Efficient Genome Editing in Setaria italica Using CRISPR/Cas9 and Base Editors

The genome editing toolbox based on CRISPR/Cas9 has brought revolutionary changes to agricultural and plant scientific research. With the development of stable genetic transformation protocols, a highly efficient genome editing system for foxtail millet (Setaria italica) is required. In the present study, we use the CRISPR/Cas9 single- and multi-gene knockout system to target the SiFMBP, SiDof4, SiBADH2, SiGBSS1, and SiIPK1 genes in the foxtail millet protoplasts to screen out highly efficient targeted sgRNAs. Then, we recovered homozygous mutant plants with most of the targeted genes through an Agrobacterium-mediated genetic transformation of foxtail millet. The mutagenesis frequency in the T0 generation was as high as 100%, and it was passed stably on to the next generation. After screening these targeted edited events, we did not detect off-target mutations at potential sites. Based on this system, we have achieved base editing successfully using two base editors (CBE and ABE) to target the SiALS and SiACC genes of foxtail millet. By utilizing CBE to target the SiALS gene, we created a homozygous herbicide-tolerant mutant plant. The current system could enhance the analysis of functional genomics and genetic improvement of foxtail millet.

SiMYB19 from Foxtail Millet (Setaria italica) Confers Transgenic Rice Tolerance to High Salt Stress in the Field

Salt stress is a major threat to crop quality and yield. Most experiments on salt stress-related genes have been conducted at the laboratory or greenhouse scale. Consequently, there is a lack of research demonstrating the merit of exploring these genes in field crops. Here, we found that the R2R3-MYB transcription factor SiMYB19 from foxtail millet is expressed mainly in the roots and is induced by various abiotic stressors such as salt, drought, low nitrogen, and abscisic acid. SiMYB19 is tentatively localized to the nucleus and activates transcription. It enhances salt tolerance in transgenic rice at the germination and seedling stages. SiMYB19 overexpression increased shoot height, grain yield, and salt tolerance in field- and salt pond-grown transgenic rice. SiMYB19 overexpression promotes abscisic acid (ABA) accumulation in transgenic rice and upregulates the ABA synthesis gene OsNCED3 and the ABA signal transduction pathway-related genes OsPK1 and OsABF2. Thus, SiMYB19 improves salt tolerance in transgenic rice by regulating ABA synthesis and signal transduction. Using rice heterologous expression analysis, the present study introduced a novel candidate gene for improving salt tolerance and increasing yield in crops grown in saline-alkali soil.

Recombinant inbred lines and next-generation sequencing enable rapid identification of candidate genes involved in morphological and agronomic traits in foxtail millet

We constructed recombinant inbred lines (RILs) between a Japanese and a Taiwanese landrace of foxtail millet and employed next-generation sequencing, such as flexible ddRAD-seq and Nanopore sequencing to identify the candidate genes involved in the crop evolution of foxtail millet. We successfully constructed a linkage map using flexible ddRAD-seq with parents and RILs and detected major QTLs for each of three traits: leaf sheath colors, spikelet-tipped bristles (stb), and days to heading (DTH). (1) For leaf sheath colors, we identified the C gene on chromosome IV. (2) We identified a homeobox (HOX14) gene for stb on chromosome II, which shows homology with HvVrs1 in barley. (3) Finally, we identified a QTL with a large effect on DTH on chromosome II. A parent of the RILs from Taiwan and Yugu1 had a Harbinger-like TE in intron 3 of this gene. We also investigated the geographical distribution of the TE insertion type of this gene and found that the insertion type is distributed in the northern part of East Asia and intensively in South and Southeast Asia, suggesting that loss/reduction of function of this gene plays an important role in spreading into the northern part of East Asia and subtropical and tropical zones.

Protective effects of bioactive peptides in foxtail millet protein hydrolysates against experimental colitis in mice

It is of great significance to develop a dietary intervention strategy to prevent inflammatory bowel disease (IBD). A millet-rich diet can ameliorate IBD, but the active ingredients and mechanisms remain...

Formulation and Quality Evaluation of Foxtail Millet and Semolina Incorporated Ready-To-Cook Upma Mix

Traditional cuisine has risen to the top of the consumer’s list of preferences. Many traditional cereal-based dishes have been processed, and instant mixes such as instant upma, idli, and dosa have been made. Comfort foods are foods that require little or no processing or cooking before consumption, making them more convenient for the user. Ready to Cook (RTC) and instant foods have grown highly popular as a result of increased urbanization and industrialization, owing to today’s lifestyle and the need for quick-to-serve cuisine.The study’s goal is to develop an RTC upma mix and evaluate its physicochemical, texture, sensory, and in vitro glycemic index. The millet was collected and pre-processing was done to develop the ready-to-cook mixes. The levels of millet incorporation ratio were 60% (V1), 70% (V2), and 80% (V3) levels. Standard procedures were used to determine the physicochemical, textural, sensory, and in vitro glycemic index. The nutritional composition of V3 was found to be high, with moisture, carbohydrate, protein, fat, fibre, soluble fibre, and insoluble fibre content of 6.4 percent, 73.6g, 8.5g, 6.2g, 6.6g, 2.4g, and 0.56g, respectively.The textural profile showed a significant difference (p<0.05) between variations in comparison with the standard. Results on sensory evaluation showed that 70% foxtail millet upma mix shows high acceptable than other. The mean in vitro glycemic index of the control upma mix was 68.7 ± 0.12, while the mean estimated glycemic index value of V1, V2, and V3 was50.5 ± 0.5, 49.8 ± 0.4, and 49.2± 0.6 respectively. Thus, the result evident that all the developed RTC upma mixes exhibited a low glycemic index and were useful for Diabetic subjects and easy to carry as a journey food.

Genome-Wide Analysis of the MADS-Box Gene Family in Foxtail Millet (Setaria Italica L.) and Expression Analyses to Reveal Their Role During Drought Stress

MADS-box gene family is a key regulatory factor family, which controls vegetative growth, reproductive development and can be used to mediate abiotic stresses in many plants. However, Knowledge of this gene family is still limited in Setaria italica. In the present study, a total of 70 SitMADS genes were identified and renamed on the basis of the chromosomal distribution of the SitMADS genes. According to gene structure, conserved motif and phylogenetic feature, the 70 SitMADSs were classified into type-Ⅰ (Mα, Mβ, Mγ) and type-Ⅱ (MIKCC and MIKC*). All of the SitMADS genes were randomly distributed on nine chromosomes, and five tandem duplicated genes and 12 pairs of duplicated gene segments were detected in the SitMADS genes family. Synteny analysis provided a high homology between SitMADS genes and OsMADS genes. A cis-element analysis inferred that SitMADS genes, except for SitMADS23, possessed at least one drought stress response and ABA(Abscisic Acid)-induced response cis-element. Real-time quantitative PCR analysis was used to detect the expression patterns of SitMADS genes in various tissues and demonstrated that the genes responded drought stress and ABA treatments. SitMADS23, SitMADS42, SitMADS51, SitMADS52, SitMADS58 and SitMADS64 were highly expressed in PEG(Polyethylene glycol) and drought stress, which suggested its important role in drought stress response. SitMADS51, SitMADS63 and SitMADS64 seemed to be responsive to ABA hormone signaling, suggesting that they were involved in the ABA signaling pathways. This paper provided a deep insight into the evolutionary characteristics of SitMADS genes. The results provide comprehensive information for further analyses of the molecular functions of the MADS-box gene family in Setaria italica.

​Development and Nutritional Evaluation of Foxtail Millet (Setaria italica) based Laddu

Backround: Foxtail millet (Setaria italica) is known for its health benefits as it is nutritionally superior to conventional food grains. Laddu are ball-shaped sweets which are popular in India and are often served at festive or religious occasions. Hence, an attempt was made to develop foxtail millet based value added laddu. Methods: Besan laddu was taken as control. Optimized foxtail millet laddu were nutritionally evaluated for proximate composition, sugars and minerals. Paired ‘t’ test was used to compare the physical parameters and nutrient composition of besan and foxtail millet laddu. Result: The developed foxtail millet laddu had the 11.61, 17.52, 2.64, 1.11 and 66.85% per 100g of protein, fat, crude fibre, ash and carbohydrate respectively. There was no significant difference in sugar composition between the control and the optimised laddu. However, it was observed that the calcium, iron, zinc, copper and manganese of foxtail millet laddu were high as compared to control laddu.