Genetic diversity and population structure analysis of Durum wheat (Triticum turgidum L.) genotypes using whole genome DArTseq-generated SilicoDArT markers

Document Type : Research Paper

Authors

1 PhD Student in Plant Genetics and Breeding, Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran

2 Department of Agronomy, Plant Breeding and Biotechnology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran.

3 Department of Plant breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran

4 Department of Agronomy & Plant Breeding, College of AgricultureIslamic Azad University, Sanandaj BranchSanandajIran

5 Faculty member of Sararud Dryland Agricultural Research Center, Kermanshah

Abstract

Objective Durum wheat (Triticum turgidum) with an average annual production of 40 million tons, is the tenth most important and common crop grown worldwide. The aim of this study was to analysis the genetic diversity and population structure of durum wheat genotypes for knowledge and apply in future genomic studies using SilicoDArT markers generated by DarTseq. Materials and Methods The DNA of 94 durum wheat genotypes were extracted by CTAB method from fresh leaves. The quality and quantity of extracted DNA were measured using spectrophotometer and adjusted to 50 ng / μl. The DNA samples were processed at Diversity Array Technology Pty, Ltd, Australia (https://www.diversityarrays.com) for DArTseq analyses using genotyping by sequencing Platform. Genetic diversity and population structure analysis were performed on the remaining 7882 markers using: Power Markerv.3.25, DARwinver 5.0, STRUCTURE2.1., GenAlexv. 6.41 and Rv3.2.3 software. Results The amount of polymorphic information content (PIC) of SilicoDArT markers ranged from 0.023 to 0.499 with an average of 0.38. The mean reproducibility and call rate of sequences in all linkage groups were above 0.98 and 0.92, respectively. The number of mapped SilicoDArT markers varied from 300 markers in the linkage group (Chr1A) to 853 markers in the linkage group (Chr7B). Chromosome size covered by SilicoDArT markers ranged from 829200 kbp in the linkage group (Chr3B) to 589293.786 kbp in the linkage group (Chr1A). The results of cluster analysis by Neighbor-Joining (NJ) method, population structure and discriminant analysis of principal components were highly consistent with each other and clearly divided the studied genotypes into four distinct groups. Genetic diversity among populations was primarily within the population (76.36 vs. 23.64%). Conclusions The relatively high number of subpopulations and the presence of high genetic diversity among and within populations were the characteristics of studied durum wheat genotypes in this study. Therefore, considering the loss of 84% genetic diversity of durum wheat during the early domestication processes, these populations can be used as a valuable resource in basic and applied research in breeding projects.

Keywords

References

 
Agrama H A, WenGui Y, Lee F, et al. (2009) Genetic assessment of a mini-core subset developed from the USDA Rice Genebank. Crop Sci 49, 1336–1346.
Akbari M, Wenzl P, Caig V, et al. (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113, 1409–1420.
Alam M, Neal J, O’Connor K, et al. (2018) Ultra-high- throughput DArTseq-based silicoDArT and SNP markers for genomic studies in macadamia. PLoS One 13(8), e0203465.
Alsaleh A, Baloch FS, Derya M, et al. (2015) Genetic linkage map of Anatolian durum wheat derived from a cross of Kunduru-1149 × Cham1. Plant Mol Biol Rep 33, 209–220.
Altıntaş S, Toklu F, Kafkas S, et al. (2008) Estimating genetic diversity in durum and bread wheat cultivars from Turkey using AFLP and SAMPL markers. Plant Breeding 127, 9 –14.
Balfourier F, Bouchet S, Robert S, et al. (2019) Worldwide phylogeography and history of wheat genetic diversity. Sci Adv 5, eaav0536.
Baloch FS, Alsaleh A, Shahid MQ, et al. (2017) A Whole Genome DArTseq and SNP Analysis for Genetic Diversity Assessment in Durum Wheat from Central Fertile Crescent. PLoS One 12(1), e0167821.
Baloch FS, Andeden EE, Alsaleh A, et al. (2016) High levels of segregation distortion in the molecular linkage map of bread wheat representing WANA (West Asia and North Africa) region. Turk J Agric For 40, 352–364.
Barrett B A, and Kidwell K K (1998) AFLP-based genetic diversity assessment   among   wheat   cultivars   from   the   Pacific   Northwest. Crop Sci 38, 1261–1271.  
Beres BL, Rahmani E, Clarke JM, et al. (2020) A Systematic Review of Durum Wheat: Enhancing Production Systems by Exploring Genotype, Environment, and Management (G _ E _ M) Synergies. Front Plant Sci 11, 568657.
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32, 314–331.
Brinez B, Blair MW, Kilian A, et al. (2012) A whole genome DArT assay to assess germplasm collection diversity in common beans. Mol Breeding 30, 181–193.
Brown, A H D (1989). Core collections: a practical approach to genetic resources management. Genome 31, 818–824.
CRP-WHEAT (2016). Wheat Agri-Food Systems Proposal 2017-2022". Research Program on Wheat, (CGIAR). Available online at:https://cgspace.cgiar.org/handle/10947/4421? show=full
de Vicente MC, Guzmán FA, Engels J, Rao VR (2005) Genetic characterization and its use in decision making for the conservation of crop germplasm. The Role of Biotechnology, Villa Gualino, Turin, Italy, 5–7 March 2005.
Edwards D, Batley J, Snowdon RJ (2013) Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet 126, 1–11.
El Bakkali A, Haouane H, Moukhli A, et al. (2013). Construction of core collections suitable for association mapping to optimize use of Mediterranean olive (Olea europaea l.) genetic resources. PLoS One 8, e61265.
Elshire RJ, Glaubitz JC, Sun Q, et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6, e19379.
Etminan A, Pour-Aboughadareh A, Mohammadi R, et al. (2018) Applicability of CAAT Box-derived Polymorphism (CBDP) Markers for Analysis of Genetic Diversity in Durum Wheat. Cereal Res Commun 46, 1-9.
 
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14, 2611–2620.
Falconer D S, and MacKay T F C (1996). Introduction to Quantitative Genetics. Longman Group Limited.
Fayaz F, Aghaee M, Talebi R, Azadi A (2019) Genetic diversity and molecular characterization of iranian durum wheat landraces (Triticum turgidum durum (Desf.) Husn.) using DArT markers. Biochem Genet 57, 98–116.
Frankham R (2005). Genetics and extinction. Biol Conserv 126, 131–140.
Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 2015, 431487.
Grzebelus D, Iorizzo M, Senalik D, et al. (2014) Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers. Mol Breeding 33, 625–637.
Heffner EL, Sorrells ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49, 1–12.
Jombart T (2008) Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24(11),1403–1405.
Kilian A, Huttner E, Wenzl P, et al. (2003) The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. In: Tuberosa R, Phillips RL, Gale M (eds) Proceedings of the international congress In the wake of the double helix: from the green revolution to the gene revolution, Bologna, pp 443–461.
Liu K, Muse SV (2005) Power Marker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128–2129.
Luan S, Chiang TY, and Gong X U N (2006) High genetic diversity vs. low genetic differentiation in nouelia insignis (Asteraceae), a narrowly distributed and endemic species in China, revealed by ISSR fingerprinting. Ann Bot 98, 583 –589.
Luo M-C, Yang Z-L, You F, et al. (2007) The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication. Theor Appl Genet 114, 947–959.
Mahboubi M, Mehrabi R, Naji AM, Talebi R. 2020. Whole‑genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping‑by‑sequencing DArTseq platform. Biotech10:48, 1-13.
Marzario S, Logozzo G, David JL, et al. (2018) Molecular genotyping (SSR) and agronomic phenotyping for utilization of durum wheat (Triticum durum Desf.) ex-situ collection from southern Italy: a combined approach including pedigreed varie- ties. Genes 9: 465.
Masood MS, Javaid A, Rabbani MA, Anwar R (2005) Phenotypic diversity and trait association in bread wheat (Triticum aestivum L.) landraces from Baluchistan, Pakistan. Pak J Bot 37: 949.
Moragues M, Moralejo M, Sorrells ME, Royo C (2007) Dispersal of durum wheat [Triticum turgidum L. ssp. turgidum convar. durum (Desf.) MacKey] landraces across the Mediterranean basin assessed by AFLPs and microsatellites. Genet Resour Crop Ev 54, 1133–1144.
Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotechnol 14, 214–219.
Murray M G, & Thompson W F (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19), 4321–4325.
Nadeem MA, Habyarimana E, Ciftci V, et al. (2018) Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS One 13, e0205363.
Ndjiondjop M-N, Semagn K, Gouda AC, et al. (2017) Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq. Front Plant Sci 8:1748.
Nielsen NH, Backes G, Stougaard J, et al. (2014) Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PLoS One 9, e94000.
Novoselovic D, Bentley AR, Šimek R, et al. (2016) Characterizing Croatian wheat germplasm diversity and structure in a European context by DArT markers. Front Plant Sci 7:184.
O¨ zkan H, Brandolini A, Scha¨ fer-Pregl R, Salamini F (2002) AFLP analysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey. Mol Biol Evol 19, 1797–1801.
O’Connor K, Kilian A, Hayes B, et al. (2019) Population structure, genetic diversity and linkage disequilibrium in a macadamia breeding population using SNP and silicoDArT markers. Tree Genet Genomes 15:24.
Oliveira HR, Campana MG, Jones H, et al. (2012) Tetraploid wheat landraces in the Mediterranean basin: taxonomy, evolution and genetic diversity. PLoS One 7, e37063.
Ouborg N J, Piquot Y, and Groenendael J M (1999). Population genetics, molecular markers and the study of dispersal in plants. J Ecol 87, 551–568.
Pandey MK, Upadhyaya HD, Rathore A, et al. (2014) Genome wide association studies for 50 agronomic traits in peanut using the ‘Reference Set’ comprising 300 genotypes from 48 countries of the semi-arid tropics of the world. PLoS One 9(8), e105228.
Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Sci Publishers, Enfield, pp 43–76.
Perrier X, Jacquemoud-Collet JP (2006) DARwin software. https://darwin.cirad.fr/darwin.
Peterson GW, Dong Y, Horbach C, Fu Y-B (2014) Genotyping-by-sequencing for plant genetic diversity analysis: a lab guide for SNP genotyping. Diversity 6, 665–680.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multi-locus genotype data. Genetics 155, 945–959.
R Core Team (2014) R: a language and environment for statistical computing. R Core Team, Vienna.
Reif J C, Zhang P, Dreisigacker S, et al. (2005) Wheat   genetic   diversity trends during domestication and breeding. Theor Appl Genet 110, 859–864.
Ren J, Sun D, Chen L, et al. (2013) Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci 14, 7061–7088.
Rubenstein DK, Heisey P, Shoemaker R, et al. (2005) Crop genetic resources: an economic appraisal. United States Department of Agriculture (USDA). Eco Inf Bull 2 (www.ers.usda.gov).
Sagawa CHD, Cristofani-Yaly M, Novelli VM, et al. (2018) Assessing genetic diversity of Citrus by DArT_seq™ genotyping. Plant Biosyst 152, 593–598.
Seyedimoradi H, Talebi R, Kanouni H, et al. (2020) Genetic diversity and population structure analysis of chickpea (Cicer arietinum L.) advanced breeding lines using whole‑genome DArTseq‑generated SilicoDArT markers. Braz J Bot 43, 541–549.
Talebi R, Fayyaz F (2012) Quantitative evaluation of genetic diversity in Iranian modern cultivars of wheat (Triticum aestivum L.) using morphological and amplified fragment length polymorphism (AFLP) markers. Biharean Biol 6,14–18.
Van de Wouw M, van Hintum T, Kik C, et al. (2010) Genetic diversity trends in twentieth century crop cultivars: a meta-analysis. Theor Appl Genet 120, 1241–1252.
Varshney RK, Pandey MK, Bohra A, et al. (2019) Toward the sequence-based breeding in legumes in the post-genome sequencing era. Theor Appl Genet 132, 797–816.
Yan W, Rutger J N, Bryant R J, et al. (2007) Development and evaluation of a core subset of the USDA rice germplasm collection. Crop Sci 47, 869–878.
Zeven AC (2000) Traditional maintenance breeding of landraces: 1. Data by crop. Euphytica 116, 65–85.
Zhang LY, Liu DC, Guo XL, et al. (2011) Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers. Bmc Genet 12:42.
Agricultural Biotechnology Journal
Volume 13, Issue 3
October 2021
Pages 43-68

Files

Share

How to cite

Statistics