A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system

Abstract

If you are citing a reference for the first time in these legends, please include all new references in the Online Methods References section, and carry on the numbering from the main References section of the paper. Extended DataFig. 1 Alternative splicing site of the PHYC gene in xiaomi a, RNA-Seq reads of Jingu21. xiaomi genome sequences were used as reference genome. The blue vertical line shows the G-T mutation site. b, RNA-seq reads of xiaomi. The wrong splicing site was marked by a red arrow. Extended Data Fig. 2 Phenotypic and molecular characterization of the xiaomi-2 mutant a, Forty-day-old plants of Jingu21 (wild type, left) and xiaomi-2 (right) plants grown under natural long-day conditions. b, Heading date of Jingu21and xiaomi-2 under natural field conditions. The heading date of ≥ 20 plants was measured for each replicate (n = 3 biologically independent replicates, ≥ 102 in total). The bottom and top of boxes represent the first and third quartile, respectively. The middle line is the median and the whiskers represent the maximum and minimum values. Statistical analysis was performed using two-tailed Wilcoxon rank-sum test. c, A mature small-sized xiaomi-2 plant (right) compared to Jingu21 (left), at the 68th day in field. d, Plant height of Jingu21 and xiaomi-2 under natural field conditions. The plant height of ≥ 23 plants was measured for each replicate (n = 3 biologically independent replicates, ≥ 83 in total). e, Molecular charicterization of xiaomi-2. Exons and introns are denoted by filled boxes and lines, respectively. P2F and P2R represent a pair of primers used to amplify the fragments harboring the mutation site from the segregating M3 individuals (Primer sequences are listed in SupplementaryTable 3). c, Structure of PHYC and its mutation version deduced according to mutations in xiaomi-2. Scale bars, 10 cm in a and c. Extended Data Fig. 3 Sequence alignment of the GAF domain of PHYC in foxtail millet and its homologs software. Red box indicates the conserved residue Leu across all listed species that is substituted with His in xiaomi-2, demonstrating its functional importance for PHYC. Accession numbers for the aligned sequences: Arabidopsis thaliana NP_198433, Brachypodium distachyon XP_003559446, Brassica napus XP_013680236, Ipomoea nil XP_019162785, Oryza sativa AAF66603, Panicum miliaceum, RLN42126, Solanum lycopersicum NP_001307446, Sorghum bicolor XP_002466441, Triticum aestivum AAU06208, Vitis vinifera ACC6096 and Zea mays XP_008665426. PHYC protein in Jingu21 is presented as for Setaria italica (Si9G09200).Extended Data Fig. 4 Hi-C interaction matrices show the pairwise correlations between ordered scaffolds along the 9 pseudomolecules correlation. in T1 transgenic seeds as visualized for GFP expression or multiple (c) T-DNA insertions were scanned with a dissection microscope equipped with UV light. All experiments were performed for eight independent biological repeats, and similar results were obtained. Scale bars, 2 mm. Extended Data Fig. 6 PCR confirmation of the site-specif...

Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

“…is one of the oldest domesticated diploid C 4 crops and has been widely cultivated in northern China for more than 11,500 years [1,2]. It has characteristics of selffertilization, relatively small genome size (~490 MB), short life cycle (~12 weeks), and rich germplasm resources, and has become an ideal model plant for C 4 grasses [3][4][5][6][7]. Compared with Arabidopsis thaliana and Oryza sativa, foxtail millet is abiotic stress tolerant particularly to drought and salinity and can make efficient use of light energy.…”

“…At the same time, the draft genome sequence of another cultivar Zhanggu was also completed, with about 423 Mb of the genome assembled and 38,801 genes identified [ 12 ]. Until 2020, a reference-grade genome of an indoor-cultivated rapid-cycling mini foxtail millet mutant Xiaomi comprising 429.94 Mb of sequences was assembled based on single-molecule real-time subread sequences [ 3 ]. Deciphering of the millet genome provides a unique resource for millet genetic breeding.…”

Foxtail Millet Stress Associated Protein Gene SiSAP4 Enhances Drought Stress Tolerance in Transgenic Arabidopsis

“…Foxtail millet not only has the characteristics of strong adaptability to drought and infertility, but also has a small genome size, genetic diversity and short life cycle. Therefore, it can be a valuable resource for abiotic stress resistant gene exploration (Muthamilarasan and Prasad 2015;Yang et al 2020). At present, the research on functional genomic data of foxtail millet including the annotation and functional characterization of genes involved in abiotic stress responses has been not analyzed.…”

Comparative Analysis of Flavonoid Metabolites in Foxtail Millet (Setaria italica) with Different Eating Quality

“…In this flavonoid metabolic network, one gene may be involved in regulating the biosynthesis of multiple metabolites, or on the contrary, multiple genes may also be related to the same flavonoid. At present, a rapid-cycling mini foxtail millet mutant, xiaomi , has provided us with a good resource for deeper exploration of these genes [ 61 ]. Moreover, the complex structure of flavonoids poses a considerable challenge to their identification.…”