Correspondence

quantification, real-time PCR, rumen, stearic acid producers

Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost-Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays

Kompetitive allele-specific polymerase chain reaction (KASP) assays have emerged as cost-effective marker assays especially for molecular breeding applications. Therefore, a set of 96 informative single nucleotide polymorphisms (SNPs) was used to develop KASP assays in groundnut or peanut (Arachis spp.). Developed assays were designated as groundnut KASP assay markers (GKAMs) and screened on 94 genotypes (validation set) that included parental lines of 27 mapping populations, seven synthetic autotetraploid and amphidiploid lines, and 19 wild species accessions. As a result, 90 GKAMs could be validated and 73 GKAMs showed polymorphism in the validation set. Validated GKAMs were screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships. Cluster analysis of marker allelic data grouped accessions according to their genome type, subspecies, and botanical variety. The subspecies Arachis hypogaea L. subsp. fastigiata Waldron and A. hypogaea subsp. hypogaea formed distinct cluster; however, some overlaps were found indicating their frequent intercrossing during the course of evolution. The wild species, having diploid genomes, were grouped into a single cluster. The average polymorphism information content value for polymorphic GKAMs was 0.32 in the validation set and 0.31 in the reference set. These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species

One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

The rumen microbial metagenome associated with high methane production in cattle

Acknowledgements The Rowett Institute of Nutrition and Health and SRUC are funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The project was supported by Defra and the DA funded Agricultural Greenhouse Gas Inventory Research Platform, the Technology Strategy Board (Project No: TP 5903–40240) and the Biotechnology and Biological Sciences Research Council (BBSRC; BB/J004243/1, BB/J004235/1). Our thanks are due to the excellent support staff at the SRUC Beef and Sheep Research Centre, Edinburgh, and to Silvia Ramos Garcia for help in interrogating the data. MW and RR contributed equally to the paper and should be considered as joint last authors.Peer reviewedPublisher PD

Peptide hydrolysis by human colonic bacteria is also a biphasic process carried out by Bacteroides-like organisms

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