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Theses

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2020 - 20212
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Subject: Biotechnology and molecular Biology × End date: 2021 × Start date: 2020 × Type: Thesis × Thesis Type: Ph.D ×
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    ThesisItemOpen Access
    Genome-wide association mapping in barley for terminal heat tolerance and malting quality
    (CCSHAU, Hisar, 2021-07) Verma, Swati; Yashveer, Shikha
    Barley (Hordeum vulgare L.), is one of the major cereal crops and has been cultivated since ancient times in different parts of the world. In particular, heat stress at the post-heading stage causes considerable yield reduction due to the stress. Understanding the genetic variation, changes in physiological processes, and level of genetic diversity existing among genotypes are needed to produce new cultivars not only having a high tolerance to heat stress, but also displaying high yield. So to address this challenge, a panel of 316 diverse barley genotypes (AM2017) were procured. It was evaluated under two conditions timely-sown (TS) and late-sown (LS) conditions in two seasons of 2017-18 and 2018-19 at CCSHAU, Hisar. Ten agro-morphological, four physiological, and five grain malting quality traits were studied. Genetic diversity and population structure were explored in the AM2017 panel after genotyping it with the 50 K iSelect Illumina Barley SNP array. A set of 36,793 SNP markers, covering a genetic distance of 991.82 cM with an average marker density of 37.09 SNPs/cM, was obtained after quality filtration. The gene diversity (GD) and Polymorphic Information Content (PIC) at the genome level were 0.362 and 0.289, respectively. The phenotypic results showed a clear reduction in trait performance under the LS condition. Marker-trait associations (MTAs) were estimated using the compressed mixed linear model. Based on the estimated MTAs and linkage disequilibrium (LD) decay observed in the genome, putative QTL was identified as associated with the traits studied. The most robust QTL observed under both sowing conditions were further studied and validated using the previously reported QTL. Several traits were found to have QTL that was not found to be reported. The combination of analyses using SNPs and changes in physiological traits provided useful information on genomic regions taking part in heat stress tolerance.
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    ThesisItemOpen Access
    Molecular approaches for detection and forecasting of wheat yellow rust
    (CCSHAU, Hisar, 2020-03) Rizwana Rehsawla; Yadav, Neelam R.
    Yellow or stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating airborne disease that affects bread wheat in the major wheat growing regions of India. The understanding of the origin, evolution, pathogenicity, avirulence/virulence behaviour of Pst is very important for the development of more effective management strategies to combat the disease spread. To understand inter and intraspecific phylogenetic relationship among Indian Pst pathotypes, multigene sequence analysis was done. Molecular marker study along with sequencing technology was used to collect information, which was more effective than virulence characterization. The molecular diversity analysis among 13 different Pst pathotypes showed two major cluster formations at similarity coefficient of 0.78. Sometimes, all three wheat rust or two rusts in combination occur simultaneously in the field. Under such conditions identification and differentiation of the yellow rust is needed for precise identification and high throughput DNA based detection protocols. To address this problem PCR based markers were developed which can specifically detect and differentiate Pst from two other rust species of Puccinia and other wheat pathogens. DNA-based methods such as conventional PCR have revolutionized plant disease detection; they are not very reliable at asymptomatic stage. Therefore, a simple and reproducible LAMP assay was developed which could detect the pathogen at an early stage i.e. 3rd day of post infection without any visible sign of pathogen attack on the leaf sample using LAMP primers available in public domain. Four novel sets of LAMP primers from ketopantotate reductase gene were also designed for Pst detection which worked successfully. Biosensing by electrochemical and SPR for the detection of yellow rust was also undertaken. Electrochemical based sensing was done using different sequences of Pst specific genes as probes. Linear response over wide DNA concentration range from 10 pg/μl to 115ng/μl was obtained with a high sensitivity, accuracy and reproducibility. The lowest detection limit was observed for microRNA like RNA 1 gene i.e. 10 pg/μl. Electrochemical DNA based biosensing was developed to distinguish between the yellow rust susceptible and resistant wheat genotypes using TaATG8j gene sequence. Linear response over wide DNA concentration range from 1 ng/μl to 50 ng/μl was obtained with detection limit of 4 pg/μl. The SPR biosensor demonstrated high specificity and long shelf life thus promising its application in Pst diagnosis. The developed biosensor exhibited a high sensitivity (0.18°/ (ng/μl)), good linearity, low detection limit (1 ng/μl) and high specificity over a wide concentration range of DNA (1–150 ng/μl).