1
|
Lu G, Li Q. Complete mitochondrial genome of Syzygium samarangense reveals genomic recombination, gene transfer, and RNA editing events. FRONTIERS IN PLANT SCIENCE 2024; 14:1301164. [PMID: 38264024 PMCID: PMC10803518 DOI: 10.3389/fpls.2023.1301164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
Wax apple (Syzygium samarangense) is a commercial fruit that belongs to one of the most species-rich tree genera in the world. We report here the first complete S. samarangense mitogenome obtained using a hybrid assembly strategy. The mitogenome was a 530,242 bp circular molecule encoding 61 unique genes accounting for 7.99% of the full-length genome. Additionally, 167 simple sequence repeats, 19 tandem repeats, and 529 pairs of interspersed repeats were identified. Long read mapping and Sanger sequencing revealed the involvement of two forward repeats (35,843 bp and 22,925 bp) in mediating recombination. Thirteen homologous fragments in the chloroplast genome were identified, accounting for 1.53% of the mitogenome, and the longest fragment was 2,432 bp. An evolutionary analysis showed that S. samarangense underwent multiple genomic reorganization events and lost at least four protein-coding genes (PCGs) (rps2, rps7, rps11, and rps19). A total of 591 RNA editing sites were predicted in 37 PCGs, of which nad1-2, nad4L-2, and rps10-2 led to the gain of new start codons, while atp6-1156, ccmFC-1315 and rps10-331 created new stop codons. This study reveals the genetic features of the S. samarangense mitogenome and provides a scientific basis for further studies of traits with an epistatic basis and for germplasm identification.
Collapse
Affiliation(s)
- Guilong Lu
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
- College of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Qing Li
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| |
Collapse
|
2
|
Hassan AH, Mokhtar MM, El Allali A. Transposable elements: multifunctional players in the plant genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1330127. [PMID: 38239225 PMCID: PMC10794571 DOI: 10.3389/fpls.2023.1330127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.
Collapse
Affiliation(s)
- Asmaa H. Hassan
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Morad M. Mokhtar
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| |
Collapse
|
3
|
Lu G, Wang W, Mao J, Li Q, Que Y. Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications. BMC PLANT BIOLOGY 2023; 23:541. [PMID: 37924024 PMCID: PMC10625231 DOI: 10.1186/s12870-023-04529-9] [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: 08/13/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Mitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported. RESULTS This study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019 bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (≥ 50 bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437 bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523 bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3). CONCLUSIONS This study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.
Collapse
Affiliation(s)
- Guilong Lu
- College of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Wenhua Wang
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China
| | - Juan Mao
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China
| | - Qing Li
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China.
| | - Youxiong Que
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
4
|
Qin DD, Liu R, Xu F, Dong G, Xu Q, Peng Y, Xu L, Cheng H, Guo G, Dong J, Li C. Characterization of a barley ( Hordeum vulgare L.) mutant with multiple stem nodes and spikes and dwarf ( msnsd) and fine-mapping of its causal gene. FRONTIERS IN PLANT SCIENCE 2023; 14:1189743. [PMID: 37484471 PMCID: PMC10359901 DOI: 10.3389/fpls.2023.1189743] [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: 03/20/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023]
Abstract
Introduction Multiple nodes and dwarf mutants in barley are a valuable resource for identifying genes that control shoot branching, vegetative growth and development. Methods In this study, physiological, microscopic and genetic analysis were conducted to characterize and fine-map the underling gene of a barley mutant with Multiple Stem Nodes and Spikes and Dwarf (msnsd), which was selected from EMS- and 60Co-treated barley cv. Edamai 934. Results and discussion The msnsd mutant had more stem nodes, lower plant height and a shorter plastochron than Edamai 934. Moreover, the mutant had two or more spikes on each tiller. Microscopic analysis showed that the dwarf phenotype of msnsd resulted from reduced cell lengths and cell numbers in the stem. Further physiological analysis showed that msnsd was GA3-deficient, with its plant height increasing after external GA3 application. Genetic analysis revealed that a single recessive nuclear gene, namely, HvMSNSD, controlled the msnsd phenotype. Using a segregating population derived from Harrington and the msnsd mutant, HvMSNSD was fine-mapped on chromosome 5H in a 200 kb interval using bulked segregant analysis (BSA) coupled with RNA-sequencing (BSR-seq), with a C-T substitution in the exon of HvTCP25 co-segregating with the msnsd phenotype. RNA-seq analysis showed that a gene encoding gibberellin 2-oxidase 8, a negative regulator of GA biosynthesis, was upregulated in the msnsd mutant. Several known genes related to inflorescence development that were also upregulated and enriched in the msnsd mutant. Collectively, we propose that HvMSNSD regulates the plastochron and morphology of reproductive organs, likely by coordinating GA homeostasis and changed expression of floral development related genes in barley. This study offers valuable insights into the molecular regulation of barley plant architecture and inflorescence development.
Collapse
Affiliation(s)
- Dandan D. Qin
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Hubei, Wuhan, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei, Wuhan, China
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei, Wuhan, China
| | - Rui Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Hubei, Wuhan, China
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei, Wuhan, China
| | - Fuchao Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Hubei, Wuhan, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei, Wuhan, China
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei, Wuhan, China
| | - Guoqing Dong
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei, Wuhan, China
| | - Qing Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Hubei, Wuhan, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei, Wuhan, China
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei, Wuhan, China
| | - Yanchun Peng
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Hubei, Wuhan, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei, Wuhan, China
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei, Wuhan, China
| | - Le Xu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Hubei, Jingzhou, China
| | - Hongna Cheng
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Hubei, Wuhan, China
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Hubei, Jingzhou, China
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Dong
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Hubei, Wuhan, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei, Wuhan, China
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei, Wuhan, China
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| |
Collapse
|
5
|
Lu G, Zhang K, Que Y, Li Y. Assembly and analysis of the first complete mitochondrial genome of Punica granatum and the gene transfer from chloroplast genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1132551. [PMID: 37416882 PMCID: PMC10320729 DOI: 10.3389/fpls.2023.1132551] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
Pomegranate (Punica granatum L.) is one of the oldest fruits with edible, medicinal and ornamental values. However, there is no report on the mitochondrial genome of pomegranate. In this study, the mitochondrial genome of P. granatum was sequenced, assembled and analyzed in detail, while the chloroplast genome was assembled using the same set of data. The results showed that the P. granatum mitogenome had a multi branched structure, using BGI + Nanopore mixed assembly strategy. The total genome length was 404,807 bp, with the GC content of 46.09%, and there were 37 protein coding genes, 20 tRNA genes and three rRNA genes. In the whole genome, 146 SSRs were identified. Besides, 400 pairs of dispersed repeats were detected, including 179 palindromic, 220 forward and one reverse. In the P. granatum mitochondrial genome, 14 homologous fragments of chloroplast genome were found, accounting for 0.54% of the total length. Phylogenetic analysis showed that among the published mitochondrial genomes of related genera, P. granatum had the closest genetic relationship with Lagerstroemia indica of Lythraceae. The 580 and 432 RNA editing sites were predicted on 37 protein coding genes of mitochondrial genome using BEDTools software and online website PREPACT respectively, but all were from C to U, of which ccmB and nad4 gene were most frequently edited, with 47 sites. This study provides a theoretical basis for understanding the evolution of higher plants, species classification and identification, and will also be useful for further utilization of pomegranate germplasm resources.
Collapse
Affiliation(s)
- Guilong Lu
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Kai Zhang
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanfeng Li
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Zhao Y, Huang Y, Gao Y, Wang Y, Wu H, Zhu H, Lu X, Ma Q. An EMS-induced allele of the brachytic2 gene can reduce plant height in maize. PLANT CELL REPORTS 2023; 42:749-761. [PMID: 36754893 DOI: 10.1007/s00299-023-02990-2] [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: 10/30/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
D129 is an EMS-induced mutant with dwarf phenotype, which has important breeding potential to cultivate new varieties suitable for high-density planting in maize Plant height is one of the important agronomic traits that affecting maize planting density, identification of superior dwarf mutants can provide important genetic materials for breeding new varieties suitable for high-density planting. In this study, we identified a dwarf mutant, d129, from maize EMS-induced mutant population. Gene mapping indicated that a G-to-A transition in the second exon of the br2 gene was responsible for the dwarf phenotype of the d129 mutant using MutMap method, which was further validated through allelism testing. Compared with WT plants, the average plant height and ear height of d129 were reduced by 26.67% and 39.43%, respectively, mainly due to a decrease in internode length. Furthermore, the d129 mutant exhibited increased internode diameter, which is important for increasing planting density due to the lodging resistance may be enhanced. Endogenous hormone measurement demonstrated that the contents of IAA and GA3 in the internode of the mutant were significantly lower than that of WT plants. RNA-seq analysis indicated that at least fifteen auxin-responsive and signaling-related genes exhibited differential expression, and some genes involved in cell development and other types of hormone signaling pathways, were also identified from the differential expressed genes. These genes may be related to the reduced hormone contents and decreased elongation of internode cells of the d129 mutant. Our study provided a novel dwarf mutant which can be applied in maize breeding to cultivate new varieties suitable for high-density planting.
Collapse
Affiliation(s)
- Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Breeding Engineering of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yuanxiang Huang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Breeding Engineering of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yajie Gao
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Breeding Engineering of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yixiao Wang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Breeding Engineering of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hongying Wu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Breeding Engineering of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hongjia Zhu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Breeding Engineering of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaoduo Lu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
- Key Laboratory of Breeding Engineering of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| |
Collapse
|
8
|
Ramakrishnan M, Papolu PK, Mullasseri S, Zhou M, Sharma A, Ahmad Z, Satheesh V, Kalendar R, Wei Q. The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome. PLANT CELL REPORTS 2023; 42:3-15. [PMID: 36401648 DOI: 10.1007/s00299-022-02945-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement. Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed.
Collapse
Affiliation(s)
- Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert's College (Autonomous), Kochi, 682018, Kerala, India
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, University of Helsinki, Biocenter 3, Viikinkaari 1, F1-00014, Helsinki, Finland.
- Institute of Plant Biology and Biotechnology (IPBB), Timiryazev Street 45, 050040, Almaty, Kazakhstan.
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| |
Collapse
|
9
|
Zhao S, Li X, Song J, Li H, Zhao X, Zhang P, Li Z, Tian Z, Lv M, Deng C, Ai T, Chen G, Zhang H, Hu J, Xu Z, Chen J, Ding J, Song W, Chang Y. Genetic dissection of maize plant architecture using a novel nested association mapping population. THE PLANT GENOME 2022; 15:e20179. [PMID: 34859966 DOI: 10.1002/tpg2.20179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The leaf angle (LA), plant height (PH), and ear height (EH) are key plant architectural traits influencing maize (Zea mays L.) yield. However, their genetic determinants have not yet been well-characterized. Here, we developed a maize advanced backcross-nested association mapping population in Henan Agricultural University (HNAU-NAM1) comprised of 1,625 BC1 F4 /BC2 F4 lines. These were obtained by crossing a diverse set of 12 representative inbred lines with the common GEMS41 line, which were then genotyped using the MaizeSNP9.4K array. Genetic diversity and phenotypic distribution analyses showed considerable levels of genetic variation. We obtained 18-88 quantitative trait loci (QTLs) associated with LA, PH, and EH by using three complementary mapping methods, named as separate linkage mapping, joint linkage mapping, and genome-wide association studies. Our analyses enabled the identification of ten QTL hot-spot regions associated with the three traits, which were distributed on nine different chromosomes. We further selected 13 major QTLs that were simultaneously detected by three methods and deduced the candidate genes, of which eight were not reported before. The newly constructed HNAU-NAM1 population in this study will further broaden our insights into understanding of genetic regulation of plant architecture, thus will help to improve maize yield and provide an invaluable resource for maize functional genomics and breeding research.
Collapse
Affiliation(s)
- Sheng Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xueying Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Junfeng Song
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural Univ., Beijing, 100193, China
| | - Huimin Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Xiaodi Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Peng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- College of Life Science and Technology, Guangxi Univ., Nanning, 530004, China
| | - Zhimin Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Zhiqiang Tian
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Meng Lv
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Ce Deng
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Tangshun Ai
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural Univ., Wuhan, 430070, China
| | - Hui Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jianlin Hu
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zhijun Xu
- Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524013, China
| | - Jiafa Chen
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Junqiang Ding
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural Univ., Beijing, 100193, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| |
Collapse
|
10
|
Phenotypic Characterization and Differential Gene Expression Analysis Reveal That Dwarf Mutant dwf Dwarfism Is Associated with Gibberellin in Eggplant. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7050114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dwarfism is a desirable trait in eggplant breeding, as it confers higher lodging resistance and allows simplified management and harvest. However, a few dwarf mutants have been reported, and the molecular mechanism underlying dwarfism in eggplant is completely unknown. Here, we report a dwarf mutant (dwf) isolated from an ethyl methyl sulfonate (EMS)-induced mutant library. The hypocotyl length, plant height, and length of internode cells of dwf were significantly decreased compared to those of the wild-type parent ‘14-345’ (WT). Differential gene expression analysis revealed that GA-related genes, including GA2ox and DELLA, were up-regulated whereas the gibberellin (GA3) content decreased in dwf. Moreover, exogenous GA3 treatment significantly increased the relative growth rate of dwf compared to WT, further indicating the important roles of GA in regulating the dwarf phenotype of dwf. Collectively, our findings shed light on GA-mediated dwarfism in dwf plants and offer a good germplasm that could be used for eggplant dwarfism breeding in the future.
Collapse
|
11
|
Strable J. Developmental genetics of maize vegetative shoot architecture. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:19. [PMID: 37309417 PMCID: PMC10236122 DOI: 10.1007/s11032-021-01208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/13/2023]
Abstract
More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01208-1.
Collapse
Affiliation(s)
- Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 USA
| |
Collapse
|