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Chian Teng Ong Elizabeth M Ross Gry B Boe-Hansen Conny Turni Ben J Hayes Ala E Tabor 《Journal of animal science》2022,100(1)
Animal metagenomic studies, in which host-associated microbiomes are profiled, are an increasingly important contribution to our understanding of the physiological functions, health and susceptibility to diseases of livestock. One of the major challenges in these studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of metagenomic profiling. This is the first study comparing the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. We compared the new method of Oxford Nanopore Technologies (ONT) adaptive sequencing, which can be used to target or eliminate defined genetic sequences, to standard ONT sequencing, Illumina 16S rDNA amplicon sequencing, and Illumina shotgun sequencing. The efficiency of each method in recovering the metagenomic data and recalling the metagenomic profiles was assessed. ONT adaptive sequencing yielded a higher amount of metagenomic data than the other methods per 1 Gb of sequence data. The increased sequencing efficiency of ONT adaptive sequencing consequently reduced the amount of raw data needed to provide sufficient coverage for the metagenomic samples with high host-to-microbe DNA ratio. Additionally, the long reads generated by ONT adaptive sequencing retained the continuity of read information, which benefited the in-depth annotations for both taxonomical and functional profiles of the metagenome. The different methods resulted in the identification of different taxa. Genera Clostridium, which was identified at low abundances and categorized under Order “Unclassified Clostridiales” when using the 16S rDNA amplicon sequencing method, was identified to be the dominant genera in the sample when sequenced with the three other methods. Additionally, higher numbers of annotated genes were identified with ONT adaptive sequencing, which also produced high coverage on most of the commonly annotated genes. This study illustrates the advantages of ONT adaptive sequencing in improving the amount of metagenomic data derived from microbiome samples with high host-to-microbe DNA ratio and the advantage of long reads in preserving intact information for accurate annotations. 相似文献
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In the Andean region, the Preduza project and its partners combined breeding for durable disease resistance using locally
adapted cultivars and farmer participatory methods. The approach taken resembles participatory variety selection (PVS). Farmers
participated in the selection of advanced materials, rather than finished cultivars. This paper describes this approach and
reports experiences with farmers–breeders collaboration.
As breeders involved farmers as participants, they learned more about the most important criteria of male and female farmers
for preferred cultivars in the marginal environments of Andean cropping systems. This approach encouraged the use of locally
adapted cultivars (often landraces), made the breeders less dependent on foreign materials, and has resulted in selection
and development of new wheat, barley, common bean, quinoa, potato and maize cultivars.
Breeding programmes based on crossing locally adapted cultivars followed by selection by the breeders in the early phases
of the breeding programmes and by participatory selection with the farmers in the more advanced stages of the breeding programmes
appeared successful. It became clear that breeders must be well acquainted with the farmer preferences such as the requirements
for specific agronomic, storage, processing and marketing traits.
Over a period of five years the centralized formal breeding approach predominantly based on material produced by the international
institutes was replaced by decentralized breeding approaches based largely on local germplasm with extensive farmer participation. 相似文献
13.
Erica gracilis is an important bedding plant in Northern Europe. Due to self-incompatibility, the development of new varieties was largely based on mutant selection from the predominant variety ’Glasers Rote‘. By crossing ’Glasers Rote‘ with wild types from South Africa in the 1980th, new cross-based varieties arose. Since the cultivation of cross-based varieties, precocious floral withering has been observed more frequently in production areas, suggesting that successful fertilization through open-pollination induces early floral senescence. A cluster analysis of current varieties based on AFLP markers confirmed the close relationship of old varieties and showed the expanded genetic diversity of cross-based varieties. Cross-experiments revealed that both, crosses of ’Glasers Rote‘-based genotypes with new cross-based genotypes and crosses between new genotypes, were successful. In contrast, selfings as well as crosses between old genotypes failed to produce seeds due to inhibition of pollen tube growth. Interestingly, we detected one self-compatible genotype, which provides new possibilities for breeding. No significant effect of open-pollination on the flowering period was observed by studying 16 genotypes, including old and new ones. This circumstance allows the mixed cultivation of different varieties in one production area. However, the flowering period was significantly affected by genotype and environment, suggesting that environmentally adapted varieties with long flowering periods can be bred. 相似文献
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Can cultivars from participatory plant breeding improve seed provision to small-scale farmers? 总被引：1，自引：0，他引：1
Seed provision for small-scale farmers deals with multiple constraints. These include, on the supply side, high seed production
costs and poor adaptedness of the cultivars, and on the demand side, anticyclical demand and low and variable sales. Approaches
to improve seed provision to this sector of farmers have so far not been very successful. This paper discusses how well-adapted
cultivars developed through participatory plant breeding (PPB) initiatives create new opportunities for production and distribution
of quality seed. It reviews supply and demand-side issues, based on research and experiences with seed production. Given better
adaptation of PPB-cultivars, the diffusion of seed of PPB initiatives should not be a major bottleneck. But constraints in
the provision of quality seed from cultivars that are commonly used remain and need to be addressed. Major points of attention
are cost-effective seed production and distribution, high information linked transaction costs, and appropriate seed production
technology. Research on these issues is needed to understand farmers’ seed demand. At the same time, these issues need to
be taken into account in new seed production initiatives that apply integrated approaches. Long term commitment by farmers
to produce, distribute and use seeds is a condition. Even if seed production is not economically sustainable at household
or organization level, farmer-based seed systems generate benefits to society as a whole that justify long term public investment
to maintain them. 相似文献
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Invertebrates are an expansive and diverse group of animals that have had little attention regarding anesthesia and analgesia. Economic use, environmental awareness, laboratory research, and increasing demand for invertebrates as pets has lead to a greater desire for knowledge for these animals in the veterinary medical community. With the increasing number of animal welfare regulations, various scientific studies have improved the overall knowledge of invertebrate medicine, but much more research is required to fully understand anesthesia techniques in the different species treated by veterinarians. Analgesia is a controversial and often neglected topic with invertebrates because of the common belief that invertebrates do not feel pain. Recently, the idea that invertebrates do not feel pain has been challenged with the discovery of nociceptive pathways similar to those in vertebrates. This article presents a general overview of anesthetics and analgesics used in selective invertebrate taxa. 相似文献