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Chandra T, Jaiswal S, Tomar RS, Iquebal MA, Kumar D. Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources. PLANTA 2024; 260:103. [PMID: 39304579 DOI: 10.1007/s00425-024-04520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
MAIN CONCLUSION Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
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Ye XX, Chen YQ, Wu JS, Zhong HQ, Lin B, Huang ML, Fan RH. Biochemical and Transcriptome Analysis Reveals Pigment Biosynthesis Influenced Chlorina Leaf Formation in Anoectochilus roxburghii (Wall.) Lindl. Biochem Genet 2024; 62:1040-1054. [PMID: 37528284 DOI: 10.1007/s10528-023-10432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/15/2023] [Indexed: 08/03/2023]
Abstract
Anoectochilus roxburghii (Wall.) Lindl is a perennial herb of the Orchidaceae family; a yellow-green mutant and a yellow mutant were obtained from the wild type, thereby providing good material for the study of leaf color variation. Pigment content analysis revealed that chlorophyll, carotenoids, and anthocyanin were lower in the yellow-green and yellow mutants than in the wild type. Transcriptome analysis of the yellow mutant and wild type revealed that 78,712 unigenes were obtained, and 599 differentially expressed genes (120 upregulated and 479 downregulated) were identified. Using the Kyoto Encyclopedia of Genes and Genomes pathway analysis, candidate genes involved in the anthocyanin biosynthetic pathway (five unigenes) and the chlorophyll metabolic pathway (two unigenes) were identified. Meanwhile, the low expression of the chlorophyll and anthocyanin biosynthetic genes resulted in the absence of chlorophylls and anthocyanins in the yellow mutant. This study provides a basis for similar research in other closely related species.
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Affiliation(s)
- Xiu-Xian Ye
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Yi-Quan Chen
- Institute of Agricultural Engineering Technology, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Jian-She Wu
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Huai-Qin Zhong
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Bing Lin
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China
| | - Min-Ling Huang
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China.
| | - Rong-Hui Fan
- Institute of Crop Sciences, Fujian Academy of Agricultural Science, Fuzhou, Fujian, China.
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Liu T, Liu X, He J, Dong K, Zhang L, Li Y, Ren R, Yang T. Comparative transcriptome analysis and genetic dissection of vegetative branching traits in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:39. [PMID: 38294546 DOI: 10.1007/s00122-023-04524-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE Two major genetic loci, qTN5.1 and qAB9.1, were identified and finely mapped to the 255 Kb region with one potential candidate gene for tiller number and the 521 Kb region with eight candidate genes for axillary branch number, respectively. Vegetative branching including tillering and axillary branching are vital traits affecting both the plant architecture and the biomass in cereal crops. However, the mechanism underlying the formation of vegetative branching in foxtail millet is largely unknown. Here, a foxtail millet cultivar and its bushy wild relative Setaria viridis accession were used to construct segregating populations to identify candidate genes regulating tiller number and axillary branch number. Transcriptome analysis using vegetative branching bud samples of parental accessions was performed, and key differentially expressed genes and pathways regulating vegetative branching were pointed out. Bulk segregant analysis on their F2:3 segregating population was carried out, and a major QTL for tiller number (qTN5.1) and two major QTLs for axillary branch number (qAB2.1 and qAB9.1) were detected. Fine-mapping strategy was further performed on F2:4 segregate population, and Seita.5G356600 encoding β-glucosidase 11 was identified as the promising candidate gene for qTN5.1, and eight genes, especially Seita.9G125300 and Seita.9G125400 annotated as B-S glucosidase 44, were finally identified as candidate genes for regulating axillary branching. Findings in this study will help to elucidate the genetic basis of the vegetative branching formation of foxtail millet and lay a foundation for breeding foxtail millet varieties with ideal vegetative branching numbers.
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Affiliation(s)
- Tianpeng Liu
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yawei Li
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China.
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Han H, Zhou Y, Liu H, Chen X, Wang Q, Zhuang H, Sun X, Ling Q, Zhang H, Wang B, Wang J, Tang Y, Wang H, Liu H. Transcriptomics and Metabolomics Analysis Provides Insight into Leaf Color and Photosynthesis Variation of the Yellow-Green Leaf Mutant of Hami Melon ( Cucumis melo L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1623. [PMID: 37111847 PMCID: PMC10143263 DOI: 10.3390/plants12081623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 06/16/2023]
Abstract
Leaf color mutants are ideal materials for studying the regulatory mechanism of chloroplast development and photosynthesis. We isolated a cucumis melo spontaneous mutant (MT), which showed yellow-green leaf phenotype in the whole growing period and could be inherited stably. We compared its leaves with the wild type (WT) in terms of cytology, physiology, transcriptome and metabolism. The results showed that the thylakoid grana lamellae of MT were loosely arranged and fewer in number than WT. Physiological experiments also showed that MT had less chlorophyll content and more accumulation of reactive oxygen species (ROS) than WT. Furthermore, the activity of several key enzymes in C4 photosynthetic carbon assimilation pathway was more enhanced in MT than WT. Transcriptomic and metabolomic analyses showed that differential expression genes and differentially accumulated metabolites in MT were mainly co-enriched in the pathways related to photosystem-antenna proteins, central carbon metabolism, glutathione metabolism, phenylpropanoid biosynthesis and flavonoid metabolism. We also analyzed several key proteins in photosynthesis and chloroplast transport by Western blot. In summary, the results may provide a new insight into the understanding of how plants respond to the impaired photosynthesis by regulating chloroplast development and photosynthetic carbon assimilation pathways.
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Affiliation(s)
- Hongwei Han
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China; (H.H.)
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Yuan Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200030, China
| | - Huifang Liu
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Xianjun Chen
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China; (H.H.)
| | - Qiang Wang
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Hongmei Zhuang
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Xiaoxia Sun
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China; (H.H.)
| | - Qihua Ling
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200030, China
| | - Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei 235000, China
| | - Baike Wang
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Juan Wang
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Yaping Tang
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Hao Wang
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830002, China
| | - Huiying Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China; (H.H.)
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Feng Y, Li Y, Zhao Y, Shi H. Physiological, transcriptome and co-expression network analysis of chlorophyll-deficient mutants in flue-cured tobacco. BMC PLANT BIOLOGY 2023; 23:153. [PMID: 36944910 PMCID: PMC10031990 DOI: 10.1186/s12870-023-04169-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Photosynthetic pigments in higher plants, including chlorophyll (Chl) and carotenoids, are crucial for photosynthesis and photoprotection. Chl-deficient tobacco seedlings generally have a lower photosynthesis rate and higher nitrate-nitrogen (NO3-N) content, which causes a profound influence on tobacco yield and quality. In this study, a stable albino leaf mutant (Al) and slight-green leaf mutant (SG) obtained from the common flue-cured tobacco (Nicotiana tabacum L.) cultivar 'Zhongyan 100' (ZY100) by mutagenesis with ethyl methanesulfonate (EMS) were used as materials. The differences between the Chl-deficient mutants and the wild-type (WT) were analyzed in terms of biomass, photosynthetic fluorescence parameters, and carbon- and nitrogen-related physiological parameters. RNA sequencing (RNA-seq) and weighted gene co-expression network analysis (WGCNA) were used to explore the key pathways and candidate genes regulating differentiated chlorophyll and nitrate content. RESULTS The results showed that, when compared to the WT, the Chl content and biomass of mutant plants were considerably lower while the NO3-N content was substantially elevated. The net photosynthetic rate, photosynthetic fluorescence parameters, carbohydrate, soluble protein, and carbon- and nitrogen-related enzyme activities all decreased in leaves of mutants and the development of chloroplasts was abnormal. Applying more nitrogen improved the growth and development of mutants, whereas NO3-N content distinctively increased compared with that of the WT. Through transcriptome sequencing, the downregulated genes in mutants were enriched in plant hormone signal transduction and nitrogen metabolism, which are involved in pigment biosynthesis and the carbon fixation pathway. In addition, two hub genes and seven transcription factors identified from the blue module through WGCNA were likely to be key candidate factors involved in chlorophyll synthesis and nitrate accumulation. CONCLUSION Our results demonstrated that differences in chlorophyll and nitrate content were caused by the combined effects of chloroplast development, photosynthesis, as well as related biological activity. In addition, transcriptome results provide a bioinformatics resource for further functional identification of key pathways and genes responsible for differences in chlorophyll and nitrate content in tobacco plants.
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Affiliation(s)
- Yuqing Feng
- College of Tobacco, Henan Agricultural University, Zhengzhou, 450000, Henan, P. R. China
| | - Yujing Li
- College of Tobacco, Henan Agricultural University, Zhengzhou, 450000, Henan, P. R. China
| | - Yuanyuan Zhao
- College of Tobacco, Henan Agricultural University, Zhengzhou, 450000, Henan, P. R. China
| | - Hongzhi Shi
- College of Tobacco, Henan Agricultural University, Zhengzhou, 450000, Henan, P. R. China.
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Zhang P, Ni Y, Jiao Z, Li J, Wang T, Yao Z, Jiang Y, Yang X, Sun Y, Li H, He D, Niu J. The wheat leaf delayed virescence of mutant dv4 is associated with the abnormal photosynthetic and antioxidant systems. Gene X 2023; 856:147134. [PMID: 36586497 DOI: 10.1016/j.gene.2022.147134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
Chlorophyll (Chl) is a key pigment for wheat (Triticum aestivum L.) photosynthesis, consequently impacts grain yield. A wheat mutant named as delayed virescence 4 (dv4) was obtained from cultivar Guomai 301 (wild type, WT) treated with ethyl methane sulfonate (EMS). The seedling leaves of dv4 were shallow yellow, apparently were chlorophyll deficient. They started to turn green at the jointing stage and returned to almost ordinary green at the heading stage. Leaf transcriptome comparison of Guomai 301 and dv4 at the jointing stage showed that most differentially expressed genes (DEGs) of transcription and translation were highly expressed in dv4, one key gene nicotianamine aminotransferase A (NAAT-A) involved in the synthesis and metabolism pathways of tyrosine, methionine and phenylalanine was significantly lowly expressed. The expression levels of the most photosynthesis related genes, such as photosystem I (PS I), ATPase and light-harvesting chlorophyll protein complex-related homeotypic genes, and protochlorophyllide reductase A (PORA) were lower; but macromolecule degradation and hypersensitivity response (HR) related gene heat shock protein 82 (HSP82) was highly expressed. Compared to WT, the contents of macromolecules such as proteins and sugars were reduced; the contents of Chl a, Chl b, total Chl, and carotenoids in leaves of dv4 were significantly less at the jointing stage, while the ratio of Chl a / Chl b was the same as that of WT. The net photosynthetic rate, stomatal conductance and transpiration rate of dv4 were significantly lower. The H2O2 content were higher, while the contents of total phenol and malondialdehyde (MDA), antioxidant enzyme activities were lower in leaves of dv4. In conclusion, the reduced contents of macromolecules and photosynthetic pigments, the abnormal photosynthetic and antioxidant systems were closely related to the phenotype of dv4.
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Affiliation(s)
- Peipei Zhang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, Henan, China
| | - Zhixin Jiao
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Junchang Li
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Ting Wang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Ziping Yao
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yumei Jiang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Xiwen Yang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yulong Sun
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Huijuan Li
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Dexian He
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Jishan Niu
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China.
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Liang H, He Q, Zhang H, Zhi H, Tang S, Wang H, Meng Q, Jia G, Chang J, Diao X. Identification and haplotype analysis of SiCHLI: a gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:24. [PMID: 36739566 DOI: 10.1007/s00122-023-04309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
We cloned and developed functional markers for the SiCHLI gene, which is responsible for the yellow-green color of leaves in foxtail millet, a frequently used marker trait in the hybrid breeding of foxtail millet by using bulked segregant analysis sequencing and haplotype analysis on the F2 and core-collected nature populations. The color of leaves has been widely used as a marker for the hybrid breeding of foxtail millet; however, few related gene have been cloned to date. Here, we used two F2 populations generated from crosses between the highly male-sterile material 125A with yellow-green leaves, and CG58 and S410, which have green leaves, to identify the genes underlying the yellow-green color of the leaves of foxtail millet. The leaves of 125A seedlings were yellow-green, but they became green at the heading stage. The content of chlorophyll a and chlorophyll b was lower, the number of thylakoid lamellae and grana was reduced, and the chloroplasts was more rounded in 125A than in S410 at the yellow-green leaf stage; however, no differences were observed between 125A and S410 in these traits and photosynthetic at the heading stage. Bulked segregant analysis and map-based cloning revealed that the SiCHLI gene is responsible for the leaf colors of 125A. A nonsynonymous mutation (C/T) in exon 3 causes yellow-green leaves in 125A at the seedling stage. Haplotype analysis of the SiCHLI gene in 596 core collected accessions revealed a new haplotype associated with high photosynthetic metabolic potential at the heading and mature stages, which could be used to enhance sterile lines with yellow-green leaves. We developed a functional marker that will facilitate the identification of foxtail millet accessions with the different types of yellow-green leaves. Generally, our study provides new genetic resources to guide the future marker-assisted or target-base editing in foxtail millet hybrid breeding.
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Affiliation(s)
- Hongkai Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang Meng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Jinhua Chang
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China.
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Cheng M, Meng F, Mo F, Qi H, Wang P, Chen X, Liu J, Ghanizadeh H, Zhang H, Wang A. Slym1 control the color etiolation of leaves by facilitating the decomposition of chlorophyll in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111457. [PMID: 36089196 DOI: 10.1016/j.plantsci.2022.111457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Photosynthesis, as an important biological process of plants, produces organic substances for plant growth and development. Although the molecular mechanisms of photosynthesis had been well investigated, the relationship between chlorophyll synthesis and photosynthesis remains largely unknown. The leaf-color mutant was an ideal material for studying photosynthesis and chlorophyll synthesis, which had been seldom investigated in tomato. Here, we obtained a yellow leaf tomato mutant ym (The mutant plants from the line of zs4) in field. Transmission electron microscopy (TEM) and photosynthetic parameters results demonstrated that chloroplast's structure was obviously destroyed and photosynthetic capacity gets weak. The mutant was hybridized with the control to construct the F2 segregation population for sequencing. Slym1 gene, controlling yellow mutant trait, was identified using Bulked Segregation Analysis. Slym1 was up-regulated in the mutant and Slym1 was located in the nucleus. The genes associated with photosynthesis and chlorophyll synthesis were down-regulated in Slym1-OE transgenic tomato plants. The results suggested that Slym1 negatively regulate photosynthesis. Photosynthetic pigment synthesis related genes HEMA, HEMB1, CHLG and CAO were up-regulated in Slym1 silencing plants. The redundant Slym1 binding the intermediate proteins MP resulting in hindering the interaction between MP and HY5 due to the Slym1 with a high expression level in ym mutant, lead to lots of the HY5 with unbound state accumulates in cells, that could accelerate the decomposition of chlorophyll. Therefore, the yellow leaf-color mutant ym could be used as an ideal material for further exploring the relationship between leaf color mutant and photosynthesis and the specific mechanism.
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Affiliation(s)
- Mozhen Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Fanyue Meng
- College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Fulei Mo
- College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Haonan Qi
- College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Peiwen Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Jiayin Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China; College of Arts and Sciences, Northeast Agricultural University, Harbin, China.
| | - Hossein Ghanizadeh
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand.
| | - He Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
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9
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Wang Y, Wang J, Chen L, Meng X, Zhen X, Liang Y, Han Y, Li H, Zhang B. Identification and function analysis of yellow-leaf mutant (YX-yl) of broomcorn millet. BMC PLANT BIOLOGY 2022; 22:463. [PMID: 36167497 PMCID: PMC9513943 DOI: 10.1186/s12870-022-03843-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/12/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Broomcorn millet is highly tolerant to drought and barren soil. Changes in chlorophyll content directly affect leaf color, which subsequently leadsleading to poor photosynthetic performance and reduced crop yield. Herein, we isolated a yellow leaf mutant (YX-yl) using a forward genetics approach and evaluated its agronomic traits, photosynthetic pigment content, chloroplast ultrastructure, and chlorophyll precursors. Furthermore, the molecular mechanism of yellowing was explored using transcriptome sequencing. RESULTS The YX-yl mutant showed significantly decreased plant height and low yield. The leaves exhibited a yellow-green phenotype and poor photosynthetic capacity during the entire growth period. The content of chlorophyll a, chlorophyll b, and carotenoids in YX-yl leaves was lower than that in wild-type leaves. Chlorophyll precursor analysis results showed that chlorophyll biosynthesis in YX-yl was hindered by the conversion of porphobilinogen to protoporphyrin IX. Examination of chloroplast ultrastructure in the leaves revealed that the chloroplasts of YX-yl accumulated on one side of the cell. Moreover, the chloroplast structure of YX-yl was degraded. The inner and outer membranes of the chloroplasts could not be distinguished well. The numbers of grana and grana thylakoids in the chloroplasts were low. The transcriptome of the yellowing mutant YX-yl was sequenced and compared with that of the wild type. Nine chlorophyll-related genes with significantly different expression profiles were identified: PmUROD, PmCPO, PmGSAM, PmPBDG, PmLHCP, PmCAO, PmVDE, PmGluTR, and PmPNPT. The proteins encoded by these genes were located in the chloroplast, chloroplast membrane, chloroplast thylakoid membrane, and chloroplast matrix and were mainly involved in chlorophyll biosynthesis and redox-related enzyme regulation. CONCLUSIONS YX-yl is an ideal material for studying pigment metabolism mechanisms. Changes in the expression patterns of some genes between YX-yl and the wild type led to differences in chloroplast structures and enzyme activities in the chlorophyll biosynthesis pathway, ultimately resulting in a yellowing phenotype in the YX-yl mutant. Our findings provide an insight to the molecular mechanisms of leaf color formation and chloroplast development in broomcorn millet.
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Affiliation(s)
- Yushen Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, Shanxi, China, 030801
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production With High-Quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Junjie Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Liqing Chen
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Xiaowei Meng
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Xiaoxi Zhen
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Yinpei Liang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, Shanxi, China, 030801
| | - Hongying Li
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801
| | - Bin Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China, 030801.
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, Shanxi, China, 030801.
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production With High-Quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu, Shanxi, China, 030801.
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, Shanxi, China, 030801.
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10
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Ye S, Yang J, Huang Y, Liu J, Ma X, Zhao L, Ma C, Tu J, Shen J, Fu T, Wen J. Bulk segregant analysis-sequencing and RNA-Seq analyses reveal candidate genes associated with albino phenotype in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:994616. [PMID: 36119587 PMCID: PMC9478516 DOI: 10.3389/fpls.2022.994616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Inheritable albino mutants are excellent models for exploring the mechanism of chloroplast biogenesis and development. However, only a few non-lethal albino mutations have been reported to date in Brassica species. Here, we describe a resynthesized Brassica napus mutant, whose leaf, stem, and silique tissues showed an inheritable albino phenotype under field conditions after the bud stage but green phenotype in the greenhouse during the whole growing season, indicating that the albino phenotype depends on environmental conditions. Compared with the green leaves of the field-grown wild-type (GL) and greenhouse-grown mutant (WGL) plants, white leaves of the field-grown mutant (WL) showed significantly lower chlorophyll contents and structural defects in chloroplasts. Genetic analysis revealed that the albino phenotype of WL is recessive and is controlled by multiple genes. Bulk segregant analysis-sequencing (BSA-Seq) indicated that the candidate regions responsible for the albino phenotype spanned a total physical distance of approximately 49.68 Mb on chromosomes A03, A07, A08, C03, C04, C06, and C07. To gain insights into the molecular mechanisms that control chloroplast development in B. napus, we performed transcriptome (RNA-Seq) analysis of GL, WGL, and WL samples. GO and KEGG enrichment analyses suggested that differentially expressed genes (DEGs) associated with leaf color were significantly enriched in photosynthesis, ribosome biogenesis and chlorophyll metabolism. Further analysis indicated that DEGs involved in chloroplast development and chlorophyll metabolism were likely the main factors responsible for the albino phenotype in B. napus. A total of 59 DEGs were screened in the candidate regions, and four DEGs (BnaC03G0522600NO, BnaC07G0481600NO, BnaC07G0497800NO, and BnaA08G0016300NO) were identified as the most likely candidates responsible for the albino phenotype. Altogether, this study provides clues for elucidating the molecular mechanisms underlying chloroplast development in B. napus.
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11
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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12
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Wang F, Chen N, Shen S. iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism of Golden-Yellow Leaf Mutant in Hybrid Paper Mulberry. Int J Mol Sci 2021; 23:127. [PMID: 35008552 PMCID: PMC8745438 DOI: 10.3390/ijms23010127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022] Open
Abstract
Plant growth and development relies on the conversion of light energy into chemical energy, which takes place in the leaves. Chlorophyll mutant variations are important for studying certain physiological processes, including chlorophyll metabolism, chloroplast biogenesis, and photosynthesis. To uncover the mechanisms of the golden-yellow phenotype of the hybrid paper mulberry plant, this study used physiological, cytological, and iTRAQ-based proteomic analyses to compare the green and golden-yellow leaves of hybrid paper mulberry. Physiological results showed that the mutants of hybrid paper mulberry showed golden-yellow leaves, reduced chlorophyll, and carotenoid content, and increased flavonoid content compared with wild-type plants. Cytological observations revealed defective chloroplasts in the mesophyll cells of the mutants. Results demonstrated that 4766 proteins were identified from the hybrid paper mulberry leaves, of which 168 proteins displayed differential accumulations between the green and mutant leaves. The differentially accumulated proteins were primarily involved in chlorophyll synthesis, carotenoid metabolism, and photosynthesis. In addition, differentially accumulated proteins are associated with ribosome pathways and could enable plants to adapt to environmental conditions by regulating the proteome to reduce the impact of chlorophyll reduction on growth and survival. Altogether, this study provides a better understanding of the formation mechanism of the golden-yellow leaf phenotype by combining proteomic approaches.
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Affiliation(s)
- Fenfen Wang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naizhi Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China;
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China;
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13
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Zhang H, Tang S, Schnable JC, He Q, Gao Y, Luo M, Jia G, Feng B, Zhi H, Diao X. Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1. FRONTIERS IN PLANT SCIENCE 2021; 12:743782. [PMID: 34858451 PMCID: PMC8632227 DOI: 10.3389/fpls.2021.743782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/13/2021] [Indexed: 05/03/2023]
Abstract
Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the "Yugu1" variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, "SSR41", which is morphologically similar to, and readily cross-pollinates with, "Yugu1". High-throughput resequencing of "SSR41" identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used "SSR41" and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.
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Affiliation(s)
- Hui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Sha Tang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - James C. Schnable
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Qiang He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanzhu Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingzhao Luo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Hui Zhi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianmin Diao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Physiological and Molecular Analysis Reveals the Differences of Photosynthesis between Colored and Green Leaf Poplars. Int J Mol Sci 2021; 22:ijms22168982. [PMID: 34445687 PMCID: PMC8396459 DOI: 10.3390/ijms22168982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Leaf coloration changes evoke different photosynthetic responses among different poplar cultivars. The aim of this study is to investigate the photosynthetic difference between a red leaf cultivar (ZHP) and a green leaf (L2025) cultivar of Populus deltoides. In this study, ‘ZHP’ exhibited wide ranges and huge potential for absorption and utilization of light energy and CO2 concentration which were similar to those in ‘L2025’ and even showed a stronger absorption for weak light. However, with the increasing light intensity and CO2 concentration, the photosynthetic capacity in both ‘L2025’ and ‘ZHP’ was gradually restricted, and the net photosynthetic rate (Pn) in ‘ZHP’ was significantly lower than that in ‘L2025’under high light or high CO2 conditions, which was mainly attributed to stomatal regulation and different photosynthetic efficiency (including the light energy utilization efficiency and photosynthetic CO2 assimilation efficiency) in these two poplars. Moreover, the higher anthocyanin content in ‘ZHP’ than that in ‘L2025’ was considered to be closely related to the decreased photosynthetic efficiency in ‘ZHP’. According to the results from the JIP-test, the capture efficiency of the reaction center for light energy in ‘L2025’ was significantly higher than that in ‘ZHP’. Interestingly, the higher levels of light quantum caused relatively higher accumulation of QA- in ‘L2025’, which blocked the electron transport and weakened the photosystem II (PSII) performance as compared with ‘ZHP’; however, the decreased capture of light quantum also could not promote the utilization of light energy, which was the key to the low photosynthetic efficiency in ‘ZHP’. The differential expressions of a series of photosynthesis-related genes further promoted these specific photosynthetic processes between ‘L2025’ and ‘ZHP’.
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15
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Gao J, Chen T, Jiang C, Wang T, Huang O, Zhang X, Liu J. Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis. PeerJ 2021; 9:e11586. [PMID: 34221719 PMCID: PMC8231315 DOI: 10.7717/peerj.11586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
Abstract
Color variation in plant tissues is a common phenomenon accompanied with a series of biological changes. In this study, a special-phenotype Aquilaria sinensis (GS) with color variation of leaf was firstly reported, and DNA barcode sequences showed GS samples could not be discriminated clearly with the normal A. sinensis sample (NS), which suggested that the variety was not the cause of the GS formation. To reveal the characteristics of GS compared to NS, the anatomical and transcriptome sequencing studies were carried out. In microscopic observation, the leaves of golden-vein-leaf sample (LGS) and normal-vein-leaf sample (LNS) showed significant differences including the area of the included phloem in midrib and the thickness parameters of palisade and spongy tissues; the stems of golden-vein-leaf sample (SGS) and normal-vein-leaf sample (SNS) were also different in many aspects such as the area of vessels and included phloem. In addition, the structure of chloroplast was more complete in the midrib of LNS than that of LGS, and some particles suspected as virus were found through transmission electron microscope as well. Genes upregulated in LGS in contrast with LNS were mainly enriched in photosynthesis. As for stems, most of the genes upregulated in SGS compared to SNS were involved in translation and metabolism processes. The pathways about photosynthesis and chlorophyll metabolism as well as some important transcription factors may explain the molecular mechanism of the unique phenotypes of leaves and the genes related to suberin biosynthesis may result in the difference of stems. In addition, the genes about defense response especially biotic stress associated with numerous pathogenesis-related (PR) genes upregulated in LGS compared to LNS indicated that the pathogen may be the internal factor. Taken together, our results reveal the macro- and micro-phenotype variations as well as gene expression profiles between GS and NS, which could provide valuable clues for elucidating the mechanism of the color variation of Aquilaria.
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Affiliation(s)
- Jiaqi Gao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Tong Chen
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tielin Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ou Huang
- Guangdong Shangzhengtang Group Co., Ltd, Dongguan, China
| | - Xiang Zhang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Juan Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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16
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Hunt HV, Przelomska NAS, Campana MG, Cockram J, Bligh HFJ, Kneale CJ, Romanova OI, Malinovskaya EV, Jones MK. Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing. THE PLANT GENOME 2021; 14:e20081. [PMID: 33543599 PMCID: PMC8638668 DOI: 10.1002/tpg2.20081] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 05/11/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping-by-sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet-green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515-SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.
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Affiliation(s)
- Harriet V. Hunt
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Natalia A. S. Przelomska
- Comparative Plant and Fungal BiologyRoyal Botanic GardensKewRichmondTW9 3AEUK
- Department of AnthropologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
| | - James Cockram
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | | | - Catherine J. Kneale
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Olga I. Romanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russia
| | | | - Martin K. Jones
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
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17
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Yang Z, Zhang H, Li X, Shen H, Gao J, Hou S, Zhang B, Mayes S, Bennett M, Ma J, Wu C, Sui Y, Han Y, Wang X. A mini foxtail millet with an Arabidopsis-like life cycle as a C 4 model system. NATURE PLANTS 2020; 6:1167-1178. [PMID: 32868891 DOI: 10.1038/s41477-020-0747-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 07/20/2020] [Indexed: 05/12/2023]
Abstract
Foxtail millet (Setaria italica) is an important crop species and an emerging model plant for C4 grasses. However, functional genomics research on foxtail millet is challenging because of its long generation time, relatively large stature and recalcitrance to genetic transformation. Here we report the development of xiaomi, a rapid-cycling mini foxtail millet mutant as a C4 model system. Five to six generations of xiaomi can be grown in a year in growth chambers due to its short life cycle and small plant size, similar to Arabidopsis. A point mutation in the Phytochrome C (PHYC) gene was found to be causal for these characteristics. PHYC encodes a light receptor essential for photoperiodic flowering. A reference-grade xiaomi genome comprising 429.94 Mb of sequence was assembled and a gene-expression atlas from 11 different tissues was developed. These resources, together with an established highly efficient transformation system and a multi-omics database, make xiaomi an ideal model system for functional studies of C4 plants.
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Affiliation(s)
- Zhirong Yang
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- College of Arts and Sciences, Shanxi Agricultural University, Taigu, China
| | - Haoshan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xukai Li
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Huimin Shen
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Jianhua Gao
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Siyu Hou
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Bin Zhang
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Sean Mayes
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Malcolm Bennett
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yuanhuai Han
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China.
- College of Agriculture, Shanxi Agricultural University, Taigu, China.
| | - Xingchun Wang
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China.
- College of Life Sciences, Shanxi Agricultural University, Taigu, China.
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18
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Yu X, Wang L, Xu K, Kong F, Wang D, Tang X, Sun B, Mao Y. Fine Mapping to Identify the Functional Genetic Locus for Red Coloration in Pyropia yezoensis Thallus. FRONTIERS IN PLANT SCIENCE 2020; 11:867. [PMID: 32655600 PMCID: PMC7324768 DOI: 10.3389/fpls.2020.00867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/27/2020] [Indexed: 05/26/2023]
Abstract
Pyropia yezoensis, commonly known as "Nori" or "Laver" is an economically important marine crop. In natural or selected populations of P. yezoensis, coloration mutants are frequently observed. Various coloration mutants are excellent materials for genetic research and study photosynthesis. However, the candidate gene controlling the Pyropia coloration phenotype remains unclear to date. QTL-seq, in combination with kompetitive allele-specific PCR (KASP) and RNA-seq, can be generally applied to population genomics studies to rapidly identify genes that are responsible for phenotypes showing extremely opposite traits. Through cross experiments between the wild line RZ and red-mutant HT, offsprings with 1-4 sectors chimeric blade were generated. Statistical analyses revealed that the red thallus coloration phenotype is conferred by a single nuclear allele. Two-pair populations, consisting of 24 and 56 wild-type/red-type single-genotype sectors from F1 progeny, were used in QTL-seq to detect a genomic region in P. yezoensis harboring the red coloration locus. Based on a high-quality genome, we first identified the candidate region within a 3.30-Mb region at the end of chromosome 1. Linkage map-based QTL analysis was used to confirm the candidate region identified by QTL-seq. Then, four KASP markers developed in this region were used to narrow down the candidate region to a 1.42-Mb region. Finally, we conducted RNA-seq to focus on 13 differentially expressed genes and further predicted rcl-1, which contains one non-synonymous SNP [A/C] in the coding region that could be regulating red thallus coloration in P. yezoensis. Our results provide novel insights into the underlying mechanism controlling blade coloration, which is a desirable trait in algae.
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Affiliation(s)
- Xinzi Yu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lu Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Kuipeng Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Dongmei Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Bin Sun
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunxiang Mao
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
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19
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Yang P, Li Y, He C, Yan J, Zhang W, Li X, Xiang F, Zuo Z, Li X, Zhu Y, Liu X, Zhao X. Phenotype and TMT-based quantitative proteomics analysis of Brassica napus reveals new insight into chlorophyll synthesis and chloroplast structure. J Proteomics 2019; 214:103621. [PMID: 31863931 DOI: 10.1016/j.jprot.2019.103621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/27/2019] [Accepted: 12/13/2019] [Indexed: 12/20/2022]
Abstract
The conversion of light energy into chemical energy in leaves is very important for plant growth and development. During this process, chlorophylls and their derivatives are indispensable as their fundamental role in the energy absorption and transduction activities. Chlorophyll variation mutants are important materials for studying chlorophyll metabolism, chloroplast biogenesis, photosynthesis and related physiological processes. Here, a chlorophyll-reduced mutant (crm1) was isolated from ethyl methanesulfonate (EMS) mutagenized Brassica napus. Compared to wild type, crm1 showed yellow leaves, reduced chlorophyll content, fewer thylakoid stacks and retarded growth. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 4575 proteins were identified from the chloroplast of Brassica napus leaves, and 466 of which displayed differential accumulations between wild type and crm1. The differential abundance proteins were found to be involved in chlorophyll metabolism, photosynthesis, phagosome and proteasome. Our results suggest that the decreased abundance of chlorophyll biosynthetic enzymes, proteins involved in photosynthesis might account for the reduced chlorophyll content, impaired thylakoid structure, and reduction of plant productivity. The increased abundance of proteins involved in phagosome and proteasome pathways might allow plants to adapt the proteome to environmental conditions to ensure growth and survival due to chlorophyll reduction. BIOLOGICAL SIGNIFICANCE: Photosynthesis, which consists of light and dark reactions, is fundamental to biomass production. Chloroplast is regarded as the main site for photosynthesis. During photosynthesis, the pigment chlorophyll is essential for light harvesting and energy transfer. This work provides new insights into protein expression patterns, and enables the identification of many attractive candidates for investigation of chlorophyll biosynthesis, chloroplast structure and photosynthesis in Brassica napus. These findings may be applied to improve the photosynthetic efficiency by genetic engineering in crops.
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Affiliation(s)
- Piao Yang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Yaxing Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chongsheng He
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Jindong Yan
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Wei Zhang
- Hunan Agricultural University, College of Agronnomy, Changsha, Hunan 410128, China
| | - Xin Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Fujiang Xiang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinmei Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Yonghua Zhu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Xuanming Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China.
| | - Xiaoying Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China.
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20
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Gao S, Gao W, Liao X, Xiong C, Yu G, Yang Q, Yang C, Ye Z. The tomato WV gene encoding a thioredoxin protein is essential for chloroplast development at low temperature and high light intensity. BMC PLANT BIOLOGY 2019; 19:265. [PMID: 31221088 PMCID: PMC6585109 DOI: 10.1186/s12870-019-1829-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 05/13/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Chloroplast biogenesis, a complex process in higher plants, is the key to photoautotrophic growth in plants. White virescent (wv) mutants have been used to unfold the molecular mechanisms underlying the regulation of chloroplast development and chloroplast gene expression in plants. However, most of genes controlling white virescent phenotype still remain unknown. RESULTS In this study, we identified a temperature- and light intensity-sensitive mutant, named as wv. The content of chlorophyll was dramatically decreased in the immature leaves of wv mutant under the conditions of low temperature and high-light intensity. TEM observation showed that the chloroplasts in the young leaves of wv mutant lacked an organized thylakoid membrane, whereas crescent-shaped chloroplasts with well-developed stromal and stacked grana thylakoids in the mature leaves were developed. Immunoblot analyses suggested that proteins of photosynthetic complexes were decreased substantially in wv mutants. Based on map-based cloning and transgenic analysis, we determined that the wv phenotype was caused by single base mutation in the first intron of WV gene, which encoded a thioredoxin protein with 365 amino acids. qRT-PCR analysis revealed that the expression of WV gene was significantly down-regulated in wv mutant. In addition, knockdown of WV gene through RNAi also resulted in white virescent young leaves, suggesting that the mutation possibly blocks the differentiation of chloroplasts through inhibiting the expression of WV gene. Furthermore, the expression of WV peaked in apical buds and gradually decreased along with the developmental stage, which was consistent with the wv mutant phenotype. Expression analysis of chloroplast-encoded genes by qRT-PCR showed that the wv mutation affected the expression pattern of chloroplast-encoded PEP dependent genes. CONCLUSION Our results suggested that wv mutant was sensitive to low temperature and light intensity. WV gene was essential for chloroplast differentiation. A single base mutation in the first intron resulted in down-regulation of WV gene expression, which inhibited the expression of chloroplast-encoded genes, thereby blocking chloroplast formation and chlorophyll synthesis.
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Affiliation(s)
- Shenghua Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430070, Hubei, China
| | - Wenjing Gao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Cheng Xiong
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Gang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qihong Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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21
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Zhang S, Wu X, Cui J, Zhang F, Wan X, Liu Q, Zhong Y, Lin T. Physiological and transcriptomic analysis of yellow leaf coloration in Populus deltoides Marsh. PLoS One 2019; 14:e0216879. [PMID: 31112574 PMCID: PMC6529213 DOI: 10.1371/journal.pone.0216879] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/30/2019] [Indexed: 12/17/2022] Open
Abstract
Populus deltoides Marsh has high ornamental value because its leaves remain yellow during the non-dormant period. However, little is known about the regulatory mechanism of leaf coloration in P. deltoides Marsh. Thus, we analyzed the physiological and transcriptional differences of yellow leaves (mutant) and green leaves (wild-type) of P. deltoides Marsh. Physiological experiments showed that the contents of chlorophyll (Chl) and carotenoid were lower in mutant leaves, and the flavonoid content did not differ significantly between mutant and wild-type leaves. Transcriptomic sequencing was further used to identify 153 differentially expressed genes (DEGs). Functional classifications based on Gene Ontology enrichment and Genome enrichment analysis indicated that the DEGs were involved in Chl biosynthesis and flavonoid biosynthesis pathways. Among these, geranylgeranyl diphosphate (CHLP) genes associated with Chl biosynthesis showed down-regulation, while chlorophyllase (CLH) genes associated with Chl degradation were up-regulated in yellow leaves. The expression levels of these genes were further confirmed using quantitative real-time PCR (RT-qPCR). Furthermore, the estimation of the main precursors of Chl confirmed that CHLP is a vital enzyme for the yellow leaf color phenotype. Consequently, the formation of yellow leaf color is due to the disruption of Chl synthesis or catabolism rather than flavonoid synthesis. These results contribute to our understanding of mechanisms and regulation of leaf color variation in poplar at the transcriptional level.
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Affiliation(s)
- Shuzhen Zhang
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaolu Wu
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jie Cui
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fan Zhang
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xueqin Wan
- College of Forestry of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qinglin Liu
- College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu Zhong
- College of Forestry of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tiantian Lin
- College of Forestry of Sichuan Agricultural University, Chengdu, Sichuan, China
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22
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Physiological and Transcriptome Analysis of a Yellow-Green Leaf Mutant in Birch (Betula platyphylla × B. Pendula). FORESTS 2019. [DOI: 10.3390/f10020120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chlorophyll (Chl)-deficient mutants are ideal materials for the study of Chl biosynthesis, chloroplast development, and photosynthesis. Although the genes encoding key enzymes related to Chl biosynthesis have been well-characterized in herbaceous plants, rice (Oryza sativa L.), Arabidopsis (Arabidopsis thaliana), and maize (Zea mays L.), yellow-green leaf mutants have not yet been fully studied in tree species. In this work, we explored the molecular mechanism of the leaf color formation in a yellow-green leaf mutant (yl). We investigated the differentially expressed genes (DEGs) between yl and control plants (wild type birch (WT) and BpCCR1 overexpression line 11, (C11)) by transcriptome sequencing. Approximately 1163 genes (874 down-regulated and 289 up-regulated) and 930 genes (755 down-regulated and 175 up-regulated) were found to be differentially expressed in yl compared with WT and C11, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs revealed that photosynthesis antenna proteins represent the most significant enriched pathway. The expressions of photosynthesis antenna proteins are crucial to the leaf color formation in yl. We also found that Chl accumulate, leaf anatomical structure, photosynthesis, and growth were affected in yl. Taken together, our results not only provide the difference of phenomenal, physiological, and gene expression characteristics in leaves between yl mutant and control plants, but also provide a new insight into the mutation underlying the chlorotic leaf phenotype in birch.
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23
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Wang Z, Zhao K, Pan Y, Wang J, Song X, Ge W, Yuan M, Lei T, Wang L, Zhang L, Li Y, Liu T, Chen W, Meng W, Sun C, Cui X, Bai Y, Wang X. Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory. BMC Genomics 2018; 19:665. [PMID: 30208846 PMCID: PMC6134603 DOI: 10.1186/s12864-018-5051-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional domains. Results As to sequence divergence, TTF genes were previously divided into five subfamilies, I-V. We found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years’ evolution. Six amino acid sites of the SIP1 subfamily possibly were likely subjected to significant positive selection. Highest expression level was observed in the spica, with the SIP1 subfamily having highest expression level. As to the origination and expansion of the gene family, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Overtime, starting from the subfamily O, certain genes evolved to form subfamilies III and I, and later from subfamily I to develop subfamilies II and V. The oldest gene, Si1g016284, has the most structural changes, and a high expression in different tissues. What’s more interesting is that it may have bridge the interaction with different proteins. Conclusions By performing phylogenetic analysis using non-plant species, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Starting from the subfamily O, certain genes evolved to form other subfamilies. Our work will contribute to understanding the structural and functional innovation of Trihelix transcription factor, and the evolutionary trajectory. Electronic supplementary material The online version of this article (10.1186/s12864-018-5051-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenyi Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
| | - Kanglu Zhao
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yuxin Pan
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Jinpeng Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Weina Ge
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Min Yuan
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Tianyu Lei
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Li Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Lan Zhang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yuxian Li
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Tao Liu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Wei Chen
- Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Wenjing Meng
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Changkai Sun
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiaobo Cui
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yun Bai
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiyin Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
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24
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Hu H, Mauro-Herrera M, Doust AN. Domestication and Improvement in the Model C4 Grass, Setaria. FRONTIERS IN PLANT SCIENCE 2018; 9:719. [PMID: 29896214 PMCID: PMC5986938 DOI: 10.3389/fpls.2018.00719] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/14/2018] [Indexed: 05/17/2023]
Abstract
Setaria viridis (green foxtail) and its domesticated relative S. italica (foxtail millet) are diploid C4 panicoid grasses that are being developed as model systems for studying grass genomics, genetics, development, and evolution. According to archeological evidence, foxtail millet was domesticated from green foxtail approximately 9,000 to 6,000 YBP in China. Under long-term human selection, domesticated foxtail millet developed many traits adapted to human cultivation and agricultural production. In comparison with its wild ancestor, foxtail millet has fewer vegetative branches, reduced grain shattering, delayed flowering time and less photoperiod sensitivity. Foxtail millet is the only present-day crop in the genus Setaria, although archeological records suggest that other species were domesticated and later abandoned in the last 10,000 years. We present an overview of domestication in foxtail millet, by reviewing recent studies on the genetic regulation of several domesticated traits in foxtail millet and discuss how the foxtail millet and green foxtail system could be further developed to both better understand its domestication history, and to provide more tools for future breeding efforts.
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Affiliation(s)
| | | | - Andrew N. Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, United States
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25
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Wu H, Shi N, An X, Liu C, Fu H, Cao L, Feng Y, Sun D, Zhang L. Candidate Genes for Yellow Leaf Color in Common Wheat ( Triticum aestivum L.) and Major Related Metabolic Pathways according to Transcriptome Profiling. Int J Mol Sci 2018; 19:ijms19061594. [PMID: 29843474 PMCID: PMC6032196 DOI: 10.3390/ijms19061594] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/05/2023] Open
Abstract
The photosynthetic capacity and efficiency of a crop depends on the biosynthesis of photosynthetic pigments and chloroplast development. However, little is known about the molecular mechanisms of chloroplast development and chlorophyll (Chl) biosynthesis in common wheat because of its huge and complex genome. Ygm, a spontaneous yellow-green leaf color mutant of winter wheat, exhibits reduced Chl contents and abnormal chloroplast development. Thus, we searched for candidate genes associated with this phenotype. Comparative transcriptome profiling was performed using leaves from the yellow leaf color type (Y) and normal green color type (G) of the Ygm mutant progeny. We identified 1227 differentially expressed genes (DEGs) in Y compared with G (i.e., 689 upregulated genes and 538 downregulated genes). Gene ontology and pathway enrichment analyses indicated that the DEGs were involved in Chl biosynthesis (i.e., magnesium chelatase subunit H (CHLH) and protochlorophyllide oxidoreductase (POR) genes), carotenoid biosynthesis (i.e., β-carotene hydroxylase (BCH) genes), photosynthesis, and carbon fixation in photosynthetic organisms. We also identified heat shock protein (HSP) genes (sHSP, HSP70, HSP90, and DnaJ) and heat shock transcription factor genes that might have vital roles in chloroplast development. Quantitative RT-PCR analysis of the relevant DEGs confirmed the RNA-Seq results. Moreover, measurements of seven intermediate products involved in Chl biosynthesis and five carotenoid compounds involved in carotenoid-xanthophyll biosynthesis confirmed that CHLH and BCH are vital enzymes for the unusual leaf color phenotype in Y type. These results provide insights into leaf color variation in wheat at the transcriptional level.
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Affiliation(s)
- Huiyu Wu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Narong Shi
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Xuyao An
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Cong Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Hongfei Fu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | - Li Cao
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
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26
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Zhang S, Zhi H, Li W, Shan J, Tang C, Jia G, Tang S, Diao X. SiYGL2 Is Involved in the Regulation of Leaf Senescence and Photosystem II Efficiency in Setaria italica (L.) P. Beauv. FRONTIERS IN PLANT SCIENCE 2018; 9:1308. [PMID: 30233633 PMCID: PMC6131628 DOI: 10.3389/fpls.2018.01308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 08/20/2018] [Indexed: 05/20/2023]
Abstract
A yellow-green leaf mutant was isolated from EMS-mutagenized lines of Setaria italica variety Yugu1. Map-based cloning revealed the mutant gene is a homolog of Arabidopsis thaliana AtEGY1. EGY1 (ethylene-dependent gravitropism-deficient and yellow-green 1) is an ATP-independent metalloprotease (MP) that is required for chloroplast development, photosystem protein accumulation, hypocotyl gravitropism, leaf senescence, and ABA signal response in A. thaliana. However, the function of EGY1 in monocotyledonous C4 plants has not yet been described. The siygl2 mutant is phenotypically characterized by chlorotic organs, premature senescence, and damaged PS II function. Sequence comparisons of the AtEGY1 and SiYGL2 proteins reveals the potential for SiYGL2 to encode a partially functional protein. Phenotypic characterization and gene expression analysis suggested that SiYGL2 participates in the regulation of chlorophyll content, leaf senescence progression, and PS II function. Additionally, our research will contribute to further characterization of the mechanisms regulating leaf senescence and photosynthesis in S. italica, and in C4 plants in general.
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27
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Wang J, Wang Z, Du X, Yang H, Han F, Han Y, Yuan F, Zhang L, Peng S, Guo E. A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq. PLoS One 2017. [PMID: 28644843 PMCID: PMC5482450 DOI: 10.1371/journal.pone.0179717] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.
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Affiliation(s)
- Jun Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
- * E-mail: (JW); (EG)
| | - Zhilan Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Xiaofen Du
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Huiqing Yang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Fang Han
- Research Institute of Agriculture Sciences of Yanan, Yanan, Shaanxi, China
| | - Yuanhuai Han
- Shanxi Agricultural University, Taigu, Shanxi, China
| | - Feng Yuan
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Linyi Zhang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Shuzhong Peng
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, Shanxi, China
- Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, China
- * E-mail: (JW); (EG)
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Xiang J, Tang S, Zhi H, Jia G, Wang H, Diao X. Loose Panicle1 encoding a novel WRKY transcription factor, regulates panicle development, stem elongation, and seed size in foxtail millet [Setaria italica (L.) P. Beauv.]. PLoS One 2017; 12:e0178730. [PMID: 28570666 PMCID: PMC5453597 DOI: 10.1371/journal.pone.0178730] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 05/19/2017] [Indexed: 01/29/2023] Open
Abstract
Panicle development is an important agronomic trait that aids in determining crop productivity. Foxtail millet and its wild ancestor green foxtail have recently been used as model systems to dissect gene functions. Here, we characterized a recessive mutant of foxtail millet, loose-panicle 1 (lp1), which showed pleiotropic phenotypes, such as a lax primary branching pattern, aberrant branch morphology, semi-dwarfism, and enlarged seed size. The loose panicle phenotype was attributed to increased panicle lengths and decreased primary branch numbers. Map-based cloning, combined with high-throughput sequencing, revealed that LP1, which encodes a novel WRKY transcription factor, is responsible for the mutant phenotype. A phylogenetic analysis revealed that LP1 belongs to the Group I WRKY subfamily, which possesses two WRKY domains (WRKY I and II). A single G-to-A transition in the fifth intron of LP1 resulted in three disorganized splicing events in mutant plants. For each of these aberrant splice variants, the normal C2H2 motif in the WRKY II domain was completely disrupted, resulting in a loss-of-function mutation. LP1 mRNA was expressed in all of the tissues examined, with higher expression levels observed in inflorescences, roots, and seeds at the grain-filling stage. A subcellular localization analysis showed that LP1 predominantly accumulated in the nucleus, which confirmed its role as a transcriptional regulator. This study provides novel insights into the roles of WRKY proteins in regulating reproductive organ development in plants and may help to develop molecular markers associated with crop yields.
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Affiliation(s)
- Jishan Xiang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm Enhancement/College of Agronomy, Gansu Agricultural University, Lanzhou, People’s Republic of China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Chifeng University, Chifeng, People’s Republic of China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm Enhancement/College of Agronomy, Gansu Agricultural University, Lanzhou, People’s Republic of China
- * E-mail: (HJW); (XMD)
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- * E-mail: (HJW); (XMD)
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30
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Pant SR, Irigoyen S, Doust AN, Scholthof KBG, Mandadi KK. Setaria: A Food Crop and Translational Research Model for C 4 Grasses. FRONTIERS IN PLANT SCIENCE 2016; 7:1885. [PMID: 28018413 PMCID: PMC5156725 DOI: 10.3389/fpls.2016.01885] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/29/2016] [Indexed: 05/23/2023]
Affiliation(s)
- Shankar R. Pant
- Texas A&M AgriLife Research and Extension Center, Texas A&M University SystemWeslaco, TX, USA
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Texas A&M University SystemWeslaco, TX, USA
| | - Andrew N. Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State UniversityStillwater, OK, USA
| | - Karen-Beth G. Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University SystemWeslaco, TX, USA
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
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Huang P, Shyu C, Coelho CP, Cao Y, Brutnell TP. Setaria viridis as a Model System to Advance Millet Genetics and Genomics. FRONTIERS IN PLANT SCIENCE 2016; 7:1781. [PMID: 27965689 PMCID: PMC5124564 DOI: 10.3389/fpls.2016.01781] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/11/2016] [Indexed: 05/18/2023]
Abstract
Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.
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