Sorghum is the main food crop in arid and semi-arid regions of the world, which is of great significance to food security, marginal land use and dietary structure in arid and semi-arid regions. Since the first generation of grain hybrid sorghum was introduced in China in 1958, in order to adapt to mechanized harvesting and reduce labor costs, the plant height of cultivated hybrid sorghum has experienced the change process of high stalk, middle stalk, middle dwarf and dwarf. the green revolution of Chinese grain hybrid sorghum has been completed in the past two decades. This paper summarizes the reasons, history and current situation of grain sorghum dwarfing breeding in China. It shows the trend of decreasing plant height and increasing yield of sorghum varieties in China in the past 60 years. The important germplasms created in the process of green revolution of grain sorghum in China were listed. Through the analysis of genetic relationship, it was found that the dwarf source of restorer line in China came from Chinese local variety Sanchisan, and the dwarf source was traced back to Tx3197B due to the utilization of foreign germplasm Tx3197 A, Tx3197 B. The cloning, variation sites, dwarfing mechanism of sorghum dwarf genes dw1, dw2 and dw3, which play an important role in the green revolution of sorghum, and the contributions of predecessors in exploring new plant height QTLs were reviewed. The dwarfing mechanism of sorghum was different from that of gibberellin regulation system (GA) in rice and wheat. dw1 reduced plant height by regulating the brassinosteroid system (BR) to shorten the length of internodes. dw2 and dw3 encode KIPK protein kinase and auxin efflux transporter (ABCB1), respectively, which regulate the transport of auxin (IAA) to shorten the length of internodes and reduce plant height. The dwarfing genes of dw1, dw2 and dw3 had multiple effects on maturity, spike length, spike grain weight, leaf area while reducing plant height. The distribution and application of dw1, dw2 and dw3 dwarf genes in backbone sterile lines and restorer lines were analyzed by molecular markers and sequencing techniques. It was found that the dwarf genes used more in sorghum restorer lines in China were only dw3, and the combination of dw1dw3 and dw2dw3 formed by dw1, dw2 and dw3 was more widely used in sterile lines. The problems and solutions of sorghum green revolution in China were discussed. It is expected to provide guidance for further improving the process of sorghum green revolution in China and cultivating new germplasm and new varieties with major breakthroughs in yield and stress resistance.

Seed industry was the ‘chip’ of agricultural development, and original innovation have played essential roles in maintaining stable development of modern agriculture. The No. 1 central document of China released in 2021 has put forward requirements of original innovation researches essential for supporting further developments of Chinese crop seed industry. Foxtail millet is a traditional crop species cultivated for both forage and grain food consumption in China, and to date, foxtail millet was still widely planted as minor cereals in China with the largest scale of field production and commercial consumption across the globe. Foxtail millet was originated from China and cultivated for thousands of years to ensure development of Chinese agricultural culture and field crop production. Original innovation in foxtail millet has promoted initial development of foxtail millet seed industry based on operation of herbicide-resistant varieties in recent decades, including breakthroughs in areas of heterosis utilization, herbicide resistant breeding, dwarfing variety creation and genomics study of this important crop species. Achievements of fundamental researches including germplasm characterization, development of breeding tools, coordination and regulation of vital traits, seeds propagation and truth identification of commercial varieties have provided more opportunities for further development of the seed industry of foxtail millet. However, challenges of seed industry development still exist in China, including deficiency of excellent germplasms, backward breeding approaches, inharmonious of yield and quality characters, unclear criterion of seed propagation and market supervision problems. Future direction of original innovation studies related to foxtail millet seed industry were as follows: 1) Large scale breeding systems constructed from utilizations of crop phenomics and genomic modification technologies, double haploid breeding and genome selection tools, identification and pyramiding of superior haplotypes; 2) Seeds production, store and quality supervision systems constructed from techniques of development and water content of commercial seeds, and establishment of molecular fingerprints and efficient utilization of heterosis in foxtail millet; 3) Construction of innovation system through integrating education, research and promotion sectors of seed industry and stimulate personnel training in China.

Foxtail millet (Setaria italica) is an important crop and an emerging model plant. Photoperiodic flowering is a key determinant of its production and geographic expansion. In this study, we found that SiPRR37 is responsible for the major quantitative trait locus (QTL) Heading date 2 (Hd2) identified in 680 foxtail millets using a genome-wide association study. Overexpression of SiPRR37 in foxtail millet significantly delayed the heading date under both natural long-day and short-day conditions. CRISPR/Cas9-induced Siprr37 mutants exhibited earlier flowering in long-day conditions but later flowering in short-day conditions. The critical day length (CDL) for the reversal of Siprr37’s function was around 14.3 h. Haplotype analysis revealed that accessions with the Tc1-Mariner transposon insertion in SiPRR37 (Hap 1) flowered significantly earlier at higher latitudes, and later at lower latitudes, indicating that natural variants of SiPRR37 exert dual functions in flowering regulation according to geographic latitude. The gradual, successive decrease in the frequency of Hap 2 from low to high latitudes, with the concurrent increase of Hap 1, demonstrates that these haplotypes have undergone artificial selection. Further F_ST analysis demonstrated that SiPRR37 has contributed to the ecological adaption of foxtail millet. Additionally, we reveal that OsPRR37 promotes flowering in rice, while GmPRR37 may only inhibit flowering in soybean. Further diurnal expression and transgenic analyses suggest that the dual function of SiPRR37 might depend on SiHd1. Our study uncovered the distinct functional reversal of SiPRR37 and functional diversification of PRR37 homologs in SD crops. These findings not only enrich knowledge about the regulation of photoperiodic flowering, but also contribute to genetic improvement of crops’ regional adaptability.

Plant height is an essential characteristic of agronomic traits, and an ideal plant height is essential for achieving high crop yields. Foxtail millet (Setaria italica) has become a novel diploid C₄ model crop. The proteomic profiles of the internode, node, and leaf in two foxtail millet varieties with different heights, Ci846 and Yugu 18, were investigated at the jointing stage in this study. There were different degrees of enrichment in various processes, such as plant hormone signal transduction, the MAPK signaling pathway, and others. In particular, the proper content of auxin could activate downstream SiARFs-SiSAURs expression, which enhances the length of internodes. Haplotype analysis of SiSAUR-like revealed two differential haplotypes of associated plant height, Hap1 and Hap2. The molecular marker SiSAUR-like-FCM1-2 can effectively separate materials into Hap1 and Hap2. Two additional genes, designated SiGH3 and SiTCH4, were found to be associated with plant height regulation. In conclusion, this study not only uncovers the crucial role of auxin regulators in modulating plant height during the jointing stage but also provides molecular markers that will be invaluable for molecular breeding efforts. The findings of this research help to elucidate the molecular mechanisms of plant height determination that can be used for crop variety innovation and breeding.

Salt stress is a global constraint on agricultural production. Therefore, the development of salt tolerant plants has become a current research hotspot. While salt tolerance has evolved more frequently in C₄ grass lineages, few studies have explored the molecular bases underlying salt stress tolerance in the C₄ crop foxtail millet. In this study, we used a multi-pronged approach spanning the omics analyses of transcriptomes and physiological analysis of the C₃ crop rice and the C₄ model crop foxtail millet to investigate their responses to salt stress. The results revealed that compared to C₃ rice, C₄ foxtail millet has upregulated abscisic acid (ABA) and notably reduced CK biosynthesis and signaling transduction under salt stress. Salt stress in C₃ rice plants triggered rapid downregulation of photosynthesis related genes, which was coupled with severely reduced net photosynthetic rates. In the salt-treated C₃ rice and C₄ foxtail millet, some stress responsive transcription factors (TFs), such as AP2/ERF, WRKY and MYB, underwent strong and distinct transcriptional changes. Based on a weighted gene co-expression network analysis (WGCNA), the AP2/ERF transcription factor Rice Starch Regulator1 SiRSR1 (Seita.3G044600) was identified as a key regulator of the salt stress response. To confirm its function, we generated OsRSR1-knockout lines using CRISPR/Cas9 genome editing in rice and its upstream repressor SimiR172a-overexpressing (172a-OE) transgenic plants in foxtail millet, which both showed increased salt tolerance. Overall, this study not only provides new insights into the convergent regulation of the salt stress responses of foxtail millet and rice, but it also sheds light on the divergent signaling networks between them in response to salt stress.

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.

Foxtail millet (Setaria italica) is an important C₄ model crop; however, due to its high-density planting and high stature, lodging at the filling stage resulted in a serious reduction in yield and quality. Therefore, it is imperative to identify and deploy the genes controlling foxtail millet plant height. In this study, we used a semi-dwarf line 263A and an elite high-stalk breeding variety, Chuang 29 to construct an F₂ population to identify dwarf genes. We performed transcriptome analysis (RNA-seq) using internode tissues sampled at three jointing stages of 263A and Chuang 29, as well as bulk segregant analysis (BSA) on their F₂ population. A total of 8918 differentially expressed genes (DEGs) were obtained from RNA-seq analysis, and GO analysis showed that DEGs were enriched in functions such as "gibberellin metabolic process" and "oxidoreductase activity", which have previously been shown to be associated with plant height. A total 593 mutated genes were screened by BSA-seq method. One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines, and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions, which indicated they play a crucial role in plant height determination. Among them, we found a gibberellin biosynthesis related GA20 oxidase gene (Seita.5G404900), which had a single-base deletion at the third exon, leading to the frameshift mutation at 263A. Cleaved amplified polymorphic sequence assay and association analysis proved the single-base deletion in Seita.5G404900 co-segregated with dwarf phenotype in two independent F₂ populations planted in entirely different environments. Taken together, the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height, and the molecular marker will be useful for marker-assisted dwarf breeding.

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, SiBOR1, 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 SiBOR1. SiBOR1 encoded a membrane-localized B efflux transporter, co-orthologous to the rice BOR1 protein. SiBOR1 was dominantly expressed in panicles and displayed a distinct expression pattern from those of its orthologs in other species. The induced mutation in SiBOR1 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. qPCR analysis identified several key genes, including phenylalanine ammonia-lyase (SiPAL) and jasmonate-ZIM-domain (SiJAZ) genes, responsive to B-deficient conditions. These results indicate that SiBOR1 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.

Male sterility is a common biological phenomenon in plant kingdom and has been used to generate male-sterile lines, which are important genetic resources for commercial hybrid seed production. Although increasing numbers of male-sterility genes have been identified in rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), few male-sterility-related genes have been characterized in foxtail millet (Setaria italica). In this study, we isolated a male-sterile ethyl methanesulfonate-generated mutant in foxtail millet, no pollen 1 (sinp1), which displayed abnormal Ubisch bodies, defective pollen exine and complete male sterility. Using bulk segregation analysis, we cloned SiNP1 and confirmed its function with CRISPR/Cas9 genome editing. SiNP1 encoded a putative glucose-methanol-choline oxidoreductase. Subcellular localization showed that the SiNP1 protein was preferentially localized to the endoplasmic reticulum and was predominantly expressed in panicle. Transcriptome analysis revealed that many genes were differentially expressed in the sinp1 mutant, some of which encoded proteins putatively involved in carbohydrate metabolism, fatty acid biosynthesis, and lipid transport and metabolism, which were closely associated with pollen wall development. Metabolome analysis revealed the disturbance of flavonoids metabolism and fatty acid biosynthesis in the mutant. In conclusion, identification of SiNP1 provides a candidate male-sterility gene for heterosis utilization in foxtail millet and gives further insight into the mechanism of pollen reproduction in plants.

Two potential BRASSINAZOLE RESISTANT 1 (BZR1) homologs were downregulated by brassinosteroids (BRs) in Setaria italica roots. Functional analysis showed that BR regulates the dephosphorylation and nuclear localization of SiBZR1 and that SiBZR1 binds conserved BZR1-recognizing cis elements. In comparison with the wild type, SiBZR1-overexpressing S. italica seedlings were more sensitive to BR-inhibited primary root growth and drought stress, indicating that SiBZR1 is a positive regulator of BR signaling and a negative regulator of drought tolerance in S. italica. PLETHORA-LIKE 1 (SiPLT-L1) was found to be a direct target gene of SiBZR1 in S. italica roots. The expression of SiPLT-L1 was downregulated by SiBZR1. SiPLT-L1-overexpressing S. italica was less sensitive to BR-inhibited root growth and more tolerant to drought stress, possibly owing to the upregulation of drought-inducible Dehydrin-family genes.