Genetic diversity and population structure of bread wheat varieties grown in Bulgaria based on microsatellite and phenotypic analyses

References

• FAOSTAT-Crops and livestock products [Internet]. [cited 2021 Sep 23]. Available from: http://www.fao.org/faostat/en/#data/QCL
   Google Scholar
• Giraldo P, Benavente E, Manzano-Agugliaro F, et al. Worldwide research trends on wheat and barley: a bibliometric comparative analysis. Agronomy. 2019;9(7):352.
   Web of Science ®Google Scholar
• Shewry PR, Hey SJ. The contribution of wheat to human diet and health. Food Energy Secur. 2015;4(3):178–202.
   PubMed Web of Science ®Google Scholar
• Nielsen NH, Backes G, Stougaard J, et al. Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PLoS One. 2014;9(4):e94000.
   PubMed Web of Science ®Google Scholar
• World population prospects – population division – United Nations [Internet]. [cited 2021 Sep 23]. Available from: https://population.un.org/wpp/
   Google Scholar
• Khan MK, Pandey A, Thomas G, et al. Genetic diversity and population structure of wheat in India and Turkey. AoB Plants [Internet]. [cited 2015 Aug 25]. Available from:
   Google Scholar
• Heal G, Walker B, Levin S, et al. Genetic diversity and interdependent crop choices in agriculture. Resour Energy Econ. 2004;26(2):175–184.
   Web of Science ®Google Scholar
• Fu Y-B, Somers DJ. Genome-wide reduction of genetic diversity in wheat breeding. Crop Sci. 2009;49(1):161–168.
   Web of Science ®Google Scholar
• Gupta PK, Varshney RK, Sharma PC, et al. Molecular markers and their applications in wheat breeding. Plant Breed. 1999;118(5):369–390.
   Web of Science ®Google Scholar
• Gupta PK, Varshney RK. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica. 2000;113(3):163–185. doi:10.1023/A:1003910819967.
   Web of Science ®Google Scholar
• Cui F, Zhang N, Fan X, et al. Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep. 2017;7(1):3788.
   PubMedGoogle Scholar
• Yang X, Tan B, Liu H, et al. Genetic diversity and population structure of Asian and European common wheat accessions based on genotyping-by-sequencing. Front Genet. 2020;11:580782.
   PubMed Web of Science ®Google Scholar
• Tomar V, Dhillon GS, Singh D, et al. Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.). PeerJ. 2021;9:e11593.
   PubMed Web of Science ®Google Scholar
• Deng P, Wang M, Feng K, et al. Genome-wide characterization of microsatellites in triticeae species: abundance, distribution and evolution. Sci Rep. 2016;6:32224.
   PubMed Web of Science ®Google Scholar
• Xu J, Liu L, Xu Y, et al. Development and characterization of simple sequence repeat markers providing genome-wide coverage and high resolution in maize. DNA Res. 2013;20(5):497–509.
   PubMed Web of Science ®Google Scholar
• Blake VC, Woodhouse MR, Lazo GR, et al. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database. 2019;2019:baz065.
   PubMedGoogle Scholar
• Chao S, Zhang W, Akhunov E, et al. Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol Breeding. 2009;23(1):23–33.
   Web of Science ®Google Scholar
• Peleg Z, Fahima T, Krugman T, et al . Genomic dissection of drought resistance in durum wheat x wild emmer wheat recombinant inbreed line population. Plant Cell Environ. 2009;32(7):758–779.
   PubMed Web of Science ®Google Scholar
• Pinto RS, Reynolds MP, Mathews KL, et al. Heat and drought adaptive QTL in a wheat population designed to minimize confounding agronomic effects. Theor Appl Genet. 2010;121(6):1001–1021.
   PubMed Web of Science ®Google Scholar
• Mondal S, Mason RE, Huggins T, et al. QTL on wheat (Triticum aestivum L.) chromosomes 1B, 3D and 5A are associated with constitutive production of leaf cuticular wax and may contribute to lower leaf temperatures under heat stress. Euphytica. 2015;201(1):123–130.
   Web of Science ®Google Scholar
• Gupta PK, Balyan HS, Gahlaut V. QTL analysis for drought tolerance in wheat: Present status and future possibilities. Agronomy. 2017;7(1):5.
   Google Scholar
• Belete Y, Shimelis H, Laing M, et al. Genetic diversity and population structure of bread wheat genotypes determined via phenotypic and SSR marker analyses under drought-stress conditions. J. Crop Improv. 2021;35(3):303–325.
   Web of Science ®Google Scholar
• Wiśniewska H, Surma M, Krystkowiak K, et al. Simultaneous selection for yield-related traits and susceptibility to Fusarium head blight in spring wheat RIL population. Breed Sci. 2016;66(2):281–292.
   PubMed Web of Science ®Google Scholar
• Zhu Z, Bonnett D, Ellis M, et al. Characterization of Fusarium head blight resistance in a CIMMYT synthetic-derived bread wheat line. Euphytica. 2016;208(2):367–375.
   Web of Science ®Google Scholar
• Zhang Z, Friesen TL, Simons KJ, et al. Development, identification, and validation of markers for marker-assisted selection against the Stagonospora nodorum toxin sensitivity genes Tsn1 and Snn2 in wheat. Mol Breeding. 2009;23(1):35–49.
   Web of Science ®Google Scholar
• Kumar S, Röder MS, Tripathi SB, et al. Mendelization and fine mapping of a bread wheat spot blotch disease resistance QTL. Mol Breeding. 2015;35(11):218.
   Web of Science ®Google Scholar
• Singh V, Singh G, Chaudhury A, et al. Phenotyping at hot spots and tagging of QTLs conferring spot blotch resistance in bread wheat. Mol Biol Rep. 2016;43(11):1293–1303.
   PubMed Web of Science ®Google Scholar
• See PT, Moffat CS. Evaluation of a novel molecular marker associated with the tan spot disease response in wheat. Agriculture. 2021;11(6):513.
   Google Scholar
• Goutam U, Kukreja S, Yadav R, et al. Recent trends and perspectives of molecular markers against fungal diseases in wheat. Front Microbiol. 2015;6:861.
   PubMed Web of Science ®Google Scholar
• Zhu X-G, Long SP, Ort DR. What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? Curr Opin Biotechnol. 2008;19(2):153–159.
   PubMed Web of Science ®Google Scholar
• Zhang Q, Maroof MAS, Kleinhofs A. Comparative diversity analysis of rflps and isozymes within and among populations of Hordeum vulgare ssp. spontaneum. Genetics. 1993;134(3):909–916.
   PubMed Web of Science ®Google Scholar
• Bhandari H, Bhanu A, Srivastava K, et al. Assessment of genetic diversity in crop plants – an overview. Adv Plants Agric Res. 2017;7:279–286.
   Google Scholar
• Röder MS, Korzun V, Wendehake K, et al. A microsatellite map of wheat. Genetics. 1998;149(4):2007–2023.
   PubMed Web of Science ®Google Scholar
• Gupta K, Balyan S, Edwards J, et al. Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet. 2002;105(2-3):413–422.
   PubMed Web of Science ®Google Scholar
• Song QJ, Shi JR, Singh S, et al. Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet. 2005;110(3):550–560.
   PubMed Web of Science ®Google Scholar
• Sourdille P, Guyomarc’h H, Baron C, et al. Improvement of the genetic maps of wheat using new microsatellite markers plant & animal genome IX. Final Abstracts Guide. 2001;167
   Google Scholar
• Hayden M, Nguyen TM, Waterman A, et al. Multiplex-ready PCR: a new method for multiplexed SSR and SNP genotyping. BMC Genomics. 2008;9:80.
   PubMed Web of Science ®Google Scholar
• Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 2005;21(9):2128–2129.
   PubMed Web of Science ®Google Scholar
• Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol. 1983;19(2):153–170.
   PubMed Web of Science ®Google Scholar
• Subramanian B, Gao S, Lercher MJ, et al. Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees. Nucleic Acids Res. 2019;47(W1):W270–W275.
   PubMed Web of Science ®Google Scholar
• Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945–959.
   PubMed Web of Science ®Google Scholar
• Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010;11:94.
   PubMed Web of Science ®Google Scholar
• Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol. 2005;14(8):2611–2620.
   PubMed Web of Science ®Google Scholar
• Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012;4(2):359–361.
   Web of Science ®Google Scholar
• Jost L . G(ST) and its relatives do not measure differentiation. Mol Ecol. 2008;17(18):4015–4026.
   PubMed Web of Science ®Google Scholar
• Almeida GD, Makumbi D, Magorokosho C, et al. QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance. Theor Appl Genet. 2013;126(3):583–600.
   PubMed Web of Science ®Google Scholar
• Todorovska E, Zheleva D, Kolev S, et al. Microsatellite variation in genomic regions responsible for agro-ecological adaptation of wheat. Biotechnol Biotechnol Equip. 2009;23(sup1):960–964.
   Web of Science ®Google Scholar
• Landjeva S, Korzun V, Ganeva G. Evaluation of genetic diversity among Bulgarian winter wheat (Triticum aestivum L.) varieties during the period 1925–2003 using microsatellites. Genet Resour Crop Evol. 2006;53(8):1605–1614.
   Web of Science ®Google Scholar
• Roussel V, Koenig J, Beckert M, et al. Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor Appl Genet. 2004;108(5):920–930.
   PubMed Web of Science ®Google Scholar
• Arora A, Kundu S, Dilbaghi N, et al. Population structure and genetic diversity among Indian wheat varieties using microsatellite (SSR) markers. AJCS. 2014;8:1281–1289.
   Google Scholar
• Zhang D, Bai G, Zhu C, et al. Genetic diversity, population structure, and linkage disequilibrium in U.S. elite winter wheat. Plant Genome 2010 [Internet]. [cited 2021 Sep 23]. Available from: https://doi.org/10.3835/plantgenome2010.03.0004
   Google Scholar
• Chen X, Min D, Yasir TA, et al. Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS One. 2012;7(9):e44510.
   PubMed Web of Science ®Google Scholar
• Dubcovsky J, Dvorak J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science. 2007;316(5833):1862–1866.
   PubMed Web of Science ®Google Scholar
• Zhang X, Liu D, Yang W, et al. Development of a new marker system for identifying the complex members of the low-molecular-weight glutenin subunit gene family in bread wheat (Triticum aestivum L.). Theor Appl Genet. 2011;122(8):1503–1516.
   PubMed Web of Science ®Google Scholar
• Le Couviour F, Faure S, Poupard B, et al. Analysis of genetic structure in a panel of elite wheat varieties and relevance for association mapping. Theor Appl Genet. 2011;123(5):715–727.
   PubMed Web of Science ®Google Scholar
• Tehseen MM, Istipliler D, Kehel Z, et al. Genetic diversity and population structure analysis of Triticum aestivum L. landrace panel from Afghanistan. Genes (Basel). 2021;12(3):340.
   PubMed Web of Science ®Google Scholar
• Aleksandrov V, Kartseva T, Alqudah AM, et al. Genetic diversity, linkage disequilibrium and population structure of Bulgarian bread wheat assessed by genome-wide distributed SNP markers: from old germplasm to semi-dwarf cultivars. Plants. 2021;10(6):1116.
   Google Scholar
• Maccaferri M, Sanguineti MC, Noli E, et al. Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breeding. 2005;15(3):271–290.
   Web of Science ®Google Scholar
• White J, Law JR, MacKay I, et al. The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor Appl Genet. 2008;116(3):439–453.
   PubMed Web of Science ®Google Scholar
• Hao C, Wang L, Ge H, et al. Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS One. 2011;6(2):e17279.
   PubMed Web of Science ®Google Scholar
• Vassileva V, Vaseva I, Dimitrova A. Expression profiling of DNA methyltransferase genes in wheat genotypes with contrasting drought tolerance. Bulg J Agric Sci. 2019;25:845–851.
   Web of Science ®Google Scholar
• Genc Y, Oldach K, Gogel B, et al. Quantitative trait loci for agronomic and physiological traits for a bread wheat population grown in environments with a range of salinity levels. Mol Breeding. 2013;32(1):39–59.
   Web of Science ®Google Scholar
• Mladenov V, Dimitrijević M, Petrović S, et al. Agronomic performance of wheat cultivars and their molecular characterization. Genetika. 2018;50(2):591–602.
   Google Scholar
• Paillard S, Schnurbusch T, Tiwari R, et al. QTL analysis of resistance to Fusarium head blight in Swiss winter wheat (Triticum aestivum L.). Theor Appl Genet. 2004;109(2):323–332.
   PubMed Web of Science ®Google Scholar
• Maccaferri M, Sanguineti MC, Demontis A, et al. Association mapping in durum wheat grown across a broad range of water regimes. J Exp Bot. 2011;62(2):409–438.
   PubMed Web of Science ®Google Scholar
• Peleg Z, Fahima T, Korol AB, et al. Genetic analysis of wheat domestication and evolution under domestication. J Exp Bot. 2011;62(14):5051–5061.
   PubMed Web of Science ®Google Scholar
• Krishnappa G, Singh AM, Chaudhary S, et al. Molecular mapping of the grain iron and zinc concentration, protein content and thousand kernel weight in wheat (Triticum aestivum L.). PLoS One. 2017;12(4):e0174972.
   PubMed Web of Science ®Google Scholar
• Darzi-Ramandi H, Shariati V, Tavakol E, et al. Detection of consensus genomic regions associated with root architecture of bread wheat on groups 2 and 3 chromosomes using QTL meta–analysis. AJCS. 2017;11.
   Google Scholar
• Li HM, Liang H, Li Z, et al. Dynamic QTL analysis of protein content and glutamine synthetase activity in recombinant inbred wheat lines. Genet Mol Res. 2015;14(3):8706–8715. doi:10.4238/2015.July.31.19.
   PubMed Web of Science ®Google Scholar