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Zhang Y, Yuan Y, Xi H, Zhang Y, Gao C, Ma M, Huang Q, Li F, Yang Z. Promotion of apoplastic oxidative burst by artificially selected GhCBSX3A enhances Verticillium dahliae resistance in upland cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2154-2168. [PMID: 38558071 DOI: 10.1111/tpj.16736] [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: 11/29/2023] [Revised: 02/21/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
Verticillium wilt (VW) is a devasting disease affecting various plants, including upland cotton, a crucial fiber crop. Despite its impact, the genetic basis underlying cotton's susceptibility or defense against VW remains unclear. Here, we conducted a genome-wide association study on VW phenotyping in upland cotton and identified a locus on A13 that is significantly associated with VW resistance. We then identified a cystathionine β-synthase domain gene at A13 locus, GhCBSX3A, which was induced by Verticillium dahliae. Functional analysis, including expression silencing in cotton and overexpression in Arabidopsis thaliana, confirmed that GhCBSX3A is a causal gene at the A13 locus, enhancing SAR-RBOHs-mediated apoplastic oxidative burst. We found allelic variation on the TATA-box of GhCBSX3A promoter attenuated its expression in upland cotton, thereby weakening VW resistance. Interestingly, we discovered that altered artificial selection of GhCBSX3A_R (an elite allele for VW) under different VW pressures during domestication and other improved processes allows specific human needs to be met. Our findings underscore the importance of GhCBSX3A in response to VW, and we propose a model for defense-associated genes being selected depending on the pathogen's pressure. The identified locus and gene serve as promising targets for VW resistance enhancement in cotton through genetic engineering.
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Affiliation(s)
- Yihao Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, National Wheat Innovation Center and Center for Crop Genome Engineering, Zhengzhou, 450001, Henan, China
| | - Yuan Yuan
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hongfang Xi
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yaning Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Chenxu Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
| | - Meng Ma
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qian Huang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China
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Wang T, Duan S, Xu C, Wang Y, Zhang X, Xu X, Chen L, Han Z, Wu T. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nat Commun 2023; 14:7377. [PMID: 37968318 PMCID: PMC10651928 DOI: 10.1038/s41467-023-43270-7] [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: 01/19/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
Structural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar 'Granny Smith' and the widely cultivated cultivar 'Red Fuji'. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs. We also observe CNVs that are positively correlated with expression levels of the genes they are associated with. Furthermore, we show that the noncoding RNA generated from a 209 bp insertion in the intron of mitogen-activated protein kinase homology encoding gene, MMK2, regulates the gene expression and affects fruit coloration. Moreover, we identify overlapping SVs associated with fruit quality and biotic resistance. This pan-genome uncovers possible contributions of CNVs to gene expression and highlights the role of SVs in apple domestication and economically important traits.
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Affiliation(s)
- Ting Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shiyao Duan
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Chen Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China.
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China.
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Wang X, Jin B, Yan W, Wang J, Xu J, Cai C, Qi X, Xu Q, Yang X, Xu X, Chen X. Cucumber abscisic acid 8'-hydroxylase Csyf2 regulates yellow flesh by modulating carotenoid biosynthesis. PLANT PHYSIOLOGY 2023; 193:1001-1015. [PMID: 37394925 DOI: 10.1093/plphys/kiad383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 07/04/2023]
Abstract
Cucumber (Cucumis sativus L.) flesh is typically colorless or pale green. Flesh with yellow or orange pigment, determined mainly by carotenoid content and composition, is mostly found in semi-wild Xishuangbanna cucumber, which has a very narrow genetic background. Here, we identified a spontaneous cucumber mutant with yellow flesh (yf-343), which accumulated more β-cryptoxanthin and less lutein than regular cultivated European glasshouse-type cucumbers. Genetic analysis revealed that the yellow flesh phenotype was controlled by a single recessive gene. Through fine mapping and gene sequencing, we identified the candidate gene C. sativus yellow flesh 2 (Csyf2), encoding an abscisic acid (ABA) 8'-hydroxylase. Overexpression and RNAi-silencing of Csyf2 in cucumber hairy roots produced lower and higher ABA contents than in non-transgenic controls, respectively. Further, RNA-seq analysis suggested that genes related to ABA signal transduction were differentially expressed in fruit flesh between yf-343 and its wild type, BY, with white flesh. The carotenoid biosynthesis pathway was specifically enriched in fruit flesh at 30 days after pollination when yf-343 fruit flesh turns yellow. Our findings highlight a promising target for gene editing to increase carotenoid content, expanding our genetic resources for pigmented cucumber flesh breeding for improving the nutritional quality of cucumber.
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Affiliation(s)
- Xueting Wang
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Boyan Jin
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Wenjing Yan
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jiaxi Wang
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jun Xu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Congxi Cai
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xiaohua Qi
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Qiang Xu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xiaodong Yang
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xuewen Xu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xuehao Chen
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Chen H, Liu X, Li S, Yuan L, Mu H, Wang Y, Li Y, Duan W, Fan P, Liang Z, Wang L. The class B heat shock factor HSFB1 regulates heat tolerance in grapevine. HORTICULTURE RESEARCH 2023; 10:uhad001. [PMID: 36938570 PMCID: PMC10018785 DOI: 10.1093/hr/uhad001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/28/2022] [Indexed: 06/01/2023]
Abstract
Grape is a widely cultivated crop with high economic value. Most cultivars derived from mild or cooler climates may not withstand increasing heat stress. Therefore, dissecting the mechanisms of heat tolerance in grapes is of particular significance. Here, we performed comparative transcriptome analysis of Vitis davidii 'Tangwei' (heat tolerant) and Vitis vinifera 'Jingxiu' (heat sensitive) grapevines after exposure to 25°C, 40°C, or 45°C for 2 h. More differentially expressed genes (DEGs) were detected in 'Tangwei' than in 'Jingxiu' in response to heat stress, and the number of DEGs increased with increasing treatment temperatures. We identified a class B Heat Shock Factor, HSFB1, which was significantly upregulated in 'Tangwei', but not in 'Jingxiu', at high temperature. VdHSFB1 from 'Tangwei' and VvHSFB1 from 'Jingxiu' differ in only one amino acid, and both showed similar transcriptional repression activities. Overexpression and RNA interference of HSFB1 in grape indicated that HSFB1 positively regulates the heat tolerance. Moreover, the heat tolerance of HSFB1-overexpressing plants was positively correlated to HSFB1 expression level. The activity of the VdHSFB1 promoter is higher than that of VvHSFB1 under both normal and high temperatures. Promoter analysis showed that more TATA-box and AT~TATA-box cis-elements are present in the VdHSFB1 promoter than the VvHSFB1 promoter. The promoter sequence variations between VdHSFB1 and VvHSFB1 likely determine the HSFB1 expression levels that influence heat tolerance of the two grape germplasms with contrasting thermotolerance. Collectively, we validated the role of HSFB1 in heat tolerance, and the knowledge gained will advance our ability to breed heat-tolerant grape cultivars.
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Affiliation(s)
- Haiyang Chen
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinna Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenchang Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546, USA
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Huayuan Mu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Yang Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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Savinkova LK, Sharypova EB, Kolchanov NA. On the Role of TATA Boxes and TATA-Binding Protein in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1000. [PMID: 36903861 PMCID: PMC10005294 DOI: 10.3390/plants12051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
For transcription initiation by RNA polymerase II (Pol II), all eukaryotes require assembly of basal transcription machinery on the core promoter, a region located approximately in the locus spanning a transcription start site (-50; +50 bp). Although Pol II is a complex multi-subunit enzyme conserved among all eukaryotes, it cannot initiate transcription without the participation of many other proteins. Transcription initiation on TATA-containing promoters requires the assembly of the preinitiation complex; this process is triggered by an interaction of TATA-binding protein (TBP, a component of the general transcription factor TFIID (transcription factor II D)) with a TATA box. The interaction of TBP with various TATA boxes in plants, in particular Arabidopsis thaliana, has hardly been investigated, except for a few early studies that addressed the role of a TATA box and substitutions in it in plant transcription systems. This is despite the fact that the interaction of TBP with TATA boxes and their variants can be used to regulate transcription. In this review, we examine the roles of some general transcription factors in the assembly of the basal transcription complex, as well as functions of TATA boxes of the model plant A. thaliana. We review examples showing not only the involvement of TATA boxes in the initiation of transcription machinery assembly but also their indirect participation in plant adaptation to environmental conditions in responses to light and other phenomena. Examples of an influence of the expression levels of A. thaliana TBP1 and TBP2 on morphological traits of the plants are also examined. We summarize available functional data on these two early players that trigger the assembly of transcription machinery. This information will deepen the understanding of the mechanisms underlying transcription by Pol II in plants and will help to utilize the functions of the interaction of TBP with TATA boxes in practice.
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Chen Y, Bao W, Hong W, Dong X, Gong M, Cheng Q, Mao K, Yao C, Liu Z, Wang N. Evaluation of eleven kiwifruit genotypes for bicarbonate tolerance and characterization of two tolerance-contrasting genotypes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:202-213. [PMID: 36427382 DOI: 10.1016/j.plaphy.2022.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Screening bicarbonate-tolerant genotypes is an environmentally-friendly and long-term effective strategy to cope with bicarbonate-induced chlorosis in fruit crops grown on calcareous soils. We investigated eleven genotypes from four kiwifruit species (Actinidia chinensis, A. macrosperma, A. polygama, and A. valvata) for differences in bicarbonate tolerance. We also characterized the physiological and molecular differences in two contrasting genotypes of this group. In the first experiment, bicarbonate-treated plantlets were irrigated with 3.0 g L-1 CaCO3 and 5.04 g L-1 NaHCO3 in peat and perlite medium culture. Based on principal component analysis, weight-based membership function method and cluster analysis, the tested genotypes were classified into three groups: (1) tolerant, including YX, Av-1, Acd, Ap, Av-2, and QM; (2) moderately tolerant, including Av-3, Am, Av-4, and HWD; and (3) sensitive, including only QH. In the second experiment, QH (bicarbonate-sensitive) and YX (bicarbonate-tolerant) were grown in sand culture with 4.0 g L-1 CaCO3 and 0.84 g L-1 or 1.26 g L-1 NaHCO3. Compared with QH, YX showed a better ability to take up iron (Fe) by roots and to transport Fe from roots to shoots in the bicarbonate treatments, probably due to a better capacity to protect from oxidative damage and to excrete protons, and a differential expression of genes associated with Fe uptake and translocation, including HA8, IRT1, YSL3 and NRAMP3. The results can facilitate identifying potential resources for bicarbonate tolerance and breeding new rootstocks, and contribute to the elucidation of the bicarbonate tolerance mechanisms in the genus Actinidia.
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Affiliation(s)
- Yuanlei Chen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenwu Bao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Weijin Hong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaoke Dong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Manyu Gong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Quanqi Cheng
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ke Mao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China; State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunchao Yao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhande Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Nannan Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Yang X, Wu B, Liu J, Zhang Z, Wang X, Zhang H, Ren X, Zhang X, Wang Y, Wu T, Xu X, Han Z, Zhang X. A single QTL harboring multiple genetic variations leads to complicated phenotypic segregation in apple flesh firmness and crispness. PLANT CELL REPORTS 2022; 41:2379-2391. [PMID: 36208306 DOI: 10.1007/s00299-022-02929-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Within a QTL, the genetic recombination and interactions among five and two functional variations at MdbHLH25 and MdWDR5A caused much complicated phenotype segregation in apple FFR and FCR. The storability of climacteric fruit like apple is a quantitative trait. We previously identified 62 quantitative trait loci (QTLs) associating flesh firmness retainability (FFR) and flesh crispness retainability (FCR), but only a few functional genetic variations were identified and validated. The genetic variation network controlling fruit storability is far to be understood and diagnostic markers are needed for molecular breeding. We previously identified overlapped QTLs F16.1/H16.2 for FFR and FCR using an F1 population derived from 'Zisai Pearl' × 'Red Fuji'. In this study, five and two single-nucleotide polymorphisms (SNPs) were identified on the candidate genes MdbHLH25 and MdWDR5A within the QTL region. The SNP1 A allele at MdbHLH25 promoter reduced the expression and SNP2 T allele and/or SNP4/5 GT alleles at the exons attenuated the function of MdbHLH25 by downregulating the expression of the target genes MdACS1, which in turn led to a reduction in ethylene production and maintenance of higher flesh crispness. The SNPs did not alter the protein-protein interaction between MdbHLH25 and MdWDR5A. The joint effect of SNP genotype combinations by the SNPs on MdbHLH25 (SNP1, SNP2, and SNP4) and MdWDR5A (SNPi and SNPii) led to a much broad spectrum of phenotypic segregation in FFR and FCR. Together, the dissection of these genetic variations contributes to understanding the complicated effects of a QTL and provides good potential for marker development in molecular breeding.
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Affiliation(s)
- Xianglong Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jing Liu
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Zhongyan Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuan Wang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Haie Zhang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xuejun Ren
- Testing and Analysis Center, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
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OsTBP2.1, a TATA-Binding Protein, Alters the Ratio of OsNRT2.3b to OsNRT2.3a and Improves Rice Grain Yield. Int J Mol Sci 2022; 23:ijms231810795. [PMID: 36142708 PMCID: PMC9503026 DOI: 10.3390/ijms231810795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
The OsNRT2.3a and OsNRT2.3b isoforms play important roles in the uptake and transport of nitrate during rice growth. However, it is unclear which cis-acting element controls the transcription of OsNRT2.3 into these specific isoforms. In this study, we used a yeast one-hybrid assay to obtain the TATA-box binding protein OsTBP2.1, which binds to the TATA-box of OsNRT2.3, and verified its important role through transient expression and RNA-seq. We found that the TATA-box of OsNRT2.3 mutants and binding protein OsTBP2.1 together increased the transcription ratio of OsNRT2.3b to OsNRT2.3a. The overexpression of OsTBP2.1 promoted nitrogen uptake and increased rice yield compared with the wild-type; however, the OsTBP2.1 T-DNA mutant lines exhibited the opposite trend. Detailed analyses demonstrated that the TATA-box was the key cis-regulatory element for OsNRT2.3 to be transcribed into OsNRT2.3a and OsNRT2.3b. Additionally, this key cis-regulatory element, together with the binding protein OsTBP2.1, promoted the development of rice and increased grain yield.
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Hao P, Lv X, Fu M, Xu Z, Tian J, Wang Y, Zhang X, Xu X, Wu T, Han Z. Long-distance mobile mRNA CAX3 modulates iron uptake and zinc compartmentalization. EMBO Rep 2022; 23:e53698. [PMID: 35254714 PMCID: PMC9066076 DOI: 10.15252/embr.202153698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/25/2022] [Accepted: 02/24/2022] [Indexed: 12/15/2022] Open
Abstract
Iron deficiency in plants can lead to excessive absorption of zinc; however, important details of this mechanism have yet to be elucidated. Here, we report that MdCAX3 mRNA is transported from the leaf to the root, and that MdCAX3 is then activated by MdCXIP1. Suppression of MdCAX3 expression leads to an increase in the root apoplastic pH, which is associated with the iron deficiency response. Notably, overexpression of MdCAX3 does not affect the apoplastic pH in a MdCXIP1 loss-of-function Malus baccata (Mb) mutant that has a deletion in the MdCXIP1 promoter. This deletion in Mb weakens MdCXIP1 expression. Co-expression of MdCAX3 and MdCXIP1 in Mb causes a decrease in the root apoplastic pH. Furthermore, suppressing MdCAX3 in Malus significantly reduces zinc vacuole compartmentalization. We also show that MdCAX3 activated by MdCXIP1 is not only involved in iron uptake, but also in regulating zinc detoxification by compartmentalizing zinc in vacuoles to avoid iron starvation-induced zinc toxicity. Thus, mobile MdCAX3 mRNA is involved in the regulation of iron and zinc homeostasis in response to iron starvation.
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Affiliation(s)
- Pengbo Hao
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Xinmin Lv
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Mengmeng Fu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Zhen Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Ji Tian
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yi Wang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, China
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Fan Z, Wu Y, Zhao L, Fu L, Deng L, Deng J, Ding D, Xiao S, Deng X, Peng S, Pan Z. MYB308-mediated transcriptional activation of plasma membrane H + -ATPase 6 promotes iron uptake in citrus. HORTICULTURE RESEARCH 2022; 9:uhac088. [PMID: 35685222 PMCID: PMC9171118 DOI: 10.1093/hr/uhac088] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/30/2022] [Indexed: 05/15/2023]
Abstract
Iron-deficiency chlorosis is a common nutritional disorder in crops grown on alkaline or calcareous soils. Although the acclimation mechanism to iron deficiency has been investigated, the genetic regulation of iron acquisition is still unclear. Here, by comparing the iron uptake process between the iron-poor-soil-tolerant citrus species Zhique (ZQ) and the iron-poor-soil-sensitive citrus species trifoliate orange (TO), we discovered that enhanced root H + efflux is crucial for the tolerance to iron deficiency in ZQ. The H+ efflux is mainly regulated by a plasma membrane-localized H+-ATPase, HA6, the expression of which is upregulated in plants grown in soil with low iron content, and significantly higher in the roots of ZQ than TO. Overexpression of the HA6 gene in the Arabidopsis thaliana aha2 mutant, defective in iron uptake, recovered the wild-type phenotype. In parallel, overexpression of the HA6 gene in TO significantly increased iron content of plants. Moreover, an iron deficiency-induced transcription factor, MYB308, was revealed to bind the promoter and activate the expression of HA6 in ZQ in yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays. Overexpression of MYB308 in ZQ roots significantly increased the expression level of the HA6 gene. However, MYB308 cannot bind or activate the HA6 promoter in TO due to the sequence variation of the corresponding MYB308 binding motif. Taking these results together, we propose that the MYB308 could activate HA6 to promote root H+ efflux and iron uptake, and that the distinctive MYB308-HA6 transcriptional module may be, at least in part, responsible for the iron deficiency tolerance in citrus.
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Affiliation(s)
- Zhengyan Fan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifang Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liuying Zhao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Lina Fu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Lile Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiarui Deng
- Chenggu Fruit Industry Technical Guidance Station, Shaanxi 723200, China
| | - Dekuan Ding
- Chenggu Fruit Industry Technical Guidance Station, Shaanxi 723200, China
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research & Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, Rockville, MD 20850, USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shu’ang Peng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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11
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Lv X, Sun Y, Hao P, Zhang C, Tian J, Fu M, Xu Z, Wang Y, Zhang X, Xu X, Wu T, Han Z. RBP differentiation contributes to selective transmissibility of OPT3 mRNAs. PLANT PHYSIOLOGY 2021; 187:1587-1604. [PMID: 34618059 PMCID: PMC8566248 DOI: 10.1093/plphys/kiab366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Long-distance mobile mRNAs play key roles in gene regulatory networks that control plant development and stress tolerance. However, the mechanisms underlying species-specific delivery of mRNA still need to be elucidated. Here, the use of grafts involving highly heterozygous apple (Malus) genotypes allowed us to demonstrate that apple (Malus domestica) oligopeptide transporter3 (MdOPT3) mRNA can be transported over a long distance, from the leaf to the root, to regulate iron uptake; however, the mRNA of Arabidopsis (Arabidopsis thaliana) oligopeptide transporter 3 (AtOPT3), the MdOPT3 homolog from A. thaliana, does not move from shoot to root. Reciprocal heterologous expression of the two types of mRNAs showed that the immobile AtOPT3 became mobile and moved from the shoot to the root in two woody species, Malus and Populus, while the mobile MdOPT3 became immobile in two herbaceous species, A. thaliana and tomato (Solanum lycopersicum). Furthermore, we demonstrated that the different transmissibility of OPT3 in A. thaliana and Malus might be caused by divergence in RNA-binding proteins between herbaceous and woody plants. This study provides insights into mechanisms underlying differences in mRNA mobility and validates the important physiological functions associated with this process.
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Affiliation(s)
- Xinmin Lv
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yaqiang Sun
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Pengbo Hao
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Cankui Zhang
- Department of Agronomy and Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Ji Tian
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Mengmeng Fu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhen Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
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12
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Gan Z, Yuan X, Shan N, Wan C, Chen C, Xu Y, Xu Q, Chen J. AcWRKY40 mediates ethylene biosynthesis during postharvest ripening in kiwifruit. PLANT SCIENCE 2021; 309:110948. [PMID: 34134847 DOI: 10.1016/j.plantsci.2021.110948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
WRKY transcription factors belong to a superfamily that is involved in many important biological processes, including plant development and senescence. However, little is known about the transcriptional regulation mechanisms of WRKY genes involved in kiwifruit postharvest ripening. Here, we isolated a WRKY gene from the kiwifruit genome and named it AcWRKY40. AcWRKY40 is a nucleus-localized protein that possesses transcriptional activation activity. The expression of AcWRKY40 was detected, and the gene responded to ethylene treatment during kiwifruit postharvest ripening, indicating its involvement in this process at the transcriptional level. We found multiple cis-acting elements related to maturation and senescence in the AcWRKY40 promoter. GUS activity analysis showed that its promoter activity was induced by exogenous ethylene. Yeast one-hybrid and dual-luciferase assays demonstrated that AcWRKY40 binds to the promoters of AcSAM2, AcACS1, and AcACS2 to activate them. In addition, transient transformations showed that AcWRKY40 enhances the expression of AcSAM2, AcACS1, and AcACS2. Taken together, these results suggest that AcWRKY40 is involved in kiwifruit postharvest ripening, possibly by regulating the expression of genes related to ethylene biosynthesis, thus deepening our understanding of the regulatory mechanisms of WRKY transcription factors in fruit ripening.
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Affiliation(s)
- Zengyu Gan
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xin Yuan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Nan Shan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chunpeng Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chuying Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yunhe Xu
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qin Xu
- Agriculture and Rural Bureau of Gongcheng Yao Autonomous County, Guilin, 542500, China
| | - Jinyin Chen
- Jiangxi Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits and Vegetables, Jiangxi Agricultural University, Nanchang, 330045, China; College of Materials and Chemical Engineering, Pingxiang University, Pingxiang, 330075, China.
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13
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Jia D, Wu P, Shen F, Li W, Zheng X, Wang Y, Yuan Y, Zhang X, Han Z. Genetic variation in the promoter of an R2R3-MYB transcription factor determines fruit malate content in apple (Malus domestica Borkh.). PLANT PHYSIOLOGY 2021; 186:549-568. [PMID: 33624810 PMCID: PMC8154052 DOI: 10.1093/plphys/kiab098] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/13/2021] [Indexed: 05/25/2023]
Abstract
Deciphering the mechanism of malate accumulation in apple (Malus domestica Borkh.) fruits can help to improve their flavor quality and enhance their benefits for human health. Here, we analyzed malate content as a quantitative trait that is determined mainly by genetic effects. In a previous study, we identified an R2R3-MYB transcription factor named MdMYB44 that was a candidate gene in qtl08.1 (quantitative trait locus mapped to chromosome 8) of fruit malate content. In the present study, we established that MdMYB44 negatively regulates fruit malate accumulation by repressing the promoter activity of the malate-associated genes Ma1 (Al-Activated Malate Transporter 9), Ma10 (P-type ATPase 10), MdVHA-A3 (V-type ATPase A3), and MdVHA-D2 (V-type ATPase D2). Two single-nucleotide polymorphisms (SNPs) in the MdMYB44 promoter, SNP A/G and SNP T/-, were experimentally shown to associate with fruit malate content. The TATA-box in the MdMYB44 promoter in the presence of SNP A enhances the basal activity of the MdMYB44 promoter. The binding of a basic-helix-loop-helix transcription factor MdbHLH49 to the MdMYB44 promoter was enhanced by the presence of SNP T, leading to increased MdMYB44 transcript levels and reduced malate accumulation. Furthermore, MdbHLH49 interacts with MdMYB44 and enhances MdMYB44 activity. The two SNPs could be used in combination to select for sour or non-sour apples, providing a valuable tool for the selection of fruit acidity by the apple breeding industry. This research is important for understanding the complex molecular mechanisms of fruit malate accumulation and accelerating the development of germplasm innovation in apple species and cultivars.
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Affiliation(s)
- Dongjie Jia
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Peng Wu
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Fei Shen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei Li
- College of Horticulture, Institute for Horticultural Plants, China Agricultural University, Beijing 100193, China
| | - Xiaodong Zheng
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongzhang Wang
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongbing Yuan
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xinzhong Zhang
- College of Horticulture, Institute for Horticultural Plants, China Agricultural University, Beijing 100193, China
| | - Zhenhai Han
- College of Horticulture, Institute for Horticultural Plants, China Agricultural University, Beijing 100193, China
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14
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Wu B, Shen F, Wang X, Zheng WY, Xiao C, Deng Y, Wang T, Yu Huang Z, Zhou Q, Wang Y, Wu T, Feng Xu X, Hai Han Z, Zhong Zhang X. Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL-based genomics-assisted prediction. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1022-1037. [PMID: 33319456 PMCID: PMC8131039 DOI: 10.1111/pbi.13527] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/29/2020] [Accepted: 12/06/2020] [Indexed: 05/24/2023]
Abstract
Retention of flesh texture attributes during cold storage is critical for the long-term maintenance of fruit quality. The genetic variations determining flesh firmness and crispness retainability are not well understood. The objectives of this study are to identify gene markers based on quantitative trait loci (QTLs) and to develop genomics-assisted prediction (GAP) models for apple flesh firmness and crispness retainability. Phenotype data of 2664 hybrids derived from three Malus domestica cultivars and a M. asiatica cultivar were collected in 2016 and 2017. The phenotype segregated considerably with high broad-sense heritability of 83.85% and 83.64% for flesh firmness and crispness retainability, respectively. Fifty-six candidate genes were predicted from the 62 QTLs identified using bulked segregant analysis and RNA-seq. The genotype effects of the markers designed on each candidate gene were estimated. The genomics-predicted values were obtained using pyramiding marker genotype effects and overall mean phenotype values. Fivefold cross-validation revealed that the prediction accuracy was 0.5541 and 0.6018 for retainability of flesh firmness and crispness, respectively. An 8-bp deletion in the MdERF3 promoter disrupted MdDOF5.3 binding, reduced MdERF3 expression, relieved the inhibition on MdPGLR3, MdPME2, and MdACO4 expression, and ultimately decreased flesh firmness and crispness retainability. A 3-bp deletion in the MdERF118 promoter decreased its expression by disrupting the binding of MdRAVL1, which increased MdPGLR3 and MdACO4 expression and reduced flesh firmness and crispness retainability. These results provide insights regarding the genetic variation network regulating flesh firmness and crispness retainability, and the GAP models can assist in apple breeding.
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Affiliation(s)
- Bei Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Fei Shen
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xuan Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Wen Yan Zheng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Chen Xiao
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yang Deng
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Yu Huang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Qian Zhou
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Yi Wang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Ting Wu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xue Feng Xu
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Hai Han
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Xin Zhong Zhang
- College of HorticultureChina Agricultural UniversityBeijingChina
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15
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Wu B, Shen F, Chen CJ, Liu L, Wang X, Zheng WY, Deng Y, Wang T, Huang ZY, Xiao C, Zhou Q, Wang Y, Wu T, Xu XF, Han ZH, Zhang XZ. Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life. THE PLANT GENOME 2021; 14:e20084. [PMID: 33605090 DOI: 10.1002/tpg2.20084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/13/2020] [Indexed: 05/18/2023]
Abstract
Room-temperature shelf life is a key factor in fresh market apple (Malus domestica Borkh.) quality and commercial value. To investigate the genetic and molecular mechanism underlying apple shelf life, quantitative trait loci (QTL) were identified using bulked segregant analysis via sequencing (BSA-seq). Ethylene emission, flesh firmness, or crispness of apple fruit from 1,273 F1 plants of M. asiatica Nakai 'Zisai Pearl' × M. domestica 'Golden Delicious' were phenotyped prior to and during 6 wk of room-temperature storage. Segregation of ethylene emission and the flesh firmness or crispness traits was detected in the population. Thirteen QTL, including three major ones, were identified on chromosome 03, 08, and 16. A candidate gene encoding pectin acetylesterase, MdPAE10, from the QTL Z16.1 negatively affected fruit shelf life. A 379-bp deletion in the coding sequence of MdPAE10 disrupted its function. A single nucleotide polymorphism (SNP) in the MdPAE10 promoter region reduced its transcription activity. These findings provided insight into the genetic control of fruit shelf life and can be potentially used in apple marker-assisted selection.
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Affiliation(s)
- Bei Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Chi Jie Chen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Li Liu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xuan Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Wen Yan Zheng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yang Deng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Ting Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhen Yu Huang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Chen Xiao
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Qian Zhou
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xue Feng Xu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhen Hai Han
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xin Zhong Zhang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
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16
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Bai Q, Shen Y, Huang Y. Advances in Mineral Nutrition Transport and Signal Transduction in Rosaceae Fruit Quality and Postharvest Storage. FRONTIERS IN PLANT SCIENCE 2021; 12:620018. [PMID: 33692815 PMCID: PMC7937644 DOI: 10.3389/fpls.2021.620018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/11/2021] [Indexed: 05/12/2023]
Abstract
Mineral nutrition, taken up from the soil or foliar sprayed, plays fundamental roles in plant growth and development. Among of at least 14 mineral elements, the macronutrients nitrogen (N), potassium (K), phosphorus (P), and calcium (Ca) and the micronutrient iron (Fe) are essential to Rosaceae fruit yield and quality. Deficiencies in minerals strongly affect metabolism with subsequent impacts on the growth and development of fruit trees. This ultimately affects the yield, nutritional value, and quality of fruit. Especially, the main reason of the postharvest storage loss caused by physiological disorders is the improper proportion of mineral nutrient elements. In recent years, many important mineral transport proteins and their regulatory components are increasingly revealed, which make drastic progress in understanding the molecular mechanisms for mineral nutrition (N, P, K, Ca, and Fe) in various aspects including plant growth, fruit development, quality, nutrition, and postharvest storage. Importantly, many studies have found that mineral nutrition, such as N, P, and Fe, not only affects fruit quality directly but also influences the absorption and the content of other nutrient elements. In this review, we provide insights of the mineral nutrients into their function, transport, signal transduction associated with Rosaceae fruit quality, and postharvest storage at physiological and molecular levels. These studies will contribute to provide theoretical basis to improve fertilizer efficient utilization and fruit industry sustainable development.
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Zheng C, Shen F, Wang Y, Wu T, Xu X, Zhang X, Han Z. Intricate genetic variation networks control the adventitious root growth angle in apple. BMC Genomics 2020; 21:852. [PMID: 33261554 PMCID: PMC7709433 DOI: 10.1186/s12864-020-07257-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified in crops. However, the underlying mechanisms of the RGA remain poorly understood, especially in apple rootstocks. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock. Results Bulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., large RGA) and ‘M9’ (M. pumila Mill., small RGA). With RNA sequencing (RNA-seq) and parental resequencing, six major functional genes were identified and constituted two genetic variation networks for the RGA. Two single nucleotide polymorphisms (SNPs) of the MdLAZY1 promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP of MdDREB2A and MdIAA1 affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within the MdNPR5 promoter damaged the interaction between MdNPR5 and MdLBD41, while one SNP of MdLBD41 interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on the MdNPR5 promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°. Conclusions Six diagnostic markers, SNP592, G122, b13, Z312, S1272, and S1288, were used to identify two intricate genetic variation networks that control the RGA and may provide new insights into the accuracy of the molecular markers. The QTLs and SNP markers can potentially be used to select deep-rooted apple rootstocks.
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Affiliation(s)
- Caixia Zheng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Jiménez-Morales E, Aguilar-Hernández V, Aguilar-Henonin L, Guzmán P. Molecular basis for neofunctionalization of duplicated E3 ubiquitin ligases underlying adaptation to drought tolerance in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:474-492. [PMID: 33164265 DOI: 10.1111/tpj.14938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Multigene families in plants expanded from ancestral genes via gene duplication mechanisms constitute a significant fraction of the coding genome. Although most duplicated genes are lost over time, many are retained in the genome. Clusters of tandemly arrayed genes are commonly found in the plant genome where they can promote expansion of gene families. In the present study, promoter fusion to the GUS reporter gene was used to examine the promoter architecture of duplicated E3 ligase genes that are part of group C in the Arabidopsis thaliana ATL family. Acquisition of gene expression by AtATL78, possibly generated from defective AtATL81 expression, is described. AtATL78 expression was purportedly enhanced by insertion of a TATA box within the core promoter region after a short tandem duplication that occurred during evolution of Brassicaceae lineages. This gene is associated with an adaptation to drought tolerance of A. thaliana. These findings also suggest duplicated genes could serve as a reservoir of tacit genetic information, and expression of these duplicated genes is activated upon acquisition of core promoter sequences. Remarkably, drought transcriptome profiling in response to rehydration suggests that ATL78-dependent gene expression predominantly affects genes with root-specific activities.
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Affiliation(s)
- Estela Jiménez-Morales
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, 36824, México
| | - Victor Aguilar-Hernández
- CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
| | - Laura Aguilar-Henonin
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, 36824, México
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, 36824, México
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19
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Sun Y, Hao P, Lv X, Tian J, Wang Y, Zhang X, Xu X, Han Z, Wu T. A long non-coding apple RNA, MSTRG.85814.11, acts as a transcriptional enhancer of SAUR32 and contributes to the Fe-deficiency response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:53-67. [PMID: 31991023 DOI: 10.1111/tpj.14706] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 05/26/2023]
Abstract
Iron (Fe) is an essential plant nutrient and its deficiency typically limits plant growth. Long non-coding (lnc) RNAs are involved in adaptive responses to nutrient stress; however, it is not known whether they function in the regulation of the canonical Fe-deficiency response. The expression of Malus domestica (apple) lncRNA MSTRG.85814 is induced by Fe deficiency, as identified by high-throughput strand-specific RNA-seq analysis of an apple homograft system. MSTRG.85814 has a complex structure, with 13 predicted RNA sequence variants, four of which are upregulated in the roots of plants experiencing Fe deficiency. We found that one MSTRG.85814 splice variant (MSTRG.85814.11) positively modulated its cis target mRNA derived from the small auxin upregulated gene SAUR32. This in turn promoted the expression of SAUR32 and caused an increase in the expression of a plasma membrane proton ATPase, AHA10. Using a pH imaging technique, a significant decrease in the apoplastic pH was observed to occur in the root tips of MSTRG.85814.11 or SAUR32-overexpressing apple plants. Thus MSTRG.85814.11 was shown to positively promote SAUR32 expression, which then activated proton extrusion involved in the Fe-deficiency response. These results reveal a mechanism by which lncRNA promotes environmental Fe-deficiency stress adaption.
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Affiliation(s)
- Yaqiang Sun
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Pengbo Hao
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinmin Lv
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ji Tian
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
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20
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Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing. Int J Mol Sci 2019; 20:ijms20225783. [PMID: 31744249 PMCID: PMC6887749 DOI: 10.3390/ijms20225783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 01/04/2023] Open
Abstract
ATP-binding cassette (ABC) transporters constitute a large, diverse, and ubiquitous superfamily that is involved in a broad range of processes. The completion of genome sequencing provides an opportunity to understand the phylogenetic history of the ABC transporter superfamily among Rosaceae species. This study identified a total of 1323 ABC transporter genes from nine Rosaceae genomes: 191 from Malus domestica, 174 from Pyrus communis, 138 from Prunus persica, 118 from Prunus avium, 141 from Prunus dulcis, 122 from Fragaria vesca, 98 from Rubus occidentalis, 162 from Prunus mume, and 179 from Rosa chinensis. Their chemical characterization, phylogenetic analysis, chromosomal localization, gene structure, gene duplication, and tissue-specific expression were studied. Their subcellular localization, transmembrane structures, and protein motifs were predicted. All the ABC transporter genes were grouped into eight subfamilies on the basis of their phylogenetic relationships and structural features. Furthermore, cis-element and expression analysis of 10 potential phytohormone transporters in MdABCG subfamily genes were also performed. Loss of the W-box in the promoter region of MdABCG28 was found to reduce the gene expression level and was linked to the dwarfing phenotype in apple rootstocks. MdABCG28 overexpression promoted shoot growth of atabcg14 mutants in Arabidopsis.
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21
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Mapping Gene Markers for Apple Fruit Ring Rot Disease Resistance Using a Multi-omics Approach. G3-GENES GENOMES GENETICS 2019; 9:1663-1678. [PMID: 30910819 PMCID: PMC6505150 DOI: 10.1534/g3.119.400167] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Apple fruit ring rot (FRR), caused by Botryosphaeria dothidea, is a worldwide disease that impacts Asian apple production regions. However, no substantial progress has thus far been made toward the mapping of candidate genes or the development of effective genetic makers. In this five-year study, the resistance of 1,733 F1 hybrids from the cross ‘Jonathan’ × ‘Golden Delicious’ was phenotyped by non-wounding inoculation with four B. dothidea isolates. We first conducted systematic comparison of different analytic strategies for bulk segregant analysis by re-sequencing (BSA-Seq) and obtained suitable one for outbreeding species such as Malus. Forty-six quantitative trait loci (QTL) for resistance/susceptibility to the four isolates, including one QTL ‘hotspot’ on chromosome 14, were identified via BSA-Seq. Using integrated multi-omics strategies including RNA-sequencing, parental re-sequencing, BSA-Seq and meta-analysis of RNA-sequencing, fifty-seven candidate genes and corresponding functional mutations from the QTL were predicted. Functional mutations located on the candidate genes were validated using kompetitive allele-specific PCR in hybrids and Malus germplasm accessions with extremely resistant/susceptible phenotypes. Ten effective markers for apple ring rot were developed. The results provide an example of rapid candidate gene mapping for complex traits in outbreeding species.
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22
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Feng Y, Liu J, Zhai L, Gan Z, Zhang G, Yang S, Wang Y, Wu T, Zhang X, Xu X, Han Z. Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks. PLANT, CELL & ENVIRONMENT 2019; 42:424-436. [PMID: 29989184 DOI: 10.1111/pce.13403] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 05/20/2023]
Abstract
Plants experiencing salt-induced stress often reduce cytokinin levels during the early phases of stress-response. Interestingly, we found that the cytokinin content in the apple rootstock "robusta" was maintained at a high level under salt stress. Through screening genes involved in cytokinin biosynthesis and catabolism, we found that the high expression levels of IPT5b in robusta roots were involved in maintaining the high cytokinin content. We identified a 42 bp deletion in the promoter region of IPT5b, which elevated IPT5b expression levels, and this deletion was linked to salt tolerance in robusta×M.9 segregating population. The 42 bp deletion resulted in the deletion of a Proline Response Element (ProRE), and our results suggest that ProRE negatively regulates IPT5b expression in response to proline. Under salt stress, the robusta cultivar maintains high cytokinin levels as IPT5b expression cannot be inhibited by proline due to the deletion of ProRE, leading to improve salt tolerance.
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Affiliation(s)
- Yi Feng
- College of Horticulture, China Agricultural University, Beijing, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jing Liu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Longmei Zhai
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zengyu Gan
- College of Horticulture, China Agricultural University, Beijing, China
| | - Guifen Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
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23
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Jia D, Shen F, Wang Y, Wu T, Xu X, Zhang X, Han Z. Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes: MdSAUR37, MdPP2CH and MdALMTII. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:427-443. [PMID: 29750477 DOI: 10.1111/tpj.13957] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 05/21/2023]
Abstract
Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, using MapQTL and BSA-seq (bulk segregant analysis using next generation sequencing) with two independent pedigree-based populations, we identified four major genome-wide QTLs responsible for apple fruit acidity. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single-nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37 and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H+ -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on the MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the fundamental physiological basis of quantitative genetics.
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Affiliation(s)
- Dongjie Jia
- Institute for Horticultural Plants, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Fei Shen
- Institute for Horticultural Plants, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- Institute for Horticultural Plants, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- Institute for Horticultural Plants, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- Institute for Horticultural Plants, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- Institute for Horticultural Plants, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- Institute for Horticultural Plants, College of Horticulture, China Agricultural University, Beijing, 100193, China
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24
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Zhao B, Cao J, Hu G, Chen Z, Wang L, Shangguan X, Wang L, Mao Y, Zhang T, Wendel JF, Chen X. Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation. THE NEW PHYTOLOGIST 2018; 218:1061-1075. [PMID: 29465754 PMCID: PMC6079642 DOI: 10.1111/nph.15063] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 01/17/2018] [Indexed: 05/18/2023]
Abstract
Cotton cultivars have evolved to produce extensive, long, seed-born fibers important for the textile industry, but we know little about the molecular mechanism underlying spinnable fiber formation. Here, we report how PACLOBUTRAZOL RESISTANCE 1 (PRE1) in cotton, which encodes a basic helix-loop-helix (bHLH) transcription factor, is a target gene of spinnable fiber evolution. Differential expression of homoeologous genes in polyploids is thought to be important to plant adaptation and novel phenotypes. PRE1 expression is specific to cotton fiber cells, upregulated during their rapid elongation stage and A-homoeologous biased in allotetraploid cultivars. Transgenic studies demonstrated that PRE1 is a positive regulator of fiber elongation. We determined that the natural variation of the canonical TATA-box, a regulatory element commonly found in many eukaryotic core promoters, is necessary for subgenome-biased PRE1 expression, representing a mechanism underlying the selection of homoeologous genes. Thus, variations in the promoter of the cell elongation regulator gene PRE1 have contributed to spinnable fiber formation in cotton. Overexpression of GhPRE1 in transgenic cotton yields longer fibers with improved quality parameters, indicating that this bHLH gene is useful for improving cotton fiber quality.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Jun‐Feng Cao
- Plant Stress Biology CenterInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
- Plant Science Research CenterShanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai201602China
| | - Guan‐Jing Hu
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Zhi‐Wen Chen
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Lu‐Yao Wang
- Nanjing Agricultural UniversityNanjingJiangsu210095China
| | - Xiao‐Xia Shangguan
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Ling‐Jian Wang
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Ying‐Bo Mao
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Tian‐Zhen Zhang
- Nanjing Agricultural UniversityNanjingJiangsu210095China
- Zhejiang UniversityHangzhouZhejiang310058China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Xiao‐Ya Chen
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
- Plant Science Research CenterShanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai201602China
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25
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Han Z, Hu Y, Lv Y, Rose JKC, Sun Y, Shen F, Wang Y, Zhang X, Xu X, Wu T, Han Z. Natural Variation Underlies Differences in ETHYLENE RESPONSE FACTOR17 Activity in Fruit Peel Degreening. PLANT PHYSIOLOGY 2018; 176:2292-2304. [PMID: 29431631 PMCID: PMC5841710 DOI: 10.1104/pp.17.01320] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/28/2018] [Indexed: 05/09/2023]
Abstract
Through natural or human selection, many fleshy fruits have evolved vivid external or internal coloration, which often develops during ripening. Such developmental changes in color are associated with the biosynthesis of pigments as well as with degreening through chlorophyll degradation. Here, we demonstrated that natural variation in the coding region of the gene ETHYLENE RESPONSE FACTOR17 (ERF17) contributes to apple (Malus domestica) fruit peel degreening. Specifically, ERF17 mutant alleles with different serine (Ser) repeat insertions in the coding region exhibited enhanced transcriptional regulation activity in a dual-luciferase reporter assay when more Ser repeats were present. Notably, surface plasmon resonance analysis showed that the number of Ser repeats affected the binding activity of ERF17 to the promoter sequences of chlorophyll degradation-related genes. In addition, overexpression of ERF17 in evergreen apples altered the accumulation of chlorophyll. Furthermore, we demonstrated that ERF17 has been under selection since the origin of apple tree cultivation. Taken together, these results reveal allelic variation underlying an important fruit quality trait and a molecular genetic mechanism associated with apple domestication.
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Affiliation(s)
- Zhenyun Han
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yanan Hu
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yuanda Lv
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - Yaqiang Sun
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, People's Republic of China
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