Cereal Genomics: Methods and Protocols

1. A Low-Cost High-throughput Method for Plant Genomic DNA Isolation

Prateek Gupta, Hymavathi Salava, Yellamaraju Sreelakshmi, and Rameshwar Sharma

2. Cereal Genomics Databases and Plant Genetic Resources in Crop Improvement

Robert J Henry

3. Integrated Genomic Strategies for Cereal Genetic Enhancement: Combining QTL and Association Mapping

Anurag Daware, Swarup K. Parida, and Akhilesh K. Tyagi

4. Sequencing and Assembling Genomes and Chromosomes of Cereal Crops

Marcelo Helguera

5. Cost-effective Profiling of Mutator Transposon Insertions in Maize by Next-generation Sequencing

Xinyan Zhang, Meixia Zhao, and Damon Lisch

6. Relative Expression Analysis of target genes by using Reverse transcription-Quantitative PCR

Rocío Liliana Gómez and Lorena Noelia Sendín

7. DNA Methylation and Transcriptomic Next Generation Technologies in Cereal Genomics

Cynthia G. Soto-Cardinault, Fátima Duarte-Aké, Clelia De-la-Peña , and Elsa Góngora-Castillo

8. Genome-wide Identification of Regulatory DNA Elements in Crop Plants

9. Genome-wide Profiling of Histone Modifications with ChIP-seq

William A. Ricci, Laura Levin, and Xiaoyu Zhang

10. Whole-genome Bisulfite Sequencing and Epigenetic Variation in Cereal Methylomes

Taiji Kawakatsu

Chen Chen and Kevin Begcy

12. Analysis of Epigenetic Modifications during Vegetative and Reproductive Development in Cereals using Chromatin Immunoprecipitation (ChIP)

Kevin Begcy and Thomas Dresselhaus

13. Cereal Circular RNAs (circRNAs): An Overview of the Computational Resources for Identification and Analysis

14. Emerging Genome Engineering Tools in Crop Research and Breeding

Andriy Bilichak, Daniel Gaudet, and John Laurie

15. CRISPR/Cas9-mediated Targeted Mutagenesis in Wheat Doubled Haploids

Alison M. R. Ferrie, Pankaj Bhowmik, Nandhakishore Rajagopalan, and Sateesh Kagale

16. Genetic Transformation of Protoplasts Isolated from Leaves of Lolium temulentum and Lolium perenne

Huw R. Davis, Anne L. Maddison, Dylan W. Phillips, and Huw D. Jones

17. Agrobacterium Transformation in the Rice Genome

Asuka Nishimura

18. 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, and Katsura Izui