Cereal Genomics: Methods and Protocols

Front Matter ....Pages i-xi
 A Low-Cost High-Throughput Method for Plant Genomic DNA Isolation  (Prateek Gupta, Hymavathi Salava, Yellamaraju Sreelakshmi, Rameshwar Sharma)....Pages 1-7
 Cereal Genomics Databases and Plant Genetic Resources in Crop Improvement  (Robert J. Henry)....Pages 9-14
 Integrated Genomic Strategies for Cereal Genetic Enhancement: Combining QTL and Association Mapping  (Anurag Daware, Swarup K. Parida, Akhilesh K. Tyagi)....Pages 15-25
 Sequencing and Assembling Genomes and Chromosomes of Cereal Crops  (Marcelo Helguera)....Pages 27-37
 Cost-Effective Profiling of Mutator Transposon Insertions in Maize by Next-Generation Sequencing  (Xinyan Zhang, Meixia Zhao, Damon Lisch)....Pages 39-50
 Relative Expression Analysis of Target Genes by Using Reverse Transcription-Quantitative PCR  (Rocío Liliana Gómez, Lorena Noelia Sendín)....Pages 51-63
 DNA Methylation and Transcriptomic Next-Generation Technologies in Cereal Genomics  (Cynthia G. Soto-Cardinault, Fátima Duarte-Aké, Clelia De-la-Peña, Elsa Góngora-Castillo)....Pages 65-84
 Genome-Wide Identification of Regulatory DNA Elements in Crop Plants  (Zhanjie Li, Kai Wang)....Pages 85-99
 Genome-Wide Profiling of Histone Modifications with ChIP-Seq  (William A. Ricci, Laura Levin, Xiaoyu Zhang)....Pages 101-117
 Whole-Genome Bisulfite Sequencing and Epigenetic Variation in Cereal Methylomes  (Taiji Kawakatsu)....Pages 119-128
 Genome-Wide Identification of Allele-Specific Gene Expression in a Parent-of-Origin Specific Manner  (Chen Chen, Kevin Begcy)....Pages 129-139
 Analysis of Epigenetic Modifications During Vegetative and Reproductive Development in Cereals Using Chromatin Immunoprecipitation (ChIP)  (Kevin Begcy, Thomas Dresselhaus)....Pages 141-156
 Cereal Circular RNAs (circRNAs): An Overview of the Computational Resources for Identification and Analysis  (Luis M. Vaschetto, Celso Gaspar Litholdo Jr, Lorena Noelia Sendín, Claudia Mabel Terenti Romero, María Paula Filippone)....Pages 157-163
 Emerging Genome Engineering Tools in Crop Research and Breeding  (Andriy Bilichak, Daniel Gaudet, John Laurie)....Pages 165-181
 CRISPR/Cas9-Mediated Targeted Mutagenesis in Wheat Doubled Haploids  (Alison M. R. Ferrie, Pankaj Bhowmik, Nandhakishore Rajagopalan, Sateesh Kagale)....Pages 183-198
 Genetic Transformation of Protoplasts Isolated from Leaves of Lolium temulentum and Lolium perenne  (Huw R. Davis, Anne L. Maddison, Dylan W. Phillips, Huw D. Jones)....Pages 199-205
 Agrobacterium Transformation in the Rice Genome  (Asuka Nishimura)....Pages 207-216
 In Vivo Phosphorylation: Development of Specific Antibodies to Detect the Phosphorylated PEPC Isoform for the C4 Photosynthesis in Zea mays  (Yoshihisa Ueno, Kumiko Yoshizawa-Kumagaye, Junji Emura, Tomoko Urabe, Taku Yoshiya, Tsuyoshi Furumoto et al.)....Pages 217-240
Back Matter ....Pages 241-247