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    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, Muhammad
    There 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.
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    Application of SolCAP Genotyping in Potato (Solanum tuberosum L.) Association Mapping
    (NLM (Medline), 2023) Yousaf, Muhammad Farhan; Zia, Muhammad Abu Bakar; Naeem, Muhammad
    Potato 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.
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    Genetic engineering techniques in potato
    (Elsevier, 2024) Zia, Muhammad Abu Bakar; Ijaz, Muhammad; Sami-ul-Allah; Aslam, Roohi; Naeem, Muhammad; Gul, Alvina; Butt, Razmia Sabahat
    Potato is the world's number one nongrain commodity and the fourth most common commodity overall after maize, rice, and wheat. In terms of cell culture, potato exhibits a high level of docility. It also has an extended history of applications in biotechnology for the improvement of crops. The recent genomic revolution has significantly enhanced the overall understanding of the genetic makeup of all crops. Crop genome sequences have reformed our view and understanding of genome association and genome development. Recent updated knowledge in markers along with advanced phenotyping, genotyping-by-sequencing (GBS), and genome-wide association studies (GWAS) has led to the development of new ways of determining marker-trait associations that can withstand genome-based breeding programs. The accessibility of sequencing of genomic data has permitted editing of the genome (localized mutagenesis) for obtaining sequences of genes that are anticipated by breeders. In the realm of potato breeding, some genetic features such as genomics, genetic mapping, and marker application have also given breeders tasks to accomplish. Several strategies have been formulated to describe potato loci, contender genes and alleles, and their associated genotypes and phenotypes. This chapter highlights how genomics technologies can be modified to meet the needs of potato breeders to enhance potato improvement through the use of next-generation phenotyping, GWAS, and genome editing tools. © 2024 Elsevier Inc. All rights reserved.
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    Genome-wide association studies (GWAS) revealed a genetic basis associated with floral traits in potato germplasm
    (Tubitak Scientific & Technological Research Council Turkey, 2022) Zia, Muhammad Abu Bakar; Demirel, Ufuk; Nadeem, Muhammad Azhar; Ali, Fawad; Dawood, Ahmad; Ijaz, Muhammad; Caliskan, Mehmet Emin
    Potato is an important noncereal staple crop serving as a source of food for a large number of the world's population. Genomewide association study (GWAS) analysis has become a useful tool to uncover the genetic basis of important plant traits by revealing significant association with the trait of interest. The present study aimed to explore the phenotypic diversity and to identify the genetic basis associated with important floral traits. A total of 237 tetraploid potato genotypes were used as plant material, and field experiments were conducted according to augmented block design for two consecutive years (2016, 2017). Analysis of variance for the studied floral traits reflected highly significant genotypic effects. Mean data for both years revealed the significant variation for pistil length (5.53 to 9.92 mm), stamen length (6.04 to 9.26 mm), and pistil length above stamen (1.31 to 4.47 mm). Pearson's correlation analysis reflected a highly significant and positive correlation of pistil length with stamen length (r = 0.42) and pistil length above stamen (r = 0.28). Principal component analysis was performed, and the first two PCs were considered accounting for a total of 81.2% variation. Constellation plot divided the studied potato panel into two main populations on the basis of stamen and pistil length. A total of 12,720SNP markers were used for the marker-trait association, and a total of 15 markers were found significantly associated with studied traits across both years. Identifying the same markers across both years helped in the validation of the obtained marker-trait associations. The identified significant markers reflected some of the putative candidate genes that might be beneficial in potato breeding programs. To the best of our knowledge, this is the first study identifying the genetic basis of important floral traits and might be helpful to the scientific community interested in potato marker-assisted breeding in these traits.
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    Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel
    (Springer, 2020) Zia, Muhammad Abu Bakar; Demirel, Ufuk; Nadeem, Muhammad Azhar; Caliskan, Mehmet Emin
    Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Nigde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r(2) value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.
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    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 Khalid
    Abiotic 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.
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    Recent advances in potato (solanum tuberosum L.) breeding
    (Springer International Publishing, 2021) Aksoy, Emre; Demirel, Ufuk; Bakhsh, Allah; Zia, Muhammad Abu Bakar; Naeem, Muhammad; Saeed, Faisal; Çalişkan, Sevgi
    Potato (Solanum tuberosum L.) is an annual dicotyledonous tuber crop originating from the Americas and now distributed all over the world. A member of the Solanaceae family, potato is the fourth most produced food crop and the first non-cereal crop in the world. Potato is a staple food with its high potentiality in fighting malnutrition in the world since potato tubers are known sources of vitamins, proteins, carbohydrates and minerals. Moreover, it generates higher yield compared to the other crops; hence, it is one of the most notable crops to eliminate hunger and poverty. Therefore, sustainable potato production is important for food security and social welfare in future climate-change scenarios. However, it is very sensitive to environmental conditions and climate change due to its shallow root system. Therefore, future potato breeding programs should focus on enhancement of abiotic and biotic stress tolerance by utilizing the natural germplasm conserved in different gene banks. Moreover, potato breeding should benefit from the effectiveness and ease of molecular techniques such as marker-assisted selection, genome-wide association studies, functional genomics and transgenics. Development of new potato varieties can also be achieved via genetic engineering and genome editing. Disease-free potato seed production requires integration of tissue culture methods in plant breeding. As a staple food for millions, the potato has an extraordinarily rich past, and a bright future. The demand for potato will increase in future, which will be the driving force behind the potato research. © Springer Nature Switzerland AG 2021.