Abstract
Durum wheat is grown mainly in rain-fed regions of Iran and the Mediterranean district under stressful conditions. Different environmental conditions and agricultural practices among ancient communities have led to the development of locally adapted genotypes known as landraces. Landraces are a valued source of genetic variety and show definite adaptation to local environmental conditions according to their home of origin. This study aimed to explore linkage disequilibrium (LD) analysis and the population structure and genetic diversity of Iranian durum wheat landraces. In this study, population structure and genome-wide LD were investigated in 129 durum landrace accessions using 1500 DArT markers. Both structure and discriminant analysis of principal components obviously subdivided the sample collection into seven distinct groups centered on key ancestors and regions of origin of the germplasm. Genetic diversity among the populations was primarily within population (68 vs. 32%). Mean LD values across the entire population sample decayed below r2 of 0.11 after 1 cM. LD decay of genomes A and B of Iranian durum wheat landrace is approximately 2–3 cM (r2 = 0.11) and approximately 0.5 cM (r2 = 0.12), respectively. Altogether, low LD decay, a high number of subpopulations, and the high existence of genetic diversity among and within populations were characteristics of the Iranian durum landrace collection. Hence, the existing genetic diversity within the population can be associated with the very long evolutionary history of plants in Iran. The populations we studied are hence presented as a valuable resource that can be used in basic and applied research in durum wheat breeding.
Similar content being viewed by others
References
Akbari M, Wenzl P, Caig V, Carling J, **a L, Yang S, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113(8):1409–1420
Alipour H, Bihamta MR, Mohammadi Peyghambari VSA, Bai G, Zhang G (2017) Genoty**-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Front Plant Sci 8(2017):1293. https://doi.org/10.3389/fpls.2017.01293
Badr A, Sch R, El Rabey H, Effgen S, Ibrahim H, Pozzi C, Rohde W, Salamini F (2000) On the origin and domestication history of barley (Hordeum vulgare). Mol Biol Evol 17(4):499–510
Barcaccia G, Molinari L, Porfiri O, Veronesi F (2002) Molecular characterization of emmer (Triticum dicoccon Schrank) Italian landraces. Genet Resour Crop Evol 49(4):417–428
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association map** of complex traits in diverse samples. Bioinformatics 23:2633–2635
Chen X, Min D, Yasir TA, Hu YG (2012) Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PloS ONE 7(9):e44510
Comadran J, Thomas W, Van Eeuwijk F, Ceccarelli S, Grando S, Stanca A, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A (2009) Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-map** population for the Mediterranean basin. Theor Appl Genet 119(1):175–187
de Carvalho MAP, Bebeli PJ, Bettencourt E, Costa G, Dias S, Dos Santos TM, Slaski JJ (2013) Cereal landraces genetic resources in worldwide GeneBanks: a review. Agron Sustain Dev 33(1):177–203
Dreisigacker S, Zhang P, Warburton M, Skovmand B, Hoisington D, Melchinger A (2005) Genetic diversity among and within CIMMYT wheat landrace accessions investigated with SSRs and implications for plant genetic resources management. Crop Sci 45(2):653–661
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. https://doi.org/10.1007/s12686-011-9548-7
El-Esawi MA, Witczak J, Abomohra AE-F, Ali HM, Elshikh MS, Ahmad M (2018) Analysis of the genetic diversity and population structure of Austrian and Belgian wheat germplasm within a regional context based on DArT Markers. Genes 9(1):47
Ennos R (1994) Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72(3):250–259
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. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4):1567–1587
Fayaz F, Mardi M, Aghaee M, Darvish F, Talebi R (2013) Phenotypic diversity analysis of grain yield and yellow pigment content in germplasm collected from Iranian durum wheat (Triticum turgidum L.) landraces. Arch Agron Soil Sci 59:1339–1357
Flint-Garcia SA, Thornsberry JM, Buckler IV ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54(1):357–374
Garavito A, Montagnon C, Guyot R, Bertrand B (2016) Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico. BMC Plant Biol 16:242. https://doi.org/10.1186/s12870-016-0933-y
Hao C, Perretant MR, Choulet F, Wang L, Paux E, Sourdille P, Zhang X, Feuillet C, Balfourier F (2010) Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations. Theor Appl Genet 121(7):1209–1225
Hao C, Wang L, Ge H, Dong Y, Zhang X (2011) Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS ONE 6(2):e17279
Harlan JR (1986) Plant domestication: diffuse origins and diffusions. The origin and domestication of cultivated plants. Elsevier, Amsterdam, pp 21–34
Holsinger K, Weir B (2009) Genetics in geographically structured populations: defining, estimating and interpreting FST. Nat Rev Genet 10:639–650
Horvath A, Didier A, Koenig J, Exbrayat F, Charmet G, Balfourier F (2009) Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.). Theor Appl Genet 119(8):1523–1537
Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genoty**. Nucleic Acids Res 29(4):e25–e25
Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11(1):94
Kovi MR, Fjellheim S, SandveS R, Larsen A, Rudi H, Asp T, Kent MP, Rognli OA (2015) Population structure, genetic variation, and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance. Front Plant Sci 6:929
Laidò G, Marone D, Russo MA, Colecchia SA, Mastrangelo AM, De Vita P et al (2014) Linkage disequilibrium and genome-wide association map** in tetraploid wheat (Triticum turgidum L.). PLoS ONE 9(4):e95211. https://doi.org/10.1371/journal.pone.0095211
Lopes MS, El-Basyoni I, Baenziger PS, Singh S, Royo C, Ozbek K, Aktas H, Ozer E, Ozdemir F, Manickavelu A, Ban T, Vikram P (2015) Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J Exp Bot 66(12):3477–3486. https://doi.org/10.1093/jxb/erv122
Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15(3):271–290
Marone D, Panio G, Ficco DB, Russo MA, De Vita P, Papa R, Rubiales D, Cattivelli L, Mastrangelo AM (2012) Characterization of wheat DArT markers: genetic and functional features. Mol Genet Genom 287(9):741–753
Moragues M, del Moral LFG, Moralejo M, Royo C (2006) Yield formation strategies of durum wheat landraces with distinct pattern of dispersal within the Mediterranean basin I: yield components. Field Crops Res 95(2):194–205
Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N (2017) DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32:261–285
Novoselović D, Bentley AR, Šimek R, Dvojković K, Sorrells ME, Gosman N, Horsnell R, Drezner G, Šatović Z (2016) Characterizing Croatian wheat germplasm diversity and structure in a European context by DArT markers. Front Plant Sci 7:184. https://doi.org/10.3389/fpls.2016.00184
Peleg Z, Saranga Y, Suprunova T et al (2008) Genetic diversity and population structure of tetraploid wheats (Triticum turgidum L.) estimated by SSR, DArT and pedigree data. Theor Appl Genet 117:103. https://doi.org/10.1007/s00122-008-0756-9
Perrier X, Jacquemoud-Collet J (2006) DARwin: dissimilarity analysis and representation for Windows 5.0.158. CIRAD, Montpellier
Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65(1):220–228
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959
R Core Team (2014) R: a language and environment for statistical computing. R Core Team, Vienna
Ruiz M, Giraldo P, Royo C, Villegas D, Aranzana MJ, Carrillo JM (2012) Diversity and genetic structure of a collection of Spanish durum wheat landraces. Crop Sci 52(5):2262–2275
Sohail QTS, Kilian A, Eltayeb AE, Tanaka H, Tsujimoto H (2012) Development of diversity array technology (DArT) markers for assessment of population structure and diversity in Aegilops tauschii. Breed Sci 62(1):38–45
Somers DJ, Banks T, DePauw R, Fox S, Clarke J, Pozniak C, McCartney C (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50(6):557–567
Stodart B, Mackay M, Raman H (2008) Assessment of molecular diversity in landraces of bread wheat (Triticum aestivum L.) held in an ex situ collection with diversity arrays technology (DArT™). Crop Pasture Sci 58(12):1174–1182
Tahir M, Turchetta T, Anwar R, Lafiandra D (1996) Assessment of genetic variability in hexaploid wheat landraces of Pakistan based on polymorphism for HMW glutenin subunits. Genet Resour Crop Evol 43(3):211–220
Weir B (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Assoc. Inc., Sunderland, MA
Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD et al (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS ONE 4:e8451
Zhang L, Liu D, Guo X, Yang W, Sun J, Wang D, Sourdille P, Zhang A (2011) Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers. BMC Genet 12(1):42
Acknowledgements
This research project was supported by grants from Islamic Azad University Sanandaj branch (Project Number 11-12-1-37345). We gratefully acknowledge the Iran National Gene Bank and Dr. Mostafa Aghaee for providing the germplasm for this study.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Fayaz, F., Aghaee Sarbarzeh, M., Talebi, R. et al. Genetic Diversity and Molecular Characterization of Iranian Durum Wheat Landraces (Triticum turgidum durum (Desf.) Husn.) Using DArT Markers. Biochem Genet 57, 98–116 (2019). https://doi.org/10.1007/s10528-018-9877-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10528-018-9877-2