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RESEARCH ARTICLE
Contents Vol 75(3)

Genetic variability of maize (Zea mays) germplasm from Iran: genotyping with a maize 600K SNP array and genome-wide scanning for selection signatures

Sorour Arzhang https://orcid.org/0000-0002-4114-2828 A , Reza Darvishzadeh https://orcid.org/0000-0001-5991-4411 A B * , Hadi Alipour https://orcid.org/0000-0003-0086-002X A * , Hamid Hatami Maleki https://orcid.org/0000-0001-7179-861X C and Sara Dezhsetan https://orcid.org/0000-0003-3739-1343 D
+ Author Affiliations
- Author Affiliations

A Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.

B Institute of Biotechnology, Urmia University, Urmia, Iran.

C Department of Plant Production and Genetics, Faculty of Agriculture, University of Maragheh, Maragheh, Iran.

D Department of Plant Production and Genetics, Faculty of Agriculture, University of Mohaghegh Ardabili, Ardabil, Iran.

* Correspondence to: r.darvishzadeh@urmia.ac.ir, ha.alipour@urmia.ac.ir

Handling Editor: Enrico Francia

Crop & Pasture Science 75, CP23288 https://doi.org/10.1071/CP23288
Submitted: 20 October 2023  Accepted: 9 February 2024  Published: 5 March 2024

© 2024 The Author(s) (or their employer(s)). Published by CSIRO Publishing

Abstract

Context

Maize (Zea mays L.) is one of the most economically important plants of the cereal family; it has value as human food, livestock feed, and as a component of industrial products.

Aims

This study focused on genetic diversity and existence of genetic divergence among promising maize inbred lines in Iran.

Methods

A commercial maize 600K SNP (single-nucleotide polymorphism) array was used to inspect genetic variability among 93 maize inbred lines.

Key results

The rate of transition mutation was twice as high as transversion mutation, and the density of detected SNPs was greater close to telomere regions of maize chromosomes. Considering the fluctuation of observed, expected and total heterozygosity and fixation index values across maize chromosomes, as well as polymorphism information content values, there is a high level of genetic variability among the studied maize panel. In addition, discriminant analysis of the principal components revealed four subpopulations in which the subpopulation ‘Line’ was distinct from other subpopulations and had no genomic overlap with them. Selection signature analysis revealed 177 regions harbouring 75 genes that differentiate among subgroups. Detected genes had a role in the mitogen-activated protein kinase signalling pathway, spliceosome, protein processing in endoplasmic reticulum, and hormone signal transduction.

Conclusions

We conclude that remarkable genetic diversity and differentiation exists among the studied maize subpopulations. The most differentiated SNPs among the subpopulations were associated with important biological processing genes and pathways.

Implications

The findings provide valuable insights for future maize breeding programs through exploitation of heterosis, as well as marker-assisted selection.

Keywords: DAPC, Fst index, genetic diversity, heterosis, mutation, selection signature, SNP markers, Zea mays.

References

Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Research 12, 1805-1814.
| Crossref | Google Scholar | PubMed |

Andorf C, Beavis WD, Hufford M, Smith S, Suza WP, Wang K, Woodhouse M, Yu J, Lübberstedt T (2019) Technological advances in maize breeding: past, present and future. Theoretical and Applied Genetics 132, 817-849.
| Crossref | Google Scholar | PubMed |

Arca M, Mary-Huard T, Gouesnard B, Bérard A, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD (2021) Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array. Frontiers in Plant Science 11, 568699.
| Crossref | Google Scholar | PubMed |

Badu-Apraku B, Garcia-Oliveira AL, Petroli CD, Hearne S, Adewale SA, Gedil M (2021) Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa. BMC Plant Biology 21, 96.
| Crossref | Google Scholar | PubMed |

Beadle G (1939) Teosinte and the origin of maize. Journal of Heredity 30, 245-247.
| Crossref | Google Scholar |

Blair MW, Cortés AJ, Penmetsa RV, Farmer A, Carrasquilla-Garcia N, Cook DR (2013) A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 126, 535-548.
| Crossref | Google Scholar | PubMed |

Boakyewaa Adu G, Badu-Apraku B, Akromah R, Garcia-Oliveira AL, Awuku FJ, Gedil M (2019) Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers. PLoS ONE 14, e0214810.
| Crossref | Google Scholar |

Buckler ES, Gaut BS, McMullen MD (2006) Molecular and functional diversity of maize. Current Opinion in Plant Biology 9, 172-176.
| Crossref | Google Scholar | PubMed |

Choukan R, Warburton ML (2005) Use of SSR data to determine relationships among early maturing Iranian maize inbred lines. Maydica 50, 163-170.
| Google Scholar |

Choukan R, Hossainzadeh A, Ghannadha M R, Warburton ML, Talei AR, Mohammadi SA (2006) Use of SSR data to determine relationships and potential heterotic groupings within medium to late maturing Iranian maize inbred lines. Field Crops Research 95, 212-222.
| Crossref | Google Scholar |

Deng N, Zhou H, Fan H, Yuan Y (2017) Single nucleotide polymorphisms and cancer susceptibility. Oncotarget 8, 110635-110649.
| Crossref | Google Scholar | PubMed |

Dube SP, Sibiya J, Kutu F (2023) Genetic diversity and population structure of maize inbred lines using phenotypic traits and single nucleotide polymorphism (SNP) markers. Scientific Reports 13, 17851.
| Crossref | Google Scholar | PubMed |

Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379.
| Crossref | Google Scholar | PubMed |

FAOSTAT (2017) Database of Food and Agriculture Organization of the United Nations. Available at http://www.fao.org/faostat/en/#data/QC/visualize

Ertiro BT, Semagn K, Das B, Olsen M, Labuschagne M, Worku M, Wegary D, Azmach G, Ogugo V, Keno T, Abebe B, Chibsa T, Menkir A (2017) Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers. BMC Genomics 18, 777.
| Crossref | Google Scholar | PubMed |

Fageria NK, Baligar VC, Jones CA (2010) Corn. In ‘Growth and mineral nutrition of field crops’. pp. 30. (CRC Press: Boca Raton) doi:10.1201/b10160

Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner E-M, Hansen M, Joets J, Le Paslier M-C, McMullen MD, Montalent P, Rose M, Schön C-C, Sun Q, Walter H, Martin OC, Falque M (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE 6, e28334.
| Crossref | Google Scholar | PubMed |

Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9, e90346.
| Crossref | Google Scholar | PubMed |

Goudet J (2005) HIERFSTAT, a package for R to compute and test hierarchical F -statistics. Molecular Ecology Notes 5, 184-186.
| Crossref | Google Scholar |

Hallauer AR, Carena MJ, Miranda Filho JB (1988) ‘Quantitative genetics in maize breeding.’ 2nd edn. pp. 468 (Iowa State University Press: Ames, Iowa)

Holtz Y, Ardisson M, Ranwez V, Besnard A, Leroy P, Poux G, Roumet P, Viader V, Santoni S, David J (2016) Genotyping by sequencing using specific allelic capture to build a high density genetic map of durum wheat. PLoS ONE 11, e0154609.
| Crossref | Google Scholar | PubMed |

Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403-1405.
| Crossref | Google Scholar | PubMed |

Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11, 94.
| Crossref | Google Scholar | PubMed |

Knaus BJ, Grünwald NJ (2017) VCFR: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources 17, 44-53.
| Crossref | Google Scholar | PubMed |

Li T, Qu J, Tian X, Lao Y, Wei N, Wang Y, Hao Y, Zhang X, Xue J, Xu S (2020) Identification of ear morphology genes in maize (Zea mays L.) using selective sweeps and association mapping. Frontiers in Genetics 11, 747.
| Crossref | Google Scholar | PubMed |

Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128-2129.
| Crossref | Google Scholar |

Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, Berkman PJ, Lai K, Batley J, Edwards D (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1, 370-382.
| Crossref | Google Scholar | PubMed |

Mammadov JA, Chen W, Ren R, Pai R, Marchione W, Yalçin F, Witsenboer H, Greene TW, Thompson SA, Kumpatla SP (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize (Zea mays L.) genome for use in marker-assisted breeding. Theoretical and Applied Genetics 121, 577-588.
| Crossref | Google Scholar | PubMed |

Mayer M, Hölker AC, Presterl T, Ouzunova M, Melchinger AE, Schön C-C (2022) Genetic diversity of European maize landraces: dataset on the molecular and phenotypic variation of derived doubled-haploid populations. Data in Brief 42, 108164.
| Crossref | Google Scholar | PubMed |

Nosrati M, Asadollahpour Nanaei H, Amiri Ghanatsaman Z, Esmailizadeh A (2019) Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep. Reproduction in Domestic Animals 54, 358-364.
| Crossref | Google Scholar |

Oliveira LSd, Schuster I, Novaes E, Pereira WA (2021) SNP genotyping for fast and consistent clustering of maize inbred lines into heterotic groups. Crop Breeding and Applied Biotechnology 21, e367121110.
| Crossref | Google Scholar |

Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z (2017) Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Molecular Plant 10, 1047-1064.
| Crossref | Google Scholar | PubMed |

Razi M, Amiri ME, Darvishzadeh R, Doulati Baneh H, Alipour H, Martínez-Gómez P (2020) Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits. Molecular Biology Reports 47, 7593-7606.
| Crossref | Google Scholar | PubMed |

Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard R (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences 81, 8014-8018.
| Crossref | Google Scholar | PubMed |

Serba DD, Muleta KT, St. Amand P, Bernardo A, Bai G, Perumal R, Bashir E (2019) Genetic diversity, population structure, and linkage disequilibrium of pearl millet. The Plant Genome 12, 180091.
| Crossref | Google Scholar |

Shahabzadeh Z, Darvishzadeh R, Mohammadi R, Jafari M, Alipour H (2022) High-throughput single nucleotide polymorphism genotyping reveals population structure and genetic diversity of tall fescue (Festuca arundinacea) populations. Crop & Pasture Science 73, 1070-1084.
| Crossref | Google Scholar |

Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KFX, Schön C-C (2014) A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics 15, 823.
| Crossref | Google Scholar |

Van Inghelandt D, Melchinger AE, Lebreton C, Stich B (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theoretical and Applied Genetics 120, 1289-1299.
| Crossref | Google Scholar | PubMed |

Vuylsteke M, Mank R, Brugmans B, Stam P, Kuiper M (2000) Further characterization of AFLP data as a tool in genetic diversity assessments among maize (Zea mays L.) inbred lines. Molecular Breeding 6, 265-276.
| Crossref | Google Scholar |

Xu C, Ren Y, Jian Y, Guo Z, Zhang Y, Xie C, Fu J, Wang H, Wang G, Xu Y, Li P, Zou C (2017) Development of a maize 55 K SNP array with improved genome coverage for molecular breeding. Molecular Breeding 37, 20.
| Crossref | Google Scholar | PubMed |

Xu G, Zhang X, Chen W, Zhang R, Li Z, Wen W, Warburton ML, Li J, Li H, Yang X (2022) Population genomics of Zea species identifies selection signatures during maize domestication and adaptation. BMC Plant Biology 22, 72.
| Crossref | Google Scholar | PubMed |

Zhang X, Zhang H, Li L, Lan H, Ren Z, Liu D, Wu L, Liu H, Jaqueth J, Li B, Pan G, Gao S (2016) Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers. BMC Genomics 17, 697.
| Crossref | Google Scholar | PubMed |

Zhu X-M, Shao X-Y, Pei Y-H, Guo X-M, Li J, Song X-Y, Zhao M-A (2018) Genetic diversity and genome-wide association study of major ear quantitative traits using high-density SNPs in maize. Frontiers in Plant Science 9, 966.
| Crossref | Google Scholar | PubMed |