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This second volume details new and updated methods on biology of various cellular processes and agronomic traits and come up with better strategies to improve legume crops. Chapters guide readers through legume genomic resources, legume pangenome and organelle genome construction, transcriptome analysis, DNA methylation analysis, double-digest restriction site-associated DNA sequencing; target enrichment sequencing via probe capture, genomic selection and transformation methods; prediction of long non-coding RNAs and secondary structures, genome-wide mining of disease resistance gene analogs; genome editing, and bioactive compound and phosphoproteome analysis. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Legume Genomics: Methods and Protocols, Second Edition aims to be comprehensive guide for researchers in the field.
List of contents
Legume pangenome construction using an iterative mapping and assembly approach.- Large-scale Identification of Transposon Insertion Polymorphisms in Leguminous Plants from Paired-End WGS Data.- Comprehensive Method for Soybean Cultivar Identification Using MGIseq, VCF2GENOME, and REST API.- Methods for Construction of Core Collections using SNP Markers.- Interspecific Hybridization Using Cicer Microphyllum Royle Ex Benth. for the Genomic Reconstruction of Cultivated Chickpea (Cicer arietinum L.).- Local haplotyping analysis for flowering time in soybean using crosshap.- Method for Genome-Wide Association Study: a soybean example.- Method to Establish Intergeneric or Interspecific Hybrids through Genomic In Situ Hybridization (GISH).- Method for dissection of genomic loci associated with chickpea root penetration traits in compact soil.- Method for ATAC Sequencing Data Analysis for Understanding Chromatin Biology in Legumes.- Protein Extraction Protocol for Legumes Compatible with Detergent - Gel Fractionation and Mass Spectrometry.- Isolation of cytoskeleton and cytoskeleton-bound polysome, and identification of cytoskeletal proteins from a grain legume.- A multi-omics approach for microbiome data analysis in legumes.- A computational pipeline for the identification of RNA virome in legumes.- Identification of tRNA-derived fragments in legumes.- Applications of the Soybean Expression Atlas in Genomics and Transcriptomics Research.- TAIL-PCR for Recovery of Tnt1 Flanking Sequences in Chickpea: A Tool for Functional Genomics Studies.- CRISPR/Cas9-Based Gene Editing in Soybean.- Expression Analysis of ROS Related Genes During Germination of Chickpea (Cicer Arietinum L.) Seeds.- Flow Cytometry and K-mer Based Approach for Genome Size Estimation of Clusterbean: A Case Study.
Summary
This second volume details new and updated methods on biology of various cellular processes and agronomic traits and come up with better strategies to improve legume crops. Chapters guide readers through legume genomic resources, legume pangenome and organelle genome construction, transcriptome analysis, DNA methylation analysis, double-digest restriction site-associated DNA sequencing; target enrichment sequencing via probe capture, genomic selection and transformation methods; prediction of long non-coding RNAs and secondary structures, genome-wide mining of disease resistance gene analogs; genome editing, and bioactive compound and phosphoproteome analysis. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions tothe material, lists of necessary materials and reagents, step-by-step, readilyreproducible laboratory protocols, and a Notes section which highlightstips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Legume Genomics: Methods and Protocols, Second Edition aims to be comprehensive guide forresearchers in the field.
