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      Genome-wide association study and its applications in the non-model crop Sesamum indicum

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          Abstract

          Background

          Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame.

          Results

          In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame.

          Conclusions

          Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12870-021-03046-x.

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          Most cited references144

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          Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

          Michiru Nishita, Seung-Yeol Park, Tadashi Nishio … (2017)
          Signaling through the Ror2 receptor tyrosine kinase promotes invadopodia formation for tumor invasion. Here, we identify intraflagellar transport 20 (IFT20) as a new target of this signaling in tumors that lack primary cilia, and find that IFT20 mediates the ability of Ror2 signaling to induce the invasiveness of these tumors. We also find that IFT20 regulates the nucleation of Golgi-derived microtubules by affecting the GM130-AKAP450 complex, which promotes Golgi ribbon formation in achieving polarized secretion for cell migration and invasion. Furthermore, IFT20 promotes the efficiency of transport through the Golgi complex. These findings shed new insights into how Ror2 signaling promotes tumor invasiveness, and also advance the understanding of how Golgi structure and transport can be regulated.
          Article 0 comments Cited 3398 times – based on 0 reviews     Review now
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            Double-slit photoelectron interference in strong-field ionization of the neon dimer

            Maksim Kunitski, Nicolas Eicke, Pia Huber … (2019)
            Wave-particle duality is an inherent peculiarity of the quantum world. The double-slit experiment has been frequently used for understanding different aspects of this fundamental concept. The occurrence of interference rests on the lack of which-way information and on the absence of decoherence mechanisms, which could scramble the wave fronts. Here, we report on the observation of two-center interference in the molecular-frame photoelectron momentum distribution upon ionization of the neon dimer by a strong laser field. Postselection of ions, which are measured in coincidence with electrons, allows choosing the symmetry of the residual ion, leading to observation of both, gerade and ungerade, types of interference.
            Article 0 comments Cited 2518 times – based on 0 reviews     Review now
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              Inference of Population Structure Using Multilocus Genotype Data

              Jonathan Pritchard, Matthew Stephens, Peter Donnelly … (2001)
              We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
              Article 0 comments Cited 2337 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Komivi Dossa: dossakomivi@gmail.com
                Linhai Wang: linhai827@163.com
                Journal
                Journal ID (nlm-ta): BMC Plant Biol
                Journal ID (iso-abbrev): BMC Plant Biol
                Title: BMC Plant Biology
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2229
                Publication date (Electronic): 22 June 2021
                Publication date PMC-release: 22 June 2021
                Publication date Collection: 2021
                Volume: 21
                Electronic Location Identifier: 283
                Affiliations
                [1 ]GRID grid.464406.4, ISNI 0000 0004 1757 9469, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, ; No.2 Xudong 2nd Road, Wuhan, 430062 China
                [2 ]Humera Agricultural Research Center of Tigray Agricultural Research Institute, Humera, Tigray Ethiopia
                [3 ]GRID grid.8191.1, ISNI 0000 0001 2186 9619, Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, , Université Cheikh Anta Diop, ; BP 5005 Dakar-Fann, 10700 Dakar, Senegal
                [4 ]GRID grid.412037.3, ISNI 0000 0001 0382 0205, Laboratory of Genetics, Horticulture and Seed Sciences, Faculty of Agronomic Sciences, , University of Abomey-Calavi, ; 01 BP 526, Cotonou, Republic of Benin
                [5 ]GRID grid.8191.1, ISNI 0000 0001 2186 9619, Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, , Université Cheikh Anta Diop, ; BP 5005 Dakar-Fann, 10700 Dakar, Senegal
                Article
                Publisher ID: 3046
                DOI: 10.1186/s12870-021-03046-x
                PMC ID: 8218510
                PubMed ID: 34157965
                SO-VID: 3526c0df-0ed3-4619-bc8b-117f6dd25933
                Copyright © © The Author(s) 2021
                License:

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                Date received : 25 October 2020
                Date accepted : 17 May 2021
                Categories
                Subject: Review
                Custom metadata
                issue-copyright-statement © The Author(s) 2021

                ScienceOpen disciplines: Plant science & Botany
                Keywords: gwas,sesame,statistical models,genomics assisted breeding
                Data availability:
                ScienceOpen disciplines: Plant science & Botany
                Keywords: gwas, sesame, statistical models, genomics assisted breeding

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