. Our results suggest that production efficiency in Japanese agriculture could be improved by raising the data visualization level and introducing smart agricultural technology. We also found that Japanese agriculture efficiency can be improved by introducing smart agricultural technology even if the data visualization level remains low. Smart agricultural technology automatically visualizes information and optimizes conditions without relying on the farmer's information literacy. At Japanese agriculture sites, the current smart agricultural technology introduction rate is less than 50%. To effectively disseminate smart agricultural technologies in the future, a policy should be implemented that promotes the development of a standardized package of smart agricultural technologies that can improve efficiency to some extent through default operation. With such a package, smart agriculture could be expanded without resorting to improving farmers' information literacy. Agricultural sites in Japan are thought to be currently engaged in developing such a standardized package of smart agricultural technologies.

Genetic relationships among emu populations in Japanese farms based on mitochondrial and microsatellite DNA polymorphisms.

Emus (Dromaius novaehollandiae) are expected to become a novel poultry species for producing eggs, meat, and oil. In our previous studies, Japanese emu populations were predicted to have reduced genetic diversity through inbreeding. For a sustainable emu industry in Japan, it is necessary to understand the current genetic structure and relationships in dispersed farms. In this study, we investigated the genetic structure and relationships of six Japanese emu farms based on mitochondrial DNA and microsatellite polymorphisms. We analyzed the DNA sequences of the mitochondrial D-loop region in 157 individuals and detected four haplotypes with four nucleotide substitution sites (Hap-a, Hap-b, Hap-c, and Hap-d). Analysis of molecular variance revealed that 43.6% of total variance was "among population," and the FST value was 0.436 with significant genetic differentiation (P < 0.001). In microsatellite analysis, the expected (HE ) and observed (HO ) heterozygosities were 0.53-0.64 and 0.44-0.59, respectively. Phylogenetic trees and STRUCTURE analysis revealed that the six Japanese farmed emu populations could be divided into four genetically differentiated groups. Therefore, we identified genetic resources that may be useful in extending the genetic diversity of Japanese farms and are predicted to contribute to the conservation and reconstruction of populations.

Judging the Perle Japonaise: The Techno-Legal Separation of Culture from Nature in 1920s Paris.

This article traces the making of a techno-legal apparatus to regulate a new object: the "cultured" pearl. In the early 1920s, round pearls cultivated on Japanese farms provoked alarm within the Paris association whose members traded more pearls than anywhere in Europe. Despite their claims to be connoisseurs of surfaces, anti-cultivation pearl dealers in Paris asserted that a pearl's identity could only be ascertained by examining its inner structure. By mid-decade, dedicated pearl testing laboratories appeared and supported French court rulings about what to call the products of Japanese pearl cultivation in relation to "natural" pearls. The meanings of nature and culture were not fixed, but transformed in the 1920s, amid legal and technical efforts to know la perle japonaise inside out.

일제강점기 구마모토(熊本)농장 화호지장에 관한 연구

This study focused on the Hwaho farm among Japanese farms that were at the center of rural exploitation during the Japanese colonial period. The contents of the study examined who Kumamoto, the owner of the farm, was, how he entered Chosun and Hwaho-ri, and how much land he owned. And what kind of buildings were in the Hwaho farm during the Japanese colonial period, how they were arranged, and how the space was organized according to the arrangement of buildings. Hwaho farm, the subject of the study, was the farm that managed the most land among Kumamoto's farms. Currently, farmer’s housing, Japanese employee housing, warehouses, and medical examination centers remain. In addition to Kumamoto, other Japanese and related buildings remain throughout the town. However, in recent years, a number of houses of enemy property such as Daue House, Sowha Ryokan, and shops are being destroyed without any records or investigations, so this study aims to record academic records of houses of enemy property remaining in Hwaho-ri Village.

Exportation of Manpower: A Case Study of Chinese Seasonal Laborers in an Agricultural District in Hokkaido

Chiebun District in Hokkaido, one of Japan’s largest vegetable- producing districts, has a long history of accepting agricultural laborers from China. Previously, farms in Chiebun District recruited seasonal laborers from the northeastern part of China, where per-capita income is much lower than China’s national average. At that time, the main reason Chinese laborers came to work in Chiebun District was to earn money. However, because of wage increases in China, it became difficult for Chiebun District farms to recruit these seasonal laborers. Around the same time, consumers’ demands for new types of vegetables were increasing in other regions such as Hebei, Henan, and Shandon Provinces, creating the need to train the farmers in these areas. Farms in Chiebun District provide comfortable living and working conditions for Chinese laborers. In return, the Chinese laborers, as indispensable manpower, contribute to the prosperity of the local agricultural industry in Chiebun District. As such, Chiebun District presents a model of a reciprocal relationship between Japanese farms and Chinese seasonal laborers.

ヒラ(技能実習ビザ)から幹部(技術ビザ)にも広がる外国人労働力:農業通年雇用者不足下の外国人の急速な量的質的拡大

ヒラ(技能実習ビザ)から幹部(技術ビザ)にも広がる外国人労働力:農業通年雇用者不足下の外国人の急速な量的質的拡大

Manure Compost Is a Potential Source of Tetracycline-Resistant Escherichia coli and Tetracycline Resistance Genes in Japanese Farms.

Manure compost has been thought of as a potential important route of transmission of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) from livestock to humans. To clarify the abundance of ARB and ARGs, ARB and ARGs were quantitatively determined in tetracycline-resistant Escherichia coli (harboring the tetA gene)-spiked feces in simulated composts. In the simulated composts, the concentration of spiked E. coli decreased below the detection limit at day 7. The tetA gene remained in manure compost for 20 days, although the levels of the gene decreased. Next, to clarify the field conditions of manure compost in Japan, the quantities of tetracycline-resistant bacteria, tetracycline resistance genes, and residual tetracyclines were determined using field-manure-matured composts in livestock farms. Tetracycline-resistant bacteria were detected in 54.5% of tested matured compost (6/11 farms). The copy number of the tetA gene and the concentrations of residual tetracyclines in field manure compost were significantly correlated. These results suggest that the use of antimicrobials in livestock constitutes a selective pressure, not only in livestock feces but also in manure compost. The appropriate use of antimicrobials in livestock and treatment of manure compost are important for avoiding the spread of ARB and ARGs.

養豚場における食肉検査結果の決定要因の主成分分析による解析法

食肉検査結果を生産者に還元し，衛生的な食肉生産を促進する事業が複数の自治体で進められているが，食肉検査結果と家畜の飼養条件の関係に関する報告は少ない．両者は多次元のデータであるため関係の解析が困難であることが問題となるが，主成分分析を用いれば多次元データを低次元のデータに縮約でき，この問題を克服できる．そこで，食肉検査データを含む多次元データから主成分分析により，肥育豚の廃棄，産子数及び子豚死亡率に係る3つの指標を作成し，それぞれとアンケート調査によって得た家畜の飼養条件との関係を重回帰分析した．重回帰分析で有意差が認められた飼養条件につき，縮約前のデータと飼養条件の関係を一般化線形混合モデル（GLMM）で分析した結果，オールイン・オールアウト，出荷日齢，断尾など6種の決定要因が示唆された．

カンボジア国における日本国への外国人技能実習生送出し

This study is to show the actual function of Japanese technical intern trainees from abroad by the interview surveys with A & B sending companies in Cambodia and returnees from Japan back to Cambodia. With the help of these companies and Japanese supervising organizations, Japanese farms, especially in vegetable ones, have accepted many trainees from developing countries to enable large-scale farming. In the survey, the trainees mentioned they had brought enough money to present the new houses to their parents and had got their carrier for the new job in the Japanese-affiliated companies.

Life cycle assessment of beef cow‐calf systems with and without grazing on abandoned cultivated lands in Japan

AbstractBeef production contributes to environmental problems, such as climate change, air pollution and water pollution. Our objective was to determine how much the introduction of beef cow grazing on abandoned lands into a housing system (housed in barns throughout the year) alters environmental impacts. We used life cycle assessment to evaluate the environmental impacts of beef cow‐calf systems with and without grazing on abandoned cultivated lands, on 11 Japanese farms. The functional unit was one marketed beef calf (Japanese Black) at 8 months of age. A reduction of global warming potential (GWP), acidification potential (AP) and eutrophication potential (EP) was found in all five grazing systems (including an experimental farm), compared with the average values for housing systems. A reduction of energy consumption was also found in the five grazing systems; however, the reduction was not large in one farm. Feed transportation and production were the main contributors to energy consumption, and unless there is a decrease in the energy consumption associated with these two processes, the energy consumption throughout the life cycle will not decrease. Thus, the introduction of grazing on abandoned lands can reduce environmental impacts, but the effects can be weakened or offset depending on the amount of imported feed. In the experimental farm with a grazing system, the reduction of GWP, AP, EP and energy consumption compared with the average values for the housing systems was 32, 48, 48 and 45%, respectively. In the four commercial farms with grazing systems, the reduction of GWP, AP, EP and energy consumption was 11–24, 13–22, 19–24 and 2–21%, respectively, which we regard as possible reductions in a real life situation. We conclude that a large reduction of environmental impacts could not be achieved solely through the introduction of grazing.

Characterization of multi-antibiotic-resistant Escherichia coli Isolated from beef cattle in Japan.

The emergence of multiple-antibiotic-resistance bacteria is increasing, which is a particular concern on livestock farms. We previously isolated 1,347 antimicrobial-resistant (AMR) Escherichia coli strains from the feces of beef cattle on 14 Japanese farms. In the present study, the genetic backgrounds and phylogenetic relationships of 45 AMR isolates were characterized by the chromosome phylotype, AMR phenotype, AMR genotype, and plasmid type. These isolates were classified into five chromosome phylotypes, which were closely linked to the farms from which they were isolated, suggesting that each farm had its own E. coli phylotype. AMR phenotype and plasmid type analyses yielded 8 and 14 types, all of which were associated with the chromosomal phylotype and, thus, to the original farms. AMR genotype analysis revealed more variety, with 16 types, indicating both inter- and intra-farm diversity. Different phylotype isolates from the same farm shared highly similar plasmid types, which indicated that plasmids with AMR genes could be transferred between phylotypes, thereby generating multi-antibiotic-resistant microorganisms. This ecological study demonstrated that the chromosome phylotype was strongly correlated with the farm from which they were isolated, while the AMR phenotype, genotype, and plasmid type were generally correlated with the chromosome phylotype and farm source.

酪農地域の生産情報の統合と生産情報を用いた疫学研究のススメ

A dairy farm owns much production data that are governed by some different cooperative societies. When we use those production data to study, we have to collect the data from some societies, integrate them using ID number of cattle or farm name, and use to analyze the association between a factor of research interest and production problems. Environment of dairy cattle in Japanese farms becomes diverse depending on the climate characteristics, self-sufficiency ratio for forage, land area for grass production, and so on. Most disorders in dairy cattle are known as environmental multifactorial problem. If a lot of risk factors for disorders are accumulated, as a result of that, some cattle become subclinical or clinical diseases. Therefore, to investigate an association with a problem in farms, we have to consider a number of factors in wide area and should select observational studies of epidemiology to large database. Now only a few scientists try to study about the field problems using production data in Japan. The reason for the number of the scientists has some possible causes, for example 1) no uniform management system for production data, 2) the cumbersome procedure to collect the production data, and 3) a few educational curriculum or training class to handle the production data. We have to think strategically into the future that we will unify all Japanese production data and make a system how to use the data for maintaining and improving Japanese livestock agriculture. Nobody doubts that Japanese production data is a repository of useful information. Shall we start epidemiological study using production data in Japanese dairy farms?

土地利用型農業における精密農業の普及条件―農業用ＧＰＳ機器市場と農業経営の対応の日米比較―

The objective of this paper is to give a prospect for the conditions of market penetration of precision farming (PA) technologies in field crop farms through the comparison of Japan and US situation. This paper focuses not only on farmers' adoption of PA technologies but also on the suppliers of PA equipments since they are under different situations of PA market and infrastructure. As a result of interview surveys, some technologies are not available to Japanese farms and most available equipments are more expensive than the US price due to the market size and language interpretation cost. GPS guidance systems are cost efficient for the Japanese farms if they can reduce less than 1% of factor input and labor cost, which is likely to be low enough to adopt them.

Euthanasia for Gilts and Sows on Japanese Commercial Farms

動物福祉の観点から，欧米では，病気や外傷などの問題があった繁殖雌豚に対して安楽死が実行されている。しかし，国内の生産農場における安楽死の現状については報告されていない。本研究の目的は，日本の生産農場における雌豚の安楽死率と安楽死リスクの測定，安楽死された雌豚とその他の雌豚における分娩後の週毎の雌豚割合の比較とした。本研究では，101農場における2001年から2004年に出生した62,742頭の雌豚の生涯記録を用いた。101農場のうち，25農場（24.8％）が安楽死を行っていた。この25農場において，安楽死雌豚の農場平均割合（±標準誤差）は1.27±0.38％であり，幅は0.06％から8.44％であった。この25農場における21,094頭の雌豚では，安楽死，死亡，淘汰雌豚の割合は，それぞれ1.7％，9.7％，88.6％であった。安楽死雌豚の平均淘汰産次と生涯生存日数は3.3±0.13産，717.2±18.58日であった。年間安楽死率は0.63％であった。安楽死雌豚348頭のうち，53.7％が起立不能，25.0％が四肢障害という理由によって安楽死されていた。安楽死雌豚は，淘汰雌豚よりも淘汰産次が低く，生涯生存日数が短かったが（P＜0.05），死亡雌豚とは差がみられなかった。産次0, 1，2の安楽死リスクは，それぞれ0.23％，0.27％，0.23％であった。また，産次が3産から6産に上がるにつれて，安楽死リスクは0.22％から0.59％に上がった。分娩後0, 1，2週における雌豚割合は，安楽死雌豚が2.7％，21.6％，8.4％，死亡雌豚が9.8％，24.1％，11.1％，淘汰雌豚が0.1％，1.3％，2.6％であった。結論として，国内生産農場では繁殖雌豚への安楽死はあまり実施されていなかった。安楽死雌豚の淘汰パターンは死亡雌豚と同様であった。動物福祉の観点から，歩行困難等を示す雌豚は，死亡を待つのでなく，安楽死させることが望ましい。

Euthanasia for Gilts and Sows on Japanese Commercial Farms

Euthanasia for Gilts and Sows on Japanese Commercial Farms