BGI Completes Sequencing Of Foxtail Millet Genome
May 15, 2012

BGI Completes Sequencing Of Foxtail Millet Genome

A report published in the online journal Nature Biotechnology states that BGI, the world´s biggest genomics organization, in collaboration with Zhangjiakou Academy of Agricultural Science, has successfully completed the analysis and genome sequence of foxtail millet (Setaria italica). Foxtail millet is the second most widely grown kind of millet.

Published on May 13, 2012, the results of the study provide a vital resource for the genetic advancement and study of foxtail millet, as well as other types of millet, on a genome-wide level.

Foxtail millet, the number one crop grown in ancient China, is a major cereal crop that provides feed for animals and food for humans in dry or semi-arid locations. The small genome size of this plant (~490M) makes it an important model for functional gene studies and comparative genomics. Other factors that make foxtail millet so vital are its complete collection of germplasm, its genetic diversity (with over six thousand varieties), and its availability of efficient transformation platforms. Developmentally it is very similar to important biofuel grasses including napier grass and switchgrass.

"The lower yield of traditional cultivars has largely limited cultivation and utilization of foxtail millet." Dr. Gengyun Zhang, Vice President of BGI, stated.  He also said, "Hybrid cultivars, recently developed by Professor Zhihai Zhao in Zhangjiakou Agricultural Academy of Science, doubled the yield of foxtail millet. I expect that the results of this study could set an example of applying the genome sequence to better understanding and quicker developing new varieties of a neglected crop with higher yield, better grain quality and stress tolerance."

BGI researchers conducting next-generation sequencing and de novo assembly for "Zhang gu", a strain of foxtail millet from Northern China, found that the concluding genome assembly was 423 Mb. They predicted that 38,801 protein-coding genes would be found, out of which ~81% were revealed.  In addition to these findings, using a set of genetic markers recognized by re-sequencing an F2 population of "Zhang gu" crossing a different strain named "A2" (the most utilized female strain of hybrid foxtail millet), the researchers created a high density genetic linkage map.

After comparing the rice genome and the newly understood foxtail millet genome, researchers discovered the rules and the foxtail millet chromosomes tendencies to change. This is imperative in understanding the evolution of the foxtail millet genome.  "We found nine foxtail millet chromosomes were formed after three chromosomal reshuffling events." Dr. Zhang Stated. He also said, "Of the three events, two occurred after divergence of foxtail millet from rice, followed by a specific reshuffling after divergence of millet from sorghum."

Foxtail millet, a diploid C4 panicoid crop, has provided insight into how C3 plants form into C4 plants. Within environments with higher daytime temperatures, drought, nitrogen or CO2 limitation, and intense sunlight, C4 plants are better adapted for survival than C3 plants. Using the foxtail millet genome to carefully analyze the evolution of several crucial genes in C4 photosynthesis pathways, researchers found that possibly every gene in the C4 carbon fixation pathway are also present in C3 plants, therefore showing that the emergence of C4 pathways may result from functional and/or expressional alterations of the genes.

Researchers also established that by using the foxtail millet genome, mapping of the quantitative trait loci could be possible. They also utilized the genome to help pinpoint herbicide resistant genes, and in doing so successfully located the gene for sethoxydim resistance.

Dr. Zhang stated, “The decoding of whole genome sequence is an essential and important step to reveal the secrets of genetic control of crops, which could serve as an important platform for biological studies and breeding."