Broadening and exploiting the genetic base of white lupin

White lupin is a European crop with a long history of domestication and high potential interest for high-protein food or feedstuff. This report aims to summarize the research steps that were undertaken to (i) verify the extent of genetic diversity exploited by modern breeding, (ii) identify elite bitter-seed landraces and sweet-seed germplasm aimed to broaden the genetic base for European breeding, (iii) assess the genetic variation for tolerance to key abiotic stresses in the germplasm of the novel genetic base, and (iv) verify the potential of genomic models based on genotyping-bysequencing (GBS) SNP data to select simultaneously and cost-efficiently for some complex traits. Molecular diversity patterns of 83 landraces from nine major historical cropping regions and 15 commercial varieties confirmed that modern plant breeding exploited only a modest part of the crop genetic variation. Germplasm evaluation experiments for adaptation to severe drought or calcareous soil revealed substantial genetic variation (Annicchiarico and Thami-Alami, 2012; Annicchiarico et al., 2018), which, along with other information, was exploited to identify four elite landraces and four elite, sweet-seed lines that acted as parents of a broadly-based population. Some 144 sweet-seed lines extracted from this population were evaluated for grain yield under severe drought in a managed environment of Italy and for adaptation to moderately calcareous soil in a spring-sown environment of the Netherlands and an autumn-sown environment of Greece. We report on the observed line variation for these traits, and on the construction of genomic selection models and their ability to predict the line adaptation to drought or lime soil based on cross validations. Genome-enabled models may be used also to select for tolerance to anthracnose and the sweet-seed trait

Ancient DNA Suggests Dwarf and ‘Giant’ Emu Are Conspecific

) is unclear. King Island Emu were mainly distinguished by their much smaller size and a reported darker colour compared to modern Emu. oxidase subunit I (COI) region (1,544 bp), as well as a region of the melanocortin 1 receptor gene (57 bp) were sequenced using a multiplex PCR approach. The results show that haplotypes for King Island Emu fall within the diversity of modern Emu.These data show the close relationship of these emu when compared to other congeneric bird species and indicate that the King Island and modern Emu share a recent common ancestor. King Island emu possibly underwent insular dwarfism as a result of phenotypic plasticity. The close relationship between the King Island and the modern Emu suggests it is most appropriate that the former should be considered a subspecies of the latter. Although both taxa show a close genetic relationship they differ drastically in size. This study also suggests that rates of morphological and neutral molecular evolution are decoupled

Aboriginal Australian mitochondrial genome variation - An increased understanding of population antiquity and diversity

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ∼55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia's first settlers. © The Author(s) 2017

Kritische Prestatie Indicatoren, kans of bedreiging voor bio-sector? : Sturen op maatschappelijke doelen moet landbouwtransitie versnellen

De opgaven op het gebied van biodiversiteit, klimaatverandering, circulariteit, landschapskwaliteit, lucht-, bodem- en waterkwaliteit en dierenwelzijn zijn groot. In het landelijk gebied speelt de landbouw een sleutelrol. Met behulp van doelsturing wil de overheid de sector ruimte bieden om maatregelen zelf in te vullen. Dit zou bij de biologische sector als muziek in de oren moeten klinken

Adelie penguins and temperature changes in Antarctica: a long-term view

During the summer months, Adélie penguins represent the dominant biomass of terrestrial Antarctica. Literally millions of individuals nest in ice-free areas around the coast of the continent. Hence, these modern populations of Adélie penguins have often been championed as an ideal biological indicator of ecological and environmental changes that we currently face. In addition, Adélie penguins show an extraordinary record of sub-fossil remains, dating back to the late Pleistocene. At this time, temperatures were much lower than now. Hence, this species offers unique long-term information, at both the genomic and ecological levels, about how a species has responded to climate change over more than 40 000 years

Ancient mtDNA sequences from the First Australians revisited

The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains similar to 1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

NoWhole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.European Research Council grant (INTERRUPTB; no. 311725), European Research Council grant (TB-ACCELERATE; no. 638553), Foundation for Innovative New Diagnostics, German Center for Infection Research (DZIF), Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy (EXC 22167–390884018), FWO Odysseus G0F8316N, US National Institutes of Health BD2K K01 (MRF ES026835), Agence Nationale de la Recherche (ANR-16-CD35-0009