Browsing by Author "Nadeem, Muhammad Azhar"

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Correction: Population Structure, Genetic Diversity, and GWAS Analyses with GBS-Derived SNPs and Silicodart Markers Unveil Genetic Potential for Breeding and Candidate Genes for Agronomic and Root Quality Traits in an International Sugar Beet Germplasm Collection
(BMC, 2025) Bahjat, Noor Maiwan; Yildiz, Mehtap; Nadeem, Muhammad Azhar; Morales, Andres; Wohlfeiler, Josefina; Baloch, Faheem Shahzad; Cavagnaro, Pablo Federico
Dna Molecular Markers in Plant Breeding: Current Status and Recent Advancements in Genomic Selection and Genome Editing
(Taylor & Francis Ltd, 2018) Nadeem, Muhammad Azhar; Nawaz, Muhammad Amjad; Shahid, Muhammad Qasim; Dogan, Yildiz; Comertpay, Gonul; Yildiz, Mehtap; Baloch, Faheem Shehzad
With the development of molecular marker technology in the 1980s, the fate of plant breeding has changed. Different types of molecular markers have been developed and advancement in sequencing technologies has geared crop improvement. To explore the knowledge about molecular markers, several reviews have been published in the last three decades; however, all these reviews were meant for researchers with advanced knowledge of molecular genetics. This review is intended to be a synopsis of recent developments in molecular markers and their applications in plant breeding and is devoted to early researchers with a little or no knowledge of molecular markers. The progress made in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a more comprehensive understanding of molecular markers and provided deeper insights into the diversity available for crops and greatly complemented breeding stratagems. Genotyping-by-sequencing and association mapping based on next-generation sequencing technologies have facilitated the identification of novel genetic markers for complex and unstructured populations. Altogether, the history, the types of markers, their application in plant sciences and breeding, and some recent advancements in genomic selection and genome editing are discussed.
Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the Ipbs-Retrotransposon Marker System
(Mdpi, 2019) Karik, Unal; Nadeem, Muhammad Azhar; Habyarimana, Ephrem; Ercisli, Sezai; Yildiz, Mehtap; Yilmaz, Abdurrahim; Baloch, Faheem Shehzad
Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon's information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant.
Genetic Characterization of Rheum Ribes (Wild Rhubarb) Genotypes in Lake Van Basin of Turkey Through Issr and Ssr Markers
(Friends Science Publishers, 2019) Ekincialp, Aytekin; Erdinc, Ceknas; Turan, Sibel; Cakmakci, Ozlem; Nadeem, Muhammad Azhar; Baloch, Faheem Shehzad; Sensoy, Suat
Rheum ribes L. (wild rhubarb) is one of the less known plants to the world and the only species from the Rheum genus present in Turkey. In this study, one R. rhabarbarum (as check genotype) and 80 R. ribes genotypes were collected from different geographical locations of Turkey for the investigation of diversity and genetic structure using ISSR (Inter Simple Sequence Repeat) and SSR (Simple Sequence Repeats) markers. SSR markers reflected higher (100%) polymorphism as compared to the ISSR marker. However, ISSR markers produced higher average Polymorphism Information Content (PIC) value (0.805) than the SSR markers (0.724). A Similar range of (PIC) values with ISSR markers was found greater (0.935-0.395) as compared to the range of SSR makers (0.88-0.47). Using Jaccard similarity index, genetic distance was measured for both markers and average genetic distance was found to be higher with ISSR markers as compared to the SSR markers. Neighbor-joining analysis clustered genotypes into 3 groups for both marker systems. During this study some distinct genotypes like R. rhabarbarum, YYUERC19, YYUERCO9 and YYUNIER65 were investigated that can be used as candidate parents for the development of R. ribes L. varieties. Structure analysis grouped the genotypes according to altitude by clustering genotypes having at more than 2000 m in one group and genotypes less than 2000 m altitude in another group. Genetic variations observed in this study can be applied to investigate various traits of interest for the R. ribes L. breeding. (C) 2019 Friends Science Publishers
Genetic Diversity Analysis in the Turkish Pepper Germplasm Using Ipbs Retrotransposon-Based Markers
(Tubitak Scientific & Technological Research Council Turkey, 2020) Yildiz, Mehtap; Kocak, Metin; Nadeem, Muhammad Azhar; Cavagnaro, Pablo; Barboza, Karina; Baloch, Faheem Shehzad; Keles, Davut
Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean 8.6 bands/primer), of which similar to 92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPG MA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper gennplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.
Identification of Genetic Basis Associated With Agronomic Traits in a Global Safflower Panel Using Genome-Wide Association Study
(Tubitak Scientific & Technological Research Council Turkey, 2021) Ali, Fawad; Nadeem, Muhammad Azhar; Habyarimana, Ephrem; Altaf, Muhammad Tanveer; Barut, Muzaffer; Kurt, Cemal; Baloch, Faheem Shehzad
Safflower is an underutilized and minor oilseed crop that received less attention from the scientific community compared to other oilseed crops like soybean and sunflower. Exploring the genetic basis associated with agronomic traits is crucial for marker-assisted breeding of safflower. A genome-wide association study was conducted using a total of 12,232 DArTseq markers to identify the marker-trait association for important agronomic traits in an international safflower panel derived from 26 different geographical countries of the world. Statistically significant genotypic effects (p < 0.05) were observed across mean data of both locations (Pakistan and Turkey). Moderate to high heritability estimates were observed for the studied traits. Studied material showed higher performance for all traits except seeds per capitulum in Pakistan compared to Turkey. Phenotypic diversity for important agronomic traits, such as plant height (60.08 to 121.48 cm), capitula per plant (8.7 to 80.4), seeds per capitulum (15 to 42.05), and seed yield per plant (4.85 to 51.02 g), was illustrated. Seed yield per plant showed a highly significant and positive correlation with capitula per plant (0.4985***). Constellation plot analysis resulted in four groups, i.e. A, B, C, and D. Genotyping by sequencing resulted in 12,232 DArTseq markers being used for the investigation of marker-trait association through mixed linear model (Q + K) approach. DArT-38077549 showed significant association with capitula per plant, while two markers (DArT-22763576, DArT-22763253) were associated with plant height. A total of two markers (DArT-38079422, DArT-100043360) were associated with seeds per capitulum. A total of five DArTseq markers showed significant association with seed yield per plant and maximum variation was resulted by DArT-100004992. The results of this study provide a new insight to understand the genetic basis associated with agronomic traits in safflower. We envisage that significant markers identified through this investigation may be applicable in future safflower marker-assisted breeding programs.