The Amaranth Genome

✍ Scribed by Dinesh Adhikary; Michael K. Deyholos; John P. Délano-Frier

• Publisher: Springer Nature
• Year: 2021
• Tongue: English
• Leaves: 194
• Category: Library

✦ Synopsis

This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

✦ Table of Contents

Preface to the Series
Preface
Contents
Contributors
Abbreviations
1 Genome and Transcriptome of Amaranth Species
Abstract
1.1 Introduction
1.2 Amaranth Draft Genome
1.3 Amaranth Transcriptome
1.3.1 Amaranth Transcriptome on Herbicide Resistance
1.3.2 Amaranth Transcriptome on Stress Response
1.3.3 Amaranth Transcriptome on Genome Rearrangement Assessment
1.3.4 Amaranth Transcriptome on Seed Development
1.3.5 Amaranth Transcriptome on Leaf Pigmentation
1.3.6 Amaranth Transcriptome on Flowering Genes
1.4 Amaranth Sequence Information in Public Databases
1.5 Experimental Design and Transcriptome Study
1.6 Final Remarks
References
2 Organelle Genomics: The Chloroplast Genome of Amaranth
Abstract
2.1 Introduction
2.2 Chloroplast Genome Sequencing
2.3 Chloroplast Genome Assembly Details
2.3.1 Codon Usage Pattern
2.3.2 Simple Sequence Repeat Content
2.3.3 Repeated Sequences
2.3.4 Variation Content
2.4 Phylogenetic Analysis
2.5 Genetic Diversity in Amaranths
2.6 Perspectives on Future Genetic Improvements
Conflict of Interest
References
3 Genetic and Phenotypic Odyssey: Voyage of the Grain Amaranths from the Americas to the Old World
Abstract
3.1 Early Evidence of Grain Amaranths in the Old World
3.2 The Asian Grain Amaranths
3.3 Taxonomic Revision of the Amaranths
3.4 Pre-Columbian or Post-Columbian Introduction of the Grain Amaranths
3.5 Modern Dissemination and Use of Amaranths in the Old World
3.6 Conclusions
References
4 Genetics of Betalain Pigments in Amaranth Species
Abstract
4.1 Introduction
4.2 Betalains in Amaranthus Species
4.2.1 Type of Betalains in Amaranthus Species
4.2.2 Betalains in Other Plant Species
4.3 Divergence of Betalains from Anthocyanins
4.3.1 Betalains Versus Anthocyanins
4.3.2 Evolutionary Relationship of Betalains and Anthocyanins
4.4 Functional Analysis of Betalain Pigments in Biotic and Abiotic Stresses
4.4.1 Abiotic Stress
4.4.2 Biotic Stress
4.5 Betalain Biosynthesis Pathway Genes
4.5.1 Betalain Biosynthesis Pathway
4.5.2 Reverse Genetics Work in Amaranth
4.6 Perspectives on Future Research and Genetic Improvements
4.7 Conclusions
Acknowledgements
References
5 Molecular Characterisation of Seed Storage Proteins (SSPs) in Grain Amaranth
Abstract
5.1 Amaranth Species Used for Grain Production
5.2 Seeds Morphological Characteristics
5.3 Proximate Seed Composition of Wild and Cultivated Amaranth Species
5.4 Amaranth Seed Proteins According to Osborne’s Classification
5.4.1 Albumins
5.4.2 Globulins
5.4.3 Prolamins
5.4.4 Glutelins
5.5 Biosynthesis and Accumulation of SSPs
5.6 Improvement of the Functional Properties of Amaranth Globulins
5.7 Phylogenetic Relationships of Amaranth Seed Storage Proteins
5.7.1 Albumins
5.7.2 Globulins
5.8 SSPs Genetics
5.9 Conclusions
Acknowledgements
References
6 Genetic Diversity in Amaranth and Its Close Relatives
Abstract
6.1 Introduction
6.2 Classification of Amaranths on the Bases of Their Use
6.3 Genetic Diversity in Amaranth and Their Wild Relatives
6.3.1 Morphological Approach
6.3.2 Biochemical Approach
6.3.3 Cytological Approach
6.3.4 Molecular Approach
6.4 Amaranth Germplasm Collection
6.5 Amaranth Varieties of India
6.6 Importance and Applications of Amaranth
6.7 Conclusion
References
7 Searching for an Identity: Functional Characterization of Taxonomically Restricted Genes in Grain Amaranth
Abstract
7.1 Introduction
7.2 Identification of TRGs
7.3 Features of TRGs
7.4 TRGs in Grain Amaranth
7.5 Work in Progress
7.6 Final Comments
References
8 How to Overcome Recalcitrance? Novel Strategies and Recent Advances in the Genetic Transformation of Grain Amaranth
Abstract
8.1 How It All Started: Agrobacterium-Mediated Transformation
8.2 Variants of the Classical Agrobacterium Transformation Method: Are They Better?
8.3 Increasing Transformation Efficiency in Recalcitrant Crops
8.4 The Long and Winding Road Leading to the Best Procedure to Transform Grain Amaranth
8.5 A Light at the End of the Tunnel? Combined Use of A. rhizogenes and A. tumefaciens for the Generation of Transformed A. hypochondriacus Plants
8.6 Genetic Improvement of Amaranth Through γ-Irradiation
8.7 Conclusions
References
9 Polyploidy and Hybridization for Amaranth Crop Improvement
Abstract
9.1 Introduction
9.2 Potential of Amaranth as a Future Crop for the Management of Climate’s Change Impact
9.2.1 Climate Change
9.2.2 Potential of Amaranth
9.3 Amaranth: Hybridization Versus Evolutionary Process
9.4 Polyploidy in Amaranths
9.4.1 Indonesian Amaranths
9.5 Amaranth Crop Improvement
9.6 Conclusion
References
10 Amaranth Transcription Factors in Response to Biotic and Abiotic Stresses
Abstract
10.1 Introduction
10.2 Identification of Amaranth TFs Involved in Stresses Tolerance
10.2.1 MYB Transcription Factor
10.2.2 bHLH Transcription Factor
10.2.3 WRKY Transcription Factor
10.3 Functional Studies of Amaranth TFs Conferring Stress Tolerance
10.3.1 AhERF-TF Conferred Tolerance to Water Stress by ABA-Independent Mechanisms
10.3.2 Dof TF Provided Tolerance to Salt Stress by ABA-Dependent and ABA-Independent Pathways
10.3.3 NF-YC Increase Water Stress Resistance by Partly ABA-Dependent
10.4 Conclusions
Acknowledgements
References