Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

Kevin J. Tsai, Mei-Yeh Jade Lu, Kai-Jung Yang, Mengyun Li, Yuchuan Teng, Shihmay Chen, Maurice S. B. Ku, Wen-Hsiung Li
2016 Scientific Reports  
The diploid C 4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular
more » ... cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains. Setaria italica, commonly known as foxtail millet, is the second-most widely planted species of millets in the world and an important grain crop model 1-3 . It is widely grown as a grain or forage crop in temperate and subtropical Asia and parts of southern Europe, North America, South America, Australia and North Africa. Cultivation of the species dates back to 5000-6000 BC in China 4 , where the species can grow under harsh, arid environments. However, despite its biological and agricultural importance, the species remains understudied in terms of genomic architecture, partly because of its lack of popularity due to low nutritional value 5 , lack of iodine and indigenous selectivity to specific parts of Africa and Asia, and partly because of the lack of a complete assembly and annotation. From a genomics perspective, there have been several mappings of genetic markers for foxtail millet 6,7 and even physiological QTL mappings for its close relative pearl millet 8 . However, studies on the genetic architecture of drought tolerance and biomass are limited and currently confined to cross-species studies 9,10 . To date, there have only been two published genome assemblies and annotations of foxtail millet, neither of which had reached over 86% of the estimated genome size 11,12 . The two publications referenced different estimated genome sizes for foxtail millet (490 Mbp and 510 Mbp), but we have chosen to use 490 Mbp throughout this work because it is a more recent reference 12 .
doi:10.1038/srep35076 pmid:27734962 pmcid:PMC5062080 fatcat:uf4fwlurfnhdfocfkdhrvwwrce