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Saripalli G, Adhikari L, Amos C, Kibriya A, Ahmed HI, Heuberger M, Raupp J, Athiyannan N, Wicker T, Abrouk M, Wallace S, Hosseinirad S, Chhuneja P, Livesay J, Rawat N, Krattinger SG, Poland J, Tiwari V. Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits. Commun Biol 2023; 6:835. [PMID: 37573415 PMCID: PMC10423216 DOI: 10.1038/s42003-023-05189-z] [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: 01/24/2023] [Accepted: 07/26/2023] [Indexed: 08/14/2023] Open
Abstract
Einkorn wheat (Triticum monococcum) is an ancient grain crop and a close relative of the diploid progenitor (T. urartu) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars.
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Affiliation(s)
- Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20783, USA
| | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Cameron Amos
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Ashraf Kibriya
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sydney Wallace
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20783, USA
| | - Seyedali Hosseinirad
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20783, USA
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Janelle Livesay
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20783, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20783, USA
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Vijay Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20783, USA.
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Luo J, Huang W, Yan J, Fang Z, Ren M. The GzMYB-7D1 gene of Guizimai No.1 wheat is essential for seed anthocyanins accumulation and yield regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111293. [PMID: 35643602 DOI: 10.1016/j.plantsci.2022.111293] [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: 03/19/2022] [Accepted: 04/16/2022] [Indexed: 06/15/2023]
Abstract
Anthocyanins are antioxidants with important benefits for human health. Therefore, they have caught the interest of plant breeding programs. In this study, GzMYB-7D1, the key gene responsible for anthocyanin synthesis regulation in the purple Guizimai No.1 wheat, was transferred into Zhonghua 11 (ZH11) rice. Compared to wild-type ZH11, anthocyanin accumulated in the seeds of GzMYB-7D1 overexpressing lines. Furthermore, anthocyanin content kept increasing in the growing panicle of GzMYB-7D1 overexpressing lines, accumulating mostly in the rice glumes and grains during maturation, along with a concomitant steady decrease in chlorophyll. Genes related to anthocyanin synthesis, including OsPAL4, Os4CL3, OsCHS, OsDFR, OsANS, and Os3GT, exhibited much higher expression in the panicles of GzMYB-7D1 overexpressing lines than in those of wild-type ZH11. Interestingly, the grain yield per plant was significantly improved in GzMYB-7D1 overexpressing lines, as indicated by a higher tiller number per plant and branching of the secondary panicle, together with a significantly higher content of total amino acids. In conclusion, the GzMYB-7D1 gene of Guizimai No.1 wheat is essential for regulating seed anthocyanin levels and grain yield in rice, and could be applied to attain rice varieties with better nutritional value and improved yields.
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Affiliation(s)
- Jie Luo
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China
| | - Weiting Huang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China; Center of Applied Biotechnology, Wuhan University of Bioengineering, Wuhan 430415, China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing in Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Zhongming Fang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China; Center of Applied Biotechnology, Wuhan University of Bioengineering, Wuhan 430415, China.
| | - Mingjian Ren
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Agricultural Sciences, Guizhou University, Guiyang 550025, China.
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Li J, Yu Z, Zhang A, Yin Y, Tang L, Li G, Zhang P, Khan IA, Dundas I, Yang Z. Physical mapping of chromosome 7J and a purple coleoptile gene from Thinopyrum intermedium in the common wheat background. PLANTA 2021; 253:22. [PMID: 33399998 DOI: 10.1007/s00425-020-03552-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
A physical map of Thinopyrum intermedium chromosome 7J was constructed using translocation mapping, and a new seedling purple coleoptile gene was mapped to the bin of FL 0.35-0.63 of 7JS. Thinopyrum intermedium (2n = 6x = 42, JJJsJsStSt), a wild relative of common wheat, harbors numerous beneficial genes for wheat improvement. Previous studies showed that wheat-Th. intermedium partial amphiploid TAF46 and its derived addition line L1 had a purple coleoptile, which was derived from Th. intermedium chromosome 7J. To identify and physically map the purple coleoptile gene, 12 wheat-Th. intermedium 7J translocation lines were analyzed by sequential multicolor fluorescence in situ hybridization (mc-FISH), PCR-based landmark unique gene (PLUG) and intron targeting (IT) markers. A physical map of the 7J chromosome was constructed, consisting of eight chromosomal bins with 89 markers. Seedling evaluation of the coleoptile colors of all tested materials indicated that the purple coleoptile gene was located to the bin with a fraction length (FL) of 0.35-0.63 on chromosome 7JS. Furthermore, based on the syntenic relationships between Th. intermedium and wheat chromosomes, we developed a new chromosome 7J-specific EST-PCR marker from the chromosomal region corresponding to the purple coleoptile gene through the Triticeae multi-omics database. The approach of designing chromosome-specific markers has facilitated fine mapping of the Thinopyrum-specific purple coleoptile gene, and these translocation lines will be valuable for studying the function of the purple coleoptile gene in anthocyanin biosynthesis.
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Affiliation(s)
- Jianbo Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Zhihui Yu
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Ahui Zhang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Yan Yin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Lingrong Tang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Guangrong Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Imtiaz Ahmed Khan
- Faculty of Eastern Medicine, Hamdard University, Karachi, 74600, Sindh, Pakistan
| | - Ian Dundas
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia.
| | - Zujun Yang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China.
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Wang D, Cao D, Yao Y, Wang J, Li Z, Liu B. Understanding the chemical foundation and genetic mechanism of the black grain trait in quinoa by integrating metabolome and transcriptome analyses. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1822207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Dongxia Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Dong Cao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
- Laboratory of Wheat Quality Improvement, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
| | - Youhua Yao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Jinmin Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Zongren Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Baolong Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
- Laboratory of Wheat Quality Improvement, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
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Riaz B, Chen H, Wang J, Du L, Wang K, Ye X. Overexpression of Maize ZmC1 and ZmR Transcription Factors in Wheat Regulates Anthocyanin Biosynthesis in a Tissue-Specific Manner. Int J Mol Sci 2019; 20:E5806. [PMID: 31752300 PMCID: PMC6887777 DOI: 10.3390/ijms20225806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 11/17/2022] Open
Abstract
Maize ZmC1 and ZmR transcription factors belong to the MYB-type and bHLH families, respectively, and control anthocyanin biosynthesis. In this study, Agrobacterium-mediated transformation was used to generate transgenic wheat plants that overexpress ZmC1 and ZmR or both, with the objective of developing anthocyanin-enriched wheat germplasm. Three kinds of stable transgenic wheat lines were obtained. The integration of target genes in the transgenic wheat plants was confirmed by fluorescence in situ hybridization (FISH) analysis. We found that single overexpression of ZmC1 regulates pigmentation in the vegetative tissues such as coleoptiles, auricles, and stems. The single overexpression of ZmR controls the coloration in reproductive tissue like spikelets and seeds. The simultaneous overexpression of ZmC1 and ZmR showed the strongest pigmentation in almost all tissues. Furthermore, quantitative real-time PCR (qRT-PCR) analysis revealed that expression of the two transgenes, and of two conserved homologous and six associated structural genes involved in anthocyanin biosynthesis in wheat were greatly up-regulated in the transgenic plants. Similarly, quantitative analysis for anthocyanin amounts based on HPLC-MS also confirmed that the transgenic wheat plants with combined overexpression of ZmC1 and ZmR accumulated the highest quantity of pigment products. Moreover, developing seeds overexpressing ZmR exposed to light conditions showed up-regulated transcript levels of anthocyanin biosynthesis-related genes compared to dark exposure, which suggests an important role of light in regulating anthocyanin biosynthesis. This study provides a foundation for breeding wheat materials with high anthocyanin accumulation and understanding the mechanism of anthocyanin biosynthesis in wheat.
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Affiliation(s)
| | | | | | | | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (B.R.); (H.C.); (J.W.); (L.D.)
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (B.R.); (H.C.); (J.W.); (L.D.)
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Cao D, Fan J, Xi X, Zong Y, Wang D, Zhang H, Liu B. Transcriptome Analysis Identifies Key Genes Responsible for Red Coleoptiles in Triticum Monococcum. MOLECULES (BASEL, SWITZERLAND) 2019; 24:molecules24050932. [PMID: 30866466 PMCID: PMC6429503 DOI: 10.3390/molecules24050932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 11/16/2022]
Abstract
Red coleoptiles can help crops to cope with adversity and the key genes that are responsible for this trait have previously been isolated from Triticum aestivum, Triticum urartu, and Aegilops tauschii. This report describes the use of transcriptome analysis to determine the candidate gene that controls the trait for white coleoptiles in T. monococcum by screening three cultivars with white coleoptiles and two with red coleoptiles. Fifteen structural genes and two transcription factors that are involved in anthocyanin biosynthesis were identified from the assembled UniGene database through BLAST analysis and their transcript levels were then compared in white and red coleoptiles. The majority of the structural genes reflected lower transcript levels in the white than in the red coleoptiles, which implied that transcription factors related to anthocyanin biosynthesis could be candidate genes. The transcript levels of MYC transcription factor TmMYC-A1 were not significantly different between the white and red coleoptiles and all of the TmMYC-A1s contained complete functional domains. The deduced amino acid sequence of the MYB transcription factor TmMYB-A1 in red coleoptiles was homologous to TuMYB-A1, TaMYB-A1, TaMYB-B1, and TaMYB-D1, which control coleoptile color in corresponding species and contained the complete R2R3 MYB domain and the transactivation domain. TmMYB-a1 lost its two functional domains in white coleoptiles due to a single nucleotide deletion that caused premature termination at 13 bp after the initiation codon. Therefore, TmMYB-A1 is likely to be the candidate gene for the control of the red coleoptile trait, and its loss-of-function mutation leads to the white phenotype in T. monococcum.
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Affiliation(s)
- Dong Cao
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, Qinghai, China.
| | - Jiequn Fan
- Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Xingyuan Xi
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
| | - Yuan Zong
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, Qinghai, China.
| | - Dongxia Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, Qinghai, China.
| | - Huaigang Zhang
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
| | - Baolong Liu
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
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Jiang W, Liu T, Nan W, Jeewani DC, Niu Y, Li C, Wang Y, Shi X, Wang C, Wang J, Li Y, Gao X, Wang Z. Two transcription factors TaPpm1 and TaPpb1 co-regulate anthocyanin biosynthesis in purple pericarps of wheat. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2555-2567. [PMID: 29562292 PMCID: PMC5920291 DOI: 10.1093/jxb/ery101] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/08/2018] [Indexed: 05/04/2023]
Abstract
Purple pericarps of bread wheat (Triticum aestivum L.) are a useful source of dietary anthocyanins. Previous mapping results indicated that the purple pericarp trait is controlled by two complementary genes located on chromosomes 7D and 2A. However, the identity of the genes and the mechanisms by which they regulate the trait are unknown. In this study, two transcription factors were characterised as anthocyanin activators in purple pericarps: TaPpm1 (purple pericarp-MYB 1) and TaPpb1 (purple pericarp-bHLH 1). Three non-functional variants were detected in the coding sequence of TaPpm1 from non-purple seed lines, in which the function of TaPpm1 was destroyed either by insertion-induced frame shifts or truncated peptides. There were six 261-bp tandem repeats in the promoter region of TaPpb1 in the purple-grained varieties, while there was only one repeat unit present in the non-purple varieties. Furthermore, using yeast two-hybrid, dual luciferase, yeast one-hybrid, and transient assays, we were able to demonstrate that the interaction of TaPpm1 and TaPpb1 co-regulates the synthesis of anthocyanin. Overall, our results provide a better understanding of the molecular basis of anthocyanin synthesis in the wheat pericarp and indicate the existence of an integrated regulatory mechanism that controls production.
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Affiliation(s)
- Wenhui Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Tianxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenzhi Nan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Diddugodage Chamila Jeewani
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanlu Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunlian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | | | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Cong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiahuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Correspondence: or
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