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A complete reference genome assembly for foxtail millet and Setaria-db, a comprehensive database for Setaria

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Molecular Plant 2024年第2期17卷 219-222页

作者： Qiang He Chunchao Wang Qiang He Jun Zhang Hongkai Liang Zefu Lui Kun Xie Sha Tang Yuhan Zhou Bin Liu Hui Zhi Guanqing Jia Ganggang Guo Huilong Du xianmin diao State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China School of Life Sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaoding 071000China State Key Laboratory of Rice Biology&Breeding Zhejang Provincial Key Laboratory of Crop GermplasmThe Advanced Seed InstituteZhejiang UniversityHangzhouChina

Dear Editor,,Foxtail millet(Setaria italica)and its wild ancestor green foxtail(S.viridis),are two C4 genetic model plants known for their desirable traits,such as small size,short life cycle,ease of transformation,and a compact genome size(~420 Mb)(He et al.,2023).Foxtail millet stands out as the only cultivated species within the Setaria genus.As a foundational crop for ancient east Asian agriculture civilization,it possesses remarkable drought and soil-nutrient deficiency tolerance.

关键词： comprehensive soil cultivated

Salt stress responses in foxtail millet:Physiological and molecular regulation

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The Crop Journal 2023年第4期11卷 1011-1021页

作者： Changai Wu Meng Zhang Yifan Liang Lei Zhang xianmin diao State Key Laboratory of Crop Biology Engineering Center of Saline-alkali Soil Plant-microbial Joint RestorationShandong Agricultural UniversityTai’an 271018ShandongChina Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China

Foxtail millet(Setaria italica L.),a member of the Paniceae family,is a temperate and tropical grass species that is widely cultivated on the Eurasian continent.It is Chinese in origin and possesses a small genome,short growth cycle,and strong natural abiotic stress resistance.Elucidating the mechanism of millet tolerance to salt stress is becoming increasingly important with increasing soil salinization limiting crop productivity.The responses and mechanisms of tolerance to salt stress from other model plants such as Arabidopsis and rice,were compared with those from foxtail millet to summarize current research on responses to salt stress.Numerous processes are involved in these processes,including physiological reactions,sensing,signaling,and control at the transcriptional,post-transcriptional,and epigenetic levels.To increase crop productivity and agricultural sustainability,a variety of technologies can be used to investigate how salt tolerance is mediated by physiological and molecular processes in foxtail millet.

关键词： Foxtail millet Salinity Physiological responses Molecular regulation Crop productivity

Production and genetic improvement of minor cereals in China

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The Crop Journal 2017年第2期5卷 103-114页

作者： xianmin diao Institute of Crop Science Chinese Academy of Agricultural Sciences Beijing 100081 China

China is a leading country in the production of several minor cereals such as foxtail millet,Job's tears,naked oat,and naked barley.Sorghum and proso millet have also contributed greatly to Chinese agriculture.Foxtail millet,sorghum,barley,and proso millet were widely grown as major crops 60 years ago,and the reduction in their cultivation area reflects historical changes in Chinese agriculture over the past decades.Systematic germplasm collections from the 1950 s to the 1990 s gathered more than 66,690 accessions of these minor cereals,and for some of them,the Chinese germplasm collections are the largest in the world;for example,the 27,700 accessions of foxtail millet.Germplasm evaluations of each cereal species have focused mainly on drought tolerance,nutritional quality,and resistance to their main diseases.Comparisons among lines and selection of those with desirable traits were the main breeding methods for minor cereals in the 1950 s and 1960 s,but these methods were replaced by crossbreeding in the 1970 s.Newly developed cultivars have greatly changed the production situation,and many super cultivars have become milestones in crop breeding history.In this review,we describe the distribution and ecoregions,origin and domestication,and landmark varieties of several minor cereals in China.Nearly all of the minor cereals are drought-tolerant and fertilizer-efficient.The requirements for environmentally friendly crops and a more diverse food supply for humans and animals provide new opportunities to cultivate minor cereals in the drier and warmer environmental conditions that are predicted in the future.

关键词： Minor cereals Origination Germplasm management Breeding

The m^(6)A reader SiYTH1 enhances drought tolerance by affecting the messenger RNA stability of genes related to stomatal closure and reactive oxygen species scavenging in Setaria italica

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Journal of Integrative Plant Biology 2023年第12期65卷 2569-2586页

作者： Weiwei Luo Yuxiang Tang Shenglan Li Linlin Zhang Yuwei Liu Renliang Zhang xianmin diao Jingjuan Yu State Key Laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing100193 China College of Life Sciences Hebei Agricultural UniversityBaoding071001 China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing100081 China

Foxtail millet(Setaria italica),a vital drought-resistant crop,plays a significant role in ensuring food and nutritional security.However,its drought resistance mechanism is not fully understood.N6-methyladenosine(m^(6)A)modification of RNA,a prevalent epi-transcriptomic modification in eukaryotes,provides a binding site for m^(6)A readers and affects plant growth and stress responses by regulating RNA metabolism.In this study,we unveiled that the YT521-B homology(YTH)family gene SiYTH1 positively regulated the drought tolerance of foxtail millet.Notably,the siyth1 mutant exhibited reduced stomatal closure and augmented accumulation of excessive H_(2)O_(2)under drought stress.Further investigations demonstrated that SiYTH1 positively regulated the transcripts harboring m^(6)A modification related to stomatal closure and reactive oxygen species(ROS)scavenging under drought stress.SiYTH1 was uniformly distributed in the cytoplasm of SiYTH1-GFP transgenic foxtail millet.It formed dynamic liquid-like SiYTH1 cytosol condensates in response to drought stress.Moreover,the cytoplasmic protein SiYTH1 was identified as a distinct m^(6)A reader,facilitating the stabilization of its directly bound SiARDP and ROS scavenging-related transcripts under drought stress.Furthermore,natural variation analysis revealed SiYTH1AGTG as the dominant allele responsible for drought tolerance in foxtail millet.Collectively,this study provides novel insights into the intricate mechanism of m^(6)A reader-mediated drought tolerance and presents a valuable genetic resource for improving drought tolerance in foxtail millet breeding.

关键词： drought stress mRNA stability N^(6)-methyladenosine(m^(6)A)reader phase separation SiYTH1 Setaria italica

De novo creation of popcorn-like fragrant foxtail millet

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Journal of Integrative Plant Biology 2023年第11期65卷 2412-2415页

作者： Yanyan Zhang Qiang He Shihui Zhang Xinyu Man Yi Sui Guanqing Jia Sha Tang Hui Zhi Chuanyin Wu xianmin diao Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Zhongyuan Research Center Chinese Academy of Agricultural SciencesXinxiang 453000China

Aroma plays a crucial role in the sensory appeal and enjoyment of food,and it significantly impacts the grain quality of cereals,thereby influencing the value and consumption of agricultural products.For example,aromatic rice varieties like Basmati and Jasmine are renowned for their distinct aroma and command almost double the price of regular rice in the market.

关键词： cereal corn thereby

A straight-forward seed production technology system for foxtail millet(Setaria italica)

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植物学报:英文版 2023年第9期65卷 2023-2035页

作者： Wei Zhang Xiantao Qi Hui Zhi Yushuang Ren Linlin Zhang Yuanzhu Gao Yi Sui Haoshan Zhang Sha Tang Guanqing Jia Chuanxiao Xie Chuanyin Wu xianmin diao Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China

For autogamous crops, a precondition for using heterosis is to produce sufficient pure male-sterile female parents that can be used to produce hybrid seeds. To date, cytoplasmic male sterility(CMS)and environment-sensitive genic male sterility(EGMS) have been used commercially to exploit heterosis for autogamous species. However, neither CMS nor EGMS has been established for foxtail millet(Setaria italica). Here, we report on the establishment and application of a seed production technology(SPT) system for this crop.First, we established a Ds Red-based SPT system,but found that it was unsuitable because it required the use of a fluorescent device for seed sorting. Instead, we constructed an SPT system with de novo betalain biosynthesis as the selection marker. This allowed us to distinguish transgenic seeds with the naked eye, thereby facilitating the identification of SPT maintainer line seeds. In this system, a seed sorter was not required to obtain sufficient seeds. The key point of the strategy is that the seed pool of the SPT maintainer line is propagated by artificial identification and harvesting of male-fertile individuals in the field, and the male-sterile line seed pool for hybrid production is produced and propagated by free pollination of male-sterile plants with the SPT maintainer line. In a field experiment, we obtained 423.96 kg male-sterile line seeds per acre,which is sufficient to plant 700.18 acres of farmland for hybrid seed production or male-sterile line reproduction. Our study therefore describes a powerful tool for hybrid seed production in foxtail millet, and demonstrates how the SPT system can be used for a small-grained crop with high reproduction efficiency.

关键词： betalain synthesis foxtail millet hybrid breeding SiPKS2 SPT system

Foxtail millet supplementation improves glucose metabolism and gut microbiota in rats with high-fat diet/streptozotocin-induced diabetes

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Food Science and Human Wellness 2022年第1期11卷 119-128页

作者： Xin Ren Linxuan Wang Zenglong Chen Min Zhang Dianzhi Hou Yong Xue xianmin diao Ruihai Liu Qun Shen Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Engineering and Technology Research Center of Food AdditivesBeijing Technology and Business UniversityBeijing 100048China Key Laboratory Plant Protein and Grain processing National Engineering and Technology Research Center for Fruits and VegetablesCollege of Food Science and Nutritional EngineeringChina Agricultural UniversityBeijing 100083China State Key Laboratory ofIntegrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China Chinese Academy of Agricultural Sciences Beijing 100081China Institute of Comparative and Environmental Toxicology Department of Food ScienceCornell UniversityIthacaNYUnited States

Foxtail millet(FM)whole grain has received special attention in recent years.To confirm the hypoglycemic effects of FM,we investigated the effects of FM supplementation on glucose metabolism and gut microbiota in rats with high-fat diet/streptozotocin(HFD/STZ)-induced diabetes.Specifically,we fully assessed the blood biochemical profiles,pancreatic histopathology,insulin-glucagon immunofluorescence,short-chain fatty acids,and gut microbiota composition of rats with HFD/STZ-induced diabetes before and after FM supplementation.Results showed that both 30% and 48% FM supplementation significantly decreased concentrations of fasting blood glucose,60-min blood glucose,and blood triglycerides(P<0.05);additionally,48% FM supplementation significantly improved blood glucose tolerance and insulin resistance(P<0.05).However,FM supplementation could not effectively repair damage to β-cells over a short period of time.In addition,4 weeks of 48% FM supplementation siginificantly increased the relative abundance of Bifidobacterium and concentration of butyrate,suggesting that the hypoglycemic effects of FM supplementation might be partially mediated by gut microbiota.Collectively,we found a dose-dependent relationship between FM supplementation and improvement of blood glucose metabolism,but did not find a synergistic effect between FM supplementation and metformin(Met)treatment.Our findings provide further support that consuming more whole-grain FM might be beneficial to individuals suffering from type 2 diabetes.

关键词： Foxtail millet Glucose metabolism Gut microbiota Short-chain fatty acids

The boron transporter SiBOR1 functions in cell wall integrity, cellular homeostasis, and panicle development in foxtail millet

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The Crop Journal 2022年第2期10卷 342-353页

作者： Hailong Wang Sha Tang Hui Zhi Lihe Xing Haoshan Zhang Chanjuan Tang Enbo Wang Meicheng Zhao Guanqing Jia Baili Feng xianmin diao State Key Laboratory of Crop Stress Biology for Arid Areas College of AgronomyNorthwest A&F UniversityYangling 712000ShaanxiChina Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China

Boron(B) is an essential micronutrient for vascular plant growth. Both B deficiency and toxicity can impair tissue development in diverse plant species, but little is known about the effect of B on reproductive panicle development and grain yield. In this study, a mutant of Setaria italica exhibiting necrotic panicle apices was identified and designated as sibor1. Sequencing revealed a candidate gene, Si BOR1, with a G-to-A alteration at the seventh exon. Knockout transgenic lines generated by clustered regularly interspaced short palindromic repeats and their associated protein-9 also had necrotic panicles, verifying the function of Si BOR1. Si BOR1 encoded a membrane-localized B efflux transporter, co-orthologous to the rice BOR1 protein. Si BOR1 was dominantly expressed in panicles and displayed a distinct expression pattern from those of its orthologs in other species. The induced mutation in Si BOR1 caused a reduction in the B content of panicle primary branches, and B deficiency-associated phenotypes such as thicker cell walls and higher cell porosity compared with Yugu 1. Transcriptome analysis indicated that differentially expressed genes involved in cell wall biogenesis, jasmonic acid synthesis, and programmed cell death response pathways were enriched in sibor1. q PCR analysis identified several key genes, including phenylalanine ammonia-lyase(Si PAL) and jasmonate-ZIM-domain(Si JAZ) genes, responsive to B-deficient conditions. These results indicate that Si BOR1 helps to regulate panicle primary branch development to maintain grain yield in S. italica. Our findings shed light on molecular mechanisms underlying the relationship between B transport and plant development in S. italica.

关键词： Foxtail millet(Setaria italica) SiBOR1 Cell wall Panicle development Grain yield

Haplotype variation and KASP markers for SiPSY1-A key gene controlling yellow kernel pigmentation in foxtail millet

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The Crop Journal 2023年第6期11卷 1902-1911页

作者： Rongjun Zuo Yanyan Zhang Yanbing Yang Chunfang Wang Hui Zhi Linlin Zhang Sha Tang Yanan Guan Shunguo Li Ruhong Cheng Zhonglin Shang Guanqing Jia xianmin diao Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Crop Research Institute Shandong Academy of Agricultural SciencesJinan 250100ShandongChina Institute of Millet Crops Hebei Academy of Agricultural and Forestry SciencesShijiazhuang 050035HebeiChina College of Life Sciences Hebei Normal UniversityShijiazhuang 050024HebeiChina

Carotenoid biosynthesis and accumulation are important in determining nutritional and commercial value of crop products.Yellow pigmentation of mature kernels caused by carotenoids is considered a vital quality trait in foxtail millet,an ancient and widely cultivated cereal crop across the world.Genomic regions associated with yellow pigment content(YPC),lutein and zeaxanthin in foxtail millet grains were identified by genome-wide association analysis(GWAS),and SiPSY1(Phytoene synthase 1 which regulates formation of the 40-carbon backbone of carotenoids)was confirmed as the main contributor to all three components by knockout and overexpression analysis.SiPSY1 was expressed in seedlings,leaves,panicles,and mature seeds,and was subcellularly localized to chloroplasts.Transcription of SiPSY1 in 15 DAP immature grains was responsible for YPC in mature seeds.Selection of SiPSY1 combined with increased YPC in mature grains during domestication of foxtail millet was confirmed.Haplotype analysis suggested that expression level of SiPSY1 could be a selection target for future breeding programs,and a KASP marker was developed for selection of favorable SiPSY1 alleles in breeding.The results of this work will benefit nutritional and commercial improvement of foxtail millet varieties,as well as other cereal crops.

关键词： Carotenoids Lutein Zeaxanthin Marker assisted selection Setaria italica