Browsing by Author "Baloch, Faheem Shehzad"

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Advancements in Qtl Mapping and Gwas Application in Plant Improvement
(Tubitak Scientific & Technological Research Council Turkey, 2024) Altaf, Muhammad Tanveer; Tatar, Muhammed; Ali, Amjad; Liaqat, Waqas; Mortazvi, Parnaz; Kayihan, Ceyhun; Baloch, Faheem Shehzad
In modern plant breeding, molecular markers have become indispensable tools, allowing the precise identification of genetic loci linked to key agronomic traits. These markers provide critical insight into the genetic architecture of crops, accelerating the selection of desirable traits for sustainable agriculture. This review focuses on the advancements in quantitative trait locus (QTL) mapping and genome-wide association studies (GWASs), highlighting their effective roles in identifying complex traits such as stress tolerance, yield, disease resistance, and nutrient efficiency. QTL mapping identifies the significant genetic regions linked to desired traits, while GWASs enhance precision using larger populations. The integration of high-throughput phenotyping has further improved the efficiency and accuracyof QTL research and GWASs, enabling precise trait analysis across diverse conditions. Additionally, next-generation sequencing, clustered regularly interspaced short palindromic repeats (CRISPR) technology, and transcriptomics have transformed these methods, offering profound insights into gene function and regulation. Single-cell RNA sequencing further enhances our understanding of plant responses at the cellular level, especially under environmental stress. Despite this progress, however, challenges persist in optimizing methods, refining training populations, and integrating these tools into breeding programs. Future studies must aim to enhance genetic prediction models, incorporate advanced molecular technologies, and refine functional markers to tackle the challenges of sustainable agriculture.
Application of Ipbs-Retrotransposons Markers for the Assessment of Genetic Diversity and Population Structure Among Sugar Beet (Beta Vulgaris) Germplasm From Different Regions of the World
(Springer, 2025) Sadik, Gokhan; Yildiz, Mehtap; Taskin, Bilgin; Kocak, Metin; Cavagnaro, Pablo Federico; Baloch, Faheem Shehzad
Sugar beet is an important agricultural crop product that has been produced and consumed worldwide since the eighteenth century and can adapt to various climatic and soil conditions. The two fundamental building blocks of any crop improvement program are germplasm resources, which contain genetic diversity and phenotypic expression of desired traits. In this study, a total of 58 sugar beet genotypes including 12 from Turkey, 4 from India, 12 from the United States of America, 16 from Iran, 12 from England and Beta vulgaris L. subsp. maritima L. Arcang. as wild species were characterized using 15 inter-primer binding site (iPBS) markers that produced intense and polymorphic bands in the germplasm library. Using these 15 iPBS markers, 102 polymorphic bands were produced and the average number of polymorphic bands was determined as 6.8. Polymorphism information content (PIC) values ranged between 0.58 and 0.83, and the average PIC value was found to be 0.70. It was determined that the most genetically different genotypes were PI 590697-US11 and PI 171508-TR8, with a distance of 0.73. Clustering algorithms Unweighted Pair Group Method Algorithm (UPGMA) and Principal Coordinate Algorithm (PCoA) confirmed that genotypes are an important factor in clustering, and STRUCTURE analysis divided sugar beet gene resources into six populations. Also, the analysis of molecular variance (AMOVA) showed that there was 8% variance among populations and 92% variance within populations. This is the first study to investigate the genetic diversity and population structure of sugar beet germplasm using the iPBS-retrotransposon marker system. The results of this research emphasized that iPBS markers are very successful and effective in examining the genetic diversity of sugar beet germplasm. The results obtained in this study provide a theoretical basis for future selection and breeding of superior sugar beet germplasm sources.
Assessment of Genetic Diversity Among 131 Safflower (Carthamus Tinctorius L.) Accessions Using Peroxidase Gene Polymorphism (Pogp) Markers
(Springer, 2022) Yildiz, Mehtap; Altaf, Muhammad Tanveer; Baloch, Faheem Shehzad; Kocak, Metin; Sadik, Gokhan; Kuzgun, Cansu; Tuncturk, Murat
Background Safflower (Carthamus tinctorius L.) is an old oilseed crop with a 1.4 GB genome size and its flowers are used for food coloring, dyes and pharmaceutical industries. It was domesticated from its putative wild ancestor Carthamus palestinus about forty-five hundred years ago in the fertile crescent region.The current study was aimed to determine the genetic diversity, population structure and to check the applicability of iPBS-retrotransposons markers. Methods and results Eleven POGP primers yielded 70 bands of which 61 were highly polymorphic with 87.14% polymorphism. A great level of genetic variation was examined with higher values of overall gene diversity (0.27), genetic distance (0.53), number of effective alleles (1.46), Shannon's information index (0.41) and polymorphism information contents (0.71). Analysis of molecular variance revealed high genetic variation with 79% within the population. The STRUCTURE, PCoA and Neighbor-joining analysis separated the safflower germplasm into 2 major populations and 1 un-classified population. The accessions which were from Asian countries i.e., China, Afghanistan, Turkey, Iran and Pakistan were genetically similar and clustered together in both populations A and B. The maximum genetic distance was measured 0.88 between Pakistan 26 x Pakistan 24. Conclusion Findings of this research such as maximum diversity indices, higher PIC values showed the effectiveness and utility of POGP markers for the evaluation of genetic relationships among safflower accessions. The results of this study also showed that POGP markers are less effective compared to ISSRs, iPBS-retrotransposons and DArTSeq markers. AMOVA showed high genetic variation (79%) within a population and maximum genetic distance was found between the accessions Pakistan 26- Pakistan 24 and may be suggested as candidate parents for future breeding activities of safflower. The accessions from the fertile crescent region were clustered together and proved the origin of safflower domestication. This study highlights genetic variation among safflower germplasm and could be helpfull for parental selection and planning for future breeding programs.
Dna Based Ipbs-Retrotransposon Markers for Investigating the Population Structure of Pea (Pisum Sativum) Germplasm From Turkey
(Pergamon-elsevier Science Ltd, 2015) Baloch, Faheem Shehzad; Alsaleh, Ahmad; Saenz de Miera, Luis E.; Hatipoglu, Rustu; Ciftci, Vandettin; Karakoy, Tolga; Ozkan, Hakan
Retrotransposons have been highly studied in monocots; however retrotransposon diversity in dicot crops has not been well documented. Our objective was to assess the diversity harbored by field pea landraces using retrotranposon markers. In this research, molecular characterization of 104 landraces and 34 field pea breeding lines was assessed using newly developed iPBS-retrotransposon markers. The 12 iPBS-retrotransposon primers generated a total 106 scorable bands, and 81 of these were found to be polymorphic (76.4%), with an average of 6.75 polymorphic fragments per primer. Polymorphism information content (PIC) ranged from 0.33 to 0.84 with an average of 0.61. It was evident that field pea landraces from the same geographical region were often placed in different groups in the neighbor joining analysis, indicating that grouping based on genetic parameters was not closely related to the geographical origin. The population structure was determined by using STRUCTURE software, and three populations at K = 3 and five populations at K = 5 were identified among landraces. The plentiful diversity present in Turkish field pea landraces could be used as genetic resource in designing breeding program, and may also contribute to worldwide pea breeding programs. Our data also suggested a role of iPBS-retrotransposons as 'a universal marker' for molecular characterization of pea germplasm. (C) 2015 Elsevier Ltd. All rights reserved.
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 Genetic Diversity of Turkish Fig (Ficus Carica L.) Germplasm Using Inter-Primer Binding Site (Ipbs) Retrotransposon Markers
(Springer, 2024) Ucer, Viyan Acar; Aglar, Erdal; Mortazavi, Parnaz; Qureshi, Sarmad Ali; Ali, Amjad; Tatar, Muhammed; Baloch, Faheem Shehzad
The common fig belonging to the Moraceae family, is valued for its latex-producing plant parts and commercially important fruit, rich in phenolic antioxidants, nutrients, and fiber, and consumed fresh or dried. The present study aimed to assess the genetic diversity of 73 fig (Ficus carica L.) genotypes collected from the Derecik and & Ccedil;UKURCA districts of the Hakkari Province of Turkey with the inter-Primer Binding Site (iPBS)-retrotransposons marker system. Molecular characterization with 12 most polymorphic primers revealed a total of 255 scorable bands, and 2375 primer produced a maximum of 36 alleles. The polymorphism information content (PIC) was recorded in a range of 0.406-0.455. The genetic diversity indices showed a mean gene diversity of 0.33 and a Shannon's information index of 0.50. The analysis of molecular variance (AMOVA) revealed higher genetic differences within the population (96%) compared to among the population (4%). The population structure and Neighbor-joining analysis-based clustering divided the entire genotype into two groups mainly their collection point. Turkish fig germplasm exhibits significant genetic diversity, which is crucial for breeding programs aimed at enhancing the resilience and productivity of new cultivars.
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.