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Öğe DNA fingerprinting and genetic diversity analysis of world quinoa germplasm using iPBS-retrotransposon marker system(Tubitak Scientific & Technical Research Council Turkey, 2020) Barut, Muzaffer; Nadeem, Muhammad Azhar; Karaköy, Tolga; Baloch, Faheem ShehzadQuinoa is an important staple food crop for millions of impoverished rural inhabitants of the Andean region. Quinoa is considered a good source of protein,vitamins, minerals, and antioxidants. This study aimed to investigate the genetic diversity and population structure of world quinoa gennplasm originating from 8 countries through the iPBS-retrotransposon marker system. Molecular characterization was performed using the 11 most polymorphic primers. A total of 235 bands were recorded, of which 66.8% were polymorphic. Mean polymorphism information content (PIC) was 0.410. Various diversity indices including mean effective number of alleles (1.269), mean Shannon's information index (0.160) and gene diversity (0.247) revealed the existence of sufficient amount of genetic diversity in studied germplasm. Bolivia-17 and Mexico-1 were found to be genetically distinct accessions and can be suggested as candidate parents for future breeding activities. Various diversity indices were also calculated among germplasm collection counries and the results clearly showed the existence of higher genetic diversity in Bolivian and Peruvian accessions. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) grouped quinoa germplasm according to their collection country. Analysis of molecular variance (AMOVA) revealed that most of the variations (69%) in world quinoa germplasm are due to differences within populations. Findings of this study can be used for deeper understanding of the genetic relationship and in the determination of appropriate breeding and conservation strategies for quinoa.Öğe Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers(Inst Nacional Pesquisas Amazonia, 2020) Vasquez Guizado, Stalin Juan; Nadeem, Muhammad Azhar; Ali, Fawad; Barut, Muzaffer; Habyarimana, Ephrem; Pacheco Gomez, Tedi; Vargas Santillan, Jhon Antoni; Baloch, Faheem ShehzadRosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.Öğe Genetic diversity, population structure and marker- trait association for 100-seed weight in international safflower panel using silicodart marker information(MDPI AG, 2020) Ali, Fawad; Nadeem, Muhammad Azhar; Barut, Muzaffer; Habyarimana, Ephrem; Sameeullah, Muhammad; Shehzad Baloch, FaheemSafflower is an important oilseed crop mainly grown in the arid and semi-arid regions of the world. The aim of this study was to explore phenotypic and genetic diversity, population structure, and marker-trait association for 100-seed weight in 94 safflower accessions originating from 26 countries using silicoDArT markers. Analysis of variance revealed statistically significant genotypic effects (p < 0.01), while Turkey samples resulted in higher 100-seed weight compared to Pakistan samples. A Constellation plot divided the studied germplasm into two populations on the basis of their 100-seed weight. Various mean genetic diversity parameters including observed number of alleles (1.99), effective number of alleles (1.54), Shannon’s information index (0.48), expected heterozygosity (0.32), and unbiased expected heterozygosity (0.32) for the entire population exhibited sufficient genetic diversity using 12232 silicoDArT markers. Analysis of molecular variance (AMOVA) revealed that most of the variations (91%) in world safflower panel are due to differences within country groups. A model-based structure grouped the 94 safflower accessions into populations A, B, C and an admixture population upon membership coefficient. Neighbor joining analysis grouped the safflower accessions into two populations (A and B). Principal coordinate analysis (PCoA) also clustered the safflower accessions on the basis of geographical origin. Three accessions; Egypt-5, Egypt-2, and India-2 revealed the highest genetic distance and hence might be recommended as candidate parental lines for safflower breeding programs. The mixed linear model i.e., the Q + K model, demonstrated that two DArTseq markers (DArT-45483051 and DArT-15672391) had significant association (p < 0.01) for 100-seed weight. We envisage that identified DArTseq markers associated with 100-seed weight will be helpful to develop high-yielding cultivars of safflower through marker-assisted breeding in the near future.Öğe Genomics, phenomics, and next breeding tools for genetic improvement of safflower (Carthamus tinctorius L.)(Springer International Publishing, 2021) Yilmaz, Abdurrahim; Yeken, Mehmet Zahit; Ali, Fawad; Barut, Muzaffer; Nadeem, Muhammad Azhar; Yilmaz, Hilal; Naeem, MuhammadSafflower is one of the most important oilseed crops with high-quality seed oil. It can be grown especially in the arid and semiarid regions in the world. The main reason why safflower is not widely cultivated is because of its low yield. Various breeding efforts have made a significant contribution to the improvement of safflower; however, it seems necessary to exploit the potentiality of this underutilized plant. The development of new and improved safflower varieties will improve the sustainability of this crop to different environmental conditions. Classic breeding efforts made great efforts in safflower breeding; however, these techniques have been slow to develop complex traits such as yield, oil yield, some quality traits, and biotic-abiotic stress resistance. Recent advancements in molecular markers and genome sequencing technologies enhanced the breeding activities and aided the scientific community to understand and comprehensively explore the genetic diversity and population structure of safflower. Phenotypic and molecular characterization helped the construction of genetic linkage maps, leading to a better understanding of complex quantitative characters for safflower varieties. The present chapter articulates different aspects of safflower including phenomics, chemical content, origin-diffusion, similarity centers, wild relatives, genetic resources, trades, and comprehensive advancement in safflower breeding in terms of classical breeding, tissue culture, QTL mapping, association mapping, transgenic breeding, genome editing, and speed breeding. This information will lead to more short-term solutions in breeding safflower crop and will provide more practical information for breeders in the near future. © Springer Nature Switzerland AG 2021.
