Linkage disequilibrium mapping: A journey from traditional breeding to molecular breeding in crop plants

434-442Germplasms are the reservoir of agronomically important traits traditionally maintained by various tribal communities over the year. Maintaining these germplasms generations after generations has little value unless exploited for the desired agronomic traits like biotic and abiotic stress, yield attributes and nutritional enrichment. Association mapping, otherwise called linkage disequilibrium mapping, is a molecular breeding approach for characterizing complex traits with agronomic importance in crop plants. It is a systematic method for identifying novel traits and is treated as an alternative tool to traditional QTL mapping approaches, which involves correlating molecular markers with the phenotypic trait in a diversified population. The map's resolution in association mapping is based on the candidate-gene approach or genome-wide association approach. Therefore, association mapping studies offer a great perspective on crop genetic improvement. Still, considerably large-scale research is required to determine the sensible implementation of association mapping analysis in most crop plants. Currently, there is considerable interest in using association mapping approaches in crop breeding programs, which can be achieved by advanced genomic technology and the development of statistical computer software packages. Here, the linkage disequilibrium approach and its usefulness in association mapping studies, including the steps associated with it are discussed. The current status and future challenges in complex trait dissection by utilizing the linkage disequilibrium mapping in crop plants are also discussed

Genome-Wide Identification and Characterization of the Brassinazole-resistant (BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat (Triticum aestivum L.)

Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat

Comprehensive General Chemistry (GA Southern)

This LibGuides-based open textbook with MathML, adapted from OpenStax Chemistry 2nd Edition, was created through a Round 14 Textbook Transformation Grant. Each chapter contains a set of downloadable end-of-chapter problems

Textbook transformation journey: from traditional to no-cost materials

For Affordable Learning Georgia Textbook Transformation grant, our team has created no-cost textbook materials for a Comprehensive General Chemistry course for engineering majors. Our open-access materials are supplemented with video tutorials and problems with engineering applications to encourage students to engage with the course material without financial constraints. We will conduct a control-treatment study to measure the impacts of this transformation. We are collecting grade data, survey data, and web analytics to explore student textbook usage, change in learning outcomes, and change in student perception of course materials. We will present our textbook transformation journey, information on open-access resources, and preliminary findings

Textbook Transformation Journey: From Traditional to No-Cost Materials

For Affordable Learning Georgia Textbook Transformation grant, our team has created no-cost textbook materials for a Comprehensive General Chemistry course for engineering majors. Our open-access materials are supplemented with video tutorials and problems with engineering applications to encourage students to engage with the course material without financial constraints. We will conduct a control-treatment study to measure the impacts of this transformation. We are collecting grade data, survey data, and web analytics to explore student textbook usage, change in learning outcomes, and change in student perception of course materials. We will present our textbook transformation journey, information on open-access resources, and preliminary findings

Linkage disequilibrium mapping: A journey from traditional breeding to molecular breeding in crop plants

Germplasms are the reservoir of agronomically important traits traditionally maintained by various tribal communities over the year. Maintaining these germplasms generations after generations has little value unless exploited for the desired agronomic traits like biotic and abiotic stress, yield attributes and nutritional enrichment. Association mapping, otherwise called linkage disequilibrium mapping, is a molecular breeding approach for characterizing complex traits with agronomic importance in crop plants. It is a systematic method for identifying novel traits and is treated as an alternative tool to traditional QTL mapping approaches, which involves correlating molecular markers with the phenotypic trait in a diversified population. The map's resolution in association mapping is based on the candidate-gene approach or genome-wide association approach. Therefore, association mapping studies offer a great perspective on crop genetic improvement. Still, considerably large-scale research is required to determine the sensible implementation of association mapping analysis in most crop plants. Currently, there is considerable interest in using association mapping approaches in crop breeding programs, which can be achieved by advanced genomic technology and the development of statistical computer software packages. Here, the linkage disequilibrium approach and its usefulness in association mapping studies, including the steps associated with it are discussed. The current status and future challenges in complex trait dissection by utilizing the linkage disequilibrium mapping in crop plants are also discussed

Effect of Different Trichoderma asperellum Formulations on Management of Sheath Blight of Rice

Trichoderma spp. were known to have antagonistic activity against against many soil borne diseases. In this experiment we have prepared five different formulations of Trichoderma asperellum and stored them in normal temperature. Later the efficacy of all the formulations were checked against sheath blight disease of rice both in-vitro and in-vivo. Among formulations the F5 [Trichoderma grown in potato dextrose broth (500ml) + Talc(500g)] treated plants showed very good result in managing sheath blight of rice by enhancing the plant height, total number of filled grains and root length. All the formulations performed significantly better than untreated control plants. The F5 treated plants were also recorded to have less disease incidence with increased yield as compared to other formulations

Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L.

PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions

Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat (Triticum aestivum L.)

Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study’s outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat