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Lv G, Jin X, Wang H, Wang Y, Wu Q, Wu H, Jiang F, Ma Y, An Y, Zhang M, Guo Y, Li S. Cloning a novel reduced-height ( Rht) gene TaOSCA1.4 from a QTL in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1381243. [PMID: 38817937 PMCID: PMC11137288 DOI: 10.3389/fpls.2024.1381243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024]
Abstract
Reducing plant height (PH) is one of the core contents of the "Green Revolution", which began in the 1960s in wheat. A number of 27 reduced-height (Rht) genes have been identified and a great number of quantitative trait loci (QTLs) for PH have been mapped on all 21 chromosomes. Nonetheless, only several genes regulated PH have been cloned. In this study, we found the interval of QTL QPh-1B included an EST-SSR marker swes1079. According to the sequence of swes1079, we cloned the TaOSCA1.4 gene. We developed a CAPS marker to analyze the variation across a natural population. The result showed that the PH was significantly different between the two haplotypes of TaOSCA1.4-1B under most of the 12 environments and the average values of irrigation and rainfed conditions. This result further demonstrated that TaOSCA1.4 was associated with PH. Then, we validated the TaOSCA1.4 via RNAi technology. The average PHs of the wild-type (WT), RNAi lines 1 (Ri-1) and 2 (Ri-2) were 94.6, 83.6 and 79.2 cm, respectively, with significant differences between the WT and Ri-1 and Ri-2. This result indicated that the TaOSCA1.4 gene controls PH. TaOSCA1.4 is a constitutively expressed gene and its protein localizes to the cell membrane. TaOSCA1.4 gene is a member of the OSCA gene family, which regulates intracellular Ca2+ concentration. We hypothesized that knock down mutants of TaOSCA1.4 gene reduced regulatory ability of Ca2+, thus reducing the PH. Furthermore, the cell lengths of the knock down mutants are not significantly different than that of WT. We speculate that TaOSCA1.4 gene is not directly associated with gibberellin (GA), which should be a novel mechanism for a wheat Rht gene.
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Affiliation(s)
- Guangde Lv
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Tai’an Academy of Agricultural Science, Tai’an, China
| | - Xuemei Jin
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Rizhao Academy of Agricultural Science, Rizhao, China
| | - Hui Wang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Yijun Wang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Qun Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Haimeng Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | | | - Yanming Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yanrong An
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Mingxia Zhang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Ying Guo
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Sishen Li
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, China
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Liu X, Zheng S, Tian S, Si Y, Ma S, Ling HQ, Niu J. Natural variant of Rht27, a dwarfing gene, enhances yield potential in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:128. [PMID: 38733405 DOI: 10.1007/s00122-024-04636-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
KEY MESSAGE Discovery of Rht27, a dwarf gene in wheat, showed potential in enhancing grain yield by reducing plant height. Plant height plays a crucial role in crop architecture and grain yield, and semi-dwarf Reduced Height (Rht) alleles contribute to lodging resistance and were important in "Green Revolution." However, the use of these alleles is associated with some negative side effects in some environments, such as reduced coleoptile length, low nitrogen use efficiency, and reduced yield. Therefore, novel dwarf gene resources are needed to pave an alternative route to overcome these side effects. In this study, a super-dwarf mutant rht27 was obtained by the mutagenesis of G1812 (Triticum urartu, the progenitor of the A sub-genome of common wheat). Genetic analysis revealed that the dwarf phenotype was regulated by a single recessive genetic factor. The candidate region for Rht27 was narrowed to a 1.55 Mb region on chromosome 3, within which we found two potential candidate genes that showed polymorphisms between the mutant and non-mutagenized G1812. Furthermore, the natural variants and elite haplotypes of the two candidates were investigated in a natural population of common wheat. The results showed that the natural variants affect grain yield components, and the dwarf haplotypes show the potential in improving agronomic traits and grain yield. Although the mutation in Rht27 results in severe dwarf phenotype in T. urartu, the natural variants in common wheat showed desirable phenotype, which suggests that Rht27 has the potential to improve wheat yield by utilizing its weak allelic mutation or fine-tuning its expression level.
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Affiliation(s)
- Xiaolin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengwei Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, Hainan, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, Hainan, China.
| | - Jianqing Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Hainan Yazhou Bay Seed Lab, Sanya, 572024, Hainan, China.
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Zhou Y, Zhang H, Zhang S, Zhang J, Di H, Zhang L, Dong L, Lu Q, Zeng X, Liu X, Zhang N, Wang Z. The G protein-coupled receptor COLD1 promotes chilling tolerance in maize during germination. Int J Biol Macromol 2023; 253:126877. [PMID: 37716664 DOI: 10.1016/j.ijbiomac.2023.126877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023]
Abstract
The geographic range and yield of the staple crop maize (Zea mays L.) are both strongly limited by low-temperature conditions. One of the most economical and effective measures for improvement of maize production is chilling tolerance enhancement. In this study, a chilling-tolerance gene in maize, ZmCOLD1, was cloned and characterized. This gene encodes a G protein-coupled receptor that is localized to the plasma membrane and the endoplasmic reticulum. A single nucleotide polymorphism (SNP) in ZmCOLD1, SNP2738, was found to confer chilling tolerance and to have promoted maize adaptations during speciation from teosinte. Overexpression of the excellent haplotype ZmCOLD1Hap11 significantly enhanced chilling tolerance, whereas knocking down ZmCOLD1 increased sensitivity to low temperatures during the germination and seedling stages. ZmCOLD1 was associated with an influx of extracellular Ca2+, increases in abscisic acid content, and decreases in gibberellic acid and indole-3-acetic acid content under low temperatures during the germination stage. ZmCOLD1 interacted with the G protein α subunit ZmCT2 at the plasma membrane, and ZmCT2 interacted with ZmLanCL in the nucleus. These proteins are components of the chilling tolerance signaling pathway in maize that are triggered by abscisic acid and photosynthesis. These results offer novel strategies for improvement of chilling tolerance in key crop species.
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Affiliation(s)
- Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Hong Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Simeng Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Jiayue Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Ling Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Qing Lu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xianjun Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Naifu Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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Zheng Q, Yu Q, Yao W, Lv K, Zhang N, Xu W. Decoding VaCOLD1 Function in Grapevines: A Membrane Protein Enhancing Cold Stress Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19357-19371. [PMID: 38037352 DOI: 10.1021/acs.jafc.3c05101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
In globally cultivated grapevines, low-temperature stress poses a persistent challenge. Although COLD1 is recognized as a cold receptor in rice, its function in grapevine cold signaling is unclear. Here, we identified VaCOLD1, a transmembrane protein from the cold-tolerant Vitis amurensis Rupr, which is primarily located on plasma and endoplasmic reticulum membranes. Broadly expressed across multiple tissues, VaCOLD1 responds to various environmental stresses, particularly to cold. Its promoter contains distinct hormone- and stress-responsive elements, with GUS assays confirming widespread expression in Arabidopsis thaliana. Validation of interaction between VaCOLD1 and VaGPA1, together with their combined expression in yeast and grape calli, notably improved cold endurance. Overexpression of VaCOLD1 enhances cold tolerance in Arabidopsis by strengthening the CBF-COR signaling pathway. This is achieved through shielding against osmotic disturbances and modifying the expression of ABA-mediated genes. These findings emphasize the critical role of the VaCOLD1-VaGPA1 complex in mediating the response to cold stress via the CBF-COR pathway.
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Affiliation(s)
- Qiaoling Zheng
- School of Life Science, Ningxia University, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Qinhan Yu
- School of Life Science, Ningxia University, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Wenkong Yao
- College of Enology & Horticulture, Ningxia University, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Kai Lv
- College of Enology & Horticulture, Ningxia University, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Ningbo Zhang
- College of Enology & Horticulture, Ningxia University, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Weirong Xu
- School of Life Science, Ningxia University, Yinchuan, Ningxia 750021, China
- College of Enology & Horticulture, Ningxia University, Yinchuan, Ningxia 750021, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, Ningxia 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
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Hui J, Bai H, Lyu X, Ma S, Chen X, Li S. A pleiotropic QTL increased economic water use efficiency in bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1067590. [PMID: 36714690 PMCID: PMC9879270 DOI: 10.3389/fpls.2022.1067590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
Wheat is one of the most important food crops in the world and drought can severely impact on wheat productivity. The identification and deployment of genes for improved water use efficiency (WUE) can help alleviate yield loss under water limitation. In this study, a high-density genetic linkage map of wheat recombinant inbred lines (Ningchun 4 x Ningchun 27) containing 8751 specific locus amplified fragment (SLAF) tags (including 14757 SNPs), with a total map distance of 1685 cM and an average inter-marker map distance of 0.19 cM was constructed by SLAF-seq technology. The economic yield WUE and nine related traits under three water treatments was monitored over four years. The results showed that loci conditioning WUE were also associated with grain carbon isotope discrimination (CID), flag leaf chlorophyll content, plant height, 1000-grain weight, grain weight per spike and grain number per spike. One locus on chromosome 2B explained 26.3% WUE variation in multiple environments. Under good soil moisture conditions before flowering, the high CID genotype QWue.acn-2B Ningchun 27, was associated with WUE, high grain weight per spike, and kilo-grain weight. Under rain-fed conditions, the low CID genotype QWue.acn-2B Ningchun 4 tended to maintain more spike number and was associated with improved WUE and yield. The introduction of good chromosome fragments of QWue.acn-2B into elite lines by molecular marker assisted selection will boost up the cultivation of high-yield and water-saving wheat varieties.
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Affiliation(s)
- Jian Hui
- Ningxia Key Laboratory of Agricultural Biotechnology, Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia, China
| | | | | | | | | | - Shuhua Li
- Ningxia Key Laboratory of Agricultural Biotechnology, Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, Ningxia, China
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Liu H, Shi Z, Ma F, Xu Y, Han G, Zhang J, Liu D, An D. Identification and validation of plant height, spike length and spike compactness loci in common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:568. [PMID: 36471256 PMCID: PMC9724413 DOI: 10.1186/s12870-022-03968-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Plant height (PH), spike length (SL) and spike compactness (SCN) are important agronomic traits in wheat due to their strong correlations with lodging and yield. Thus, dissection of their genetic basis is essential for the improvement of plant architecture and yield potential in wheat breeding. The objective of this study was to map quantitative trait loci (QTL) for PH, SL and SCN in a recombinant inbred line (RIL) population derived from the cross 'PuBing3228 × Gao8901' (PG-RIL) and to evaluate the potential values of these QTL to improve yield. RESULTS In the current study, Five, six and ten stable QTL for PH, SL, and SCN, respectively, were identified in at least two individual environments. Five major QTL QPh.cas-5A.3, QPh.cas-6A, QSl.cas-6B.2, QScn.cas-2B.2 and QScn.cas-6B explained 5.58-25.68% of the phenotypic variation. Notably, two, three and three novel stable QTL for PH, SL and SCN were identified in this study, which could provide further insights into the genetic factors that shape PH and spike morphology in wheat. Conditional QTL analysis revealed that QTL for SCN were mainly affected by SL. Moreover, a Kompetitive Allele Specific PCR (KASP) marker tightly linked to stable major QTL QPh.cas-5A.3 was developed and verified using the PG-RIL population and a natural population. CONCLUSIONS Twenty-one stable QTL related to PH, SL, and SCN were identified. These stable QTL and the user-friendly marker KASP8750 will facilitate future studies involving positional cloning and marker-assisted selection in breeding.
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Affiliation(s)
- Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Zhipeng Shi
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feifei Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Yunfeng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Jinpeng Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, China.
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China.
- The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Ren R, Liu W, Yao M, Jia Y, Huang L, Li W, He X, Guan M, Liu Z, Guan C, Hua W, Xiong X, Qian L. Regional association and transcriptome analysis revealed candidate genes controlling plant height in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:69. [PMID: 37313473 PMCID: PMC10248621 DOI: 10.1007/s11032-022-01337-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/07/2022] [Indexed: 06/15/2023]
Abstract
Plant height is a key morphological trait in rapeseed, which not only plays an important role in determining plant architecture, but is also an important characteristic related to yield. Presently, the improvement of plant architecture is a major challenge in rapeseed breeding. This work was carried out to identify genetic loci related to plant height in rapeseed. In this study, a genome-wide association study (GWAS) of plant height was performed using a Brassica 60 K Illumina Infinium SNP array and 203 Brassica napus accessions. Eleven haplotypes containing important candidate genes were detected and significantly associated with plant height on chromosomes A02, A03, A05, A07, A08, C03, C06, and C09. Moreover, regional association analysis of 50 resequenced rapeseed inbred lines was used to further analyze these eleven haplotypes and revealed nucleotide variation in the BnFBR12-A08 and BnCCR1-C03 gene regions related to the phenotypic variation in plant height. Furthermore, coexpression network analysis showed that BnFBR12-A08 and BnCCR1-C03 were directly connected with hormone genes and transcription factors and formed a potential network regulating the plant height of rapeseed. Our results will aid in the development of haplotype functional markers to further improve plant height in rapeseed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01337-1.
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Affiliation(s)
- Rui Ren
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Min Yao
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Yuan Jia
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Luyao Huang
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wenqian Li
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Xin He
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Mei Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Zhongsong Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Chunyun Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xinghua Xiong
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128 China
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Xu Z, Wang R, Kong K, Begum N, Almakas A, Liu J, Li H, Liu B, Zhao T, Zhao T. An APETALA2/ethylene responsive factor transcription factor GmCRF4a regulates plant height and auxin biosynthesis in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:983650. [PMID: 36147224 PMCID: PMC9485679 DOI: 10.3389/fpls.2022.983650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/17/2022] [Indexed: 06/01/2023]
Abstract
Plant height is one of the key agronomic traits affecting soybean yield. The cytokinin response factors (CRFs), as a branch of the APETALA2/ethylene responsive factor (AP2/ERF) super gene family, have been reported to play important roles in regulating plant growth and development. However, their functions in soybean remain unknown. This study characterized a soybean CRF gene named GmCRF4a by comparing the performance of the homozygous Gmcrf4a-1 mutant, GmCRF4a overexpression (OX) and co-silencing (CS) lines. Phenotypic analysis showed that overexpression of GmCRF4a resulted in taller hypocotyls and epicotyls, more main stem nodes, and higher plant height. While down-regulation of GmCRF4a conferred shorter hypocotyls and epicotyls, as well as a reduction in plant height. The histological analysis results demonstrated that GmCRF4a promotes epicotyl elongation primarily by increasing cell length. Furthermore, GmCRF4a is required for the expression of GmYUCs genes to elevate endogenous auxin levels, which may subsequently enhance stem elongation. Taken together, these observations describe a novel regulatory mechanism in soybean, and provide the basis for elucidating the function of GmCRF4a in auxin biosynthesis pathway and plant heigh regulation in plants.
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Affiliation(s)
- Zhiyong Xu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruikai Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Keke Kong
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Aisha Almakas
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jun Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyu Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tao Zhao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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9
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Yang G, Zhang Y, Wei X, Cui L, Nie X. Genetic Diversity of Transcription Factor Genes in Triticum and Mining for Promising Haplotypes for Beneficial Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:899292. [PMID: 35873966 PMCID: PMC9305608 DOI: 10.3389/fpls.2022.899292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
Transcription factor (TF) is a class of the sequence-specific DNA-binding proteins that modulate the transcription of target genes, and thus regulate their expressions. Variations in TF are the crucial determinants for phenotypic traits. Although much progress has been made in the functions of TF genes in wheat, one of the most important staple crops globally, the diversity of TF genes in wheat and its progenitors are not well understood, especially the agronomically promising haplotypes have not yet been characterized. Here, we identified a total of 6,023 TF genes from hexaploid wheat through a genome-search method and classified them into 59 gene families based on the conserved domain. The characteristics and dN/dS values of these genes showed evidently selective effects. Based on re-sequencing data, we found a strong genetic bottleneck among these TF genes on A and D subgenomes while no found in B subgenome during wheat domestication. Combined with selective signals and known QTLs on the whole genome, 21 TF genes were preliminarily found to be associated with yield-related traits. The haplotype frequency of these TF genes was further investigated in bread wheat and its progenitors and 13 major haplotypes were the casual loci related to key traits. Finally, the tissue-specific TF genes were also identified using RNA-seq analysis. This study provided insights into the diversity and evolution of TF genes and the identified TF genes and excellent haplotypes associating with traits will contribute to wheat genetic improvement.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Ying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xinyu Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Licao Cui
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
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10
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Gawande ND, Hamiditabar Z, Brunetti SC, Gulick PJ. Characterization of the heterotrimeric G protein gene families in Triticum aestivum and related species. 3 Biotech 2022; 12:99. [PMID: 35463045 PMCID: PMC8938547 DOI: 10.1007/s13205-022-03156-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/01/2022] [Indexed: 11/27/2022] Open
Abstract
This study characterizes the heterotrimeric G protein gene families in Triticum aestivum, their tissue-specific expression patterns during development and in response to biotic and abiotic stress conditions. There are three Gα genes, three Gβ and 12 Gγ genes, totaling 18 genes encoding heterotrimeric G proteins in the hexaploid wheat genome. Each haploid genome of the hexaploid T. aestivum has a single gene encoding the α subunit of the heterotrimeric G protein complex, GA1, a single Gβ and four Gγ genes. Each gene has three homeologous copies in the A, B and D genomes. The physical interaction between the Gβ (Gpb) and two Gγ subunits, Gpg1 and Gpg2, was shown through bimolecular fluorescence complementation (BiFC). The gene expression in response to biotic and abiotic stresses showed both up-regulation and down-regulation of members of the gene families. Gγ2-B and Gγ2-D are significantly upregulated during heat stress, GA1-D is upregulated by cold stress and Gγ1-A and Gγ1-D were upregulated by Fusarium graminearum inoculation in a F. graminearum resistant cultivar. This suggests that these members may play roles in biotic and abiotic signaling pathways and the roles of these genes within these pathways need further investigation. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03156-9.
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Affiliation(s)
- Nilesh D. Gawande
- Biology Department, Concordia University, 7141 Sherbrooke W, Montreal, QB H4B 1R6 Canada
| | - Zeynab Hamiditabar
- Biology Department, Concordia University, 7141 Sherbrooke W, Montreal, QB H4B 1R6 Canada
| | - Sabrina C. Brunetti
- Biology Department, Concordia University, 7141 Sherbrooke W, Montreal, QB H4B 1R6 Canada
| | - Patrick J. Gulick
- Biology Department, Concordia University, 7141 Sherbrooke W, Montreal, QB H4B 1R6 Canada
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11
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Xie Y, Zeng W, Wang C, Xu D, Guo H, Xiong H, Fang H, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Fine Mapping of qd1, a Dominant Gene that Regulates Stem Elongation in Bread Wheat. Front Genet 2021; 12:793572. [PMID: 34912380 PMCID: PMC8667865 DOI: 10.3389/fgene.2021.793572] [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: 10/12/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Stem elongation is a critical phase for yield determination and, as a major trait, is targeted for manipulation for improvement in bread wheat (Triticum aestivum L.). In a previous study, we characterized a mutant showing rapid stem elongation but with no effect on plant height at maturity. The present study aimed to finely map the underlying mutated gene, qd1, in this mutant. By analyzing an F2 segregating population consisting of 606 individuals, we found that the qd1 gene behaved in a dominant manner. Moreover, by using the bulked segregant RNA sequencing (BSR-seq)-based linkage analysis method, we initially mapped the qd1 gene to a 13.55 Mb region on chromosome 4B (from 15.41 to 28.96 Mb). This result was further confirmed in F2 and BC3F2 segregating populations. Furthermore, by using transcriptome sequencing data, we developed 14 Kompetitive Allele-Specific PCR (KASP) markers and then mapped the qd1 gene to a smaller and more precise 5.08 Mb interval from 26.80 to 31.88 Mb. To develop additional markers to finely map the qd1 gene, a total of 4,481 single-nucleotide polymorphisms (SNPs) within the 5.08 Mb interval were screened, and 25 KASP markers were developed based on 10x-depth genome resequencing data from both wild-type (WT) and mutant plants. The qd1 gene was finally mapped to a 1.33 Mb interval from 28.86 to 30.19 Mb on chromosome 4B. Four candidate genes were identified in this region. Among them, the expression pattern of only TraesCS4B02G042300 in the stems was concurrent with the stem development of the mutant and WT. The qd1 gene could be used in conjunction with molecular markers to manipulate stem development in the future.
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Affiliation(s)
- Yongdun Xie
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Weiwei Zeng
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Chaojie Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Daxing Xu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Hanshun Fang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Luxiang Liu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
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12
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Sun Z, Yue Z, Liu H, Ma K, Li C. Microbial-Assisted Wheat Iron Biofortification Using Endophytic Bacillus altitudinis WR10. Front Nutr 2021; 8:704030. [PMID: 34414208 PMCID: PMC8368724 DOI: 10.3389/fnut.2021.704030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/02/2021] [Indexed: 12/20/2022] Open
Abstract
Microbial-assisted biofortification attracted much attention recently due to its sustainable and eco-friendly nature for improving nutrient content in wheat. An endophytic strain Bacillus altitudinis WR10, which showed sophistical regulation of iron (Fe) homeostasis in wheat seedlings, inspired us to test its potential for enhancing Fe biofortification in wheat grain. In this study, assays in vitro indicated that WR10 has versatile plant growth-promoting (PGP) traits and bioinformatic analysis predicted its non-pathogenicity. Two inoculation methods, namely, seed soaking and soil spraying, with 107 cfu/ml WR10 cells were applied once before sowing of wheat (Triticum aestivum L. cv. Zhoumai 36) in the field. After wheat maturation, evaluation of yield and nutrients showed a significant increase in the mean number of kernels per spike (KPS) and the content of total nitrogen (N), potassium (K), and Fe in grains. At the grain filling stage, the abundance of Bacillus spp. and the content of N, K, and Fe in the root, the stem, and the leaf were also increased in nearly all tissues, except Fe in the stem and the leaf. Further correlation analysis revealed a positive relationship between the total abundance of Bacillus spp. and the content of N, K, and Fe in grains. Seed staining confirmed the enhanced accumulation of Fe, especially in the embryo and the endosperm. Finally, using a hydroponic coculture model, qPCR quantification indicated effective colonization, internalization, translocation, and replication of strain WR10 in wheat within 48 h. Collectively, strain WR10 assisted successful Fe biofortification in wheat in the field, laying a foundation for further large-scale investigation of its applicability and effectiveness.
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Affiliation(s)
- Zhongke Sun
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.,College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Zonghao Yue
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Keshi Ma
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Chengwei Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
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13
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Xue Y, Wang J, Mao X, Li C, Li L, Yang X, Hao C, Chang X, Li R, Jing R. Association Analysis Revealed That TaPYL4 Genes Are Linked to Plant Growth Related Traits in Multiple Environment. FRONTIERS IN PLANT SCIENCE 2021; 12:641087. [PMID: 34456932 PMCID: PMC8387097 DOI: 10.3389/fpls.2021.641087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Abscisic acid (ABA), one of phytohormones, plays an important regulatory role in plant growth and development. ABA receptor PYL4 (pyrabactin resistance 1-like 4) was previously detected to be involved in plant response to a variety of stresses. TaPYL4 overexpression could enhance wheat (Triticum aestivum) drought resistance. In order to further investigate TaPYL4's role in regulating development of other major agronomic traits in wheat, genes of TaPYL4-2A, TaPYL4-2B, and TaPYL4-2D were cloned from wheat, respectively. Polymorphism analysis on TaPYL4 sequences revealed that encoding regions of the three genes were highly conserved, without any SNP (single nucleotide polymorphism) presence. However, nine SNPs and four SNPs were identified in the promoter regions of TaPYL4-2A and TaPYL4-2B, respectively. Functional molecular markers were developed based on these polymorphisms, which were then used to scan a natural population of 323 common wheat accessions for correlation analysis between genotype and the target phenotypic traits. Both TaPYL4-2A and TaPYL4-2B markers were significantly correlated with plant growth-related traits under multiple environments (well-watered, drought and heat stress treatments). The additive effects of TaPYL4-2A and TaPYL4-2B were verified by the combinational haplotype (Hap-AB1∼Hap-AB4) effects determined from field data. Cis-acting elements were analyzed in the promoters of TaPYL4-2A and TaPYL4-2B, showing that a TGA-element bound by ARFs (auxin response factors) existed only in Hap-2A-1 of TaPYL4-2A. Gene expression assays indicated that TaPYL4-2A was constitutively expressed in various tissues, with higher expression in Hap-2A-1 genotypes than in Hap-2A-2 materials. Notably, TaARF4 could act as TaPYL4-2A transcription activator in Hap-2A-1 materials, but not in Hap-2A-2 genotypes. Analysis of geographic distribution and temporal frequency of haplotypes indicated that Hap-AB1 was positively selected in wheat breeding in China. Therefore, TaPYL4-2A and TaPYL4-2B could be a valuable target gene in wheat genetic improvement to develop the ideal plant architecture.
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Affiliation(s)
- Yinghong Xue
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xi Yang
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Chenyang Hao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Runzhi Li
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Jin YN, Cui ZH, Ma K, Yao JL, Ruan YY, Guo ZF. Characterization of ZmCOLD1, novel GPCR-Type G Protein genes involved in cold stress from Zea mays L. and the evolution analysis with those from other species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:619-632. [PMID: 33854288 PMCID: PMC7981359 DOI: 10.1007/s12298-021-00966-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Maize is one of the most vital staple crops worldwide. G proteins modulate plentiful signaling pathways, and G protein-coupled receptor-type G proteins (GPCRs) are highly conserved membrane proteins in plants. However, researches on maize G proteins and GPCRs are scarce. In this study, we identified three novel GPCR-Type G Protein (GTG) genes from chromosome 10 (Chr 10) in maize, designated as ZmCOLD1-10A, ZmCOLD1-10B and ZmCOLD1-10C. Their amino acid sequences had high similarity to TaCOLD1 from wheat and OsCOLD1 from rice. They contained the basic characteristics of GTG/COLD1 proteins, including GPCR-like topology, the conserved hydrophilic loop (HL) domain, DUF3735 (domain of unknown function 3735) domain, GTPase-activating domain, and ATP/GTP-binding domain. Subcellular localization analyses of ZmCOLD1 proteins suggested that ZmCOLD1 proteins localized on plasma membrane (PM) and endoplasmic reticulum (ER). Furthermore, amino acid sequence alignment verified the conservation of the key 187th amino acid T in maize and other wild maize-relative species. Evolutionary relationship among plants GTG/COLD1 proteins family displayed strong group-specificity. Expression analysis indicated that ZmCOLD1-10A was cold-induced and inhibited by light. Together, these results suggested that ZmCOLD1 genes had potential value to improve cold tolerance and to contribute crops growth and molecular breeding.
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Affiliation(s)
- Ya-Nan Jin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
- College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, 028000 China
| | - Zhen-hai Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Ke Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Jia-Lu Yao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Yan-Ye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
| | - Zhi-Fu Guo
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866 China
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15
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Cao J, Liu K, Song W, Zhang J, Yao Y, Xin M, Hu Z, Peng H, Ni Z, Sun Q, Du J. Pleiotropic function of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE gene TaSPL14 in wheat plant architecture. PLANTA 2021; 253:44. [PMID: 33481116 PMCID: PMC7822796 DOI: 10.1007/s00425-020-03531-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/06/2020] [Indexed: 05/04/2023]
Abstract
MAIN CONCLUSION The function of SQUAMOSA PROMOTER-BINDING PROTEIN-BOX gene TaSPL14 in wheat is similar to that of OsSPL14 in rice in regulating plant height, panicle length, spikelet number, and thousand-grain weight of wheat, but differs during tiller development. TaSPL14 may regulate spike development via ethylene-response gene EIN3-LIKE 1 (TaEIL1), ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 2.11 (TaRAP2.11), and ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR 1 (TaERF1), but not DENSE AND ERECT PANICLE 1 (TaDEP1) in wheat. The SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE gene OsSPL14 from rice is considered to be a major determinant of ideal plant architecture consisting of few unproductive tillers, more grains per spike, and high resistance of stems to lodging. However, the function of its orthologous gene, TaSPL14, in wheat is unknown. Here, we reported the functional similarities and differences between TaSPL14 and OsSPL14. Similar to OsSPL14 knock-outs in rice, wheat TaSPL14 knock-out plants exhibited decreased plant height, panicle length, spikelet number, and thousand-grain weight. In contrast to OsSPL14, however, TaSPL14 did not affect tiller number. Transcriptome analysis revealed that the expression of genes related to ethylene response was significantly decreased in young spikes of TaSPL14 knock-out lines as compared with wild type. TaSPL14 directly binds to the promoters of the ethylene-response genes TaEIL1, TaRAP2.11, and TaERF1, and promotes their expression, suggesting that TaSPL14 might regulate wheat spike development via the ethylene-response pathway. The elucidation of TaSPL14 will contribute to understanding of the molecular mechanisms that underlie wheat plant architecture.
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Affiliation(s)
- Jie Cao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Kaiye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Jianing Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 People’s Republic of China
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16
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Zhang L, Guo X, Qin Y, Feng B, Wu Y, He Y, Wang A, Zhu J. The chilling tolerance divergence 1 protein confers cold stress tolerance in processing tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:34-46. [PMID: 32193092 DOI: 10.1016/j.plaphy.2020.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
Tomato (Lycopersicon esculentum Mill [Solanum lycopersicum L.].) is an important food material and cash crop, as well as a model plant for genetic evolution and molecular biology research. However, as a cold-sensitive crop originating from the tropics, the growth and development of tomato is often affected by low temperature stress. Therefore, how processing tomatoes resist this type of stress has important theoretical and practical significance. In this study, the LeCOLD1 gene was cloned from processing tomato. Subcellular localization analysis showed that LeCOLD1 was located in the plasma membrane. Real-time quantitative PCR analysis showed that LeCOLD1 was highly expressed in roots. Drought, salt and low temperatures induced the expression of COLD1. Overexpression and RNA interference vectors of LeCOLD1 were constructed and were transformed into tomato by the Agrobacterium-mediated method, and then obtaining transgenic tomato plants. It was found that LeCOLD1 increased the height of processing tomato plants and increased the length of their roots. In addition, overexpression of LeCOLD1 significantly improved the cold resistance of the plants. Overexpressing LeCOLD1 in tomato plants reduced the damage to the cell membrane, accumulation of ROS and photoinhibition of PSII, and maintained the high activity of antioxidant enzymes and the content of osmotic regulators. Further analysis revealed that during low temperature stress, the cells maintained high levels of antioxidant enzyme activity by regulating the transcription of the genes encoding these enzymes. The results show that overexpressing LeCOLD1 in tomato increases the plants' resistance to low temperatures, and that reducing LeCOLD1 expression makes the plants more sensitive to low temperatures.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Xinyong Guo
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Yujie Qin
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Bin Feng
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Yating Wu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Yaling He
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Aiying Wang
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Jianbo Zhu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China.
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17
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Liu H, Li H, Hao C, Wang K, Wang Y, Qin L, An D, Li T, Zhang X. TaDA1, a conserved negative regulator of kernel size, has an additive effect with TaGW2 in common wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1330-1342. [PMID: 31733093 PMCID: PMC7152612 DOI: 10.1111/pbi.13298] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/29/2019] [Accepted: 11/05/2019] [Indexed: 05/18/2023]
Abstract
Kernel size is an important trait determining cereal yields. In this study, we cloned and characterized TaDA1, a conserved negative regulator of kernel size in wheat (Triticum aestivum). The overexpression of TaDA1 decreased the size and weight of wheat kernels, while its down-regulation using RNA interference (RNAi) had the opposite effect. Three TaDA1-A haplotypes were identified in Chinese wheat core collections, and a haplotype association analysis showed that TaDA1-A-HapI was significantly correlated with the production of larger kernels and higher kernel weights in modern Chinese cultivars. The haplotype effect resulted from a difference in TaDA1-A expression levels between genotypes, with TaDA1-A-HapI resulting in lower TaDA1-A expression levels. This favourable haplotype was found having been positively selected during wheat breeding over the last century. Furthermore, we demonstrated that TaDA1-A physically interacts with TaGW2-B. The additive effects of TaDA1-A and TaGW2-B on kernel weight were confirmed not only by the phenotypic enhancement arising from the simultaneous down-regulation of TaDA1 and TaGW2 expression, but also by the combinational haplotype effects estimated from multi-environment field data from 348 wheat cultivars. A comparative proteome analysis of developing transgenic and wild-type grains indicated that TaDA1 and TaGW2 are involved in partially overlapping but relatively independent protein regulatory networks. Thus, we have identified an important gene controlling kernel size in wheat and determined its interaction with other genes regulating kernel weight, which could have beneficial applications in wheat breeding.
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Affiliation(s)
- Hong Liu
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Center for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangHebeiChina
| | - Huifang Li
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ke Wang
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yamei Wang
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Lin Qin
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Diaoguo An
- Center for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangHebeiChina
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Agronomy CollegeGansu Agriculture UniversityLanzhou, GansuChina
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18
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Wang K, Gong Q, Ye X. Recent developments and applications of genetic transformation and genome editing technologies in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1603-1622. [PMID: 31654081 DOI: 10.1007/s00122-019-03464-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Wheat (Triticum aestivum) is a staple crop across the world and plays a remarkable role in food supplying security. Over the past few decades, basic and applied research on wheat has lagged behind other cereal crops due to the complex and polyploid genome and difficulties in genetic transformation. A breakthrough called as PureWheat was made in the genetic transformation of wheat in 2014 in Asia, leading to a noticeable progress of wheat genome editing. Due to this great achievement, it is predicated that wheat biotechnology revolution is arriving. Genome editing technologies using zinc finger nucleases, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats-associated endonucleases (CRISR/Cas) are becoming powerful tools for crop modification which can help biologists and biotechnologists better understand the processes of mutagenesis and genomic alteration. Among the three genome editing systems, CRISR/Cas has high specificity and activity, and therefore it is widely used in genetic engineering. Generally, the genome editing technologies depend on an efficient genetic transformation system. In this paper, we summarize recent progresses and applications on genetic transformation and genome editing in wheat. We also examine the future aspects of genetic transformation and genome editing. We believe that the technologies for wheat efficient genetic engineering and functional studies will become routine with the emergence of high-quality genomic sequences.
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Affiliation(s)
- Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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19
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Chen Z, Cheng X, Chai L, Wang Z, Bian R, Li J, Zhao A, Xin M, Guo W, Hu Z, Peng H, Yao Y, Sun Q, Ni Z. Dissection of genetic factors underlying grain size and fine mapping of QTgw.cau-7D in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:149-162. [PMID: 31570967 DOI: 10.1007/s00122-019-03447-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/21/2019] [Indexed: 05/26/2023]
Abstract
Thirty environmentally stable QTL controlling grain size and/or plant height were identified, among which QTgw.cau-7D was delimited into the physical interval of approximately 4.4 Mb. Grain size and plant height (PHT) are important agronomic traits in wheat breeding. To dissect the genetic basis of these traits, we conducted a quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs). In total, 30 environmentally stable QTL for thousand grain weight (TGW), grain length (GL), grain width (GW) and PHT were detected. Notably, one major pleiotropic QTL on chromosome arm 3DS explained the highest phenotypic variance for TGW, GL and PHT, and two stable QTL (QGw.cau-4B and QGw.cau-7D) on chromosome arms 4BS and 7DS contributed greater effects for GW. Furthermore, the stable QTL controlling grain size (QTgw.cau-7D and QGw.cau-7D) were delimited into the physical interval of approximately 4.4 Mb harboring 56 annotated genes. The elite NILs of QTgw.cau-7D increased TGW by 12.79-21.75% and GW by 4.10-8.47% across all three environments. Collectively, these results provide further insight into the genetic basis of TGW, GL, GW and PHT, and the fine-mapped QTgw.cau-7D will be an attractive target for positional cloning and marker-assisted selection in wheat breeding programs.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xuejiao Cheng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhihui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Ruolin Bian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Jiang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population. G3-GENES GENOMES GENETICS 2019; 9:4045-4057. [PMID: 31611346 PMCID: PMC6893202 DOI: 10.1534/g3.119.400353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (<15°) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 data points from ∼16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30-45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5-10 chilling tolerance loci explaining 20-41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and Dw3) that were under strong directional selection in the US during the 20th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.
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