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Liu XY, Jiang RC, Ma B, Wang Y, Yang YZ, Xu C, Sun F, Tan BC. Maize requires Embryo defective27 for embryogenesis and seedling development. PLANT PHYSIOLOGY 2024; 195:430-445. [PMID: 38198212 DOI: 10.1093/plphys/kiae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
The essential role of plastid translation in embryogenesis has been established in many plants, but a retrograde signal triggered by defective plastid translation machinery that may leads to embryogenesis arrest remains unknown. In this study, we characterized an embryo defective27 (emb27) mutant in maize (Zea mays), and cloning indicates that Emb27 encodes the plastid ribosomal protein S13. The null mutant emb27-1 conditions an emb phenotype with arrested embryogenesis; however, the leaky mutant emb27-2 exhibits normal embryogenesis but an albino seedling-lethal phenotype. The emb27-1/emb27-2 trans-heterozygotes display varying phenotypes from emb to normal seeds but albino seedlings. Analysis of the Emb27 transcription levels in these mutants revealed that the Emb27 expression level in the embryo corresponds with the phenotypic expression of the emb27 mutants. In the W22 genetic background, an Emb27 transcription level higher than 6% of the wild-type level renders normal embryogenesis, whereas lower than that arrests embryogenesis. Mutation of Emb27 reduces the level of plastid 16S rRNA and the accumulation of the plastid-encoded proteins. As a secondary effect, splicing of several plastid introns was impaired in emb27-1 and 2 other plastid translation-defective mutants, emb15 and emb16, suggesting that plastome-encoded factors are required for the splicing of these introns, such as Maturase K (MatK). Our results indicate that EMB27 is essential for plastid protein translation, embryogenesis, and seedling development in maize and reveal an expression threshold of Emb27 for maize embryogenesis.
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Affiliation(s)
- Xin-Yuan Liu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Rui-Cheng Jiang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bing Ma
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yong Wang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yan-Zhuo Yang
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Chunhui Xu
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Feng Sun
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Lab of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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Vitale A, Pedrazzini E. StresSeed: The Unfolded Protein Response During Seed Development. FRONTIERS IN PLANT SCIENCE 2022; 13:869008. [PMID: 35432435 PMCID: PMC9008589 DOI: 10.3389/fpls.2022.869008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
During seed development, the endoplasmic reticulum (ER) takes care of the synthesis and structural maturation of very high amounts of storage proteins in a relatively short time. The ER must thus adjust its extension and machinery to optimize this process. The major signaling mechanism to maintain ER homeostasis is the unfolded protein response (UPR). Both storage proteins that assemble into ER-connected protein bodies and those that are delivered to protein storage vacuoles stimulate the UPR, but its extent and features are specific for the different storage protein classes and even for individual members of each class. Furthermore, evidence exists for anticipatory UPR directly connected to the development of storage seed cells and for selective degradation of certain storage proteins soon after their synthesis, whose signaling details are however still largely unknown. All these events are discussed, also in the light of known features of mammalian UPR.
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Zhang X, Zhu Y, Kremling KAG, Romay MC, Bukowski R, Sun Q, Gao S, Buckler ES, Lu F. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:273-290. [PMID: 34661697 DOI: 10.1007/s00122-021-03965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize.
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Affiliation(s)
- Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China.
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Karl A G Kremling
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
- USDA-ARS, R. W. Holley Center, Cornell University, Ithaca, NY, USA
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Hurst P, Schnable JC, Holding DR. Tandem duplicate expression patterns are conserved between maize haplotypes of the α-zein gene family. PLANT DIRECT 2021; 5:e346. [PMID: 34541444 PMCID: PMC8438537 DOI: 10.1002/pld3.346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/12/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Tandem duplication gives rise to copy number variation and subsequent functional novelty among genes as well as diversity between individuals in a species. Functional novelty can result from either divergence in coding sequence or divergence in patterns of gene transcriptional regulation. Here, we investigate conservation and divergence of both gene sequence and gene regulation between the copies of the α-zein gene family in maize inbreds B73 and W22. We used RNA-seq data generated from developing, self-pollinated kernels at three developmental stages timed to coincide with early and peak zein expression. The reference genome annotations for B73 and W22 were modified to ensure accurate inclusion of their respective α-zein gene models to accurately assess copy-specific expression. Expression analysis indicated that although the total expression of α-zeins is higher in W22, the pattern of expression in both lines is conserved. Additional analysis of publicly available RNA-seq data from a diverse population of maize inbreds also demonstrates variation in absolute expression, but conservation of expression patterns across a wide range of maize genotypes and α-zein haplotypes.
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Affiliation(s)
- Preston Hurst
- Department of Agronomy and Horticulture, Center for Plant Science InnovationUniversity of NebraskaLincolnNebraskaUSA
| | - James C. Schnable
- Department of Agronomy and Horticulture, Center for Plant Science InnovationUniversity of NebraskaLincolnNebraskaUSA
| | - David R. Holding
- Department of Agronomy and Horticulture, Center for Plant Science InnovationUniversity of NebraskaLincolnNebraskaUSA
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Parsons L, Ren Y, Yobi A, Hurst P, Angelovici R, Rodriguez O, Holding DR. Production and Selection of Quality Protein Popcorn Hybrids Using a Novel Ranking System and Combining Ability Estimates. FRONTIERS IN PLANT SCIENCE 2020; 11:698. [PMID: 32655587 PMCID: PMC7325744 DOI: 10.3389/fpls.2020.00698] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/04/2020] [Indexed: 05/27/2023]
Abstract
Popcorn varieties are agronomically sub-optimal and genetically limited compared to other maize subspecies. To increase genetic diversity and improve popcorn agronomics, dent germplasm has been introduced to popcorn with limited success and generally, major loss of popping. Between 2013 and 2018, 12 Quality Protein Popcorn (QPP) inbreds containing Quality Protein Maize (QPM) and popcorn germplasm were produced that maintained popping while carrying the opaque-2 allele conferring elevated kernel lysine. This is an opportune trait in the growing market for healthier snacks and a model for mining QPM traits into popcorn. We crossed QPP inbreds to explore the effects of heterosis on popcorn protein, popping quality, and plant agronomics and selected hybrids for further production. To rank and intermediately prescreen hybrids, we utilized a novel hybrid-ranking model adapted from a rank summation index while examining the inbred general combining ability and hybrid specific combining ability estimates for all traits. We observed a biological manifestation of heterosis by categorizing hybrids by pedigree that resulted in a stepwise progression of trait improvement. These results corroborated our hybrid selection and offered insight in basic heterosis research. Estimates for popcorn quality and agronomic trait covariances also suggest the synergistic introgression of highly vitreous dent maize (QPM) into popcorn, providing a likely explanation for the successfully maintained vitreous endosperm, protein quality and popping traits in line with a remodeled proteome. QPP hybrids maintained improved amino acid profiles although different popping methods variably affected popcorn's protein bound and free amino acid levels. This preliminary screening of QPP hybrids is enabling further quantitative selection for large-scale, complex trait comparison to currently marketed elite popcorn varieties.
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Affiliation(s)
- Leandra Parsons
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Ying Ren
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Preston Hurst
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | | | - David R. Holding
- Department of Agronomy and Horticulture, University of Nebraska – Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation – Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, United States
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