Genetic Diversity and Population Structure Analysis of Tropical Soybean (Glycine max (L.) Merrill) using Single Nucleotide Polymorphic Markers

1
Tonny Obua
Tonny Obua
2
Julius P. Sserumaga
Julius P. Sserumaga
3
Stephen O. Opiyo
Stephen O. Opiyo
4
Phinehas Tukamuhabwa
Phinehas Tukamuhabwa
5
Thomas L. Odong
Thomas L. Odong
6
Josiah Mutuku
Josiah Mutuku
7
Nasser Yao
Nasser Yao

Send Message

To: Author

GJSFR Volume 20 Issue D6

Article Fingerprint

ReserarchID

WD869

Genetic Diversity and Population Structure Analysis of Tropical Soybean (Glycine max (L.)  Merrill) using Single Nucleotide Polymorphic Markers Banner
  • English
  • Afrikaans
  • Albanian
  • Amharic
  • Arabic
  • Armenian
  • Azerbaijani
  • Basque
  • Belarusian
  • Bengali
  • Bosnian
  • Bulgarian
  • Catalan
  • Cebuano
  • Chichewa
  • Chinese (Simplified)
  • Chinese (Traditional)
  • Corsican
  • Croatian
  • Czech
  • Danish
  • Dutch
  • Esperanto
  • Estonian
  • Filipino
  • Finnish
  • French
  • Frisian
  • Galician
  • Georgian
  • German
  • Greek
  • Gujarati
  • Haitian Creole
  • Hausa
  • Hawaiian
  • Hebrew
  • Hindi
  • Hmong
  • Hungarian
  • Icelandic
  • Igbo
  • Indonesian
  • Irish
  • Italian
  • Japanese
  • Javanese
  • Kannada
  • Kazakh
  • Khmer
  • Korean
  • Kurdish (Kurmanji)
  • Kyrgyz
  • Lao
  • Latin
  • Latvian
  • Lithuanian
  • Luxembourgish
  • Macedonian
  • Malagasy
  • Malay
  • Malayalam
  • Maltese
  • Maori
  • Marathi
  • Mongolian
  • Myanmar (Burmese)
  • Nepali
  • Norwegian
  • Pashto
  • Persian
  • Polish
  • Portuguese
  • Punjabi
  • Romanian
  • Russian
  • Samoan
  • Scots Gaelic
  • Serbian
  • Sesotho
  • Shona
  • Sindhi
  • Sinhala
  • Slovak
  • Slovenian
  • Somali
  • Spanish
  • Sundanese
  • Swahili
  • Swedish
  • Tajik
  • Tamil
  • Telugu
  • Thai
  • Turkish
  • Ukrainian
  • Urdu
  • Uzbek
  • Vietnamese
  • Welsh
  • Xhosa
  • Yiddish
  • Yoruba
  • Zulu

Soybean (Glycine max (L.) Merrill) is among the most important crops worldwide due to its numerous uses in feed, food, biofuel, and significant atmospheric nitrogen fixation capability. To understand the genetic diversity and population structure of tropical soybean germplasm, 89 genotypes from diverse sources were analyzed using 7,962 SNP markers. The AMOVA results showed low diversity among and high within the populations, while the polymorphism information content (PIC) was 0.27. Both phylogenetic and principal component analysis grouped the 89 soybean genotypes into three major clusters, while population structure grouped the soybean genotypes into two subpopulations. On the other, the average Roger genetic distances within the study population was 0.34. The low diversity reported in the studied soybean germplasm pool is particularly worrying, considering the new trends of climate change and the emergence of new pests and diseases of soybean. Therefore, in order to address these challenges and develop soybean varieties with desirable traits, there is a need to broaden the genetic base of tropical soybean through the importation of germplasm from other countries.

40 Cites in Articles

References

  1. Sampson Twumasi-Ankrah,Michael Owusu,Simon Appiah,Wilhemina Pels,Doris Arthur (2012). Forecasting COVID-19 Confirmed Cases in Ghana: A Model Selection Approach.
  2. Peter Bradbury,Zhiwu Zhang,Dallas Kroon,Terry Casstevens,Yogesh Ramdoss,Edward (2007). TASSEL : Software for Association Mapping of Complex Traits in Diverse Samples.
  3. Devendra Chauhan,J Bhat,A Thakur,S Kumari,Z Hussain,C Satyawathi (2015). Molecular Characterization and Genetic Diversity Assessment in Soybean [ Glycine Max ( L .) Merr.
  4. Wu Chen,Lu Hou,Zhiyong Zhang,Xiaoming Pang,Yingyue Li (2017). Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers.
  5. V Dayaman,N Senthil,M Raveendran,N Nadarajan,P Shanmugasundaram,P Balasubramanian (2009). Diversity Analysis in Selected Indian Soybean [Glycine Max (L.) Merrill] Using Morphological and SSR Markers.
  6. M Doldi,J Vollmann,T Lelley (1997). Genetic Diversity in Soybean as Determined by RAPD and Microsatellite Analysis.
  7. Dent Earl,Bridgett Vonholdt (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method.
  8. Guillaume Evanno,Sebastien Regnaut,Jerome Goudet (2005). Detecting the number of clusters of individuals using the software <scp>structure</scp>: a simulation study.
  9. S Gupta,J Manjaya (2017). Genetic Diversity and Population Structure of Indian Soybean (Glycine Max (L.) Merr.) as Revealed by Microsatellite Markers.
  10. Raoni Gwinner,Tesfahun Setotaw,Moacir Pasqual,Joao Santos,Alan Zuffo,Everton Zambiazzi,Adriano Bruzi (2017). Genetic diversity in Brazilian soybean germplasm.
  11. D Hao,H Cheng,Z Yin,S Cui,D Zhang,H Wang,D Yu (2012). Identification of Single Nucleotide Polymorphisms and Haplotypes Associated with Yield and Yield Components in Soybean (Glycine Max) Landraces across Multiple Environments.
  12. Yegappa Hipparagi,Rakesh Singh,Debjani Choudhury,Veena Gupta (2017). Genetic Diversity and Population Structure Analysis of Kala Bhat ( Glycine Max ( L .) Merrill ) Genotypes Using SSR Markers.
  13. Mattias Jakobsson,Noah Rosenberg (2007). CLUMPP : A Cluster Matching and Permutation Program for Dealing with Label Switching and Multimodality in Analysis of Population Structure.
  14. Muhammad Khalid,F Farhatullah,Naqib Ullah Khan,Raziud Din,M Yasir Khan,M Akmal,Nasir Ali (2010). Linkage of Morphological Markers in Brassica.
  15. A Kilian,P Wenzl,E Huttner,J Carling,L Xia,H Blois,Vanessa Caig,Katarzyna Heller-Uszynska,Damian Jaccoud,Colleen Hopper,Malgorzata Aschenbrenner-Kilian,Margaret Evers,Kaiman Peng,Cyril Cayla,Puthick Hok,Grzegorz Uszynski (2012). Diversity Arrays Technology: A Generic Genome Profiling Technology on Open Platforms.
  16. Giriraj Kumawat,Gourav Singh,C Gireesh,M Shivakumar,Mamta Arya,Dinesh Agarwal,Syed Husain (2015). Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India.
  17. Zenglu Li,Randall Nelson (2001). Genetic Diversity among Soybean Accessions from Three Countries Measured by RAPDs.
  18. Ying‐hui Li,Wei Li,Chen Zhang,Liang Yang,Ru‐zhen Chang,Brandon Gaut,Li‐juan Qiu (2010). Genetic diversity in domesticated soybean (<i>Glycine max</i>) and its wild progenitor (<i>Glycine soja</i>) for simple sequence repeat and single‐nucleotide polymorphism loci.
  19. Zhangxiong Liu,Huihui Li,Zixiang Wen,Xuhong Fan,Yinghui Li,Rongxia Guan,Yong Guo,Shuming Wang,Dechun Wang,Lijuan Qiu (2017). Comparison of Genetic Diversity between Chinese and American Soybean (Glycine max (L.)) Accessions Revealed by High-Density SNPs.
  20. João Maldonado Dos Santos,Trupti Vitor,Joshi,M Saad,Yang Khan,Juexin Liu,Tri Wang,Marcelo Vuong,Francismar Fernandes De Oliveira,Dong Corrêa Marcelino-Guimarães,Henry Xu,Ricardo Nguyen,Abdelnoor Vilela (2016). Evaluation of Genetic Variation among Brazilian Soybean Cultivars through Genome Resequencing.
  21. M Malek,Y Mohd,Most Rafii,Sharmin Shahida,Ujjal Afroz,M Kumar Nath,Alam Monjurul,Mondal (2014). Morphological Characterization and Assessment of Genetic Variability , Character Association, and Divergence in Soybean Mutants.
  22. Jafar Mammadov,Rajat Aggarwal,Ramesh Buyyarapu,Siva Kumpatla (2012). SNP Markers and Their Impact on Plant Breeding.
  23. D Ojo,A Ajayi,O Oduwaye (2012). Genetic Relationships among Soybean Accessions Based on Morphological and RAPDs Techniques.
  24. Tiago Otvia,Helena Unda-Trevisoli Sandra,Mota Fabiana,Souza Laerte,Orlando Antonio (2014). Genetic divergence of roundup ready (RR) soybean cultivars estimated by phenotypic characteristics and molecular markers.
  25. N Patterson,A Price,D Reich (2006). Population structure and Eigenanalysis.
  26. Jonathan Pritchard,Matthew Stephens,Peter Donnelly (2000). Inference of Population Structure Using Multilocus Genotype Data.
  27. Jing Ren,Daokun Sun,Liang Chen,Frank You,Jirui Wang,Yunliang Peng,Eviatar Nevo,Dongfa Sun,Ming-Cheng Luo,Junhua Peng (2013). Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat.
  28. Noah Rosenberg (2004). <scp>distruct</scp>: a program for the graphical display of population structure.
  29. Nivedita Singh,Debjani Choudhury,Amit Singh,Sundeep Kumar,Kalyani Srinivasan,R Tyagi,Nivedita Singh,Rakesh Singh (2013). Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties.
  30. Snv (2011). Increased Competitiveness of the Oilseed Value Chain through Improved Information on the Markets for Soybean in Uganda.
  31. M Ssengendo,J Mayende,R Mubiru (2010). Soybean Fact Sheet: Export Potential of the Soybean Sub-Sector in Uganda.
  32. P Tantasawat,J Trongchuen,T Prajongjai,S Jenweerawat,W Chaowiset (2011). SSR Analysis of Soybean ( Glycine Max ( L .) Merr .) Genetic Relationship and Variety Identification in Thailand.
  33. Patcharin Tanya,Peerasak Srinives,Theerayut Toojinda,Apichart Vanavichit,Achara Nuntakij,Somsak Kotepong,Suk Ha Lee (2001). Unknown Title.
  34. Adalgisa Torres,Anna Grunvald,Talita Martins,Maria Santos,Noélle Lemos,Luis Silva,Mariangela Hungria (2015). Genetic structure and diversity of a soybean germplasm considering biological nitrogen fixation and protein content.
  35. Douglas Candia,Claire Ashaba,James Mukoki,Peter Jehopio,Brenda Kyasiimire (2019). NON-SCHOOL FACTORS ASSOCIATED WITH SCHOOL DROPOUTS IN UGANDA.
  36. P Tukamuhabwa,T Obua (2015). Production Guide In Uganda.
  37. G Ddamulira,O Isaac,M Kiryowa,R Akullo,M Ajero,M Logoose,A Otim,F Masika,J Mundingotto,M Matovu,I Ramathani (2001). Practices and constraints of tomato production among smallholder farmers in Uganda.
  38. A Vignal,D Milan,S Cristobal,Eggen (2002). A Review on SNP and Other Types of Molecular Markers and Their Use in.
  39. Lixia Wang,Rongxia Guan,Liu Zhangxiong,Ruzhen Chang,Lijuan Qiu (2006). Genetic Diversity of Chinese Cultivated Soybean Revealed by SSR Markers.
  40. Zhengkui Zhou,Yu Jiang,Zheng Wang,Zhiheng Gou,Jun Lyu,Weiyu Li,Yanjun Yu,Liping Shu,Yingjun Zhao,Yanming Ma,Chao Fang,Yanting Shen,Tengfei Liu,Congcong Li,Qing Li,Mian Wu,Min Wang,Yunshuai Wu,Yang Dong,Wenting Wan,Xiao Wang,Zhaoli Ding,Yuedong Gao,Hui Xiang,Baoge Zhu,Suk-Ha Lee,Wen Wang,Zhixi Tian (2015). Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean.

Funding

No external funding was declared for this work.

Conflict of Interest

The authors declare no conflict of interest.

Ethical Approval

No ethics committee approval was required for this article type.

Data Availability

Not applicable for this article.

Tonny Obua. 2020. \u201cGenetic Diversity and Population Structure Analysis of Tropical Soybean (Glycine max (L.) Merrill) using Single Nucleotide Polymorphic Markers\u201d. Global Journal of Science Frontier Research - D: Agriculture & Veterinary GJSFR-D Volume 20 (GJSFR Volume 20 Issue D6): .

Download Citation

Issue Cover
GJSFR Volume 20 Issue D6
Pg. 35- 43
Journal Specifications

Crossref Journal DOI 10.17406/GJSFR

Print ISSN 0975-5896

e-ISSN 2249-4626

Keywords
Classification
GJSFR-D Classification: FOR Code: 070199
Version of record

v1.2

Issue date

July 31, 2020

Language

English

Experiance in AR

The methods for personal identification and authentication are no exception.

Read in 3D

The methods for personal identification and authentication are no exception.

Article Matrices
Total Views: 2277
Total Downloads: 1170
2026 Trends
Research Identity (RIN)
Related Research

Published Article

Soybean (Glycine max (L.) Merrill) is among the most important crops worldwide due to its numerous uses in feed, food, biofuel, and significant atmospheric nitrogen fixation capability. To understand the genetic diversity and population structure of tropical soybean germplasm, 89 genotypes from diverse sources were analyzed using 7,962 SNP markers. The AMOVA results showed low diversity among and high within the populations, while the polymorphism information content (PIC) was 0.27. Both phylogenetic and principal component analysis grouped the 89 soybean genotypes into three major clusters, while population structure grouped the soybean genotypes into two subpopulations. On the other, the average Roger genetic distances within the study population was 0.34. The low diversity reported in the studied soybean germplasm pool is particularly worrying, considering the new trends of climate change and the emergence of new pests and diseases of soybean. Therefore, in order to address these challenges and develop soybean varieties with desirable traits, there is a need to broaden the genetic base of tropical soybean through the importation of germplasm from other countries.

Soybean (Glycine max (L.) Merrill) is among the most important crops worldwide due to its numerous uses in feed, food, biofuel, and significant atmospheric nitrogen fixation capability. To understand the genetic diversity and population structure of tropical soybean germplasm, 89 genotypes from diverse sources were analyzed using 7,962 SNP markers. The AMOVA results showed low diversity among and high within the populations, while the polymorphism information content (PIC) was 0.27. Both phylogenetic and principal component analysis grouped the 89 soybean genotypes into three major clusters, while population structure grouped the soybean genotypes into two subpopulations. On the other, the average Roger genetic distances within the study population was 0.34. The low diversity reported in the studied soybean germplasm pool is particularly worrying, considering the new trends of climate change and the emergence of new pests and diseases of soybean. Therefore, in order to address these challenges and develop soybean varieties with desirable traits, there is a need to broaden the genetic base of tropical soybean through the importation of germplasm from other countries.

Our website is actively being updated, and changes may occur frequently. Please clear your browser cache if needed. For feedback or error reporting, please email [email protected]
×

This Page is Under Development

We are currently updating this article page for a better experience.

Request Access

Please fill out the form below to request access to this research paper. Your request will be reviewed by the editorial or author team.
X

Quote and Order Details

Contact Person

Invoice Address

Notes or Comments

This is the heading

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Ut elit tellus, luctus nec ullamcorper mattis, pulvinar dapibus leo.

High-quality academic research articles on global topics and journals.

Genetic Diversity and Population Structure Analysis of Tropical Soybean (Glycine max (L.) Merrill) using Single Nucleotide Polymorphic Markers

Tonny Obua
Tonny Obua
Julius P. Sserumaga
Julius P. Sserumaga
Stephen O. Opiyo
Stephen O. Opiyo
Phinehas Tukamuhabwa
Phinehas Tukamuhabwa
Thomas L. Odong
Thomas L. Odong
Josiah Mutuku
Josiah Mutuku
Nasser Yao
Nasser Yao

Research Journals