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      Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet

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          Abstract

          Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Our study aimed at identifying genetic components involved in early drought stress tolerance as a first step toward the development of improved pearl millet varieties or hybrids. A panel of 188 inbred lines from West Africa was phenotyped under early drought stress and well-irrigated conditions. We found a strong impact of drought stress on yield components. This impact was variable between inbred lines. We then performed an association analysis with a total of 392,493 SNPs identified using Genotyping-by-Sequencing (GBS). Correcting for genetic relatedness, genome wide association study identified QTLs for biomass production in early drought stress conditions and for stay-green trait. In particular, genes involved in the sirohaem and wax biosynthesis pathways were found to co-locate with two of these QTLs. Our results might contribute to breed pearl millet lines with improved yield under drought stress.

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          Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

          Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users.
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            Proteomic Analyses Provide Novel Insights into Plant Growth and Ginsenoside Biosynthesis in Forest Cultivated Panax ginseng (F. Ginseng)

            F. Ginseng (Panax ginseng) is planted in the forest to enhance the natural ginseng resources, which have an immense medicinal and economic value. The morphology of the cultivated plants becomes similar to that of wild growing ginseng (W. Ginseng) over the years. So far, there have been no studies highlighting the physiological or functional changes in F. Ginseng and its wild counterparts. In the present study, we used proteomic technologies (2DE and iTRAQ) coupled to mass spectrometry to compare W. Ginseng and F. Ginseng at various growth stages. Hierarchical cluster analysis based on protein abundance revealed that the protein expression profile of 25-year-old F. Ginseng was more like W. Ginseng than less 20-year-old F. Ginseng. We identified 192 differentially expressed protein spots in F. Ginseng. These protein spots increased with increase in growth years of F. Ginseng and were associated with proteins involved in energy metabolism, ginsenosides biosynthesis, and stress response. The mRNA, physiological, and metabolic analysis showed that the external morphology, protein expression profile, and ginsenoside synthesis ability of the F. Ginseng increased just like that of W. Ginseng with the increase in age. Our study represents the first characterization of the proteome of F. Ginseng during development and provides new insights into the metabolism and accumulation of ginsenosides.
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              The stay-green trait.

              Stay-green (sometimes staygreen) refers to the heritable delayed foliar senescence character in model and crop plant species. In a cosmetic stay-green, a lesion interferes with an early step in chlorophyll catabolism. The possible contribution of synthesis to chlorophyll turnover in cosmetic stay-greens is considered. In functional stay-greens, the transition from the carbon capture period to the nitrogen mobilization (senescence) phase of canopy development is delayed, and/or the senescence syndrome proceeds slowly. Yield and composition in high-carbon (C) crops such as cereals, and in high-nitrogen (N) species such as legumes, reflect the source-sink relationship with canopy C capture and N remobilization. Quantitative trait loci studies show that functional stay-green is a valuable trait for improving crop stress tolerance, and is associated with the domestication syndrome in cereals. Stay-green variants reveal how autumnal senescence and dormancy are coordinated in trees. The stay-green phenotype can be the result of alterations in hormone metabolism and signalling, particularly affecting networks involving cytokinins and ethylene. Members of the WRKY and NAC families, and an ever-expanding cast of additional senescence-associated transcription factors, are identifiable by mutations that result in stay-green. Empirical selection for functional stay-green has contributed to increasing crop yields, particularly where it is part of a strategy that also targets other traits such as sink capacity and environmental sensitivity and is associated with appropriate crop management methodology. The onset and progress of senescence are phenological metrics that show climate change sensitivity, indicating that understanding stay-green can contribute to the design of appropriate crop types for future environments. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: Writing – original draft
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: Project administrationRole: Writing – original draft
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: Writing – original draft
                Role: Data curationRole: Formal analysis
                Role: ConceptualizationRole: Formal analysisRole: Resources
                Role: Data curationRole: Formal analysisRole: Writing – original draft
                Role: ConceptualizationRole: SupervisionRole: Writing – review & editing
                Role: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                25 October 2018
                2018
                : 13
                : 10
                : e0201635
                Affiliations
                [1 ] DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France
                [2 ] Laboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
                [3 ] Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Institut Sénégalais des Recherches Agricoles (ISRA), Thiès, Senegal
                [4 ] Institut Togolais de Recherche Agronomique (ITRA), Lomé, Togo
                [5 ] International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Niamey, Niger
                [6 ] AGAP, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Institut National de la Recherche Agronomique (INRA), Montpellier SupAgro, Université de Montpellier, Montpellier, France
                [7 ] Eco&Sols, IRD, CIRAD, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
                [8 ] Laboratoire mixte international Intensification Ecologique des Sols cultivés en Afrique de l’Ouest, Dakar, Senegal
                [9 ] Laboratoire National de Recherches sur les Productions Végétales (LNRPV), ISRA, Dakar, Senegal
                [10 ] Laboratoire Commun de Microbiologie IRD/ISRA/Université Cheikh Anta Diop (UCAD), Dakar, Senegal
                Louisiana State University College of Agriculture, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                [¤a]

                Current address: UMR MARBEC, (CNRS, IRD, IFREMER, UM), Montpellier, France

                [¤b]

                Current address: Earth and Life Institute-Agronomy, Université Catholique de Louvain, Louvain-La-Neuve, Belgium

                Author information
                http://orcid.org/0000-0002-1978-8446
                http://orcid.org/0000-0002-6191-723X
                http://orcid.org/0000-0002-6568-6504
                Article
                PONE-D-18-20813
                10.1371/journal.pone.0201635
                6201870
                30359386
                8fa3cc2d-fd6e-4157-992a-9231a95d6904
                © 2018 Debieu et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 13 July 2018
                : 16 October 2018
                Page count
                Figures: 6, Tables: 4, Pages: 19
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100012948, Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100007599, Agropolis Fondation;
                Award ID: AF 1301-015
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-l0-LABX-0001-0l
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-16-IDEX-0006
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002803, Fondazione Cariplo;
                Award ID: FC 2013-0891
                Award Recipient :
                This work was supported by the IRD, the French Ministry for Research and Higher Education (PhD grant to SP) and the NewPearl grant in the frame of the CERES initiative by the Agropolis Fondation (N° AF 1301-015 to LL, as part of the "Investissement d'avenir" ANR-l0-LABX-0001-0l) under the frame of I-SITE MUSE (ANR-16-IDEX-0006) and by the Fondazione Cariplo (N° FC 2013-0891).
                Categories
                Research Article
                Biology and Life Sciences
                Plant Science
                Plant Physiology
                Plant Defenses
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Pathology
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
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                Custom metadata
                All phenotypic data are within the paper and its Supporting Information files. Genotyping (GBS) data are available in genbank (acc. PRJNA492967).

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