The Saccharinae clade of the Poaceae (grass) family of flowering plants includes several important crops with a rich history of contributions to humanity and the promise of still-greater contributions, as a result of some of the highest biomass productivity levels known, resilience to drought and other environmental challenges that are likely to increase, amenability to production systems that may mitigate or even reverse losses of ecological capital such as topsoil erosion, and the recent blossoming of sorghum as a botanical and genomic model for the clade.
In Genomics of the Saccharinae, advances of the past decade and earlier are summarized and synthesized to elucidate the current state of knowledge of the structure, function, and evolution of the Sorghum, Saccharum, and Miscanthus genera, and progress in the application of this knowledge to crop improvement. As a backdrop, it is important to understand the naturally occurring diversity in each genus, its organization and distribution, and its evolutionary history. Genomic tools and methods for Saccharinae biology and improvement have improved dramatically in the past few years – a detailed summary of these tools and their applications is a central element of Genomics of the Saccharinae. Application of genomic tools to priorities in crop improvement, including understanding and manipulating plant growth and development, composition, and defense, as well as increasing the quality and productivity of seed/grain, sugar, biomass, and other value-added products under a range of conditions and inputs, are addressed.
In particular, as the first native African crop to emerge as a genomic model, sorghum offers an excellent case study of challenges and opportunities in linking new advances in biosciences to solving some of Africa's major agricultural problems. Several members of the clade, exemplified by Sorghum halepense (Johnsongrass) offer insights into weediness and invasion biology. The first sequence for a member of the clade, sorghum, as well as progress and challenges toward sequencing of additional members and the new opportunities that this will create, are also explored in Genomics of the Saccharinae. Indeed, the very complexities that have hindered study of some clade members also offer intriguing opportunities to gain insight into fundamental questions such as roles of polyploidy in agricultural productivity and post-polyploidy evolution.
Natural History and Genetic Diversity
1. Phylogenetic relationships of Saccharinae and Sorghinae Elizabeth A. Kellogg
2. The gene pool of Sorghum bicolor and its improvement. Clarissa T. Kimber, Jeff A. Dahlberg, and Stephen Kresovich
3. The gene pool of Saccharum species and their improvement. Andrew H. Paterson, Paul H. Moore, Tom L. Tew
4. The gene pool of Miscanthus species and its improvement Erik J. Sacks, John A. Juvik, Qi Lin, J. Ryan Stewart and Toshihiko Yamada
Genomic Tools, Resources and Approaches
5. The Sorghum genome sequence: a core resource for Saccharinae genomics Andrew H. Paterson
6. Transcriptome analysis in the Saccharinae Milton Yutaka Nishiyama-Jr, Fabio Vicente, Paloma Mieko Sato, Savio Siqueira Ferreira, Alan Mitchell Durham, Frank Alex Feltus, and Glaucia Mendes Souza
7. Sorghum and Sugarcane Proteomics Bongani Ndimba, R Ngara
8. Gene mutagenesis systems and resources for the Saccharinae Zhanguo Xin, Ming-Li Wang, Surinder Chopra, Pohao Wang
9. Association Genetics Strategies and Resources Jianming Yu, Martha T. Hamblin, and Mitchell R. Tuinstra
10. Sorghum transformation: overview and utility Tejinder Kumar, Arlene Howe, Shirley Sato, Ismail Dweikat, Tom Clemente
11. Genetic engineering of Saccharum Getu Beyene, Ian S. Curtis, Mona B. Damaj, Marco T. Buenrostro-Nava and T. Erik Mirkov
12. Genetic engineering of Miscanthus Dean Engler and Katrin Jakob
13. Saccharinae Bioinformatics Resources Alan R. Gingle, F. Alex Feltus
Bridging Classical and Genomic Investigations of Sorghum Biology
14. Bridging Classical and Molecular Genetics of Sorghum Plant Stature and Maturity Patrick J. Brown and Andrew H. Paterson
15. Bridging classical and molecular genetics of sorghum disease resistance Clint W. Magill
16. Bridging Conventional and Molecular Genetics of Sorghum Insect Resistance Yinghua Huang, Hari C. Sharma, and Mukesh K. Dhillon
17. Genetic enhancement of sorghum for biomass utilization Wilfred Vermerris and Ana Saballos
Early Messages pertinent to Other Crops, from Saccharinae Research
18. Comparative genomics of grasses: A Saccharinae-centric view Andrew H. Paterson, Xiyin Wang, Haibao Tang, Changsoo Kim
19. Comparative genomic analysis of C4 photosynthesis pathway evolution in grasses Xiyin Wang, Andrew H. Paterson
20. Differentiation of seed, sugar, and biomass-producing genotypes in Saccharinae species Seth C. Murray
21. Perennialism and Weediness in the Saccharinae Russell W. Jessup
Synthetic and Futuristic Perspectives
22. Bringing the benefits of sorghum genomics to Africa Segenet Kelemu, Brhane Gebrekidan, Jagger Harvey
23. Synthesis: Fundamental insights into plant biology from the Saccharinae clade Andrew Paterson
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