Abstract
Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.
Highlights
Sorghum [Sorghum bicolor (L.) Moench], which is widely grown throughout arid and semi-arid tropical regions, is the world’s fifth most important cereal crop [1]
The remaining 43,803 independent probes corresponded to 21,495 O. sativa mRNA sequences in Genbank, with their homologs in sorghum identified using the database at the Sorghum Genome Project (Department of Energy Joint Genome Institute, www.phytozome. net)
3,406 independent probes on the rice array were mapped to the S. bicolor genome with 100% sequence identity, resulting in 1,703 O. sativa genes corresponding to 2,199 S. bicolor annotated genes (416 probes mapped to 2 or 3 S. bicolor genes, data not shown)
Summary
Sorghum [Sorghum bicolor (L.) Moench], which is widely grown throughout arid and semi-arid tropical regions, is the world’s fifth most important cereal crop [1]. The use of sorghum in biofuel production promises to further increase the economic impact of this species. Sorghum bicolor is the most economically important of the approximately 30 species in the genus. Sorghum bicolor is cultivated for grain and forage, while a wild relative native from Asia [8], S. propinquum (Kunth) Hitchc., is cultivated only for forage. Sorghum propinquum is a perennial with small seeds, high levels of tillering, narrow leaves, and well-developed rhizomes [9]. Rhizomes, which are underground stems, are associated with both perenniality and biomass partitioning; in Sorghum, their growth and development is controlled by multiple genes, as revealed by genetic analysis using a S. bicolor 6 S. propinquum mapping population [10]
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