International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

Tag

GGE biplot

2 RESULTS
Bioinformatics and systems biology of plants symposiumGenomic analysis of Vavilov\’s historic chickpea landraces using GWAS, AMMI and GGE biplot analyses

Genomic analysis of Vavilov\’s historic chickpea landraces using GWAS, AMMI and GGE biplot analyses

No Comment on Genomic analysis of Vavilov\’s historic chickpea landraces using GWAS, AMMI and GGE biplot analyses

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/247.pdf”]
Alena Sokolkova1, Sergey V. Bulyntsev2, Peter L. Chang3, Noelia Carrasquila-Garcia4, Eric von Wettberg5, Margarita A. Vishnyakova6, Douglas R. Cook7, Sergey V. Nuzhdin8, Maria G. Samsonova9
1Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia, alyonasok@yandex.ru
2Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, s_bulyntsev@mail.ru
3University of Southern California, Program in Molecular and Computational Biology, Dornsife College of Letters Arts & Sciences, Los Angeles, CA 90089 USA, peterc@usc.edu
4University of California Davis, Department of Plant Pathology, Davis, CA 95616 USA, noecarras@ucdavis.edu
5University of Vermont, Department of Plant and Soil Science, Burlington, VT 05405, USA, eric.bishop-von-wettberg@uvm.edu
6Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, m.vishnyakova@vir.nw.ru
7University of California Davis, Department of Plant Pathology, Davis, CA 95616 USA, drcook@ucdavis.edu
8University of Southern California, Program in Molecular and Computational Biology, Dornsife College of Letters Arts & Sciences, Los Angeles, CA 90089 USA, snuzhdin@usc.edu
9Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia, m.g.samsonova@gmail.com

The Vavilov seed bank contains numerous landraces collected nearly hundred years ago, before intensive breeding of most crops, and thus is a potential reservoir of historic crop adaptations. Here we analyze the genomes of 407 of Vavilov\’s original landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. We performed GWAS to find associations between VIR’s chickpea accessions and phenotypic data obtained in Kuban experimental station of VIR in 2017 under infectious conditions. To find out the effects of infectious conditions on phenotypic traits, the data was subjected to AMMI and GGE biplot analyses.

Bioinformatics and systems biology of plants symposiumAnalysis of agronomic traits of mungbean (Vigna radiata) accessions from the World Vegetable Gene Bank (Taiwan)

Analysis of agronomic traits of mungbean (Vigna radiata) accessions from the World Vegetable Gene Bank (Taiwan)

No Comment on Analysis of agronomic traits of mungbean (Vigna radiata) accessions from the World Vegetable Gene Bank (Taiwan)

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/249.pdf”]
Alena Sokolkova1, Marina Burlyaeva2, Tatjana Valiannikova3, Margarita A. Vishnyakova4, Roland Schafleitner5, Cheng-Ruei Lee6, Chau-Ti Ting7, Sergey V. Nuzhdin8, Maria G. Samsonova9, Eric von Wettberg10
1Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia, alyonasok@yandex.ru
2Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, m.burlyaeva@vir.nw.ru
3Kuban Branch of Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), Krasnodar region, Russia, fitolaka61@yandex.ru
4Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, m.vishnyakova@vir.nw.ru
5World Vegetable Center, Shanhua, Tainan 74199, Taiwan, roland.schafleitner@worldveg.org
6National Taiwan University, Taipei 106, Taiwan, chengrueilee@ntu.edu.tw
7National Taiwan University, Taipei 106, Taiwan, ctting@ntu.edu.tw
8University of Southern California, Program in Molecular and Computational Biology, Dornsife College of Letters Arts & Sciences, Los Angeles, CA 90089 USA, snuzhdin@usc.edu
9Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia, m.g.samsonova@gmail.com
10University of Vermont, Department of Plant and Soil Science, Burlington, VT 05405, USA, eric.bishop-von-wettberg@uvm.edu

The World Vegetable Gene Bank, in Taiwan, houses a unique genebank of mungbean. Here we analyze the genomes of 293 accessions that represent the major market classes. GWAS analysis conducted on phenotypic data obtained in Astrakhan experimental station of VIR in 2019 and multi-environmental GWAS analysis with phenotypic data obtained in different locations and time periods (Taiwan 1984, Taiwan 2018, India 2016, Kuban 2018, Astrakhan 2019) identified a large number of genome intervals and potential gene candidates that may affect important agronomic traits. To find out the effects of different climatic conditions on phenotypic traits, the data was subjected to AMMI and GGE biplot analyses. Phenotyping the mini-core collection of mungbean in different climatic locations can estimate phenology traits such as maturation. Uncovering SNPs for these traits will speed breeding efforts for production of mungbean suitable for cultivation in temperate regions.