Browsing by Author "Patil, Gunvant B. (TTU)"
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Item Development of High-Quality Nuclei Isolation to Study Plant Root–Microbe Interaction for Single-Nuclei Transcriptomic Sequencing in Soybean(2023) D’Agostino, Leonidas W. (TTU); Yong-Villalobos, Lenin (TTU); Herrera-Estrella, Luis (TTU); Patil, Gunvant B. (TTU)Single-nucleus RNA sequencing (sNucRNA-seq) is an emerging technology that has been rapidly adopted and demonstrated to be a powerful tool for detailed characterization of each cell- and sub cell-types in complex tissues of higher eukaryotes. sNucRNA-seq has also been used to dissect cell-type-specific transcriptional responses to environmental or developmental signals. In plants, this technology is being utilized to identify cell-type-specific trajectories for the study of several tissue types and important traits, including the single-cell dissection of the genetic determinants regulating plant–microbe interactions. The isolation of high-quality nuclei is one of the prerequisite steps to obtain high-quality sNucRNA-seq results. Although nuclei isolation from several plant tissues is well established, this process is highly troublesome when plant tissues are associated with beneficial or pathogenic microbes. For example, root tissues colonized with rhizobium bacteria (nodules), leaf tissue infected with bacterial or fungal pathogens, or roots infected with nematodes pose critical challenges to the isolation of high-quality nuclei and use for downstream application. Therefore, isolation of microbe-free, high-quality nuclei from plant tissues are necessary to avoid clogging or interference with the microfluidic channel (e.g., 10× Genomics) or particle-templated emulsion that are used in sNucRNA-seq platforms. Here, we developed a simple, effective, and efficient method to isolate high-quality nuclei from soybean roots and root nodules, followed by washing out bacterial contamination. This protocol has been designed to be easily implemented into any lab environment, and it can also be scaled up for use with multiple samples and applicable to a variety of samples with the presence of microbes. We validated this protocol by successfully generating a barcoded library using the 10× Genomics microfluidic platform from tissue subjected to this procedure. This workflow was developed to provide an accessible alternative to instrument-based approaches (e.g., fluorescent cell sorting) and will expand the ability of researchers to perform experiments such as sNucRNA-seq and sNucATAC-seq on inherently heterogeneous plant tissue samples.Item Genome editing and chromosome engineering in plants(2023) Ojha, Arjun (TTU); Zhang, Feng; Patil, Gunvant B. (TTU)In the last two decades, innovations in genomics (genome reading) have advanced crop breeding and have played a central role crop improvement. Since first crop genome (rice) was published, several crop genomes are out in the public domain with an exponential increase in the number of samples per genome, improved genome assembly and development of PAN genomes (Figure 1). The availability of reference, whole genome re-sequencing (WGRS) and PAN-genomes are essential to map allelic variants (single base pair to large variations) and have advanced our knowledge toward precise gene discovery, marker development, and trait introgression (Bevan et al., 2017; Kadam et al., 2016; Patil et al., 2016; Valliyodan et al., 2021). WGRS and development of PAN genomes is one of the many payoffs of trait discovery programs and has been conducted in a variety of organism including humans, animals, and several crop species (Figure 1). The dense variation data integrated with other omics platforms (transcriptomics, phenomics, and metabolomics) improves the understanding of phenotype–genotype relationship and essential for marker-assisted breeding and gene mapping. Several crop-specific databases have been developed to accelerate the trait mapping, and this information has become an integral part of all aspects of biological research, including basic and applied plant biology (Deshmukh et al., 2021; Matthews et al., 2009). With integrated genomic technologies, researchers can now effectively identify casual genetic variants from wild/landrace relatives. Application of robust and high throughput genome engineering technologies will be essential to understand gene function and achieve targeted modification of desirable agronomic traits in a wide range of plants, especially crop species.Item High day and night temperatures impact on cotton yield and quality—current status and future research direction(2023) Saini, Dinesh K. (TTU); Impa, S. M. (TTU); McCallister, Donna (TTU); Patil, Gunvant B. (TTU); Abidi, Noureddine (TTU); Ritchie, Glen (TTU); Jaconis, S. Y.; Jagadish, Krishna S.V. (TTU)Heat waves, and an increased number of warm days and nights, have become more prevalent in major agricultural regions of the world. Although well adapted to semi-arid regions, cotton is vulnerable to high temperatures, particularly during flowering and boll development. To maintain lint yield potential without compromising its quality under high-temperature stress, it is essential to understand the effects of heat stress on various stages of plant growth and development, and associated tolerance mechanisms. Despite ongoing efforts to gather data on the effects of heat stress on cotton growth and development, there remains a critical gap in understanding the distinct influence of high temperatures during the day and night on cotton yield and quality. Also, identifying mechanisms and target traits that induce greater high day and night temperature tolerance is essential for breeding climate-resilient cotton for future uncertain climates. To bridge these knowledge gaps, we embarked on a rigorous and comprehensive review of published literature, delving into the impact of heat stress on cotton yields and the consequential losses in fiber quality. This review encompasses information on the effects of heat stress on growth, physiological, and biochemical responses, fertilization, cotton yield, and quality. Additionally, we discuss management options for minimizing heat stress-induced damage, and the benefits of integrating conventional and genomics-assisted breeding for developing heat-tolerant cotton cultivars. Finally, future research areas that need to be addressed to develop heat-resilient cotton are proposed.