GENOMIC AND TRANSCRIPTOMIC APPROACHES TOWARDS THE GENETIC IMPROVEMENT OF AN UNDERUTILISED CROPS: THE CASE OF BAMBARA GROUNDNUT

With the world population estimated to be nine billion by 2050, the need to exploit plant genetic diversity in order to increase and diversify global food supply, and minimise the over-reliance for food on a few staple crops is of the utmost importance. Bambara groundnut ( Vigna subterranea (L) Verdc.), is underutilised legume indigenous to Africa, rich in carbohydrates, with reasonable amounts of protein. It is known to be drought tolerant, able to grow on marginal lands where other major crops cannot with minimal rainfall (<700 mm) and chemical inputs. Crop improvement for abiotic stress tolerance and increasing/stabilising yield have been difficult to achieve due to the complex nature of these stresses, and the genotype x environment interaction (GxE). This review paper highlights how a number of recent technologies and approaches used for major crop research, can be translated into use in research of minor crops, using bambara groundnut as an exemplar species. Using drought tolerance as a trait of interest in this crop, we will demonstrate how limitations can affect genomic approaches for understanding traits in bambara groundnut, and, how genomic and transcriptomic methodologies developed for major crops can be applied to underutilised crops for better understanding of the genetics governing important agronomic traits. Furthermore, such approaches will allow for cross species comparison between major and minor crops, exemplified by bambara groundnut leading to improved research in such crops. This will lead to a better understanding of the role of stress-responsive genes and drought adaptation in this underutilised legume.Avec la population mondiale estim\ue9e \ue0 neuf milliards de personnes \ue0 \ue9ch\ue9ance 2050, il est imp\ue9rieux d\u2019exploiter la diversit\ue9 g\ue9n\ue9tique des plantes afin d\u2019accro\ueetre et diversifier la production globale en aliments, mais aussi r\ue9duire la d\ue9pendance \ue0 outrance de peu d\u2019 aliments de base pour l\u2019alimentation humaine. Le vouandzou ( Vigna subterranea (L) Verdc.), est une l\ue9gumineuse indig\ue8ne sous utilis\ue9e enAfrique, mais qui est riche en amidon, avec une quantit\ue9 raisonnable de proteine. Il reconnu comme \ue9tant resistant \ue0 la s\ue9cheresse, il est capable de pousser et de r\ue9aliser un cycle v\ue9g\ue9tatif et reproducteur parfait dans les zones marginales de basse pluiviom\ue9trie (<700 mm) o\uf9 d\u2019autres cultures majeures ne peuvent survivre. L\u2019am\ue9lioration des cultures pour la tol\ue9rance face aux stress abiotiques et l\u2019accroissement et la stabilization des rendements ont \ue9t\ue9 difficiles \ue0 r\ue9aliser en raison de nature complexe de ces stress et l\u2019influence de l\u2019interaction genotype-environment (GxE). Cette revue de literature montre comment les nombreuses technologies et approaches r\ue9centes utilis\ue9es par la recherche sur les cultures majeures peuvent adapt\ue9es et utilis\ue9es dans la recherhe sur les cultures mineures, en se servant du bambara groundnut comme esp\ue8ce mod\ue8le. En prenant la tolerance \ue0 la s\ue9cheresse comme caract\ue8re d\ue9sir\ue9 pour cette culture, nous allons d\ue9montrer commnents les insuffisances des approches de g\ue9nomique peuvent emp\ueacher la ma\ueetrise des caract\ue8res d\ue9sir\ue9s chez le vouandzou et comment les techniques de g\ue9nomique et de transcriptomique d\ue9velopp\ue9es pour les cultures majeures peuvent \ueatre appliqu\ue9es aux cultures sous utilis\ue9es afin de mieux comprendre les d\ue9terminants g\ue9n\ue9tiques gouvernant les caract\ue8res agronomiques. De plus, de telles approaches permettra de comparer les cultures majeures et mineures, avec ici l\u2019exemple du vouandzou qui permettra d\u2019am\ue9liorer le niveau de recherche chez de telles cultures. Cela permettra de mieux comprendre le r\uf4le des genes r\ue9pondant au stress hydrique et l\u2019adaptation \ue0 la s\ue9cheresse chez cette l\ue9gumineuse sous utilis\ue9e

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding Information: GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file : Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services. Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

3D analysis of medium field with consideration of perpendicular head-medium combinations

10.1109/APMRC.2006.365937Asia-Pacific Magnetic Recording Conference 2006, Digest of APMRC 2006