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:: Volume 14, Issue 4 (3-2022) ::
2022, 14(4): 113-134 Back to browse issues page
Assessment of Genetic Diversity and Population Structure of Barley Breeding Lines and Landraces Using SNP Markers
Farhad Ahakpaz1 , Iraj Bernosi * , Babak Abdollahi Mandoulakani , Saber Golkari , Jafar Jafarzadeh , Sripada Udupa
Associate professor, Department of Plant Production and Genetics, Uromieh University, Uromieh, West Azerbaijan, Iran
Abstract:   (1447 Views)
Genetic diversity is critical for developing broadly adapted cultivars with desirable traits. This research aimed to investigate the genetic diversity, population structure, and genome-wide linkage disequilibrium (LD) of 108 barley genotypes, including rainfed and irrigated breeding lines, cultivars, and landraces with the 50K IlluminaTM iSelect single nucleotide polymorphism (SNP) array. After quality control, 14,943 polymorphic SNPs were subjected to estimate Shannon's information index (I), Nei's gene diversity (H), polymorphic information content (PIC), fixation index (Fst), and principal component analysis (PCA). The I and H indices were 0.74 and 0.336, respectively. The PIC values were 0.367 and 0.178 for six and two-rowed barley, respectively. PCA using Nei's genetic distance identified three subpopulations. Subpopulations 1 and 2 had 0.38, and 0.29 PIC values, respectively, and were more diverse than subpopulation 3 (0.09). The Fst value was 0.381. Subpopulations 1 and 3 indicated the highest (0.379) and the lowest (0.040) genetic diversity within subpopulations, respectively. The average LD for two-rowed genotypes and subpopulation 3 was more than that for six-roweded genotypes. A high level of genetic variation and genetic differentiation among subpopulations was observed in this panel. The irrigated six-rowed types and landraces indicated higher genetic diversity, whereas rainfed two-rowed barley indicated the highest LD and the lowest genetic variation due to high selection intensity. This panel could be used for genome-wide association studies to identify the trait-marker associations in future genetic improvement programs for barley.
Keywords: Barley Genetic Resource, Population Structure, Genome-Wide Linkage Disequilibrium, Polymorphic Information Content, Single Nucleotide Polymorphism.
Full-Text [PDF 1604 kb]   (503 Downloads)    
Type of Study: Research | Subject: Special
Received: 2022/01/16 | Accepted: 2022/01/31 | Published: 2022/03/1
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Ahakpaz1 F, Bernosi I, Abdollahi Mandoulakani B, Golkari S, Jafarzadeh J, Udupa S. Assessment of Genetic Diversity and Population Structure of Barley Breeding Lines and Landraces Using SNP Markers. Journal of Biosafety 2022; 14 (4) :113-134
URL: http://journalofbiosafety.ir/article-1-450-en.html


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Volume 14, Issue 4 (3-2022) Back to browse issues page
فصل نامه علمی ایمنی زیستی Journal of Biosafety
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