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Retrotransposon-mediated DELLA transcriptional reprograming underlies semi-dominant dwarfism in foxtail millet

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The Crop Journal 2019年第4期7卷 458-468页

作者： Meicheng Zhao Hui Zhi Xue Zhang guanqing jia Xianmin Diao Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing 100081 China Center for Agricultural Research Resources Institute of Genetics and Developmental Biology Chinese Academy of Sciences Shijiazhuang 050021 Hebei China

Retrotransposons account for a large proportion of the genome and genomic variation, and play key roles in creating novel genes and diversifying the genome in many eukaryotic species. Although retrotransposons are abundant in plants, their roles had been underestimated because of a lack of research. Here, we characterized a gibberellin Acid (GA)-insensitive dwarf mutant, 84133, in foxtail millet. Map-based cloning revealed a 5.5-kb Copia-like retrotransposon insertion in DWARF1 (D1), which encodes a DELLA protein. Transcriptional analysis showed that the Copia retrotransposon mediated the transcriptional reprogramming of D1 leading to a novel N-terminal-deleted truncated DELLA transcript that was putatively driven by Copia's LTR, namely D1-TT, and another chimeric transcript. The presence of D1-TT was confirmed by protein immunodetection analysis. Furthermore, D1-TT protein was resistant to GA3 treatment compared with the intact DELLA protein due to its inability to interact with the GA receptor, SiGID1. Overexpression of D1-TT in foxtail millet resulted in dwarf plants, confirming that it determines the dwarfism of 84133. Thus, our study documents a rare instance of long terminal repeat (LTR) retrotransposon-mediated transcriptional reprograming in the plant kingdom. These results shed light on the function of LTR retrotransposons in generating new gene functions and genetic diversity.

关键词： Retrotransposon Transcriptional reprogramming DELLA Dwarf breeding Foxtail millet (Setaria italica)

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我国谷子登记品种遗传多样性分析及综合评价

作物杂志 2024年第4期 14-23页

作者：袁迪智慧王海岗张慧姚琦梁红凯王君杰陈凌刁现民贾冠清青岛农业大学农学院山东青岛266109 中国农业科学院作物科学研究所北京100081 山西农业大学农业基因资源研究中心山西太原030031

谷子登记品种在农业生产中发挥着重要的支撑作用。开展相关的多样性评估,可以指导谷子品种的生产布局和育种优异互补亲本选择,进而提高新品种培育和田间生产效率。对2011-2022年间登记的200份谷子品种进行了一年两点的农艺性状调查和分... 详细信息

谷子登记品种在农业生产中发挥着重要的支撑作用。开展相关的多样性评估,可以指导谷子品种的生产布局和育种优异互补亲本选择,进而提高新品种培育和田间生产效率。对2011-2022年间登记的200份谷子品种进行了一年两点的农艺性状调查和分析。结果表明,200份谷子登记品种变异系数范围为9.12%~21.96%,遗传多样性指数(H′)为1.9578~2.0866。区域性农艺性状分析结果表明,东北春谷区的品种变异系数高于西北春谷区和华北夏谷区,其中穗重、穗粒重具有最高的变异系数。相关性分析显示,穗重和穗粒重正相关性系数最高,穗颈长和茎粗负相关性系数最高。基于主成分分析和综合得分(F值)筛选出综合评价较好的前20个登记品种,200份登记品种中F值最高的品种为太选谷28,最低的是龙谷26。基于农艺性状进行聚类分析,200份谷子登记品种可分为4个类群,其中类群Ⅰ大部分农艺性状平均值偏高,类群Ⅳ中12个农艺性状均值较低。

关键词：谷子登记品种:农艺性状遗传多样性综合评价

Identification of no pollen 1 provides a candidate gene for heterosis utilization in foxtail millet(Setaria italica L.)

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The Crop Journal 2021年第6期9卷 1309-1319页

作者： Wei Zhang Hui Zhi Sha Tang Haoshan Zhang Yi Sui guanqing jia Chuanyin Wu Xianmin Diao Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China

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 *** 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.

关键词： Foxtail millet Setaria italica Male sterile No pollen 1 CRISPR/Cas9 Hybrid breeding

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 *** 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

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 *** 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 *** 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 ***1 was expressed in seedlings,leaves,panicles,and mature seeds,and was subcellularly localized to *** of SiPSY1 in 15 DAP immature grains was responsible for YPC in mature *** of SiPSY1 combined with increased YPC in mature grains during domestication of foxtail millet was *** 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 *** 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

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 ***, 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

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中国谷子种业创新现状与未来展望

中国农业科学 2022年第4期55卷 653-665页

作者：贾冠清刁现民中国农业科学院作物科学研究所

种业是农业发展的“芯片”，原始创新是农业可持续发展的根本动力。2021年中央一号文件明确提出推进中国农作物种业快速发展的要求，对中国农作物种业原始创新研究提出了明确期望。谷子是中国起源的传统粮饲兼用作物及特色杂粮作物，生... 详细信息

种业是农业发展的“芯片”，原始创新是农业可持续发展的根本动力。2021年中央一号文件明确提出推进中国农作物种业快速发展的要求，对中国农作物种业原始创新研究提出了明确期望。谷子是中国起源的传统粮饲兼用作物及特色杂粮作物，生产及消费规模均位居世界首位。作为粟类作物，谷子在中国农业生产及农耕文明的起始与发展过程中发挥了重要的推动和支撑作用，已有研究证实谷子在中国拥有悠久的栽培历史，并且形成了分布广泛且多样性丰富的各类种质资源。近年来，谷子在杂交品种选育及杂种优势利用、抗除草剂品种和适于机械化栽培品种推广、基因组学及功能基因研究等领域取得进展，在原始创新的推动下初步形成了以杂交品种和抗除草剂品种为经营主体的谷子种业体系，推动了谷子种业从无到有的突破。中国在谷子优异种质鉴定与创制方法研究、谷子高效育种技术途径研发、谷子关键性状的协调表达与调控规律解析、谷子良种繁育过程基本生物学属性研究以及谷子新品种真实性鉴定方法探索等方面原始创新的进步为谷子种业发展提供了支撑，形成了一套初具规模的种业原始创新技术。目前，谷子种业持续良性发展仍然面临包括优异突破性种质匮乏、育种技术水平相对滞后、品质与产量协调性不够、良种扩繁标准缺乏以及种业市场监管手段有待加强等诸多挑战。为了推进谷子种业持续快速、高效、深入的发展，未来中国谷子种业原始创新研究的主要方向包括：基于表型组学与基因组修饰技术、单倍体育种与全基因组选择技术和关键性状优异单倍型鉴定与整合技术的谷子规模化高效育种技术体系构建；基于种子发育生理调控、分子指纹及杂种优势高效利用技术的谷子种子高效生产储藏与监管技术体系构建；以及基于谷子种业产学研推一体化设计与高效整合的人才培养与创新体系构建等方面。

关键词：谷子种业原始创新现状发展趋势

Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet

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The Crop Journal 2023年第2期11卷 593-604页

作者： Mengyuan Zhu Qiang He Mingjie Lyu Tiantian Shi Qian Gao Hui Zhi Huan Wang guanqing jia Sha Tang Xiliu Cheng Rui Wanga Andi Xu Haigang Wang Zhijun Qiao Jun Liu Xianmin Diao Ying Gao National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI) Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Biotechnology Research Institute Chinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Chengdu National Agricultural Science and Technology Center Chengdu 610213SichuanChina Center for Agricultural Genetic Resources Research Shanxi Agricultural UniversityTaiyuan 030031ShanxiChina Institute of Germplasm Resources and Biotechnology Tianjin Academy of Agricultural SciencesTianjin 300112China

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 ***,it is imperative to identify and deploy the genes controlling foxtail millet plant *** 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 *** 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 *** 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 *** them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at *** amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different *** 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.

关键词： Foxtail millet Plant height Transcriptome analysis Bulk segregant analysis Functional markers Association analysis