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      Evaluation and identification of wild lentil accessions for enhancing genetic gains of cultivated varieties

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          Abstract

          Domesticated lentil has a relatively narrow genetic base globally and most released varieties are susceptible to severe biotic and abiotic stresses. The crop wild relatives could provide new traits of interest for tailoring novel germplasm and cultivated lentil improvement. The primary objective of this study was to evaluate wild lentil accessions for identification of economically viable agro-morphological traits and resistance against major biotic stresses. The study has revealed substantial variations in seed yield and its important component characters. Further, the diversity analysis of wild accessions showed two major clusters which were bifurcated into sub-clusters, thereby suggesting their wider genetic divergence. However, principal component analysis exhibited that seed yield plant -1, number of seeds plant -1, number of pods plant -1, harvest index and biological yield plant -1 contributed significantly to the total genetic variation assessed in wild lentil taxa. Moreover, some of the wild accessions collected from Syria and Turkey regions showed resistance against more than one disease indicating rich diversity of lentil genetic resources. The identification of most promising genotypes carrying resistance against major biotic stresses could be utilized in the cultivated or susceptible varieties of lentil for enhancing genetic gains. The study has also identified some trait specific accessions, which could also be taken into the consideration while planning distant hybridization in lentil.

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          Estimates of Genetic and Environmental Variability in Soybeans1

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            Classification and Characterization of Species within the Genus Lens Using Genotyping-by-Sequencing (GBS)

            Lentil (Lens culinaris ssp. culinaris) is a nutritious and affordable pulse with an ancient crop domestication history. The genus Lens consists of seven taxa, however, there are many discrepancies in the taxon and gene pool classification of lentil and its wild relatives. Due to the narrow genetic basis of cultivated lentil, there is a need towards better understanding of the relationships amongst wild germplasm to assist introgression of favourable genes into lentil breeding programs. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows multiplexing of up to 384 samples or more per library to generate genome-wide single nucleotide Polymorphism (SNP) markers. In this study, we aimed to characterize our lentil germplasm collection using a two-enzyme GBS approach. We constructed two 96-plex GBS libraries with a total of 60 accessions where some accessions had several samples and each sample was sequenced in two technical replicates. We developed an automated GBS pipeline and detected a total of 266,356 genome-wide SNPs. After filtering low quality and redundant SNPs based on haplotype information, we constructed a maximum-likelihood tree using 5,389 SNPs. The phylogenetic tree grouped the germplasm collection into their respective taxa with strong support. Based on phylogenetic tree and STRUCTURE analysis, we identified four gene pools, namely L. culinaris/L. orientalis/L. tomentosus, L. lamottei/L. odemensis, L. ervoides and L. nigricans which form primary, secondary, tertiary and quaternary gene pools, respectively. We discovered sequencing bias problems likely due to DNA quality and observed severe run-to-run variation in the wild lentils. We examined the authenticity of the germplasm collection and identified 17% misclassified samples. Our study demonstrated that GBS is a promising and affordable tool for screening by plant breeders interested in crop wild relatives.
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              Genetic diversity in major farm crops on the farm and in reserve

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Writing – original draft
                Role: Data curationRole: Formal analysis
                Role: MethodologyRole: Validation
                Role: Data curationRole: Validation
                Role: Formal analysisRole: Methodology
                Role: MethodologyRole: Validation
                Role: Data curationRole: Formal analysis
                Role: Funding acquisitionRole: Methodology
                Role: MethodologyRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 March 2020
                2020
                : 15
                : 3
                : e0229554
                Affiliations
                [1 ] Regional Station, National Bureau of Plant Genetic Resources, Shimla, India
                [2 ] National Bureau of Plant Genetic Resources, Pusa, New Delhi, India
                [3 ] CSK Himachal Pradesh Agriculture University, Palampur, India
                [4 ] Rafi Ahmad Kidwai College of Agriculture, Sehore, India
                [5 ] Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Australia
                [6 ] South Asia and China Regional Programme, International Centre for Agricultural Research in Dry Areas, DPS Marg, Pusa, New Delhi, India
                Louisiana State University College of Agriculture, UNITED STATES
                Author notes

                Competing Interests: Authors declare that they have no competing interests.

                Author information
                http://orcid.org/0000-0002-5644-9144
                Article
                PONE-D-19-35002
                10.1371/journal.pone.0229554
                7053756
                32126106
                5cf58d8c-bb06-4b51-af13-4d6a493a860e
                © 2020 Singh 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
                : 3 January 2020
                : 6 February 2020
                Page count
                Figures: 6, Tables: 5, Pages: 14
                Funding
                Authors thank the Regional Coordinator of South Asia and China Regional Programme for grant in aid to accomplish the proposed research.
                Categories
                Research Article
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Seeds
                Biology and Life Sciences
                Genetics
                Plant Genetics
                Crop Genetics
                Biology and Life Sciences
                Plant Science
                Plant Genetics
                Crop Genetics
                Biology and Life Sciences
                Plant Science
                Plant Pathology
                Plant Pathogens
                Plant Fungal Pathogens
                Powdery Mildew
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Fungal Pathogens
                Fusarium
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Fungal Pathogens
                Fusarium
                Biology and Life Sciences
                Mycology
                Fungal Pathogens
                Fusarium
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Flowering Plants
                People and Places
                Geographical Locations
                Asia
                Turkey (Country)
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                Europe
                Turkey (Country)
                People and Places
                Geographical Locations
                Asia
                Syria
                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
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Ecology and Environmental Sciences
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
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                All relevant data are within the paper and its Supporting Information files

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