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Kelsang GA, Ni L, Zhao Z. Insights from the first chromosome-level genome assembly of the alpine gentian Gentiana straminea Maxim. DNA Res 2024; 31:dsae022. [PMID: 39017645 PMCID: PMC11375616 DOI: 10.1093/dnares/dsae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/18/2024] Open
Abstract
Gentiana straminea Maxim. is a perennial herb and mainly distributed in the Qinghai-Tibetan Plateau. To adapt to the extreme environment, it has developed particular morphological, physiological, and genetic structures. Also, rich in iridoids, it is one of the original plants of traditional Chinese herb 'Qinjiao'. Herein, we present its first chromosome-level genome sequence assembly and compare it with the genomes of other Gentiana species to facilitate the analysis of genomic characteristics. The assembled genome size of G. straminea was 1.25 Gb, with a contig N50 of 7.5 Mb. A total of 96.08% of the genome sequences was anchored on 13 pseudochromosomes, with a scaffold N50 of 92.70 Mb. A total of 54,310 protein-coding genes were predicted, 80.25% of which were functionally annotated. Comparative genomic analyses indicated that G. straminea experienced two whole-genome duplication events after the γ whole-genome triplication with other eudicots, and it diverged from other Gentiana species at ~3.2 Mya. A total of 142 enzyme-coding genes related to iridoid biosynthesis were identified in its genome. Additionally, we identified differences in the number and expression patterns of iridoid biosynthetic pathway genes in G. straminea compared with two other Gentiana species by integrating whole-genome sequence and transcriptomic analyses.
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Affiliation(s)
- Gyab Ala Kelsang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Mentseekhang, Traditional Tibetan Hospital, Lhasa 850000, China
| | - Lianghong Ni
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhili Zhao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Zhang D, Gan Y, Le L, Pu L. Epigenetic variation in maize agronomical traits for breeding and trait improvement. J Genet Genomics 2024:S1673-8527(24)00028-6. [PMID: 38310944 DOI: 10.1016/j.jgg.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, China
| | - Yujun Gan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Li Y, Li D, E L, Yang J, Liu W, Xu M, Ye J. ZmDRR206 Regulates Nutrient Accumulation in Endosperm through Its Role in Cell Wall Biogenesis during Maize Kernel Development. Int J Mol Sci 2023; 24:ijms24108735. [PMID: 37240079 DOI: 10.3390/ijms24108735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Dirigent proteins (DIRs) contribute to plant fitness by dynamically reorganizing the cell wall and/or by generating defense compounds during plant growth, development, and interactions with environmental stresses. ZmDRR206 is a maize DIR, it plays a role in maintaining cell wall integrity during seedling growth and defense response in maize, but its role in regulating maize kernel development is unclear. Association analysis of candidate genes indicated that the natural variations of ZmDRR206 were significantly associated with maize hundred-kernel weight (HKW). ZmDRR206 plays a dominant role in storage nutrient accumulation in endosperm during maize kernel development, ZmDRR206 overexpression resulted in small and shrunken maize kernel with significantly reduced starch content and significantly decreased HKW. Cytological characterization of the developing maize kernels revealed that ZmDRR206 overexpression induced dysfunctional basal endosperm transfer layer (BETL) cells, which were shorter with less wall ingrowth, and defense response was constitutively activated in developing maize kernel at 15 and 18 DAP by ZmDRR206 overexpression. The BETL-development-related genes and auxin signal-related genes were down-regulated, while cell wall biogenesis-related genes were up-regulated in developing BETL of the ZmDRR206-overexpressing kernel. Moreover, the developing ZmDRR206-overexpressing kernel had significantly reduced contents of the cell wall components such as cellulose and acid soluble lignin. These results suggest that ZmDRR206 may play a regulatory role in coordinating cell development, storage nutrient metabolism, and stress responses during maize kernel development through its role in cell wall biogenesis and defense response, and provides new insights into understanding the mechanisms of kernel development in maize.
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Affiliation(s)
- Yanmei Li
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Dongdong Li
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Lizhu E
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jiayi Yang
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Wenjing Liu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Mingliang Xu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jianrong Ye
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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Chandran AKN, Sandhu J, Irvin L, Paul P, Dhatt BK, Hussain W, Gao T, Staswick P, Yu H, Morota G, Walia H. Rice Chalky Grain 5 regulates natural variation for grain quality under heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1026472. [PMID: 36304400 PMCID: PMC9593041 DOI: 10.3389/fpls.2022.1026472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Heat stress occurring during rice (Oryza sativa) grain development reduces grain quality, which often manifests as increased grain chalkiness. Although the impact of heat stress on grain yield is well-studied, the genetic basis of rice grain quality under heat stress is less explored as quantifying grain quality is less tractable than grain yield. To address this, we used an image-based colorimetric assay (Red, R; and Green, G) for genome-wide association analysis to identify genetic loci underlying the phenotypic variation in rice grains exposed to heat stress. We found the R to G pixel ratio (RG) derived from mature grain images to be effective in distinguishing chalky grains from translucent grains derived from control (28/24°C) and heat stressed (36/32°C) plants. Our analysis yielded a novel gene, rice Chalky Grain 5 (OsCG5) that regulates natural variation for grain chalkiness under heat stress. OsCG5 encodes a grain-specific, expressed protein of unknown function. Accessions with lower transcript abundance of OsCG5 exhibit higher chalkiness, which correlates with higher RG values under stress. These findings are supported by increased chalkiness of OsCG5 knock-out (KO) mutants relative to wildtype (WT) under heat stress. Grains from plants overexpressing OsCG5 are less chalky than KOs but comparable to WT under heat stress. Compared to WT and OE, KO mutants exhibit greater heat sensitivity for grain size and weight relative to controls. Collectively, these results show that the natural variation at OsCG5 may contribute towards rice grain quality under heat stress.
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Affiliation(s)
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, Philippines
| | - Tian Gao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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5
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Zheng Y. Molecular mechanisms of maize endosperm transfer cell development. PLANT CELL REPORTS 2022; 41:1171-1180. [PMID: 34689216 DOI: 10.1007/s00299-021-02807-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/14/2021] [Indexed: 05/12/2023]
Abstract
Endosperm transfer cells function as the nutrient transporter, antimicrobic barrier, and signal mediator between filial and maternal tissues. Sugar supply of maternal tissues, sugar demand of filial tissues, and requirement for defence against pathogens are three elemental factors inducing differentiation of endosperm transfer cells. Epigenetic factors, especially MEG1, moderate the key genetic factor ZmMRP-1 to activate endosperm transfer cell-specific genes that control the flange wall ingrowth formation and defensin-like protein secretion in maize. Auxin and cytokinin are primary hormones involved in development of maize endosperm transfer cells. Crosstalk between glucose and hormone signaling regulates endosperm transfer cell development via modifying ZmMRP-1 expression. This review summarizes the current knowledge on maize endosperm transfer cell development, and discusses its potential molecular mechanisms. It is expected to strengthen the theoretical basis for structural and functional optimization of endosperm transfer cells, and yield improvement of kernels in maize.
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Affiliation(s)
- Yankun Zheng
- School of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China.
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7
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Hassan MU, Islam MM, Wang R, Guo J, Luo H, Chen F, Li X. Glutamine application promotes nitrogen and biomass accumulation in the shoot of seedlings of the maize hybrid ZD958. PLANTA 2020; 251:66. [PMID: 32065312 DOI: 10.1007/s00425-020-03363-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/09/2020] [Indexed: 05/21/2023]
Abstract
Glutamine (Gln) is an efficient nitrogen source in promoting aboveground nitrogen and biomass accumulation in ZD958 (an elite maize hybrid with great potential for further genetic improvement) seedlings when conditioning a smaller but adequate root system. Amino acids account for a significant part of nitrogen (N) resources in the soil. However, how amino acid-N affects crop growth remains to be further investigated. Here, glutamine (Gln) application (80% NH4NO3 + 20% Gln; mixed N) enhanced shoot growth of the maize hybrid ZD958. N concentration in the shoot increased, which is associated with favorable increases in SPAD values, GS/GOGAT activities, and accumulation of glutamate, asparagine, total free amino acids and soluble proteins in the shoot under mixed N. On the other hand, root growth was reduced when exposed to Gln as indicated by the significantly lower dry weight, root/shoot ratio, and primary, seminal, crown, and total root lengths, as well as unfavorable physiological alterations. Up-regulation of expression of ZmAMT1.3, ZmNRT2.1, and ZmAAP2 in the root and that of ZmAMT1.1, ZmAMT1.3, and ZmLHT1 in the shoot preconditioned N over-accumulation in the shoot and facilitated shoot growth, presumably via enhancing N translocation to the shoot, when Gln was supplied. Together, Gln is an efficient N source in promoting aboveground N and biomass accumulation in ZD958 seedlings when conditioning a smaller but adequate root system. Notably, ZD958's parental lines Z58 and Chang7-2 displayed a wide range of variations in Gln responses, which may be partially attributed to single nucleotide polymorphisms (SNPs) in cis-elements and coding regions revealed in this study and much larger quantities of unidentified genetic variations between Z58 and Chang7-2. Extensive genetic divergence of these two elite inbred lines implied large potentials for further genetic improvement of ZD958 in relation to organic N use efficiency.
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Affiliation(s)
- Mahmood Ul Hassan
- The Key Laboratory of Plant-Soil Interactions, MOE, Beijing, 100193, China
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Md Monirul Islam
- The Key Laboratory of Plant-Soil Interactions, MOE, Beijing, 100193, China
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Ruifeng Wang
- The Key Laboratory of Plant-Soil Interactions, MOE, Beijing, 100193, China
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Jingyu Guo
- The Key Laboratory of Plant-Soil Interactions, MOE, Beijing, 100193, China
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Huilan Luo
- The Key Laboratory of Plant-Soil Interactions, MOE, Beijing, 100193, China
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Fanjun Chen
- The Key Laboratory of Plant-Soil Interactions, MOE, Beijing, 100193, China
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Xuexian Li
- The Key Laboratory of Plant-Soil Interactions, MOE, Beijing, 100193, China.
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China.
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8
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Wegary D, Teklewold A, Prasanna BM, Ertiro BT, Alachiotis N, Negera D, Awas G, Abakemal D, Ogugo V, Gowda M, Semagn K. Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands. Sci Rep 2019; 9:13490. [PMID: 31530852 PMCID: PMC6748982 DOI: 10.1038/s41598-019-49861-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/28/2019] [Indexed: 11/08/2022] Open
Abstract
Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30-36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.
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Affiliation(s)
- Dagne Wegary
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Adefris Teklewold
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia.
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Berhanu T Ertiro
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Demewez Negera
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Geremew Awas
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Demissew Abakemal
- Ambo Agricultural Research Center, P.O. Box 37, West Shoa, Ambo, Ethiopia
| | - Veronica Ogugo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Kassa Semagn
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya.
- Africa Rice Center (AfricaRice), M'bé Research Station, 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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Kim E, Xiong Y, Kang BH, Sung S. Identification of Long Noncoding RNAs in the Developing Endosperm of Maize. Methods Mol Biol 2019; 1933:49-65. [PMID: 30945178 DOI: 10.1007/978-1-4939-9045-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maize endosperm consists of three distinct types of tissues, including the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Compartmentalization of these tissues during endosperm differentiation makes the endosperm development an excellent model to study changes in gene expression during development. By utilizing cryo-dissection of developing endosperm, morphologically distinct samples can be obtained for transcriptome and epigenome analysis. Here, we describe methods for the isolation of tissues from developing maize endosperm and for the transcriptome analysis to identify novel long noncoding RNAs. The transcriptome data can be further analyzed to illustrate spatiotemporal changes in both coding and noncoding transcripts during the endosperm development.
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Affiliation(s)
- Eundeok Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Yuqing Xiong
- Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Byung-Ho Kang
- Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
- School of Life Sciences, State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Sibum Sung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
- International Scholar, Kyung-Hee University, Suwon, South Korea.
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Abstract
The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally distinct cells. To compare gene expression patterns involved in maize endosperm cell differentiation, we isolated transcripts from cryo-dissected endosperm specimens enriched with BETL, AL, or SE at 8, 12, and 16 days after pollination (DAP). We performed transcriptome profiling of coding and long noncoding transcripts in the three cell types during differentiation and identified clusters of the transcripts exhibiting spatio-temporal specificities. Our analysis uncovered that the BETL at 12 DAP undergoes the most dynamic transcriptional regulation for both coding and long noncoding transcripts. In addition, our transcriptome analysis revealed spatio-temporal regulatory networks of transcription factors, imprinted genes, and loci marked with histone H3 trimethylated at lysine 27. Our study suggests that various regulatory mechanisms contribute to the genetic networks specific to the functions and structures of the cell types of the endosperm.
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Doll NM, Depège-Fargeix N, Rogowsky PM, Widiez T. Signaling in Early Maize Kernel Development. MOLECULAR PLANT 2017; 10:375-388. [PMID: 28267956 DOI: 10.1016/j.molp.2017.01.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 05/26/2023]
Abstract
Developing the next plant generation within the seed requires the coordination of complex programs driving pattern formation, growth, and differentiation of the three main seed compartments: the embryo (future plant), the endosperm (storage compartment), representing the two filial tissues, and the surrounding maternal tissues. This review focuses on the signaling pathways and molecular players involved in early maize kernel development. In the 2 weeks following pollination, functional tissues are shaped from single cells, readying the kernel for filling with storage compounds. Although the overall picture of the signaling pathways regulating embryo and endosperm development remains fragmentary, several types of molecular actors, such as hormones, sugars, or peptides, have been shown to be involved in particular aspects of these developmental processes. These molecular actors are likely to be components of signaling pathways that lead to transcriptional programming mediated by transcriptional factors. Through the integrated action of these components, multiple types of information received by cells or tissues lead to the correct differentiation and patterning of kernel compartments. In this review, recent advances regarding the four types of molecular actors (hormones, sugars, peptides/receptors, and transcription factors) involved in early maize development are presented.
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Affiliation(s)
- Nicolas M Doll
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Nathalie Depège-Fargeix
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Peter M Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France.
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12
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Li L, Briskine R, Schaefer R, Schnable PS, Myers CL, Flagel LE, Springer NM, Muehlbauer GJ. Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias. BMC Genomics 2016; 17:875. [PMID: 27814670 PMCID: PMC5097351 DOI: 10.1186/s12864-016-3194-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/22/2016] [Indexed: 01/08/2023] Open
Abstract
Background Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. Results To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks – maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. Conclusions Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types, duplication ages and co-expression consequences. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3194-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.,National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Roman Briskine
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Robert Schaefer
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lex E Flagel
- Monsanto Company, Chesterfield, MO, 63017, USA.,Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA. .,Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA.
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Zhang X, Hirsch CN, Sekhon RS, de Leon N, Kaeppler SM. Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1907-17. [PMID: 26826570 PMCID: PMC4783370 DOI: 10.1093/jxb/erw006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Seed size is an important component of grain yield and a key determinant trait for crop domestication. The Krug Yellow Dent long-term selection experiment for large and small seed provides a valuable resource to dissect genetic and phenotypic changes affecting seed size within a common genetic background. In this study, inbred lines derived from Krug Large Seed (KLS) and Krug Small Seed (KSS) populations and reciprocal F1 crosses were used to investigate developmental and molecular mechanisms governing seed size. Seed morphological characteristics showed striking differences between KLS and KSS inbred lines, and the reciprocal cross experiment revealed a strong maternal influence on both seed weight and seed size. Quantification of endosperm area, starchy endosperm cell size, and kernel dry mass accumulation indicated a positive correlation between seed size, endosperm cell number, and grain filling rate, and patterns of grain filling in reciprocal crosses mirrored that of the maternal parent. Consistent with the maternal contribution to seed weight, transcriptome profiling of reciprocal F1 hybrids showed substantial similarities to the maternal parent. A set of differentially expressed genes between KLS and KSS inbreds were found, which fell into a broad number of functional categories including DNA methylation, nucleosome assembly, and heat stress response. In addition, gene co-expression network analysis of parental inbreds and reciprocal F1 hybrids identified co-expression modules enriched in ovule development and DNA methylation, implicating these two processes in seed size determination. These results expand our understanding of seed size regulation and help to uncover the developmental and molecular basis underlying maternal control of seed size in maize.
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Affiliation(s)
- Xia Zhang
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Rajandeep S Sekhon
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
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14
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Zhan J, Thakare D, Ma C, Lloyd A, Nixon NM, Arakaki AM, Burnett WJ, Logan KO, Wang D, Wang X, Drews GN, Yadegari R. RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. THE PLANT CELL 2015; 27:513-31. [PMID: 25783031 PMCID: PMC4558669 DOI: 10.1105/tpc.114.135657] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/28/2015] [Accepted: 02/26/2015] [Indexed: 05/18/2023]
Abstract
Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the genetic networks that regulate endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the maize (Zea mays) kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene coexpression network analysis identified coexpression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a coexpression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types.
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Affiliation(s)
- Junpeng Zhan
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Dhiraj Thakare
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Chuang Ma
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Alan Lloyd
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Neesha M Nixon
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Angela M Arakaki
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - William J Burnett
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Kyle O Logan
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Dongfang Wang
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Xiangfeng Wang
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Gary N Drews
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Ramin Yadegari
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
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15
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Park J, Cui Y, Kang BH. AtPGL3 is an Arabidopsis BURP domain protein that is localized to the cell wall and promotes cell enlargement. FRONTIERS IN PLANT SCIENCE 2015; 6:412. [PMID: 26106400 PMCID: PMC4460304 DOI: 10.3389/fpls.2015.00412] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/22/2015] [Indexed: 05/22/2023]
Abstract
The BURP domain is a plant-specific domain that has been identified in secretory proteins, and some of these are involved in cell wall modification. The tomato polygalacturonase I complex involved in pectin degradation in ripening fruits has a non-catalytic subunit that has a BURP domain. This protein is called polygalacturonase 1 beta (PG1β) and the Arabidopsis genome encodes three proteins that exhibit strong amino acid similarities with PG1β? We generated Arabidopsis lines in which expression levels of AtPGLs are altered in order to investigate the biological roles of the Arabidopsis PG1β-like proteins (AtPGLs). Among the three AtPGLs (AtPGL1-3), AtPGL3 exhibited the highest transcriptional activity throughout all developmental stages. AtPGL triple mutant plants have smaller rosette leaves than those of wild type plants because the leaf cells are smaller in the mutant plants. Interestingly, when we overexpressed AtPGL3 using a 35S promoter, leaf cells in transgenic plants grew larger than those of the wild type. A C-terminal GFP fusion protein of AtPGL3 complemented phenotypes of the triple mutant plants and it localized to the cell wall. A truncated AtPGL3-GFP fusion protein lacking the BURP domain failed to rescue the mutant phenotypes even though the GFP protein was targeted to the cell wall, indicating that the BURP domain is required for the protein's effect on cell expansion. Quantitative RT-PCR and immunoblot analyses indicated that the α-expansin 6 gene is up-regulated in the overexpressor plants. Taken together, these results indicate that AtPGL3 is an apoplastic BURP domain protein playing a role in cell expansion.
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Affiliation(s)
- Jiyoung Park
- Plant Molecular Cellular Biology Program, Microbiology and Cell Sciences, University of FloridaGainesville, FL, USA
| | - Yong Cui
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Byung-Ho Kang
- Plant Molecular Cellular Biology Program, Microbiology and Cell Sciences, University of FloridaGainesville, FL, USA
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong KongHong Kong, China
- *Correspondence: Byung-Ho Kang, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, 409 East Block Science Center, Shatin, NT, Hong Kong, China
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16
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Bai F, Settles AM. Imprinting in plants as a mechanism to generate seed phenotypic diversity. FRONTIERS IN PLANT SCIENCE 2014; 5:780. [PMID: 25674092 PMCID: PMC4307191 DOI: 10.3389/fpls.2014.00780] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/16/2014] [Indexed: 05/21/2023]
Abstract
Normal plant development requires epigenetic regulation to enforce changes in developmental fate. Genomic imprinting is a type of epigenetic regulation in which identical alleles of genes are expressed in a parent-of-origin dependent manner. Deep sequencing of transcriptomes has identified hundreds of imprinted genes with scarce evidence for the developmental importance of individual imprinted loci. Imprinting is regulated through global DNA demethylation in the central cell prior to fertilization and directed repression of individual loci with the Polycomb Repressive Complex 2 (PRC2). There is significant evidence for transposable elements and repeat sequences near genes acting as cis-elements to determine imprinting status of a gene, implying that imprinted gene expression patterns may evolve randomly and at high frequency. Detailed genetic analysis of a few imprinted loci suggests an imprinted pattern of gene expression is often dispensable for seed development. Few genes show conserved imprinted expression within or between plant species. These data are not fully explained by current models for the evolution of imprinting in plant seeds. We suggest that imprinting may have evolved to provide a mechanism for rapid neofunctionalization of genes during seed development to increase phenotypic diversity of seeds.
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Affiliation(s)
| | - A. M. Settles
- *Correspondence: A. M. Settles, Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, P. O. Box 110690, Gainesville, FL 32611-0690, USA e-mail:
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