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Öğe An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice)(Springer, 2022) Zia, Muhammad Abu Bakar; Yousaf, Muhammad Farhan; Asim, Arslan; Naeem, MuhammadThere is a significant interest while utilizing association mapping technique to determine the genes which are accountable for numerical dissimilarity of the more complex characteristics with agronomic and evolutionary significance. Recently improvements have been made in genomic technology, which motivates for the exploitation of natural diversity, and establishment of more vigorous and strong statistical analysis methods. It creates association mapping technique more demanding and reasonable to plant research programs. Genome-wide association mapping technique recognizes quantitative trait loci (QTLs) by studying the marker-trait associations which could be credited to the power of linkage disequilibrium between different molecular markers and functional polymorphisms through a pool of diversified germplasm. In this review, we will describe an overview of genetic mapping and the current status of association mapping studies in model cereal crops i.e., wheat and rice.Öğe Application of SolCAP Genotyping in Potato (Solanum tuberosum L.) Association Mapping(NLM (Medline), 2023) Yousaf, Muhammad Farhan; Zia, Muhammad Abu Bakar; Naeem, MuhammadPotato variety development entails a number of breeding steps, as well as testing and, finally, commercialization. Historically, phenotypic assesment were carried out to select and germplasm development. The US Department of Agriculture (USDA) funded the Solanaceae Coordinated Agricultural Project (SolCAP) to decode genomic resources into tools that breeders and geneticists can use. This project resulted in the creation of a genome-wide single-nucleotide polymorphism (SNP) array that can be used to evaluate elite potato-breeding germplasm. This array was used to genotype a diverse panel of Solanum species, as well as numerous biparental, diploid, and tetraploid populations. It has high marker density to generate genetic maps that can be used to identify numerous quantitative trait loci (QTLs) for agronomic, quality, biotic, and abiotic resistance traits. Up to now, numerous QTLs for important traits have been identified using new diploid and tetraploid genetic maps. SNP markers were used to assess germplasm relationships and fingerprint varieties and identify candidate genes. The Infinium 8303 SolCAP Potato array offers a common set of SNP markers that can be used for mapping, germplasm assessment, and fingerprinting with confidence. This array has also been helpful in furthering our understanding of the potato genome. Furthermore, some other Infinium potato arrays (i.e., 12 K, 20 K, and 25 K) have been genotyped, and breeders can map quantitative trait loci (QTLs) across multiple populations to improve our understanding of economically important traits and lead to marker-assisted selection (MAS) and breeding and, ultimately, improved varieties. © 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.Öğe Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato (Solanum tuberosum L.)(Springer Heidelberg, 2021) Yousaf, Muhammad Farhan; Demirel, Ufuk; Naeem, Muhammad; Caliskan, Mehmet EminTuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato (Solanum tuberosum L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software WinRHIZO (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, Q + K linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps (r(2) = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases StPP1), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, Sus3, SuSy, and StSUT1) and PVY resistance (Ry sto). The findings of our study can be employed in future breeding programs for improvement in potato production.Öğe Genomics for Abiotic Stress Resistance in Legumes(Springer International Publishing, 2023) Zia, Muhammad Abu Bakar; Ul-Allah, Sami; Sher, Ahmad; Ijaz, Muhammad; Sattar, Abdul; Yousaf, Muhammad Farhan; Chaudhry, Usman KhalidAbiotic stress is an environmental constraint that negatively influences the growth of legumes. Additionally, it is predicted that in the future, it will have devastating effects on the growth and yield of crops. Therefore, currently most of the studies are being conducted to observe the response of legume crops to ensure food for future generations. With the introduction of genomic approaches, it enabled plant scientists to screen cultivars in a more precise way by utilizing the available genomic information. It also resulted in numerous genes that play a pivotal role for stress tolerance in crops that can be positively exploited to develop tolerant cultivars. In this chapter, some of the genomic approaches have been discussed. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.Öğe Overview on domestication, breeding, genetic gain and improvement of tuber quality traits of potato using fast forwarding technique (GWAS): A review(Wiley, 2021) Naeem, Muhammad; Demirel, Ufuk; Yousaf, Muhammad Farhan; Caliskan, Sevgi; Caliskan, Mehmet EminTuber quality is the subject of great interest among the processing industry and consumers worldwide. Being a polygenic trait, its enhancement requires a systematic understanding of their genetic complexity. Molecular genetics offered valuable solutions to the challenging endeavours of slow genetic gains in conventional potato breeding. With the advent of linkage maps, molecular markers and availability of next-generation sequencing (NGS) platforms, the plant breeding programmes worldwide have achieved faster genetic gain due to marker-assisted selection (MAS). Linkage mapping detects QTLs in biparental population; alternatively, genomic and phenotypic differences can be identified by extensive genotyping and phenotyping of a germplasm panel depicting natural biological diversity to reveal QTLs, in other words, marker-trait associations. Due to advancements in the fields of genome sequencing and bioinformatics, researchers have preferred to use the genome-wide association mapping (GWAS) method for detecting QTLs due to its higher resolution. In potato, GWAS identified causative allele(s)/loci and provides reliable platform for the development of diagnostic SNP markers by employing Infinium SolCAP SNP array. Later, KASP validation markers can be developed to be used as selection markers in order to bred improved cultivars. The current review focuses on recently used approaches for genetic analyses (linkage mapping or association mapping) regarding potato tuber quality traits, provides comprehensive knowledge about breeding, genetic gain, basic genetic and statistical GWAS concepts and subsequently highlights the genetic discoveries using GWAS and KASP markers.Öğe SNP Markers Associated with Some Root, Stolon, and Tuber Traits in Tetraploid Potatoes (Solanum tuberosum L.) Grown Under Diverse Growing Systems(Springer, 2024) Yousaf, Muhammad Farhan; Demirel, Ufuk; Naeem, Muhammad; Naawe, Eric Kuopuobe; Caliskan, Mehmet EminNumerous loci, environmental factors, and their interactions have an impact on the phenotypic diversity of several significant traits in plants. One approach put forth in recent years for genetic research and finding quantitative trait loci (QTLs) responsible for the specific trait is association mapping. The purpose of the current study was to pinpoint the genetic underpins of significant underground traits in potato. A panel of 192 diverse tetraploid potato genotypes from different countries were grown under different growing conditions (i.e., aeroponics and pot) to study root, stolon and tuber traits. Significant differences (P <= 0.01) were found between the genotypes for all examined traits, and the heritability (H-2) of the traits ranged from 0.74 to 0.94. Genotyping was carried out using the SolCAP 25K array. 21,226 polymorphic SNPs were used for association mapping of underground traits. A GWASpoly R package was implemented for the marker-trait associations, and 78 genomic regions were found associated with the traits under investigation.. The history of potato breeding was reflected in LD patterns. The identified SNPs have their putative gene functions related to the root and stolon architecture and tuber growth (i.e., WRKY transcription factor, MAPK, the GTP cyclohydrolase 1 (i.e., GTPCHI), Glutathionyl-hydroquinone reductase, and pyrophosphate-fructose 6-phosphate 1-phosphotransferase subunit alpha (PFPase). The results of the present study provides a framework that could be helpful for future potato breeding programs to increase tuber production and reduce the challenges of feeding the world's population in the years to come.
