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Li W, Li Y, Shi H, Wang H, Ji K, Zhang L, Wang Y, Dong Y, Li Y. ZmMPK6, a mitogen-activated protein kinase, regulates maize kernel weight. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3287-3299. [PMID: 38457358 DOI: 10.1093/jxb/erae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
Kernel weight is a critical agronomic trait in maize production. Many genes are related to kernel weight but only a few of them have been applied to maize breeding and cultivation. Here, we identify a novel function of maize mitogen-activated protein kinase 6 (ZmMPK6) in the regulation of maize kernel weight. Kernel weight was reduced in zmmpk6 mutants and increased in ZmMPK6-overexpressing lines. In addition, starch granules, starch content, protein content, and grain-filling characteristics were also affected by the ZmMPK6 expression level. ZmMPK6 is mainly localized in the nucleus and cytoplasm, widely distributed across various tissues, and is expressed during kernel development, which is consistent with its role in kernel weight. Thus, these results provide new insights into the role of ZmMPK6, a mitogen-activated protein kinase, in maize kernel weight, and could be applied to further molecular breeding for kernel quality and yield in maize.
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Affiliation(s)
- Wenyu Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Yayong Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Huiyue Shi
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Han Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Kun Ji
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Long Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Yan Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Yongbin Dong
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
| | - Yuling Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Longzi Lake Campus, Zhengzhou, Henan 450046, China
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Liu Y, Li H, Liu J, Wang Y, Jiang C, Zhou Z, Zhuo L, Li W, Fernie AR, Jackson D, Yan J, Luo Y. The additive function of YIGE2 and YIGE1 in regulating maize ear length. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38804053 DOI: 10.1111/tpj.16851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Ear length (EL) is a key trait that greatly contributes to yield in maize. Although dozens of EL quantitative trait loci have been mapped, very few causal genes have been cloned, and the molecular mechanisms remain largely unknown. Our previous study showed that YIGE1 is involved in sugar and auxin pathways to regulate ear inflorescence meristem (IM) development and thus affects EL in maize. Here, we reveal that YIGE2, the paralog of YIGE1, regulates maize ear development and EL through auxin pathway. Knockout of YIGE2 causes a significant decrease of auxin level, IM length, floret number, EL, and grain yield. yige1 yige2 double mutants had even shorter IM and ears implying that these two genes redundantly regulate IM development and EL. The genes controlling auxin levels are differential expressed in yige1 yige2 double mutants, leading to lower auxin level. These results elucidated the critical role of YIGE2 and the redundancy between YIGE2 and YIGE1 in maize ear development, providing a new genetic resource for maize yield improvement.
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Affiliation(s)
- Yu Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Huinan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jie Liu
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ziqi Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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3
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Wang Y, Luo Y, Guo X, Li Y, Yan J, Shao W, Wei W, Wei X, Yang T, Chen J, Chen L, Ding Q, Bai M, Zhuo L, Li L, Jackson D, Zhang Z, Xu X, Yan J, Liu H, Liu L, Yang N. A spatial transcriptome map of the developing maize ear. NATURE PLANTS 2024; 10:815-827. [PMID: 38745100 DOI: 10.1038/s41477-024-01683-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024]
Abstract
A comprehensive understanding of inflorescence development is crucial for crop genetic improvement, as inflorescence meristems give rise to reproductive organs and determine grain yield. However, dissecting inflorescence development at the cellular level has been challenging owing to a lack of specific marker genes to distinguish among cell types, particularly in different types of meristems that are vital for organ formation. In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of the developing maize ear primordium, identifying 12 cell types, including 4 newly defined cell types found mainly in the inflorescence meristem. By extracting the meristem components for detailed clustering, we identified three subtypes of meristem and validated two MADS-box genes that were specifically expressed at the apex of determinate meristems and involved in stem cell determinacy. Furthermore, by integrating single-cell RNA transcriptomes, we identified a series of spatially specific networks and hub genes that may provide new insights into the formation of different tissues. In summary, this study provides a valuable resource for research on cereal inflorescence development, offering new clues for yield improvement.
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Affiliation(s)
- Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Yunfu Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiali Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenwen Shao
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjie Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaofeng Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- China National GeneBank, Shenzhen, China
| | - Tao Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- China National GeneBank, Shenzhen, China
| | - Jing Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- China National GeneBank, Shenzhen, China
| | - Lihua Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Qian Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Minji Bai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Li Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China.
- Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Shenzhen, China.
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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Bi Y, Jiang F, Zhang Y, Li Z, Kuang T, Shaw RK, Adnan M, Li K, Fan X. Identification of a novel marker and its associated laccase gene for regulating ear length in tropical and subtropical maize lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:94. [PMID: 38578443 PMCID: PMC10997716 DOI: 10.1007/s00122-024-04587-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
KEY MESSAGE This study revealed the identification of a novel gene, Zm00001d042906, that regulates maize ear length by modulating lignin synthesis and reported a molecular marker for selecting maize lines with elongated ears. Maize ear length has garnered considerable attention due to its high correlation with yield. In this study, six maize inbred lines of significant importance in maize breeding were used as parents. The temperate maize inbred line Ye107, characterized by a short ear, was crossed with five tropical or subtropical inbred lines featuring longer ears, creating a multi-parent population displaying significant variations in ear length. Through genome-wide association studies and mutation analysis, the A/G variation at SNP_183573532 on chromosome 3 was identified as an effective site for discriminating long-ear maize. Furthermore, the associated gene Zm00001d042906 was found to correlate with maize ear length. Zm00001d042906 was functionally annotated as a laccase (Lac4), which showed activity and influenced lignin synthesis in the midsection cells of the cob, thereby regulating maize ear length. This study further reports a novel molecular marker and a new gene that can assist maize breeding programs in selecting varieties with elongated ears.
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Affiliation(s)
- Yaqi Bi
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650093, China
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Ziwei Li
- Dehong Teachers' College, Luxi, 678400, China
| | - Tianhui Kuang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Ranjan K Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Muhammad Adnan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Kunzhi Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650093, China.
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
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5
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Xu D, Zeng L, Wang L, Yang DL. Rice requires a chromatin remodeler for Polymerase IV-small interfering RNA production and genomic immunity. PLANT PHYSIOLOGY 2024; 194:2149-2164. [PMID: 37992039 DOI: 10.1093/plphys/kiad624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
Transgenes are often spontaneously silenced, which hinders the application of genetic modifications to crop breeding. While gene silencing has been extensively studied in Arabidopsis (Arabidopsis thaliana), the molecular mechanism of transgene silencing remains elusive in crop plants. We used rice (Oryza sativa) plants silenced for a 35S::OsGA2ox1 (Gibberellin 2-oxidase 1) transgene to isolate five elements mountain (fem) mutants showing restoration of transgene expression. In this study, we isolated multiple fem2 mutants defective in a homolog of Required to Maintain Repression 1 (RMR1) of maize (Zea mays) and CLASSY (CLSY) of Arabidopsis. In addition to failing to maintain transgene silencing, as occurs in fem3, in which mutation occurs in NUCLEAR RNA POLYMERASE E1 (OsNRPE1), the fem2 mutant failed to establish transgene silencing of 35S::OsGA2ox1. Mutation in FEM2 eliminated all RNA POLYMERASE IV (Pol-IV)-FEM1/OsRDR2 (RNA-DEPENDENT RNA POLYMERASE 2)-dependent small interfering RNAs (siRNAs), reduced DNA methylation on genome-wide scale in rice seedlings, caused pleiotropic developmental defects, and increased disease resistance. Simultaneous mutation in 2 FEM2 homologous genes, FEM2-Like 1 (FEL1) and FEL2, however, did not affect DNA methylation and rice development and disease resistance. The predominant expression of FEM2 over FEL1 and FEL2 in various tissues was likely caused by epigenetic states. Overexpression of FEL1 but not FEL2 partially rescued hypomethylation of fem2, indicating that FEL1 maintains the cryptic function. In summary, FEM2 is essential for establishing and maintaining gene silencing; moreover, FEM2 is solely required for Pol IV-FEM1 siRNA biosynthesis and de novo DNA methylation.
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Affiliation(s)
- Dachao Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Longjun Zeng
- Institute of Crop Sciences, Yichun Academy of Sciences, Yichun, 336000 Jiangxi, China
| | - Lili Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Liu L, Zhan J, Yan J. Engineering the future cereal crops with big biological data: toward an intelligence-driven breeding by design. J Genet Genomics 2024:S1673-8527(24)00058-4. [PMID: 38531485 DOI: 10.1016/j.jgg.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.
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Affiliation(s)
- Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jimin Zhan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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7
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Feng X, Guan H, Wen Y, Zhou H, Xing X, Li Y, Zheng D, Wang Q, Zhang W, Xiong H, Hu Y, Jia L, Luo S, Zhang X, Guo W, Wu F, Xu J, Liu Y, Lu Y. Profiling the selected hotspots for ear traits in two maize-teosinte populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:74. [PMID: 38451289 DOI: 10.1007/s00122-024-04554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
KEY MESSAGE Eight selected hotspots related to ear traits were identified from two maize-teosinte populations. Throughout the history of maize cultivation, ear-related traits have been selected. However, little is known about the specific genes involved in shaping these traits from their origins in the wild progenitor, teosinte, to the characteristics observed in modern maize. In this study, five ear traits (kernel row number [KRN], ear length [EL], kernel number per row [KNR], cob diameter [CD], and ear diameter [ED]) were investigated, and eight quantitative trait loci (QTL) hotspots were identified in two maize-teosinte populations. Notably, our findings revealed a significant enrichment of genes showing a selection signature and expressed in the ear in qbdCD1.1, qbdCD5.1, qbpCD2.1, qbdED1.1, qbpEL1.1, qbpEL5.1, qbdKNR1.1, and qbdKNR10.1, suggesting that these eight QTL are selected hotspots involved in shaping the maize ear. By combining the results of the QTL analysis with data from previous genome-wide association study (GWAS) involving two natural panels, we identified eight candidate selected genes related to KRN, KNR, CD, and ED. Among these, considering their expression pattern and sequence variation, Zm00001d025111, encoding a WD40/YVTN protein, was proposed as a positive regulator of KNR. This study presents a framework for understanding the genomic distribution of selected loci crucial in determining ear-related traits.
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Affiliation(s)
- Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Huarui Guan
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Ying Wen
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Hanmei Zhou
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Xiaobin Xing
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yinzhi Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Dan Zheng
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Weixiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Hao Xiong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yue Hu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Li Jia
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Shuang Luo
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Xuemei Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Wei Guo
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, 611130, Sichuan, China.
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
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8
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Xie S, Luo H, Huang W, Jin W, Dong Z. Striking a growth-defense balance: Stress regulators that function in maize development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:424-442. [PMID: 37787439 DOI: 10.1111/jipb.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/01/2023] [Indexed: 10/04/2023]
Abstract
Maize (Zea mays) cultivation is strongly affected by both abiotic and biotic stress, leading to reduced growth and productivity. It has recently become clear that regulators of plant stress responses, including the phytohormones abscisic acid (ABA), ethylene (ET), and jasmonic acid (JA), together with reactive oxygen species (ROS), shape plant growth and development. Beyond their well established functions in stress responses, these molecules play crucial roles in balancing growth and defense, which must be finely tuned to achieve high yields in crops while maintaining some level of defense. In this review, we provide an in-depth analysis of recent research on the developmental functions of stress regulators, focusing specifically on maize. By unraveling the contributions of these regulators to maize development, we present new avenues for enhancing maize cultivation and growth while highlighting the potential risks associated with manipulating stress regulators to enhance grain yields in the face of environmental challenges.
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Affiliation(s)
- Shiyi Xie
- Maize Engineering and Technology Research Center of Hunan Province, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Hongbing Luo
- Maize Engineering and Technology Research Center of Hunan Province, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Wei Huang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiwei Jin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- Tianjin Key Laboratory of Intelligent Breeding of Major Crops, Fresh Corn Research Center of BTH, College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, 300384, China
| | - Zhaobin Dong
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
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9
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Zhang D, Gan Y, Le L, Pu L. Epigenetic variation in maize agronomical traits for breeding and trait improvement. J Genet Genomics 2024:S1673-8527(24)00028-6. [PMID: 38310944 DOI: 10.1016/j.jgg.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, China
| | - Yujun Gan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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10
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Joshi P, Soni P, Sharma V, Manohar SS, Kumar S, Sharma S, Pasupuleti J, Vadez V, Varshney RK, Pandey MK, Puppala N. Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut. Genes (Basel) 2024; 15:140. [PMID: 38397130 PMCID: PMC10888419 DOI: 10.3390/genes15020140] [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: 11/14/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.
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Affiliation(s)
- Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Pooja Soni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Sampath Kumar
- Agricultural Research Station, Andhra Pradesh Agricultural University, Anantapur 515591, India;
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Janila Pasupuleti
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Vincent Vadez
- Institut de Recherche pour le Development (IRD), Université de Montpellier, Unité Mixte de Recherche Diversité et Adaptation des Espèces (UMR DIADE), 34394 Montpellier, France;
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Naveen Puppala
- Agricultural Science Center at Clovis, New Mexico State University, Clovis, NM 88101, USA
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11
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Zhang X, Sun J, Zhang Y, Li J, Liu M, Li L, Li S, Wang T, Shaw RK, Jiang F, Fan X. Hotspot Regions of Quantitative Trait Loci and Candidate Genes for Ear-Related Traits in Maize: A Literature Review. Genes (Basel) 2023; 15:15. [PMID: 38275597 PMCID: PMC10815758 DOI: 10.3390/genes15010015] [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: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past three decades. This review aims to (1) comprehensively summarize and analyze previous studies on QTLs associated with these eight ear-related traits and identify hotspot bin regions located on maize chromosomes and key candidate genes associated with the ear-related traits and (2) compile major and stable QTLs and QTL clusters from various mapping populations and mapping methods and techniques providing valuable insights for fine mapping, gene cloning, and breeding for high-yield and high-quality maize. Previous research has demonstrated that QTLs for ear-related traits are distributed across all ten chromosomes in maize, and the phenotypic variation explained by a single QTL ranged from 0.40% to 36.76%. In total, 23 QTL hotspot bins for ear-related traits were identified across all ten chromosomes. The most prominent hotspot region is bin 4.08 on chromosome 4 with 15 QTLs related to eight ear-related traits. Additionally, this study identified 48 candidate genes associated with ear-related traits. Out of these, five have been cloned and validated, while twenty-eight candidate genes located in the QTL hotspots were defined by this study. This review offers a deeper understanding of the advancements in QTL mapping and the identification of key candidates associated with eight ear-related traits. These insights will undoubtedly assist maize breeders in formulating strategies to develop higher-yield maize varieties, contributing to global food security.
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Affiliation(s)
- Xingjie Zhang
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Jiachen Sun
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.S.); (T.W.)
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Jinfeng Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Meichen Liu
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Linzhuo Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Shaoxiong Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (X.Z.); (J.L.); (M.L.); (L.L.); (S.L.)
| | - Tingzhao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (J.S.); (T.W.)
| | - Ranjan Kumar Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (F.J.)
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12
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Shen X, Xiao B, Kaderbek T, Lin Z, Tan K, Wu Q, Yuan L, Lai J, Zhao H, Song W. Dynamic transcriptome landscape of developing maize ear. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1856-1870. [PMID: 37731154 DOI: 10.1111/tpj.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/19/2023] [Accepted: 08/26/2023] [Indexed: 09/22/2023]
Abstract
Seed number and harvesting ability in maize (Zea mays L.) are primarily determined by the architecture of female inflorescence, namely the ear. Therefore, ear morphogenesis contributes to grain yield and as such is one of the key target traits during maize breeding. However, the molecular networks of this highly dynamic and complex grain-bearing inflorescence remain largely unclear. As a first step toward characterizing these networks, we performed a high-spatio-temporal-resolution investigation of transcriptomes using 130 ear samples collected from developing ears with length from 0.1 mm to 19.0 cm. Comparisons of these mRNA populations indicated that these spatio-temporal transcriptomes were clearly separated into four distinct stages stages I, II, III, and IV. A total of 23 793 genes including 1513 transcription factors (TFs) were identified in the investigated developing ears. During the stage I of ear morphogenesis, 425 genes were predicted to be involved in a co-expression network established by eight hub TFs. Moreover, 9714 ear-specific genes were identified in the seven kinds of meristems. Additionally, 527 genes including 59 TFs were identified as especially expressed in ear and displayed high temporal specificity. These results provide a high-resolution atlas of gene activity during ear development and help to unravel the regulatory modules associated with the differentiation of the ear in maize.
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Affiliation(s)
- Xiaomeng Shen
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Bing Xiao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Tangnur Kaderbek
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Zhen Lin
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Kaiwen Tan
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Qingyu Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Lixing Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
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13
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Wu T, Shen P, Dai J, Ma Y, Feng Y. A Pathway to Assess Genetic Variation of Wheat Germplasm by Multidimensional Traits with Digital Images. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0119. [PMID: 38026469 PMCID: PMC10665127 DOI: 10.34133/plantphenomics.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023]
Abstract
In this paper, a new pathway was proposed to assess the germplasm genetic variation by multidimensional traits of wheat seeds generated from digital images. A machine vision platform was first established to reconstruct wheat germplasm 3D model from omnidirectional image sequences of wheat seeds. Then, multidimensional traits were conducted from the wheat germplasm 3D model, including seed length, width, thickness, surface area, volume, maximum projection area, roundness, and 2 new defined traits called cardioid-derived area and the index of adjustment (J index). To assess genetic variation of wheat germplasm, phenotypic coefficients of variation (PCVs), analysis of variance (ANOVA), clustering, and the defined genetic variation factor (GVF) were calculated using the extracted morphological traits of 15 wheat accessions comprising 13 offspring and 2 parents. The measurement accuracy of 3D reconstruction model is demonstrated by the correlation coefficient (R) and root mean square errors (RMSEs). Results of PCVs among all the traits show importance of multidimensional traits, as seed volume (22.4%), cardioid-derived area (16.97%), and maximum projection area (14.67%). ANOVA shows a highly significance difference among all accessions. The results of GVF innovatively reflect the connection between genotypic variance and phenotypic traits from parents to offspring. Our results confirmed that extracting multidimensional traits from digital images is a promising high-throughput and cost-efficient pathway that can be included as a valuable approach in genetic variation assessment, and it can provide useful information for genetic improvement, preservation, and evaluation of wheat germplasm.
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Affiliation(s)
- Tingting Wu
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi 712100, China
| | - Peng Shen
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianlong Dai
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuntao Ma
- College of Land Science and Technology,
China Agricultural University, Beijing 100091, China
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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14
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Sharma D, Kumari A, Sharma P, Singh A, Sharma A, Mir ZA, Kumar U, Jan S, Parthiban M, Mir RR, Bhati P, Pradhan AK, Yadav A, Mishra DC, Budhlakoti N, Yadav MC, Gaikwad KB, Singh AK, Singh GP, Kumar S. Meta-QTL analysis in wheat: progress, challenges and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:247. [PMID: 37975911 DOI: 10.1007/s00122-023-04490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.
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Affiliation(s)
- Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Anupma Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anshu Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Sofora Jan
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - M Parthiban
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Reyazul Rouf Mir
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Pradeep Bhati
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Anjan Kumar Pradhan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Aakash Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Neeraj Budhlakoti
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh C Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Kiran B Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India.
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15
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Mirza Z, Jonwal S, Saini H, Sinha AK, Gupta M. Unraveling the molecular aspects of iron-mediated OsWRKY76 signaling under arsenic stress in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108136. [PMID: 37897891 DOI: 10.1016/j.plaphy.2023.108136] [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: 09/27/2023] [Accepted: 10/22/2023] [Indexed: 10/30/2023]
Abstract
Arsenic (As) is a significant environmental element that restricts the growth and production of rice plants. Although the role of iron (Fe) to sequester As in rice is widely known, the molecular mechanism regarding As-Fe interaction remains opaque. Here, we show the differential response of two rice varieties (Ratna and Lalat) in terms of their morphological and biochemical changes in the presence of As and Fe. These results together with in-silico screening, gene expression analysis, and protein-protein interaction studies suggest the role of OsWRKY76 in Fe-mediated As stress alleviation. When OsWRKY76 is activated by MAPK signaling, it inhibits the gene expression of Fe transporters OsIRT1 and OsYSL2, which reduces the amount of Fe accumulated. However, MAPK signaling and OsWRKY76 remain down-regulated during Fe supplementation with As, which subsequently encourages the up-regulation of OsIRT1 and OsYSL2. This results in greater Fe content and decreased As accumulation and toxicity. The lower H2O2 and SOD, CAT, and APX activities were likewise seen under the As + Fe condition. Overall, results revealed the molecular aspects of Fe-mediated control of OsWRKY76 signaling and showed that Ratna is a more As tolerant variety than Lalat. Lalat, however, performs better in As stress due to the presence of Fe.
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Affiliation(s)
- Zainab Mirza
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 25, India
| | - Sarvesh Jonwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Himanshu Saini
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 25, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Meetu Gupta
- Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 25, India.
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16
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Li T, Yang H, Zhang X, Zhu L, Zhang J, Wei N, Li R, Dong Y, Feng Z, Zhang X, Xue J, Xu S. Genetic architecture of ear traits based on association mapping and co-expression networks in maize inbred lines and hybrids. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:78. [PMID: 37928364 PMCID: PMC10624778 DOI: 10.1007/s11032-023-01426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Ear traits are key contributors to grain yield in maize; therefore, exploring their genetic basis facilitates the improvement of grain yield. However, the underlying molecular mechanisms of ear traits remain obscure in both inbred lines and hybrids. Here, two association panels, respectively, comprising 203 inbred lines (IP) and 246 F1 hybrids (HP) were employed to identify candidate genes for six ear traits. The IP showed higher phenotypic variation and lower phenotypic mean than the HP for all traits, except ear tip-barrenness length. By conducting a genome-wide association study (GWAS) across multiple environments, 101 and 228 significant single-nucleotide polymorphisms (SNPs) associated with six ear traits were identified in the IP and HP, respectively. Of these significant SNPs identified in the HP, most showed complete-incomplete dominance and over-dominance effects for each ear trait. Combining a gene co-expression network with GWAS results, 186 and 440 candidate genes were predicted in the IP and HP, respectively, including known ear development genes ids1 and sid1. Of these, nine candidate genes were detected in both populations and expressed in maize ear and spikelet tissues. Furthermore, two key shared genes (GRMZM2G143330 and GRMZM2G171139) in both populations were found to be significantly associated with ear traits in the maize Goodman diversity panel with high-density variations. These findings advance our knowledge of the genetic architecture of ear traits between inbred lines and hybrids and provide a valuable resource for the genetic improvement of ear traits in maize. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01426-9.
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Affiliation(s)
- Ting Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Haoxiang Yang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xiaojun Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Liangjia Zhu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Jun Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Ningning Wei
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Ranran Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Yuan Dong
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Zhiqian Feng
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xinghua Zhang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100 Shaanxi China
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17
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Uba CU, Oselebe HO, Tesfaye AA, Abtew WG. Association mapping in bambara groundnut [Vigna subterranea (L.) Verdc.] reveals loci associated with agro-morphological traits. BMC Genomics 2023; 24:593. [PMID: 37803263 PMCID: PMC10557193 DOI: 10.1186/s12864-023-09684-9] [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: 03/12/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) are important for the acceleration of crop improvement through knowledge of marker-trait association (MTA). This report used DArT SNP markers to successfully perform GWAS on agro-morphological traits using 270 bambara groundnut [Vigna subterranea (L.) Verdc.] landraces sourced from diverse origins. The study aimed to identify marker traits association for nine agronomic traits using GWAS and their candidate genes. The experiment was conducted at two different locations laid out in alpha lattice design. The cowpea [Vigna unguiculata (L.) Walp.] reference genome (i.e. legume genome most closely related to bambara groundnut) assisted in the identification of candidate genes. RESULTS The analyses showed that linkage disequilibrium was found to decay rapidly with an average genetic distance of 148 kb. The broadsense heritability was relatively high and ranged from 48.39% (terminal leaf length) to 79.39% (number of pods per plant). The GWAS identified a total of 27 significant marker-trait associations (MTAs) for the nine studied traits explaining 5.27% to 24.86% of phenotypic variations. Among studied traits, the highest number of MTAs was obtained from seed coat colour (6) followed by days to flowering (5), while the least is days to maturity (1), explaining 5.76% to 11.03%, 14.5% to 19.49%, and 11.66% phenotypic variations, respectively. Also, a total of 17 candidate genes were identified, varying in number for different traits; seed coat colour (6), days to flowering (3), terminal leaf length (2), terminal leaf width (2), number of seed per pod (2), pod width (1) and days to maturity (1). CONCLUSION These results revealed the prospect of GWAS in identification of SNP variations associated with agronomic traits in bambara groundnut. Also, its present new opportunity to explore GWAS and marker assisted strategies in breeding of bambara groundnut for acceleration of the crop improvement.
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Affiliation(s)
- Charles U Uba
- Department of Horticulture and Plant Science, Jimma University, Jimma, Ethiopia.
| | | | - Abush A Tesfaye
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Wosene G Abtew
- Department of Horticulture and Plant Science, Jimma University, Jimma, Ethiopia
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Dong X, Luo H, Bi W, Chen H, Yu S, Zhang X, Dai Y, Cheng X, Xing Y, Fan X, Zhu Y, Guo Y, Meng D. Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm. BMC PLANT BIOLOGY 2023; 23:470. [PMID: 37803280 PMCID: PMC10557216 DOI: 10.1186/s12870-023-04473-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Genomic imprinting refers to a subset of genes that are expressed from only one parental allele during seed development in plants. Studies on genomic imprinting have revealed that intraspecific variations in genomic imprinting expression exist in naturally genetic varieties. However, there have been few studies on the functional analysis of allele-specific imprinted genes. RESULTS Here, we generated three reciprocal crosses among the B73, Mo17 and CAU5 inbred lines. Based on the transcriptome-wide analysis of allele-specific expression using RNA sequencing technology, 305 allele-specific imprinting genes (ASIGs) were identified in embryos, and 655 ASIGs were identified in endosperms from three maize F1 hybrids. Of these ASIGs, most did not show consistent maternal or paternal bias between the same tissue from different hybrids or different tissues from one hybrid cross. By gene ontology (GO) analysis, five and eight categories of GO exhibited significantly higher functional enrichments for ASIGs identified in embryo and endosperm, respectively. These functional categories indicated that ASIGs are involved in intercellular nutrient transport, signaling pathways, and transcriptional regulation of kernel development. Finally, the mutation and overexpression of one ASIG (Zm305) affected the length and width of the kernel. CONCLUSION In this study, our data will be helpful in gaining further knowledge of genes exhibiting allele-specific imprinting patterns in seeds. The gain- and loss-of-function phenotypes of ASIGs associated with agronomically important seed traits provide compelling evidence for ASIGs as crucial targets to optimize seed traits in crop plants.
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Affiliation(s)
- Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Haishan Luo
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Wenjing Bi
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hanyu Chen
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaoyu Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yuxin Dai
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xipeng Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yupeng Xing
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaoqin Fan
- Manas Agricultural Experimental Station of Xinjiang Academy of Agricultural Sciences, Changji, 832200, Xinjiang, China
| | - Yanbin Zhu
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd, Shenyang, Liaoning, 110164, China
| | - Yanling Guo
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd, Shenyang, Liaoning, 110164, China
| | - Dexuan Meng
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
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19
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Tang H, Zhang R, Wang M, Xie X, Zhang L, Zhang X, Liu C, Sun B, Qin F, Yang X. QTL mapping for flowering time in a maize-teosinte population under well-watered and water-stressed conditions. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:67. [PMID: 37601731 PMCID: PMC10435433 DOI: 10.1007/s11032-023-01413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023]
Abstract
Maize grain yield can be greatly reduced when flowering time coincides with drought conditions, which delays silking and consequently increases the anthesis-silking interval. Although the genetic basis of delayed flowering time under water-stressed conditions has been elucidated in maize-maize populations, little is known in this regard about maize-teosinte populations. Here, 16 quantitative trait loci (QTL) for three flowering-time traits, namely days to anthesis, days to silk, and the anthesis-silking interval, were identified in a maize-teosinte introgression population under well-watered and water-stressed conditions; these QTL explained 3.98-32.61% of phenotypic variations. Six of these QTL were considered to be sensitive to drought stress, and the effect of any individual QTL was small, indicating the complex genetic nature of drought resistance in maize. To resolve which genes underlie the six QTL, 11 candidate genes were identified via colocalization analysis of known associations with flowering-time-related drought traits. Among the 11 candidate genes, five were found to be differentially expressed in response to drought stress or under selection during maize domestication, and thus represented the most likely candidates underlying the drought-sensitive QTL. The results lay a foundation for further studies of the genetic mechanisms of drought resistance and provide valuable information for improving drought resistance during maize breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01413-0.
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Affiliation(s)
- Huaijun Tang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193 China
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Renyu Zhang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193 China
| | - Min Wang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193 China
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Lei Zhang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Xuan Zhang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193 China
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Baocheng Sun
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193 China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193 China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193 China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193 China
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20
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Sharma A, Sharma D, Verma SK. A systematic in silico report on iron and zinc proteome of Zea mays. FRONTIERS IN PLANT SCIENCE 2023; 14:1166720. [PMID: 37662157 PMCID: PMC10469895 DOI: 10.3389/fpls.2023.1166720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/10/2023] [Indexed: 09/05/2023]
Abstract
Zea mays is an essential staple food crop across the globe. Maize contains macro and micronutrients but is limited in essential mineral micronutrients such as Fe and Zn. Worldwide, serious health concerns have risen due to the deficiencies of essential nutrients in human diets, which rigorously jeopardizes economic development. In the present study, the systematic in silico approach has been used to predict Fe and Zn binding proteins from the whole proteome of maize. A total of 356 and 546 putative proteins have been predicted, which contain sequence and structural motifs for Fe and Zn ions, respectively. Furthermore, the functional annotation of these predicted proteins, based on their domains, subcellular localization, gene ontology, and literature support, showed their roles in distinct cellular and biological processes, such as metabolism, gene expression and regulation, transport, stress response, protein folding, and proteolysis. The versatile roles of these shortlisted putative Fe and Zn binding proteins of maize could be used to manipulate many facets of maize physiology. Moreover, in the future, the predicted Fe and Zn binding proteins may act as relevant, novel, and economical markers for various crop improvement programs.
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Affiliation(s)
- Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India
| | - Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, District Kangra, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi, Delhi, India
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21
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Wang H, Liu S, Ma S, Wang Y, Yang H, Liu J, Li M, Cui X, Liang S, Cheng Q, Shen H. Characterization of the Molecular Events Underlying the Establishment of Axillary Meristem Region in Pepper. Int J Mol Sci 2023; 24:12718. [PMID: 37628899 PMCID: PMC10454251 DOI: 10.3390/ijms241612718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Plant architecture is a major motif of plant diversity, and shoot branching patterns primarily determine the aerial architecture of plants. In this study, we identified an inbred pepper line with fewer lateral branches, 20C1734, which was free of lateral branches at the middle and upper nodes of the main stem with smooth and flat leaf axils. Successive leaf axil sections confirmed that in normal pepper plants, for either node n, Pn (Primordium n) < 1 cm and Pn+1 < 1 cm were the critical periods between the identification of axillary meristems and the establishment of the region, whereas Pn+3 < 1 cm was fully developed and formed a completely new organ. In 20C1734, the normal axillary meristematic tissue region establishment and meristematic cell identity confirmation could not be performed on the axils without axillary buds. Comparative transcriptome analysis revealed that "auxin-activated signaling pathway", "response to auxin", "response to abscisic acid", "auxin biosynthetic process", and the biosynthesis of the terms/pathways, such as "secondary metabolites", were differentially enriched in different types of leaf axils at critical periods of axillary meristem development. The accuracy of RNA-seq was verified using RT-PCR for some genes in the pathway. Several differentially expressed genes (DEGs) related to endogenous phytohormones were targeted, including several genes of the PINs family. The endogenous hormone assay showed extremely high levels of IAA and ABA in leaf axils without axillary buds. ABA content in particular was unusually high. At the same time, there is no regular change in IAA level in this type of leaf axils (normal leaf axils will be accompanied by AM formation and IAA content will be low). Based on this, we speculated that the contents of endogenous hormones IAA and ABA in 20C1734 plant increased sharply, which led to the abnormal expression of genes in related pathways, which affected the formation of Ams in leaf axils in the middle and late vegetative growth period, and finally, nodes without axillary buds and side branches appeared.
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Affiliation(s)
- Haoran Wang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Sujun Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Shijie Ma
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Yun Wang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Hanyu Yang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Jiankun Liu
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Mingxuan Li
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiangyun Cui
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Sun Liang
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
| | - Qing Cheng
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
| | - Huolin Shen
- Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China; (H.W.); (S.L.); (S.M.); (Y.W.); (H.Y.); (J.L.); (M.L.); (X.C.); (S.L.)
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
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22
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Duan H, Xue Z, Ju X, Yang L, Gao J, Sun L, Xu S, Li J, Xiong X, Sun Y, Wang Y, Zhang X, Ding D, Zhang X, Tang J. The genetic architecture of prolificacy in maize revealed by association mapping and bulk segregant analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:182. [PMID: 37555969 DOI: 10.1007/s00122-023-04434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 08/10/2023]
Abstract
KEY MESSAGE Here, we revealed maize prolificacy highly correlated with domestication and identified a causal gene ZmEN1 located in one novel QTL qGEN261 that regulating maize prolificacy by using multiple-mapping methods. The development of maize prolificacy (EN) is crucial for enhancing yield and breeding specialty varieties. To achieve this goal, we employed a genome-wide association study (GWAS) to analyze the genetic architecture of EN in maize. Using 492 inbred lines with a wide range of EN variability, our results demonstrated significant differences in genetic, environmental, and interaction effects. The broad-sense heritability (H2) of EN was 0.60. Through GWAS, we identified 527 significant single nucleotide polymorphisms (SNPs), involved 290 quantitative trait loci (QTL) and 806 genes. Of these SNPs, 18 and 509 were classified as major effect loci and minor loci, respectively. In addition, we performed a bulk segregant analysis (BSA) in an F2 population constructed by a few-ears line Zheng58 and a multi-ears line 647. Our BSA results identified one significant QTL, qBEN1. Importantly, combining the GWAS and BSA, four co-located QTL, involving six genes, were identified. Three of them were expressed in vegetative meristem, shoot tip, internode and tip of ear primordium, with ZmEN1, encodes an unknown auxin-like protein, having the highest expression level in these tissues. It suggested that ZmEN1 plays a crucial role in promoting axillary bud and tillering to encourage the formation of prolificacy. Haplotype analysis of ZmEN1 revealed significant differences between different haplotypes, with inbred lines carrying hap6 having more EN. Overall, this is the first report about using GWAS and BSA to dissect the genetic architecture of EN in maize, which can be valuable for breeding specialty maize varieties and improving maize yield.
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Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Zhengjie Xue
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xiaolong Ju
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Lu Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, People's Republic of China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Yan Wang
- Zhucheng Mingjue Tender Company Limited, Weifang, People's Republic of China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, People's Republic of China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, People's Republic of China.
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23
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Li C, Li Y, Song G, Yang D, Xia Z, Sun C, Zhao Y, Hou M, Zhang M, Qi Z, Wang B, Wang H. Gene expression and expression quantitative trait loci analyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:772-787. [PMID: 37186341 DOI: 10.1111/tpj.16260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.
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Affiliation(s)
- Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, 010070, China
| | - Yaoyao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Guangshu Song
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Di Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changhe Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuelei Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingyue Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhi Qi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, 010070, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
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24
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Dong Z, Wang Y, Bao J, Li Y, Yin Z, Long Y, Wan X. The Genetic Structures and Molecular Mechanisms Underlying Ear Traits in Maize ( Zea mays L.). Cells 2023; 12:1900. [PMID: 37508564 PMCID: PMC10378120 DOI: 10.3390/cells12141900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Maize (Zea mays L.) is one of the world's staple food crops. In order to feed the growing world population, improving maize yield is a top priority for breeding programs. Ear traits are important determinants of maize yield, and are mostly quantitatively inherited. To date, many studies relating to the genetic and molecular dissection of ear traits have been performed; therefore, we explored the genetic loci of the ear traits that were previously discovered in the genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping studies, and refined 153 QTL and 85 quantitative trait nucleotide (QTN) clusters. Next, we shortlisted 19 common intervals (CIs) that can be detected simultaneously by both QTL mapping and GWAS, and 40 CIs that have pleiotropic effects on ear traits. Further, we predicted the best possible candidate genes from 71 QTL and 25 QTN clusters that could be valuable for maize yield improvement.
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Affiliation(s)
- Zhenying Dong
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Yanbo Wang
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Jianxi Bao
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Ya’nan Li
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Zechao Yin
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Yan Long
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
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25
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Xiong X, Li J, Su P, Duan H, Sun L, Xu S, Sun Y, Zhao H, Chen X, Ding D, Zhang X, Tang J. Genetic dissection of maize (Zea mays L.) chlorophyll content using multi-locus genome-wide association studies. BMC Genomics 2023; 24:384. [PMID: 37430212 DOI: 10.1186/s12864-023-09504-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The chlorophyll content (CC) is a key factor affecting maize photosynthetic efficiency and the final yield. However, its genetic basis remains unclear. The development of statistical methods has enabled researchers to design and apply various GWAS models, including MLM, MLMM, SUPER, FarmCPU, BLINK and 3VmrMLM. Comparative analysis of their results can lead to more effective mining of key genes. RESULTS The heritability of CC was 0.86. Six statistical models (MLM, BLINK, MLMM, FarmCPU, SUPER, and 3VmrMLM) and 1.25 million SNPs were used for the GWAS. A total of 140 quantitative trait nucleotides (QTNs) were detected, with 3VmrMLM and MLM detecting the most (118) and fewest (3) QTNs, respectively. The QTNs were associated with 481 genes and explained 0.29-10.28% of the phenotypic variation. Additionally, 10 co-located QTNs were detected by at least two different models or methods, three co-located QTNs were identified in at least two different environments, and six co-located QTNs were detected by different models or methods in different environments. Moreover, 69 candidate genes within or near these stable QTNs were screened based on the B73 (RefGen_v2) genome. GRMZM2G110408 (ZmCCS3) was identified by multiple models and in multiple environments. The functional characterization of this gene indicated the encoded protein likely contributes to chlorophyll biosynthesis. In addition, the CC differed significantly between the haplotypes of the significant QTN in this gene, and CC was higher for haplotype 1. CONCLUSION This study's results broaden our understanding of the genetic basis of CC, mining key genes related to CC and may be relevant for the ideotype-based breeding of new maize varieties with high photosynthetic efficiency.
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Affiliation(s)
- Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Pingping Su
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haidong Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoyang Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
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26
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Zhu J, Wei X, Yin C, Zhou H, Yan J, He W, Yan J, Li H. ZmEREB57 regulates OPDA synthesis and enhances salt stress tolerance through two distinct signalling pathways in Zea mays. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37326336 DOI: 10.1111/pce.14644] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
In plant, APETALA2/ethylene-responsive factor (AP2/ERF)-domain transcription factors are important in regulating abiotic stress tolerance. In this study, ZmEREB57 encoding a AP2/ERF transcription factor was identified and its function was investigated in maize. ZmEREB57 is a nuclear protein with transactivation activity induced by several abiotic stress types. Furthermore, two CRISPR/Cas9 knockout lines of ZmEREB57 showed enhanced sensitivity to saline conditions, whereas the overexpression of ZmEREB57 increased salt tolerance in maize and Arabidopsis. DNA affinity purification sequencing (DAP-Seq) analysis revealed that ZmEREB57 notably regulates target genes by binding to promoters containing an O-box-like motif (CCGGCC). ZmEREB57 directly binds to the promoter of ZmAOC2 involved in the synthesis of 12-oxo-phytodienoic acid (OPDA) and jasmonic acid (JA). Transcriptome analysis revealed that several genes involved in regulating stress and redox homeostasis showed differential expression patterns in OPDA- and JA-treated maize seedlings exposed to salt stress compared to those treated with salt stress alone. Analysis of mutants deficient in the biosynthesis of OPDA and JA revealed that OPDA functions as a signalling molecule in the salt response. Our results indicate that ZmEREB57 involves in salt tolerance by regulating OPDA and JA signalling and confirm early observations that OPDA signalling functions independently of JA signalling.
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Affiliation(s)
- Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xuening Wei
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Chaoshu Yin
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Hui Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Jiahui Yan
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, China
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27
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Basu U, Parida SK. Restructuring plant types for developing tailor-made crops. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1106-1122. [PMID: 34260135 DOI: 10.1111/pbi.13666] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 05/27/2023]
Abstract
Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.
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Affiliation(s)
- Udita Basu
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Swarup K Parida
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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28
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Adel S, Carels N. Plant Tolerance to Drought Stress with Emphasis on Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112170. [PMID: 37299149 DOI: 10.3390/plants12112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 06/12/2023]
Abstract
Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.
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Affiliation(s)
- Sarah Adel
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development for Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, Brazil
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29
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Wang Y, Bi Y, Jiang F, Shaw RK, Sun J, Hu C, Guo R, Fan X. Mapping and Functional Analysis of QTL for Kernel Number per Row in Tropical and Temperate-Tropical Introgression Lines of Maize ( Zea mays L.). Curr Issues Mol Biol 2023; 45:4416-4430. [PMID: 37232750 DOI: 10.3390/cimb45050281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F7 recombinant inbred line (RIL) populations were created using a temperate-tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids.
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Affiliation(s)
- Yuling Wang
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Ranjan Kumar Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jiachen Sun
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650500, China
| | - Can Hu
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
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30
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Muthamil S, Kim HY, Jang HJ, Lyu JH, Shin UC, Go Y, Park SH, Lee HG, Park JH. Understanding the relationship between cancer associated cachexia and hypoxia-inducible factor-1. Biomed Pharmacother 2023; 163:114802. [PMID: 37146421 DOI: 10.1016/j.biopha.2023.114802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/07/2023] Open
Abstract
Cancer-associated cachexia (CAC) is a multifactorial disorder characterized by an unrestricted loss of body weight as a result of muscle and adipose tissue atrophy. Cachexia is influenced by several factors, including decreased metabolic activity and food intake, an imbalance between energy uptake and expenditure, excessive catabolism, and inflammation. Cachexia is highly associated with all types of cancers responsible for more than half of cancer-related mortalities worldwide. In healthy individuals, adipose tissue significantly regulates energy balance and glucose homeostasis. However, in metastatic cancer patients, CAC occurs mainly because of an imbalance between muscle protein synthesis and degradation which are organized by certain extracellular ligands and associated signaling pathways. Under hypoxic conditions, hypoxia-inducible factor-1 (HIF-1α) accumulated and translocated to the nucleus and activate numerous genes involved in cell survival, invasion, angiogenesis, metastasis, metabolic reprogramming, and cancer stemness. On the other hand, the ubiquitination proteasome pathway is inhibited during low O2 levels which promote muscle wasting in cancer patients. Therefore, understanding the mechanism of the HIF-1 pathway and its metabolic adaptation to biomolecules is important for developing a novel therapeutic method for cancer and cachexia therapy. Even though many HIF inhibitors are already in a clinical trial, their mechanism of action remains unknown. With this background, this review summarizes the basic concepts of cachexia, the role of inflammatory cytokines, pathways connected with cachexia with special reference to the HIF-1 pathway and its regulation, metabolic changes, and inhibitors of HIFs.
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Affiliation(s)
- Subramanian Muthamil
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Hyun Yong Kim
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Hyun-Jun Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Ji-Hyo Lyu
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Ung Cheol Shin
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea
| | - Younghoon Go
- Korean Medicine (KM)-application Center, Korea Institute of Oriental Medicine, Daegu, Republic of Korea
| | - Seong-Hoon Park
- Genetic and Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Daejeon 34141, Republic of Korea
| | - Hee Gu Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jun Hong Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Jeollanam-do, 58245, Republic of Korea; University of Science & Technology (UST), KIOM campus, Korean Convergence Medicine Major, Daejeon 34054, Republic of Korea.
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31
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Li Q, Liu N, Wu C. Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization. PLANTA 2023; 257:94. [PMID: 37031436 DOI: 10.1007/s00425-023-04126-y] [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: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.
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Affiliation(s)
- Qinglin Li
- Crop Genesis and Novel Agronomy Center, Yangling, 712100, Shaanxi, China.
| | - Ning Liu
- Shandong ZhongnongTiantai Seed Co., Ltd, Pingyi, 273300, Shandong, China
| | - Chenglai Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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32
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Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.). Genes (Basel) 2023; 14:genes14030637. [PMID: 36980909 PMCID: PMC10048783 DOI: 10.3390/genes14030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Genomic regions governing grain protein content (GPC), 1000 kernel weight (TKW), and normalized difference vegetation index (NDVI) were studied in a set of 280 bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom array and phenotyped in three environments. A total of 26 marker-trait associations (MTAs) were detected on 18 chromosomes covering the A, B, and D subgenomes of bread wheat. The GPC showed the maximum MTAs (16), followed by NDVI (6), and TKW (4). A maximum of 10 MTAs was located on the B subgenome, whereas, 8 MTAs each were mapped on the A and D subgenomes. In silico analysis suggest that the SNPs were located on important putative candidate genes such as NAC domain superfamily, zinc finger RING-H2-type, aspartic peptidase domain, folylpolyglutamate synthase, serine/threonine-protein kinase LRK10, pentatricopeptide repeat, protein kinase-like domain superfamily, cytochrome P450, and expansin. These candidate genes were found to have different roles including regulation of stress tolerance, nutrient remobilization, protein accumulation, nitrogen utilization, photosynthesis, grain filling, mitochondrial function, and kernel development. The effects of newly identified MTAs will be validated in different genetic backgrounds for further utilization in marker-aided breeding.
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33
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Gong D, Wang Y, Zhang H, Liang K, Sun Q, Qiu F. Overexpression of ZmKL9 increases maize hybrid hundred kernel weight. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:451-453. [PMID: 36331355 PMCID: PMC9946134 DOI: 10.1111/pbi.13957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/07/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Dianming Gong
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Yuanru Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Hetong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Kun Liang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Qin Sun
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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34
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Wang B, Hou M, Shi J, Ku L, Song W, Li C, Ning Q, Li X, Li C, Zhao B, Zhang R, Xu H, Bai Z, Xia Z, Wang H, Kong D, Wei H, Jing Y, Dai Z, Wang HH, Zhu X, Li C, Sun X, Wang S, Yao W, Hou G, Qi Z, Dai H, Li X, Zheng H, Zhang Z, Li Y, Wang T, Jiang T, Wan Z, Chen Y, Zhao J, Lai J, Wang H. De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis. Nat Genet 2023; 55:312-323. [PMID: 36646891 DOI: 10.1038/s41588-022-01283-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023]
Abstract
Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F1 hybrids, we found strong positive correlations between better-parent heterosis of the F1 hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.
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Affiliation(s)
- Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, China
| | - Junpeng Shi
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Lixia Ku
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Hua Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhijing Bai
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dexin Kong
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Hongbin Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yifeng Jing
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Zhouyan Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Hu Hailing Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xinyu Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Chunhui Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Xuan Sun
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Shuaishuai Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Wen Yao
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Gege Hou
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zhi Qi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing, China
| | | | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China.,Guangzhou Laboratory, Guangzhou, China
| | - Zhaoman Wan
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Yanhui Chen
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China.
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China.
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
| | - Haiyang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
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Crop germplasm: Current challenges, physiological-molecular perspective, and advance strategies towards development of climate-resilient crops. Heliyon 2023; 9:e12973. [PMID: 36711267 PMCID: PMC9880400 DOI: 10.1016/j.heliyon.2023.e12973] [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: 06/02/2022] [Revised: 01/01/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Germplasm is a long-term resource management mission and investment for civilization. An estimated ∼7.4 million accessions are held in 1750 plant germplasm centres around the world; yet, only 2% of these assets have been utilized as plant genetic resources (PGRs). According to recent studies, the current food yield trajectory will be insufficient to feed the world's population in 2050. Additionally, possible negative effects in terms of crop failure because of climate change are already being experienced across the world. Therefore, it is necessary to reconciliation of research advancement and innovation of practices for further exploration of the potential of crop germplasm especially for the complex traits associated with yield such as water- and nitrogen use efficiency. In this review, we tried to address current challenges, research gaps, physiological and molecular aspects of two broad spectrum complex traits such as water- and nitrogen-use efficiency, and advanced integrated strategies that could provide a platform for combined stress management for climate-smart crop development. Additionally, recent development in technologies that are directly related to germplasm characterization was highlighted for further molecular utilization towards the development of elite varieties.
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Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:38. [PMID: 35440054 PMCID: PMC9019968 DOI: 10.1186/s13068-022-02134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/03/2022] [Indexed: 11/10/2022]
Abstract
Background Yield is the most important and complex trait that is influenced by numerous relevant traits with very complicated interrelations. While there are a large number of studies on the phenotypic relationship and genetic basis of yield traits, systematic studies with further dissection focusing on yield are limited. Therefore, there is still lack of a comprehensive and in-depth understanding of the determination of yield. Results In this study, yield was systematically dissected at the phenotypic, genetic to molecular levels in oilseed rape (Brassica napus L.). The analysis of correlation, network, and principal component for 21 traits in BnaZN-RIL population showed that yield was determined by a complex trait network with key contributors. The analysis of the constructed high-density single nucleotide polymorphism (SNP) linkage map revealed the concentrated distribution of distorted and heterozygous markers, likely due to selection on genes controlling the growth period and yield heterosis. A total of 134 consensus quantitative trait loci (QTL) were identified for 21 traits, of which all were incorporated into an interconnecting QTL network with dozens of hub-QTL. Four representative hub-QTL were further dissected to the target or candidate genes that governed the causal relationships between the relevant traits. Conclusions The highly consistent results at the phenotypic, genetic, and molecular dissecting demonstrated that yield was determined by a multilayer composite network that involved numerous traits and genes showing complex up/down-stream and positive/negative regulation. This provides a systematic view, further insight, and exact roadmap for yield determination, which represents a significant advance toward the understanding and dissection of complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02134-w.
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Liu Y, Yi C, Liu Q, Wang C, Wang W, Han F, Hu X. Multi-Omics Profiling Identifies Candidate Genes Controlling Seed Size in Peanut. PLANTS (BASEL, SWITZERLAND) 2022; 11:3276. [PMID: 36501316 PMCID: PMC9740956 DOI: 10.3390/plants11233276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by 60Co treatment of a common peanut landrace, Huayu 22, and were designated as the "big seed" mutant lines (hybs). The length and weight of the seed in hybs were about 118% and 170% of those in wild-type (WT), respectively. We adopted a multi-omics approach to identify the genomic locus underlying the hybs mutants. We performed whole genome sequencing (WGS) of WT and hybs mutants and identified thousands of large-effect variants (SNPs and indels) that occurred in about four hundred genes in hybs mutants. Seeds from both WT and hybs lines were sampled 20 days after flowering (DAF) and were used for RNA-Seq analysis; the results revealed about one thousand highly differentially expressed genes (DEGs) in hybs compared to WT. Using a method that combined large-effect variants with DEGs, we identified 45 potential candidate genes that shared gene product mutations and expression level changes in hybs compared to WT. Among the genes, two candidate genes encoding cytochrome P450 superfamily protein and NAC transcription factors may be associated with the increased seed size in hybs. The present findings provide new information on the identification and functional research into candidate genes responsible for the seed size phenotype in peanut.
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Affiliation(s)
- Yang Liu
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life Sciences, Linyi University, Linyi 276000, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Congyang Yi
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life Sciences, Linyi University, Linyi 276000, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunhui Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenpeng Wang
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life Sciences, Linyi University, Linyi 276000, China
| | - Fangpu Han
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life Sciences, Linyi University, Linyi 276000, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojun Hu
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life Sciences, Linyi University, Linyi 276000, China
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38
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Ren H, Liu M, Zhang J, Liu P, Liu C. Effects of agronomic traits and climatic factors on yield and yield stability of summer maize ( Zea mays L) in the Huang-Huai-Hai Plain in China. FRONTIERS IN PLANT SCIENCE 2022; 13:1050064. [PMID: 36457517 PMCID: PMC9707337 DOI: 10.3389/fpls.2022.1050064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Zhengdan 958 (ZD958) is the summer maize variety with the widest planting area in Huang-Huai-Hai plain in the past 20 years. Understanding the agronomic characteristics of maize and its adaptability to climatic factors is of great significance for breeding maize varieties with high yield and stability. In this study, the experimental data of 33 experimental stations from 2005 to 2015 were analyzed to clarify the effects of different agronomic traits on yield and the correlation between agronomic traits, and to understand the effects of different climatic factors on summer maize yield and agronomic traits. The results showed that the average yield of ZD958 was 9.20 t ha-1, and the yield variation coefficient was 13.41%. There was a certainly negative correlation between high yield and high stability. Plant heights, ear heights, double ear rate, ear length, ear rows, line grain number, grain number per ear, ear diameter, cob diameter, and 1000 grains weight were significantly positive correlation with maize yield. Solar radiation before and after silking were significantly positive correlation with maize yield. Path analysis showed that changes in agronomic traits accounted for 54% of the yield variation, and changes in climate factors accounted for 26% of the yield variation. Our study showed that higher plant height, ear height, grain number per ear and 1000-grain weight, lower lodging rate, pour the discount rate and shorter bald tip long were the main reasons for high yield. Among the climatic factors, solar radiation and the lowest temperature have significant effects on the yield.
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Affiliation(s)
- Hao Ren
- College of Agronomy, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
| | - Mingyu Liu
- College of Agronomy, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
| | - Jibo Zhang
- Shandong Climate Center, Jinan, Shandong, China
| | - Peng Liu
- College of Agronomy, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, Shandong, China
| | - Cunhui Liu
- Shandong Seed Administration Station, Shandong Provincial Department of Agriculture and Rural Affairs, Jinan, Shandong, China
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Han X, Li L, Chen H, Liu L, Sun L, Wang X, Xiang Y, Wan Z, Liu C. Resequencing of 558 Chinese mungbean landraces identifies genetic loci associated with key agronomic traits. FRONTIERS IN PLANT SCIENCE 2022; 13:1043784. [PMID: 36311125 PMCID: PMC9597495 DOI: 10.3389/fpls.2022.1043784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Mungbean is a warm-season annual food legume and plays important role in supplying food and nutritional security in many tropical countries. However, the genetic basis of its agronomic traits remains poorly understood. Therefore, we resequenced 558 Chinese mungbean landraces and produced a comprehensive map of mungbean genomic variation. We phenotyped all landraces in six different environments. Genome-wide association studies (GWAS) produced 110 signals significantly associated with nine agronomic traits, for which several candidate genes were identified. Overall, this study provides new insight into the genetic architecture of mungbean agronomic traits. Moreover, the genome-wide variations identified here should be valuable resources for future breeding studies of this important food legume.
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Affiliation(s)
- Xuesong Han
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Li Li
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Hongwei Chen
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Liangjun Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Longqin Sun
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Xingmin Wang
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Yantao Xiang
- College of Agronomy, Yangtze University, Jingzhou, China
| | - Zhenghuang Wan
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
| | - Changyan Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic, Wuhan, China
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Zhou X, Li J, Wang Y, Liang X, Zhang M, Lu M, Guo Y, Qin F, Jiang C. The classical SOS pathway confers natural variation of salt tolerance in maize. THE NEW PHYTOLOGIST 2022; 236:479-494. [PMID: 35633114 DOI: 10.1111/nph.18278] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/19/2022] [Indexed: 05/27/2023]
Abstract
Sodium (Na+ ) is the major cation damaging crops in the salinised farmland. Previous studies have shown that the Salt Overly Sensitive (SOS) pathway is important for salt tolerance in Arabidopsis. Nevertheless, the SOS pathway remains poorly investigated in most crops. This study addresses the function of the SOS pathway and its association with the natural variation of salt tolerance in maize. First, we showed that a naturally occurring 4-bp frame-shifting deletion in ZmSOS1 caused the salt hypersensitive phenotype of the maize inbred line LH65. Accordingly, mutants lacking ZmSOS1 also displayed a salt hypersensitive phenotype, due to an impaired root-to-rhizosphere Na+ efflux and an increased shoot Na+ concentration. We next showed that the maize SOS3/SOS2 complex (ZmCBL4/ZmCIPK24a and ZmCBL8/ZmCIPK24a) phosphorylates ZmSOS1 therefore activating its Na+ -transporting activity, with their loss-of-function mutants displaying salt hypersensitive phenotypes. Moreover, we observed that a LTR/Gypsy insertion decreased the expression of ZmCBL8, thereby increasing shoot Na+ concentration in natural maize population. Taken together, our study demonstrated that the maize SOS pathway confers a conservative salt-tolerant role, and the components of SOS pathway (ZmSOS1 and ZmCBL8) confer the natural variations of Na+ regulation and salt tolerance in maize, therefore providing important gene targets for breeding salt-tolerant maize.
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Affiliation(s)
- Xueyan Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Jianfang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Yiqiao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ming Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Minhui Lu
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
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Zeng T, Meng Z, Yue R, Lu S, Li W, Li W, Meng H, Sun Q. Genome wide association analysis for yield related traits in maize. BMC PLANT BIOLOGY 2022; 22:449. [PMID: 36127632 PMCID: PMC9490995 DOI: 10.1186/s12870-022-03812-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the genetic basis of yield related traits contributes to the improvement of grain yield in maize. RESULTS Using 291 excellent maize inbred lines as materials, six yield related traits of maize, including grain yield per plant (GYP), grain length (GL), grain width (GW), kernel number per row (KNR), 100 kernel weight (HKW) and tassel branch number (TBN) were investigated in Jinan, in 2017, 2018 and 2019. The average values of three environments were taken as the phenotypic data of yield related traits, and they were statistically analyzed. Based on 38,683 high-quality SNP markers in the whole genome of the association panel, the MLM with PCA model was used for genome-wide association analysis (GWAS) to obtain 59 significantly associated SNP sites. Moreover, 59 significantly associated SNPs (P < 0.0001) referring to GYP, GL, GW, KNR, HKW and TBN, of which 14 SNPs located in yield related QTLs/QTNs previously reported. A total of 66 candidate genes were identified based on the 59 significantly associated SNPs, of which 58 had functional annotation. CONCLUSIONS Using genome-wide association analysis strategy to identify genetic loci related to maize yield, a total of 59 significantly associated SNP were detected. Those results aid in our understanding of the genetic architecture of maize yield and provide useful SNPs for genetic improvement of maize.
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Affiliation(s)
- Tingru Zeng
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhaodong Meng
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Runqing Yue
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shouping Lu
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wenlan Li
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wencai Li
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hong Meng
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qi Sun
- Maize Institute, Shandong Academy of Agricultural Sciences, Jinan, China
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Woldeyohannes AB, Iohannes SD, Miculan M, Caproni L, Ahmed JS, de Sousa K, Desta EA, Fadda C, Pè ME, Dell'Acqua M. Data-driven, participatory characterization of farmer varieties discloses teff breeding potential under current and future climates. eLife 2022; 11:80009. [PMID: 36052993 PMCID: PMC9439699 DOI: 10.7554/elife.80009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
In smallholder farming systems, traditional farmer varieties of neglected and underutilized species (NUS) support the livelihoods of millions of growers and consumers. NUS combine cultural and agronomic value with local adaptation, and transdisciplinary methods are needed to fully evaluate their breeding potential. Here, we assembled and characterized the genetic diversity of a representative collection of 366 Ethiopian teff (Eragrostis tef) farmer varieties and breeding materials, describing their phylogenetic relations and local adaptation on the Ethiopian landscape. We phenotyped the collection for its agronomic performance, involving local teff farmers in a participatory variety evaluation. Our analyses revealed environmental patterns of teff genetic diversity and allowed us to identify 10 genetic clusters associated with climate variation and with uneven spatial distribution. A genome-wide association study was used to identify loci and candidate genes related to phenology, yield, local adaptation, and farmers’ appreciation. The estimated teff genomic offset under climate change scenarios highlighted an area around lake Tana where teff cropping may be most vulnerable to climate change. Our results show that transdisciplinary approaches may efficiently propel untapped NUS farmer varieties into modern breeding to foster more resilient and sustainable cropping systems. Small farms support the livelihoods of about two billion people worldwide. Smallholder farmers often rely on local varieties of crops and use less irrigation and fertilizer than large producers. But smallholdings can be vulnerable to weather events and climate change. Data-driven research approaches may help to identify the needs of farmers, taking into account traditional knowledge and cultural practices to enhance the sustainability of certain crops. Teff is a cereal crop that plays a critical role in the culture and diets of Ethiopian communities. It is also a super food appreciated on international markets for its nutritional value. Rural smallholder farmers in Ethiopia rely on the crop for subsistence and income and make up the bulk of the country’s agricultural system. Many grow local varieties with tremendous genetic diversity. Scientists, in collaboration with farmers, could tap that diversity to produce more productive or climate-resilient types of teff, both for national and international markets. Woldeyohannes, Iohannes et al. produced the first large-scale genetic, agronomic and climatic study of traditional teff varieties. In the experiments, Woldeyohannes and Iohannes et al. sequenced the genomes of 366 Ethiopian teff varieties and evaluated their agronomic value in common gardens. The team collaborated with 35 local farmers to understand their preference of varieties and traits. They then conducted a genome-wide association study to assess the crops’ productivity and their adaptations to local growing conditions and farmer preferences. Genetic changes that speed up teff maturation and flowering time could meet small farmers’ needs to secure teff harvest. Woldeyohannes, Iohannes et al. also identified a region in Ethiopia, where local teff varieties may struggle to adapt to climate change. Genetic modifications may help the crop to adapt to frequent droughts that may be a common characteristic of future climates. The experiments reveal the importance of incorporating traditional knowledge from smallholder farmers into data-driven crop improvement efforts considering genetics and climate science. This multidisciplinary approach may help to improve food security and protect local genetic diversity on small farms. It may also help to ensure that agricultural advances fairly and equitably benefit small farmers.
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Affiliation(s)
- Aemiro Bezabih Woldeyohannes
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | | | - Mara Miculan
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Leonardo Caproni
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jemal Seid Ahmed
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Kauê de Sousa
- Digital Inclusion, Bioversity International, Montpellier, France.,Department of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Carlo Fadda
- Biodiversity for Food and Agriculture, Bioversity International, Nairobi, Kenya
| | - Mario Enrico Pè
- Center of Plant Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
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Tao T, Huang Q, Zuo Z, Lu Y, Su X, Xu Y, Li P, Xu C, Yang Z. Nucleotide polymorphisms of the maize ZmFWL7 gene and their association with ear-related traits. Front Genet 2022; 13:960529. [PMID: 36035151 PMCID: PMC9399371 DOI: 10.3389/fgene.2022.960529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022] Open
Abstract
Plant fw2.2-like (FWL) genes, encoding proteins harboring a placenta-specific eight domain, have been suggested to control fruit and grain size through regulating cell division, differentiation, and expansion. Here, we re-sequenced the nucleotide sequences of the maize ZmFWL7 gene, a member of the FWL family, in 256 elite maize inbred lines, and the associations of nucleotide polymorphisms in this locus with 11 ear-related traits were further detected. A total of 175 variants, including 159 SNPs and 16 InDels, were identified in the ZmFWL7 locus. Although the promoter and downstream regions showed higher nucleotide polymorphism, the coding region also possessed 61 SNPs and 6 InDels. Eleven polymorphic sites in the ZmFWL7 locus were found to be significantly associated with eight ear-related traits. Among them, two nonsynonymous SNPs (SNP2370 and SNP2898) showed significant association with hundred kernel weight (HKW), and contributed to 7.11% and 8.62% of the phenotypic variations, respectively. In addition, the SNP2898 was associated with kernel width (KW), and contributed to 7.57% of the phenotypic variations. Notably, the elite allele T of SNP2370 was absent in teosintes and landraces, while its frequency in inbred lines was increased to 12.89%. By contrast, the frequency of the elite allele A of SNP2898 was 3.12% in teosintes, and it was raised to 12.68% and 19.92% in landraces and inbred lines, respectively. Neutral tests show that this locus wasn’t artificially chosen during the process of domestication and genetic improvement. Our results revealed that the elite allelic variants in ZmFWL7 might possess potential for the genetic improvement of maize ear-related traits.
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Affiliation(s)
- Tianyun Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Qianfeng Huang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Zhihao Zuo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Xiaomin Su
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- *Correspondence: Chenwu Xu, ; Zefeng Yang,
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- *Correspondence: Chenwu Xu, ; Zefeng Yang,
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Shi X, Li W, Guo Z, Wu M, Zhang X, Yuan L, Qiu X, Xing Y, Sun X, Xie H, Tang J. Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage. BMC PLANT BIOLOGY 2022; 22:348. [PMID: 35843937 PMCID: PMC9290290 DOI: 10.1186/s12870-022-03695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Heterosis is widely used in many crops and is important for global food safety, and maize is one of the most successful crops to take advantage of heterosis. Gene expression patterns control the development of the maize ear, but the mechanisms by which heterosis affects transcriptional-level control are not fully understood. RESULTS In this study, we sampled ear inflorescence meristems (IMs) from the single-segment substitution maize (Zea mays) line lx9801hlEW2b, which contains the heterotic locus hlEW2b associated with ear width, as well as the receptor parent lx9801, the test parent Zheng58, and their corresponding hybrids Zheng58 × lx9801hlEW2b (HY) and Zheng58 × lx9801 (CK). After RNA sequencing and transcriptomic analysis, 2531 unique differentially expressed genes (DEGs) were identified between the two hybrids (HY vs. CK). Our results showed that approximately 64% and 48% of DEGs exhibited additive expression in HY and CK, whereas the other genes displayed a non-additive expression pattern. The DEGs were significantly enriched in GO functional categories of multiple metabolic processes, plant organ morphogenesis, and hormone regulation. These essential processes are potentially associated with heterosis performance during the maize ear developmental stage. In particular, 125 and 100 DEGs from hybrids with allele-specific expression (ASE) were specifically identified in HY and CK, respectively. Comparison between the two hybrids suggested that ASE genes were involved in different development-related processes that may lead to the hybrid vigor phenotype during maize ear development. In addition, several critical genes involved in auxin metabolism and IM development were differentially expressed between the hybrids and showed various expression patterns (additive, non-additive, and ASE). Changes in the expression levels of these genes may lead to differences in auxin homeostasis in the IM, affecting the transcription of core genes such as WUS that control IM development. CONCLUSIONS Our research suggests that additive, non-additive, and allele-specific expression patterns may fine-tune the expression of crucial DEGs that modulate carbohydrate and protein metabolic processes, nitrogen assimilation, and auxin metabolism to optimal levels, and these transcriptional changes may play important roles in maize ear heterosis. The results provide new information that increases our understanding of the relationship between transcriptional variation and heterosis during maize ear development, which may be helpful for clarifying the genetic and molecular mechanisms of heterosis.
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Affiliation(s)
- Xia Shi
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Weihua Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mingbo Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangge Zhang
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Liang Yuan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ye Xing
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaojing Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huiling Xie
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, Henan, 450002, China.
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45
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Li C, Guan H, Jing X, Li Y, Wang B, Li Y, Liu X, Zhang D, Liu C, Xie X, Zhao H, Wang Y, Liu J, Zhang P, Hu G, Li G, Li S, Sun D, Wang X, Shi Y, Song Y, Jiao C, Ross-Ibarra J, Li Y, Wang T, Wang H. Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding. NATURE PLANTS 2022; 8:750-763. [PMID: 35851624 DOI: 10.1038/s41477-022-01190-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.
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Affiliation(s)
- Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghui Guan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Jing
- Novogene Bioinformatics Institute, Beijing, China
| | - Yaoyao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng Liu
- Institute of Food Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xiaoqing Xie
- Institute of Food Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyan Zhao
- Institute of Maize Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanbo Wang
- Institute of Maize Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jingbao Liu
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Panpan Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Guanghui Hu
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guoliang Li
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Suiyan Li
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Dequan Sun
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiaoming Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA, USA.
- Center for Population Biology and Genome Center, University of California, Davis, CA, USA.
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Haiyang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
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46
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Lu H, Wu H, Zhu G, Yin C, Zhao L, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Identification and Fine Mapping of the Candidate Gene Controlling Multi-Inflorescence in Brassica napus. Int J Mol Sci 2022; 23:ijms23137244. [PMID: 35806247 PMCID: PMC9266383 DOI: 10.3390/ijms23137244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
As a desirable agricultural trait, multi-inflorescence (MI) fulfills the requirement of mechanized harvesting and yield increase in rapeseed (Brassica napus L.). However, the genetic mechanism underlying the multi-inflorescence trait remain poorly understood. We previously identified a difference of one pair of dominant genes between the two mapping parental materials. In this study, phenotype and expression analysis indicated that the imbalance of the CLAVATA (CLV)-WUSCHEL (WUS) feedback loop may contribute to the abnormal development of the shoot apical meristem (SAM). BnaMI was fine-mapped to a 55 kb genomic region combining with genotype and phenotype of 5768 BCF1 individuals using a traditional mapping approach. Through comparative and expression analyses, combined with the annotation in Arabidopsis, five genes in this interval were identified as candidate genes. The present findings may provide assistance in functional analysis of the mechanism associated with multi-inflorescence and yield increase in rapeseed.
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47
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Sabharwal T, Lu Z, Slocum RD, Kang S, Wang H, Jiang HW, Veerappa R, Romanovicz D, Nam JC, Birk S, Clark G, Roux SJ. Constitutive expression of a pea apyrase, psNTP9, increases seed yield in field-grown soybean. Sci Rep 2022; 12:10870. [PMID: 35760854 PMCID: PMC9237067 DOI: 10.1038/s41598-022-14821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/13/2022] [Indexed: 12/02/2022] Open
Abstract
To address the demand for food by a rapidly growing human population, agricultural scientists have carried out both plant breeding and genetic engineering research. Previously, we reported that the constitutive expression of a pea apyrase (Nucleoside triphosphate, diphosphohydrolase) gene, psNTP9, under the control of the CaMV35S promoter, resulted in soybean plants with an expanded root system architecture, enhanced drought resistance and increased seed yield when they are grown in greenhouses under controlled conditions. Here, we report that psNTP9-expressing soybean lines also show significantly enhanced seed yields when grown in multiple different field conditions at multiple field sites, including when the gene is introgressed into elite germplasm. The transgenic lines have higher leaf chlorophyll and soluble protein contents and decreased stomatal density and cuticle permeability, traits that increase water use efficiency and likely contribute to the increased seed yields of field-grown plants. These altered properties are explained, in part, by genome-wide gene expression changes induced by the transgene.
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Affiliation(s)
- Tanya Sabharwal
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Robert D Slocum
- Program in Biological Sciences, Goucher College, Towson, MD, 21204, USA
| | - Seongjoon Kang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Huan Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Han-Wei Jiang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Roopadarshini Veerappa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Dwight Romanovicz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ji Chul Nam
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Simon Birk
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Greg Clark
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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48
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An Y, Chen L, Li YX, Li C, Shi Y, Zhang D, Li Y, Wang T. Fine mapping qKRN5.04 provides a functional gene negatively regulating maize kernel row number. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1997-2007. [PMID: 35385977 DOI: 10.1007/s00122-022-04089-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Zm00001d016075 was identified by fine mapping qKRN5.04. The function of Zm00001d016075, negatively modulating maize (Zea Mays L.) kernel row number (KRN), was verified by CRISPR-Cas9. InDel308 located in the promoter of Zm00001d016075 has potential for use as a molecular marker to identify KRN in maize breeding. Kernel row number (KRN), controlled by multiple quantitative trait loci (QTLs), is one of the most important traits that relate to maize production and domestication. Here, fine mapping was conducted to study a major QTL, qKRN5.04, to a 65-kb genomic region using a progeny test strategy in an advanced backcross population, in which Nong531 (N531) and the inbred line of Silunuo (SLN) were employed as the recurrent and the donor parent, respectively. Within this region, there was only one gene (Zm00001d016075) based on the B73 reference genome. Furthermore, we performed regional association mapping using a panel of 236 diverse inbred lines and observed that all significant SNPs were located within Zm00001d016075. The expression of Zm00001d016075 was significantly higher in N531 and qKRN5.04N531 than qKRN5.04SLN, resulting from the different promoter activity of Zm00001d016075. Sequence analysis revealed that InDel308, located in the promoter of Zm00001d016075, was related to the KRN variation in different maize inbred lines. Using the CRISPR-Cas9 strategy, we determined Zm00001d016075 played a role in negatively regulating KRN and had a moderate effect on 10-kernel width, 100-kernel weight, kernels per ear, and grain yield per ear. These results provide critical insights on the genetic basis and quantitative variation for KRN.
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Affiliation(s)
- Yixin An
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yong-Xiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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49
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Genome-Wide Association Studies of Maize Seedling Root Traits under Different Nitrogen Levels. PLANTS 2022; 11:plants11111417. [PMID: 35684192 PMCID: PMC9182862 DOI: 10.3390/plants11111417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 11/21/2022]
Abstract
Nitrogen (N) is one of the important factors affecting maize root morphological construction and growth development. An association panel of 124 maize inbred lines was evaluated for root and shoot growth at seedling stage under normal N (CK) and low N (LN) treatments, using the paper culture method. Twenty traits were measured, including three shoot traits and seventeen root traits, a genome-wide association study (GWAS) was performed using the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods. The results showed that LN condition promoted the growth of the maize roots, and normal N promoted the growth of the shoots. A total of 185 significant SNPs were identified, including 27 SNPs for shoot traits and 158 SNPs for root traits. Four important candidate genes were identified. Under LN conditions, the candidate gene Zm00001d004123 was significantly correlated with the number of crown roots, Zm00001d025554 was correlated with plant height. Under CK conditions, the candidate gene Zm00001d051083 was correlated with the length and area of seminal roots, Zm00001d050798 was correlated with the total root length. The four candidate genes all responded to the LN treatment. The research results provide genetic resources for the genetic improvement of maize root traits.
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50
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Pei Y, Deng Y, Zhang H, Zhang Z, Liu J, Chen Z, Cai D, Li K, Du Y, Zang J, Xin P, Chu J, Chen Y, Zhao L, Liu J, Chen H. EAR APICAL DEGENERATION1 regulates maize ear development by maintaining malate supply for apical inflorescence. THE PLANT CELL 2022; 34:2222-2241. [PMID: 35294020 PMCID: PMC9134072 DOI: 10.1093/plcell/koac093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/12/2022] [Indexed: 05/12/2023]
Abstract
Ear length (EL) is a key trait that contributes greatly to grain yield in maize (Zea mays). While numerous quantitative trait loci for EL have been identified, few causal genes have been studied in detail. Here we report the characterization of ear apical degeneration1 (ead1) exhibiting strikingly shorter ears and the map-based cloning of the casual gene EAD1. EAD1 is preferentially expressed in the xylem of immature ears and encodes an aluminum-activated malate transporter localizing to the plasma membrane. We show that EAD1 is a malate efflux transporter and loss of EAD1 leads to lower malate contents in the apical part of developing inflorescences. Exogenous injections of malate rescued the shortened ears of ead1. These results demonstrate that EAD1 plays essential roles in regulating maize ear development by delivering malate through xylem vessels to the apical part of the immature ear. Overexpression of EAD1 led to greater EL and kernel number per row and the EAD1 genotype showed a positive association with EL in two different genetic segregating populations. Our work elucidates the critical role of EAD1 in malate-mediated female inflorescence development and provides a promising genetic resource for enhancing maize grain yield.
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Affiliation(s)
| | | | - Huairen Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaogui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhibin Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Darun Cai
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Kai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yimo Du
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jie Zang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Peiyong Xin
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuhang Chen
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juan Liu
- Author for correspondence: (H.C.); (J.L.)
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