Role of Cellulose Synthase-Like (Csl) genes in barley root growth and differentiation

Barley is a commercial important crop with multiple utilisations. It is widely used in the malting and brewing industries, and with rising attention as super food for its high dietary fibre content. Intensive studies have focused on grain development to improve grain quality to benefit agricultural practices. Less attention has been given to root development. Roots are important plant organs that provide mechanical strength to anchor plants to soil substrates. Roots are also responsible for water and nutrients capture and transportation to aerial organs to support plant development. From the root apical meristem, cells undergo rapid division to form different tissues in the meristem zone, followed by longitudinal expansion to enlarge cell size in the elongation zone, and complete final differentiation in the maturation zone to form fully functional root cells. During this process, cell wall biosynthesis and assembly are critical determinants because the rapidly enlarging cells require strength to resist internal pressure, and also flexibility to allow unidirectional cell expansion. Plant cell walls are composed of various polymers, including cellulose, hemicelluloses, and pectins, which confer distinct chemical and mechanical properties. Cell wall polysaccharide heterogeneity has been described in various tissues and species including Arabidopsis roots and barley developing grains. However, very limited knowledge on the relationships between the composition of root tip cell walls and the development of barley roots has been reported due to the complexity and heterogeneity of the roots. The work presented in this thesis aimed to identify the roles of two cell wall related genes belonging to the Cellulose Synthase-Like (Csl) family during root tip development. To gain a better understanding of gene regulation and polysaccharide composition in the barley root tip, we first analysed the expression of the Csl genes in different root regions and showed predominate expression of HvCslF3 and HvCslF9 genes in the meristem and elongation zones. Cell wall polysaccharide composition of barley root tips was determined by immunohistochemistry and glycosidic linkage analysis. To further understand the functions of the HvCslF3 and HvCslF9 genes in the barley root tip, we employed RNAi to generate knock-down mutants, and analysed the morphological and dynamic differences between the mutants and the wild-type cultivar Golden Promise. These genes are essential in maintaining seminal root elongation and cortical radial patterning of seedlings. The potential functions of HvCslF3 and HvCslF9 genes in regulating the synthesis of cell wall polysaccharides, (1,4)-β-linked glucoxylan and (1,3;1,4)-β-glucan, respectively, were revealed. This indicates that cell wall composition affects root development as a smaller root system was observed in the mutant barley seedlings. Notably, the restrictions on root development were not limited to seedlings. Indeed, we also show the reduction in the root systems and aerial tissue development in the glasshouse grown mutant plants throughout the vegetative growth. The smaller root systems resulted in limitation on water and nutrient uptake. Transportation may be the main reason behind the decreased development of aerial organs. To support this hypothesis, mathematical modelling was used to predict the difference in water and nutrients capture between the genotypes. The simulations also highlighted the variations on plant performance in response to nutrient stresses. Interestingly, the mutant root systems contain certain traits that are beneficial for the plant to tolerate low nutrient availabilities. These findings suggested a new direction in plant breeding to generate plants with more efficient root traits based on cell wall related gene expression and regulation. A phylogenetic study indicated the close relationship between the CslF and CslD gene families. The Arabidopsis genome lacks CslF genes and the plant therefore provides an excellent heterologous expression system to study the functions of HvCslF genes. By introducing the HvCslF3 gene into wild-type Arabidopsis (Col-0) plants and root hair mutants deficient in AtCslD3 and AtCslD5, we demonstrated the functional redundancy between the CslD and CslF gene families and identified a role for HvCslF3 in root hair cell file specification and root hair elongation.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 202

High-Order SNP Combinations Associated with Complex Diseases: Efficient Discovery, Statistical Power and Functional Interactions

There has been increased interest in discovering combinations of single-nucleotide polymorphisms (SNPs) that are strongly associated with a phenotype even if each SNP has little individual effect. Efficient approaches have been proposed for searching two-locus combinations from genome-wide datasets. However, for high-order combinations, existing methods either adopt a brute-force search which only handles a small number of SNPs (up to few hundreds), or use heuristic search that may miss informative combinations. In addition, existing approaches lack statistical power because of the use of statistics with high degrees-of-freedom and the huge number of hypotheses tested during combinatorial search. Due to these challenges, functional interactions in high-order combinations have not been systematically explored. We leverage discriminative-pattern-mining algorithms from the data-mining community to search for high-order combinations in case-control datasets. The substantially improved efficiency and scalability demonstrated on synthetic and real datasets with several thousands of SNPs allows the study of several important mathematical and statistical properties of SNP combinations with order as high as eleven. We further explore functional interactions in high-order combinations and reveal a general connection between the increase in discriminative power of a combination over its subsets and the functional coherence among the genes comprising the combination, supported by multiple datasets. Finally, we study several significant high-order combinations discovered from a lung-cancer dataset and a kidney-transplant-rejection dataset in detail to provide novel insights on the complex diseases. Interestingly, many of these associations involve combinations of common variations that occur in small fractions of population. Thus, our approach is an alternative methodology for exploring the genetics of rare diseases for which the current focus is on individually rare variations

Root angle is controlled by EGT1in cereal crops employing anantigravitropic mechanism

Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus anti-gravitropic offset (AGO) mechanisms. Here we report a new root angle regulatory gene termed ENHANCED GRAVITROPISM1 (EGT1) that encodes a putative AGO component, whose loss of function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes a F-box and Tubby domain containing protein which is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wildtype. Transcript profiling revealed Hvegt1 roots deregulate ROS homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shown that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic Force Microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wildtype. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery’s known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing a novel anti-gravitropic mechanism

Role of cellulose synthase-like (csl) genes in barley root growth and differentiation

Barley is a commercial important crop with multiple utilisations. It is widely used in the malting and brewing industries, and with rising attention as super food for its high dietary fibre content. Intensive studies have focused on grain development to improve grain quality to benefit agricultural practices. Less attention has been given to root development. Roots are important plant organs that provide mechanical strength to anchor plants to soil substrates. Roots are also responsible for water and nutrients capture and transportation to aerial organs to support plant development. From the root apical meristem, cells undergo rapid division to form different tissues in the meristem zone, followed by longitudinal expansion to enlarge cell size in the elongation zone, and complete final differentiation in the maturation zone to form fully functional root cells. During this process, cell wall biosynthesis and assembly are critical determinants because the rapidly enlarging cells require strength to resist internal pressure, and also flexibility to allow unidirectional cell expansion. Plant cell walls are composed of various polymers, including cellulose, hemicelluloses, and pectins, which confer distinct chemical and mechanical properties. Cell wall polysaccharide heterogeneity has been described in various tissues and species including Arabidopsis roots and barley developing grains. However, very limited knowledge on the relationships between the composition of root tip cell walls and the development of barley roots has been reported due to the complexity and heterogeneity of the roots. The work presented in this thesis aimed to identify the roles of two cell wall related genes belonging to the Cellulose Synthase-Like (Csl) family during root tip development. To gain a better understanding of gene regulation and polysaccharide composition in the barley root tip, we first analysed the expression of the Csl genes in different root regions and showed predominate expression of HvCslF3 and HvCslF9 genes in the meristem and elongation zones. Cell wall polysaccharide composition of barley root tips was determined by immunohistochemistry and glycosidic linkage analysis. To further understand the functions of the HvCslF3 and HvCslF9 genes in the barley root tip, we employed RNAi to generate knock-down mutants, and analysed the morphological and dynamic differences between the mutants and the wild-type cultivar Golden Promise. These genes are essential in maintaining seminal root elongation and cortical radial patterning of seedlings. The potential functions of HvCslF3 and HvCslF9 genes in regulating the synthesis of cell wall polysaccharides, (1,4)-β-linked glucoxylan and (1,3;1,4)-β-glucan, respectively, were revealed. This indicates that cell wall composition affects root development as a smaller root system was observed in the mutant barley seedlings. Notably, the restrictions on root development were not limited to seedlings. Indeed, we also show the reduction in the root systems and aerial tissue development in the glasshouse grown mutant plants throughout the vegetative growth. The smaller root systems resulted in limitation on water and nutrient uptake. Transportation may be the main reason behind the decreased development of aerial organs. To support this hypothesis, mathematical modelling was used to predict the difference in water and nutrients capture between the genotypes. The simulations also highlighted the variations on plant performance in response to nutrient stresses. Interestingly, the mutant root systems contain certain traits that are beneficial for the plant to tolerate low nutrient availabilities. These findings suggested a new direction in plant breeding to generate plants with more efficient root traits based on cell wall related gene expression and regulation. A phylogenetic study indicated the close relationship between the CslF and CslD gene families. The Arabidopsis genome lacks CslF genes and the plant therefore provides an excellent heterologous expression system to study the functions of HvCslF genes. By introducing the HvCslF3 gene into wild-type Arabidopsis (Col-0) plants and root hair mutants deficient in AtCslD3 and AtCslD5, we demonstrated the functional redundancy between the CslD and CslF gene families and identified a role for HvCslF3 in root hair cell file specification and root hair elongation

Role of cellulose synthase-like (csl) genes in barley root growth and differentiation

Barley is a commercial important crop with multiple utilisations. It is widely used in the malting and brewing industries, and with rising attention as super food for its high dietary fibre content. Intensive studies have focused on grain development to improve grain quality to benefit agricultural practices. Less attention has been given to root development. Roots are important plant organs that provide mechanical strength to anchor plants to soil substrates. Roots are also responsible for water and nutrients capture and transportation to aerial organs to support plant development. From the root apical meristem, cells undergo rapid division to form different tissues in the meristem zone, followed by longitudinal expansion to enlarge cell size in the elongation zone, and complete final differentiation in the maturation zone to form fully functional root cells. During this process, cell wall biosynthesis and assembly are critical determinants because the rapidly enlarging cells require strength to resist internal pressure, and also flexibility to allow unidirectional cell expansion. Plant cell walls are composed of various polymers, including cellulose, hemicelluloses, and pectins, which confer distinct chemical and mechanical properties. Cell wall polysaccharide heterogeneity has been described in various tissues and species including Arabidopsis roots and barley developing grains. However, very limited knowledge on the relationships between the composition of root tip cell walls and the development of barley roots has been reported due to the complexity and heterogeneity of the roots. The work presented in this thesis aimed to identify the roles of two cell wall related genes belonging to the Cellulose Synthase-Like (Csl) family during root tip development. To gain a better understanding of gene regulation and polysaccharide composition in the barley root tip, we first analysed the expression of the Csl genes in different root regions and showed predominate expression of HvCslF3 and HvCslF9 genes in the meristem and elongation zones. Cell wall polysaccharide composition of barley root tips was determined by immunohistochemistry and glycosidic linkage analysis. To further understand the functions of the HvCslF3 and HvCslF9 genes in the barley root tip, we employed RNAi to generate knock-down mutants, and analysed the morphological and dynamic differences between the mutants and the wild-type cultivar Golden Promise. These genes are essential in maintaining seminal root elongation and cortical radial patterning of seedlings. The potential functions of HvCslF3 and HvCslF9 genes in regulating the synthesis of cell wall polysaccharides, (1,4)-β-linked glucoxylan and (1,3;1,4)-β-glucan, respectively, were revealed. This indicates that cell wall composition affects root development as a smaller root system was observed in the mutant barley seedlings. Notably, the restrictions on root development were not limited to seedlings. Indeed, we also show the reduction in the root systems and aerial tissue development in the glasshouse grown mutant plants throughout the vegetative growth. The smaller root systems resulted in limitation on water and nutrient uptake. Transportation may be the main reason behind the decreased development of aerial organs. To support this hypothesis, mathematical modelling was used to predict the difference in water and nutrients capture between the genotypes. The simulations also highlighted the variations on plant performance in response to nutrient stresses. Interestingly, the mutant root systems contain certain traits that are beneficial for the plant to tolerate low nutrient availabilities. These findings suggested a new direction in plant breeding to generate plants with more efficient root traits based on cell wall related gene expression and regulation. A phylogenetic study indicated the close relationship between the CslF and CslD gene families. The Arabidopsis genome lacks CslF genes and the plant therefore provides an excellent heterologous expression system to study the functions of HvCslF genes. By introducing the HvCslF3 gene into wild-type Arabidopsis (Col-0) plants and root hair mutants deficient in AtCslD3 and AtCslD5, we demonstrated the functional redundancy between the CslD and CslF gene families and identified a role for HvCslF3 in root hair cell file specification and root hair elongation

Self-Calibration for the General Cable-Driven Serial Manipulator with Multi-Segment Cables

This paper focuses on the kinematic calibration problem for the general cable-driven serial manipulator (CDSM) with multi-segment cables to improve its motion control accuracy. Firstly, to fully describe the calibration parameters of cables, links, joint positions, and the transmission system, this paper proposes a new cable routing description method named cable-routing configuration struct (CRCS), which provides a complete set of parameters to be calibrated for the proposed self-calibration algorithm. Then, a self-calibration algorithm for CDSM with motor incremental encoders is proposed, which can calibrate the robot at one time only using sufficient measured motor and joint positions. Its premise, the initial cable length, needs to be calibrated. Finally, the parameters of a three-DOF (degree of freedom) six-cable CDSM were described using the CRCS description method, and a comparative experiment was carried out on the same motion controller using the parameters before and after calibration. The experiment results of trajectory tracking error showed that the calibration parameters obtained by the proposed calibration algorithm can significantly improve the motion control accuracy of the three-DOF six-cable CDSM. This verified the correctness and effectiveness of the proposed calibration algorithm

A Closed-Form Solution for the Inverse Kinematics of the 2<i>n</i>-DOF Hyper-Redundant Manipulator Based on General Spherical Joint

This paper presents a closed-form inverse kinematics solution for the 2n-degree of freedom (DOF) hyper-redundant serial manipulator with n identical universal joints (UJs). The proposed algorithm is based on a novel concept named as general spherical joint (GSJ). In this work, these universal joints are modeled as general spherical joints through introducing a virtual revolution between two adjacent universal joints. This virtual revolution acts as the third revolute DOF of the general spherical joint. Remarkably, the proposed general spherical joint can also realize the decoupling of position and orientation just as the spherical wrist. Further, based on this, the universal joint angles can be solved if all of the positions of the general spherical joints are known. The position of a general spherical joint can be determined by using three distances between this unknown general spherical joint and another three known ones. Finally, a closed-form solution for the whole manipulator is solved by applying the inverse kinematics of single general spherical joint section using these positions. Simulations are developed to verify the validity of the proposed closed-form inverse kinematics model

Self-Calibration for the General Cable-Driven Serial Manipulator with Multi-Segment Cables

This paper focuses on the kinematic calibration problem for the general cable-driven serial manipulator (CDSM) with multi-segment cables to improve its motion control accuracy. Firstly, to fully describe the calibration parameters of cables, links, joint positions, and the transmission system, this paper proposes a new cable routing description method named cable-routing configuration struct (CRCS), which provides a complete set of parameters to be calibrated for the proposed self-calibration algorithm. Then, a self-calibration algorithm for CDSM with motor incremental encoders is proposed, which can calibrate the robot at one time only using sufficient measured motor and joint positions. Its premise, the initial cable length, needs to be calibrated. Finally, the parameters of a three-DOF (degree of freedom) six-cable CDSM were described using the CRCS description method, and a comparative experiment was carried out on the same motion controller using the parameters before and after calibration. The experiment results of trajectory tracking error showed that the calibration parameters obtained by the proposed calibration algorithm can significantly improve the motion control accuracy of the three-DOF six-cable CDSM. This verified the correctness and effectiveness of the proposed calibration algorithm

A Closed-Form Solution for the Inverse Kinematics of the 2n-DOF Hyper-Redundant Manipulator Based on General Spherical Joint

This paper presents a closed-form inverse kinematics solution for the 2n-degree of freedom (DOF) hyper-redundant serial manipulator with n identical universal joints (UJs). The proposed algorithm is based on a novel concept named as general spherical joint (GSJ). In this work, these universal joints are modeled as general spherical joints through introducing a virtual revolution between two adjacent universal joints. This virtual revolution acts as the third revolute DOF of the general spherical joint. Remarkably, the proposed general spherical joint can also realize the decoupling of position and orientation just as the spherical wrist. Further, based on this, the universal joint angles can be solved if all of the positions of the general spherical joints are known. The position of a general spherical joint can be determined by using three distances between this unknown general spherical joint and another three known ones. Finally, a closed-form solution for the whole manipulator is solved by applying the inverse kinematics of single general spherical joint section using these positions. Simulations are developed to verify the validity of the proposed closed-form inverse kinematics model