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Lorenzo CD, Blasco-Escámez D, Beauchet A, Wytynck P, Sanches M, Garcia Del Campo JR, Inzé D, Nelissen H. Maize mutant screens: from classical methods to new CRISPR-based approaches. THE NEW PHYTOLOGIST 2024. [PMID: 39212458 DOI: 10.1111/nph.20084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Mutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (Zea mays) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site-directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR-Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings.
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Affiliation(s)
- Christian Damian Lorenzo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - David Blasco-Escámez
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Arthur Beauchet
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Pieter Wytynck
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Matilde Sanches
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Jose Rodrigo Garcia Del Campo
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Hilde Nelissen
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
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2
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Wu C, Luo J, Xiao Y. Multi-omics assists genomic prediction of maize yield with machine learning approaches. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:14. [PMID: 38343399 PMCID: PMC10853138 DOI: 10.1007/s11032-024-01454-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024]
Abstract
With the improvement of high-throughput technologies in recent years, large multi-dimensional plant omics data have been produced, and big-data-driven yield prediction research has received increasing attention. Machine learning offers promising computational and analytical solutions to interpret the biological meaning of large amounts of data in crops. In this study, we utilized multi-omics datasets from 156 maize recombinant inbred lines, containing 2496 single nucleotide polymorphisms (SNPs), 46 image traits (i-traits) from 16 developmental stages obtained through an automatic phenotyping platform, and 133 primary metabolites. Based on benchmark tests with different types of prediction models, some machine learning methods, such as Partial Least Squares (PLS), Random Forest (RF), and Gaussian process with Radial basis function kernel (GaussprRadial), achieved better prediction for maize yield, albeit slight difference for method preferences among i-traits, genomic, and metabolic data. We found that better yield prediction may be caused by various capabilities in ranking and filtering data features, which is found to be linked with biological meaning such as photosynthesis-related or kernel development-related regulations. Finally, by integrating multiple omics data with the RF machine learning approach, we can further improve the prediction accuracy of grain yield from 0.32 to 0.43. Our research provides new ideas for the application of plant omics data and artificial intelligence approaches to facilitate crop genetic improvements. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01454-z.
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Affiliation(s)
- Chengxiu Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yingjie Xiao
- 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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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: 6] [Impact Index Per Article: 6.0] [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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4
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Li K, Tassinari A, Giuliani S, Rosignoli S, Urbany C, Tuberosa R, Salvi S. QTL mapping identifies novel major loci for kernel row number-associated ear fasciation, ear prolificacy and tillering in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1017983. [PMID: 36704171 PMCID: PMC9871824 DOI: 10.3389/fpls.2022.1017983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/14/2022] [Indexed: 05/31/2023]
Abstract
Maize ear fasciation originates from excessive or abnormal proliferation of the ear meristem and usually manifests as flattened multiple-tipped ear and/or disordered kernel arrangement. Ear prolificacy expresses as multiple ears per plant or per node. Both ear fasciation and prolificacy can affect grain yield. The genetic control of the two traits was studied using two recombinant inbred line populations (B73 × Lo1016 and Lo964 × Lo1016) with Lo1016 and Lo964 as donors of ear fasciation and prolificacy, respectively. Ear fasciation-related traits, number of kernel rows (KRN), ear prolificacy and number of tillers were phenotyped in multi-year field experiments. Ear fasciation traits and KRN showed relatively high heritability (h 2 > 0.5) except ratio of ear diameters. For all ear fasciation-related traits, fasciation level positively correlated with KRN (0.30 ≤ r ≤ 0.68). Prolificacy and tillering were not correlated and their h 2 ranged from 0.41 to 0.78. QTL mapping identified four QTLs for ear fasciation, on chromosomes 1 (two QTLs), 5 and 7, the latter two overlapping with QTLs for number of kernel rows. Notably, at these QTLs, the Lo1016 alleles increased both ear fasciation and KRN across populations, thus showing potential breeding applicability. Four and five non-overlapping QTLs were mapped for ear prolificacy and tillering, respectively. Two ear fasciation QTLs, qFas1.2 and qFas7, overlapped with fasciation QTLs mapped in other studies and spanned compact plant2 and ramosa1 candidate genes. Our study identified novel ear fasciation loci and alleles positively affecting grain yield components, and ear prolificacy and tillering loci which are unexpectedly still segregating in elite maize materials, contributing useful information for genomics-assisted breeding programs.
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Affiliation(s)
- Kai Li
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Alberto Tassinari
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Silvia Giuliani
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Serena Rosignoli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | | | - Roberto Tuberosa
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
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Cao Y, Zhang K, Yu H, Chen S, Xu D, Zhao H, Zhang Z, Yang Y, Gu X, Liu X, Wang H, Jing Y, Mei Y, Wang X, Lefebvre V, Zhang W, Jin Y, An D, Wang R, Bosland P, Li X, Paran I, Zhang B, Giuliano G, Wang L, Cheng F. Pepper variome reveals the history and key loci associated with fruit domestication and diversification. MOLECULAR PLANT 2022; 15:1744-1758. [PMID: 36176193 DOI: 10.1016/j.molp.2022.09.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum spp.) is an important vegetable crop that provides a unique pungent sensation when eaten. Through construction of a pepper variome map, we examined the main groups that emerged during domestication and breeding of C. annuum, their relationships and temporal succession, and the molecular events underlying the main transitions. The results showed that the initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, as well as the recent appearance of large, blocky, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we identified Up, which encodes a BIG GRAIN protein involved in auxin transport, as a key domestication gene that controls erect vs pendent fruit orientation. The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. Taken together, these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.
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Affiliation(s)
- Yacong Cao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kang Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hailong Yu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Shumin Chen
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Donghui Xu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hong Zhao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhenghai Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yinqing Yang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaozhen Gu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xinyan Liu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Haiping Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yaxin Jing
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yajie Mei
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiang Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Véronique Lefebvre
- INRAE, GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, 84140 Montfavet, France
| | - Weili Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Jin
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Dongliang An
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Risheng Wang
- Institute of Vegetables, Academy of Agricultural Sciences of Guangxi, 174 Daxue East Road, Nanning 53007, P. R. China
| | - Paul Bosland
- Department of Plant and Environmental Sciences, NMSU, Las Cruces, NM 88003, USA
| | - Xixiang Li
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Ilan Paran
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Baoxi Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Giovanni Giuliano
- Biotechnology and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese, 301-00123 Roma, Italy.
| | - Lihao Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Feng Cheng
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
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6
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Wang Y, Tang Q, Kang Y, Wang X, Zhang H, Li X. Analysis of the Utilization and Prospects of CRISPR-Cas Technology in the Annotation of Gene Function and Creation New Germplasm in Maize Based on Patent Data. Cells 2022; 11:cells11213471. [PMID: 36359866 PMCID: PMC9657720 DOI: 10.3390/cells11213471] [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: 09/28/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Maize (Zea mays L.) is a food crop with the largest planting area and the highest yield in the world, and it plays a vital role in ensuring global food security. Conventional breeding methods are costly, time-consuming, and ineffective in maize breeding. In recent years, CRISPR-Cas editing technology has been used to quickly generate new varieties with high yield and improved grain quality and stress resistance by precisely modifying key genes involved in specific traits, thus becoming a new engine for promoting crop breeding and the competitiveness of seed industries. Using CRISPR-Cas, a range of new maize materials with high yield, improved grain quality, ideal plant type and flowering period, male sterility, and stress resistance have been created. Moreover, many patents have been filed worldwide, reflecting the huge practical application prospects and commercial value. Based on the existing patent data, we analyzed the development process, current status, and prospects of CRISPR-Cas technology in dissecting gene function and creating new germplasm in maize, providing information for future basic research and commercial production.
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Affiliation(s)
- Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiaoling Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuli Kang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (H.Z.); (X.L.)
| | - Xinhai Li
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (H.Z.); (X.L.)
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7
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Duan Z, Zhang M, Zhang Z, Liang S, Fan L, Yang X, Yuan Y, Pan Y, Zhou G, Liu S, Tian Z. Natural allelic variation of GmST05 controlling seed size and quality in soybean. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1807-1818. [PMID: 35642379 PMCID: PMC9398382 DOI: 10.1111/pbi.13865] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 05/26/2023]
Abstract
Seed size is one of the most important agronomic traits determining the yield of crops. Cloning the key genes controlling seed size and pyramiding their elite alleles will facilitate yield improvement. To date, few genes controlling seed size have been identified in soybean, a major crop that provides half of the plant oil and one quarter of the plant protein globally. Here, through a genome-wide association study of over 1800 soybean accessions, we determined that natural allelic variation at GmST05 (Seed Thickness 05) predominantly controlled seed thickness and size in soybean germplasm. Further analyses suggested that the two major haplotypes of GmST05 differed significantly at the transcriptional level. Transgenic experiments demonstrated that GmST05 positively regulated seed size and influenced oil and protein contents, possibly by regulating the transcription of GmSWEET10a. Population genetic diversity analysis suggested that allelic variations of GmST05 were selected during geographical differentiation but have not been fixed. In summary, natural variation in GmST05 determines transcription levels and influences seed size and quality in soybean, making it an important gene resource for soybean molecular breeding.
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Affiliation(s)
- Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shan Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Pan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Guoan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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8
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Šim�škov� M, Daneva A, Doll N, Schilling N, Cubr�a-Rad�o M, Zhou L, De Winter F, Aesaert S, De Rycke R, Pauwels L, Dresselhaus T, Brugi�re N, Simmons CR, Habben JE, Nowack MK. KIL1 terminates fertility in maize by controlling silk senescence. THE PLANT CELL 2022; 34:2852-2870. [PMID: 35608197 PMCID: PMC9338811 DOI: 10.1093/plcell/koac151] [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: 11/09/2021] [Accepted: 05/15/2022] [Indexed: 05/05/2023]
Abstract
Plant flowers have a functional life span during which pollination and fertilization occur to ensure seed and fruit development. Once flower senescence is initiated, the potential to set seed or fruit is irrevocably lost. In maize, silk strands are the elongated floral stigmas that emerge from the husk-enveloped inflorescence to intercept airborne pollen. Here we show that KIRA1-LIKE1 (KIL1), an ortholog of the Arabidopsis NAC (NAM (NO APICAL MERISTEM), ATAF1/2 (Arabidopsis thaliana Activation Factor1 and 2) and CUC (CUP-SHAPED COTYLEDON 2)) transcription factor KIRA1, promotes senescence and programmed cell death (PCD) in the silk strand base, ending the window of accessibility for fertilization of the ovary. Loss of KIL1 function extends silk receptivity and thus strongly increases kernel yield following late pollination. This phenotype offers new opportunities for possibly improving yield stability in cereal crops. Moreover, despite diverging flower morphologies and the substantial evolutionary distance between Arabidopsis and maize, our data indicate remarkably similar principles in terminating floral receptivity by PCD, whose modulation offers the potential to be widely used in agriculture.
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Affiliation(s)
| | | | - Nicolas Doll
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Neeltje Schilling
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Marta Cubr�a-Rad�o
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Liangzi Zhou
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Freya De Winter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Stijn Aesaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
- Ghent University Expertise Centre for Transmission Electron Microscopy and VIB BioImaging Core, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
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9
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Zhang Y, Jiao F, Li J, Pei Y, Zhao M, Song X, Guo X. Transcriptomic analysis of the maize inbred line Chang7-2 and a large-grain mutant tc19. BMC Genomics 2022; 23:4. [PMID: 34983391 PMCID: PMC8725412 DOI: 10.1186/s12864-021-08230-9] [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: 05/12/2021] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
Backgrounds Grain size is a key factor in crop yield that gradually develops after pollination. However, few studies have reported gene expression patterns in maize grain development using large-grain mutants. To investigate the developmental mechanisms of grain size, we analyzed a large-grain mutant, named tc19, at the morphological and transcriptome level at five stages corresponding to days after pollination (DAP). Results After maturation, the grain length, width, and thickness in tc19 were greater than that in Chang7-2 (control) and increased by 3.57, 8.80, and 3.88%, respectively. Further analysis showed that grain width and 100-kernel weight in tc19 was lower than in Chang7-2 at 14 and 21 DAP, but greater than that in Chang7-2 at 28 DAP, indicating that 21 to 28 DAP was the critical stage for kernel width and weight development. For all five stages, the concentrations of auxin and brassinosteroids were significantly higher in tc19 than in Chang7-2. Gibberellin was higher at 7, 14, and 21 DAP, and cytokinin was higher at 21 and 35 DAP, in tc19 than in Chang7-2. Through transcriptome analysis at 14, 21, and 28 DAP, we identified 2987, 2647 and 3209 differentially expressed genes (DEGs) between tc19 and Chang7-2. By using KEGG analysis, 556, 500 and 633 DEGs at 14, 21 and 28 DAP were pathway annotated, respectively, 77 of them are related to plant hormone signal transduction pathway. ARF3, AO2, DWF4 and XTH are higher expressed in tc19 than that in Chang7-2. Conclusions We found some DEGs in maize grain development by using Chang7-2 and a large-grain mutant tc19. These DEGs have potential application value in improving maize performance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08230-9.
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Affiliation(s)
- Yanrong Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Jun Li
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Yuhe Pei
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Meiai Zhao
- Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China.,College of Life Science, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xiyun Song
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China. .,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China.
| | - Xinmei Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China. .,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China.
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10
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Yassitepe JEDCT, da Silva VCH, Hernandes-Lopes J, Dante RA, Gerhardt IR, Fernandes FR, da Silva PA, Vieira LR, Bonatti V, Arruda P. Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties. FRONTIERS IN PLANT SCIENCE 2021; 12:766702. [PMID: 34721493 PMCID: PMC8553389 DOI: 10.3389/fpls.2021.766702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/15/2021] [Indexed: 05/17/2023]
Abstract
Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world's maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.
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Affiliation(s)
- Juliana Erika de Carvalho Teixeira Yassitepe
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Viviane Cristina Heinzen da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - José Hernandes-Lopes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Ricardo Augusto Dante
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Isabel Rodrigues Gerhardt
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Fernanda Rausch Fernandes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Priscila Alves da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Leticia Rios Vieira
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Vanessa Bonatti
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
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11
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Simmons CR, Lafitte HR, Reimann KS, Brugière N, Roesler K, Albertsen MC, Greene TW, Habben JE. Successes and insights of an industry biotech program to enhance maize agronomic traits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 307:110899. [PMID: 33902858 DOI: 10.1016/j.plantsci.2021.110899] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 05/18/2023]
Abstract
Corteva Agriscience™ ran a discovery research program to identify biotech leads for improving maize Agronomic Traits such as yield, drought tolerance, and nitrogen use efficiency. Arising from many discovery sources involving thousands of genes, this program generated over 3331 DNA cassette constructs involving a diverse set of circa 1671 genes, whose transformed maize events were field tested from 2000 to 2018 under managed environments designed to evaluate their potential for commercialization. We demonstrate that a subgroup of these transgenic events improved yield in field-grown elite maize breeding germplasm. A set of at least 22 validated gene leads are identified and described which represent diverse molecular and physiological functions. These leads illuminate sectors of biology that could guide crop improvement in maize and perhaps other crops. In this review and interpretation, we share some of our approaches and results, and key lessons learned in discovering and developing these maize Agronomic Traits leads.
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Affiliation(s)
- Carl R Simmons
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA.
| | - H Renee Lafitte
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Kellie S Reimann
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Norbert Brugière
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Keith Roesler
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Marc C Albertsen
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Thomas W Greene
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Jeffrey E Habben
- Corteva Agriscience, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
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12
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Wang L, Suo X, Liu Y, Liu C, Luo M. Sphingosine Promotes Embryo Biomass in Upland Cotton: A Biochemical and Transcriptomic Analysis. Biomolecules 2021; 11:525. [PMID: 33915924 PMCID: PMC8065874 DOI: 10.3390/biom11040525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/21/2022] Open
Abstract
Sphingolipids are essential membrane components and signal molecules, but their regulatory role in cotton embryo growth is largely unclear. In this study, we evaluated the effects of treatment with the sphingolipid synthesis inhibitor fumonisin B1 (FB1), the serine palmityl transferase (SPT) inhibitor myriocin, the SPT sphingolipid product DHS (d18:0 dihydrosphingosine), and the post-hydroxylation DHS product PHS (t18:0 phytosphingosine) on embryo growth in culture, and performed comparative transcriptomic analysis on control and PHS-treated samples. We found that FB1 could inhibit cotton embryo development. At the five-day ovule/embryo developmental stage, PHS was the most abundant sphingolipid. An SPT enzyme inhibitor reduced the fresh weight of embryos, while PHS had the opposite effect. The transcriptomic analysis identified 2769 differentially expressed genes (1983 upregulated and 786 downregulated) in the PHS samples. A large number of transcription factors were highly upregulated, such as zinc finger, MYB, NAC, bHLH, WRKY, MADS, and GRF in PHS-treated samples compared to controls. The lipid metabolism and plant hormone (auxin, brassinosteroid, and zeatin) related genes were also altered. Our findings provide target metabolites and genes for cotton seed improvement.
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Affiliation(s)
- Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaodong Suo
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing 400716, China;
| | - Yujie Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chen Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Ming Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China; (L.W.); (Y.L.); (C.L.)
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing 400716, China;
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13
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Zhang H, Lu Y, Ma Y, Fu J, Wang G. Genetic and molecular control of grain yield in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:18. [PMID: 37309425 PMCID: PMC10236077 DOI: 10.1007/s11032-021-01214-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/07/2021] [Indexed: 06/14/2023]
Abstract
Understanding the genetic and molecular basis of grain yield is important for maize improvement. Here, we identified 49 consensus quantitative trait loci (cQTL) controlling maize yield-related traits using QTL meta-analysis. Then, we collected yield-related traits associated SNPs detected by association mapping and identified 17 consensus significant loci. Comparing the physical positions of cQTL with those of significant SNPs revealed that 47 significant SNPs were located within 20 cQTL regions. Furthermore, intensive reviews of 31 genes regulating maize yield-related traits found that the functions of many genes were conservative in maize and other plant species. The functional conservation indicated that some of the 575 maize genes (orthologous to 247 genes controlling yield or seed traits in other plant species) might be functionally related to maize yield-related traits, especially the 49 maize orthologous genes in cQTL regions, and 41 orthologous genes close to the physical positions of significant SNPs. In the end, we prospected on the integration of the public sources for exploring the genetic and molecular mechanisms of maize yield-related traits, and on the utilization of genetic and molecular mechanisms for maize improvement. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01214-3.
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Affiliation(s)
- Hongwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Yantian Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Yuting Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Junjie Fu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
| | - Guoying Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 The People’s Republic of China
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