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Dai Z, Dong S, Cai H, Beckles DM, Guan J, Liu X, Gu X, Miao H, Zhang S. Genome-wide association analysis reveal candidate genes and haplotypes related to root weight in cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1417314. [PMID: 39086910 PMCID: PMC11288866 DOI: 10.3389/fpls.2024.1417314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Background The plant root system is critical for the absorption of water and nutrients, and have a direct influence on growth and yield. In cucumber, a globally consumed crop, the molecular mechanism of root development remains unclear, and this has implications for developing stress tolerant varieties. This study sought to determine the genetic patterns and related genes of cucumber root weight. A core cucumber germplasms population was used to do the GWAS analysis in three environments. Results Here, we investigated four root-weight related traits including root fresh weight (RFW), root dry weight (RDW), ratio of root dry weight to root fresh weight (RDFW) and the comprehensive evaluation index, D-value of root weight (DRW) deduced based on the above three traits for the core germplasm of the cucumber global repository. According to the D-value, we identified 21 and 16 accessions with light and heavy-root, respectively. We also found that the East Asian ecotype accessions had significantly heavier root than other three ecotypes. The genome-wide association study (GWAS) for these four traits reveals that 4 of 10 significant loci (gDRW3.1, gDRW3.2, gDRW4.1 and gDRW5.1) were repeatedly detected for at least two traits. Further haplotype and expression analysis for protein-coding genes positioned within these 4 loci between light and heavy-root accessions predicted five candidate genes (i.e., Csa3G132020 and Csa3G132520 both encoding F-box protein PP2-B1 for gDRW3.1, Csa3G629240 encoding a B-cell receptor-associated protein for gDRW3.2, Csa4G499330 encodes a GTP binding protein for gDRW4.1, and Csa5G286040 encodes a proteinase inhibitor for gDRW5.1). Conclusions We conducted a systematic analysis of the root genetic basis and characteristics of cucumber core germplasms population. We detected four novel loci, which regulate the root weight in cucumber. Our study provides valuable candidate genes and haplotypes for the improvement of root system in cucumber breeding.
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Affiliation(s)
- Zhuonan Dai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hexu Cai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diane M. Beckles
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Vetrova S, Alyokhina K, Engalycheva I, Kozar E, Mukhina K, Sletova M, Krivenkov L, Tikhonova T, Kameneva A, Frolova S, Chizhik V, Martynov V. Identification and Pathogenicity of Fusarium Species Associated with Onion Basal Rot in the Moscow Region of Russian Federation. J Fungi (Basel) 2024; 10:331. [PMID: 38786686 PMCID: PMC11121879 DOI: 10.3390/jof10050331] [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: 03/19/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Fusarium basal rot of onions causes large losses during storage of commercial production of onion bulbs, which in turn adversely affects the food market situation in the off-season period. There are no data on the composition of Fusarium spp., which causes onion basal rot in the Russian Federation. Therefore, our research was aimed at Fusarium spp. causing onion basal rot in the Moscow Region of the Russian Federation and studying the pathogenicity of these species for the host plant. We studied 20 isolates of Fusarium spp. collected from affected mature bulbs and seed bulbs. Species identification of the isolates was carried out using analysis of the nucleotide sequences of the three genetic loci ITS, tef1 and rpb2, as well as was based on the macro- and micromorphological characteristics of these isolates. As a result, the species F. annulatum (F. fujikuroi species complex), F. oxysporum (F. oxysporum species complex), F. acuminatum (F. tricinctum species complex) and F. solani (F. solani species complex) were identified to involve in the pathogenesis of Fusarium basal rot. We have shown for the first time that the species F. annulatum and F. acuminatum are highly aggressive and capable of causing onion basal rot. The predominant species were F. annulatum and F. oxysporum. The proportion of these species in the total number of analyzed isolates was 60% and 25%, respectively. The largest proportion (33%) of highly aggressive on mature bulbs isolates was found in the species F. annulatum. The data obtained provide practical insights for developing strategies to manage Fusarium fungi responsible for onion basal rot Moscow Region of the Russian Federation. In addition, data about species composition and aggressive isolates may be used in onion breeding for resistance to Fusarium basal rot.
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Affiliation(s)
- Svetlana Vetrova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Ksenia Alyokhina
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Irina Engalycheva
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Elena Kozar
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Kseniya Mukhina
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Maria Sletova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Leonid Krivenkov
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Tatyana Tikhonova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Alina Kameneva
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Svetlana Frolova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Vera Chizhik
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
- Federal State Budgetary Scientific Institution All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Viktor Martynov
- Federal State Budgetary Scientific Institution All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
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Dong S, Liu X, Han J, Miao H, Beckles DM, Bai Y, Liu X, Guan J, Yang R, Gu X, Sun J, Yang X, Zhang S. CsMLO8/11 are required for full susceptibility of cucumber stem to powdery mildew and interact with CsCRK2 and CsRbohD. HORTICULTURE RESEARCH 2024; 11:uhad295. [PMID: 38404593 PMCID: PMC10894460 DOI: 10.1093/hr/uhad295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/20/2023] [Indexed: 02/27/2024]
Abstract
Powdery mildew (PM) is one of the most destructive diseases that threaten cucumber production globally. Efficient breeding of novel PM-resistant cultivars will require a robust understanding of the molecular mechanisms of cucumber resistance against PM. Using a genome-wide association study, we detected a locus significantly correlated with PM resistance in cucumber stem, pm-s5.1. A 1449-bp insertion in the CsMLO8 coding region at the pm-s5.1 locus resulted in enhanced stem PM resistance. Knockout mutants of CsMLO8 and CsMLO11 generated by CRISPR/Cas9 both showed improved PM resistance in the stem, hypocotyl, and leaves, and the double mutant mlo8mlo11 displayed even stronger resistance. We found that reactive oxygen species (ROS) accumulation was higher in the stem of these mutants. Protein interaction assays suggested that CsMLO8 and CsMLO11 could physically interact with CsRbohD and CsCRK2, respectively. Further, we showed that CsMLO8 and CsCRK2 competitively interact with the C-terminus of CsRbohD to affect CsCRK2-CsRbohD module-mediated ROS production during PM defense. These findings provide new insights into the understanding of CsMLO proteins during PM defense responses.
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Affiliation(s)
- Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Jianan Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Diane M Beckles
- Department of Plant Sciences, University of California Davis, One Shield Avenue, Davis, CA 95616, USA
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Ruizhen Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
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Li C, Dong S, Beckles DM, Liu X, Guan J, Gu X, Miao H, Zhang S. GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber. FRONTIERS IN PLANT SCIENCE 2023; 14:1116214. [PMID: 37235012 PMCID: PMC10208356 DOI: 10.3389/fpls.2023.1116214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/24/2023] [Indexed: 05/28/2023]
Abstract
Low temperatures (LTs) negatively affect the percentage and rate of cucumber (Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: gLTG1.1, gLTG1.2, gLTG1.3, gLTG4.1, gLTG5.1, gLTG5.2, and gLTG6.1 after resequencing of the accessions. Of the seven loci, three, i.e., gLTG1.2, gLTG4.1, and gLTG5.2, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) for gLTG1.2, CsaV3_4G013480 (a RING-type E3 ubiquitin transferase) for gLTG4.1, and CsaV3_5G029350 (a serine/threonine-protein kinase) for gLTG5.2. The function for CsPPR (CsaV3_1G044080) in regulating LTG was confirmed, as Arabidopsis lines ectopically expressing CsPPR showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that CsPPR positively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.
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Affiliation(s)
- Caixia Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diane M. Beckles
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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A Large-Scale Genomic Association Analysis Identifies the Candidate Genes Regulating Salt Tolerance in Cucumber ( Cucumis sativus L.) Seedlings. Int J Mol Sci 2022; 23:ijms23158260. [PMID: 35897836 PMCID: PMC9332819 DOI: 10.3390/ijms23158260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Salt stress seriously restricts plant growth and development, affects yield and quality, and thus becomes an urgent problem to be solved in cucumber stress resistance breeding. Mining salt tolerance genes and exploring the molecular mechanism of salt tolerance could accelerate the breeding of cucumber germplasm with excellent salt stress tolerance. In this study, 220 cucumber core accessions were used for Genome-Wide Association Studies (GWAS) and the identification of salt tolerance genes. The salinity injury index that was collected in two years showed significant differences among the core germplasm. A total of seven loci that were associated with salt tolerance in cucumber seedlings were repeatedly detected, which were located on Chr.2 (gST2.1), Chr.3 (gST3.1 and gST3.2), Chr.4 (gST4.1 and gST4.2), Chr.5 (gST5.1), and Chr.6 (gST6.1). Within these loci, 62 genes were analyzed, and 5 candidate genes (CsaV3_2G035120, CsaV3_3G023710, CsaV3_4G033150, CsaV3_5G023530, and CsaV3_6G009810) were predicted via the functional annotation of Arabidopsis homologous genes, haplotype of extreme salt-tolerant accessions, and qRT-PCR. These results provide a guide for further research on salt tolerance genes and molecular mechanisms of cucumber seedlings.
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GWAS Reveals a Novel Candidate Gene CmoAP2/ERF in Pumpkin ( Cucurbita moschata) Involved in Resistance to Powdery Mildew. Int J Mol Sci 2022; 23:ijms23126524. [PMID: 35742978 PMCID: PMC9223685 DOI: 10.3390/ijms23126524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Pumpkin (Cucurbita moschata Duchesne ex Poir.) is a multipurpose cash crop rich in antioxidants, minerals, and vitamins; the seeds are also a good source of quality oils. However, pumpkin is susceptible to the fungus Podosphaera xanthii, an obligate biotrophic pathogen, which usually causes powdery mildew (PM) on both sides of the leaves and reduces photosynthesis. The fruits of infected plants are often smaller than usual and unpalatable. This study identified a novel gene that involves PM resistance in pumpkins through a genome-wide association study (GWAS). The allelic variation identified in the CmoCh3G009850 gene encoding for AP2-like ethylene-responsive transcription factor (CmoAP2/ERF) was proven to be involved in PM resistance. Validation of the GWAS data revealed six single nucleotide polymorphism (SNP) variations in the CmoAP2/ERF coding sequence between the resistant (IT 274039 [PMR]) and the susceptible (IT 278592 [PMS]). A polymorphic marker (dCAPS) was developed based on the allelic diversity to differentiate these two haplotypes. Genetic analysis in the segregating population derived from PMS and PMR parents provided evidence for an incomplete dominant gene-mediated PM resistance. Further, the qRT-PCR assay validated the elevated expression of CmoAP2/ERF during PM infection in the PMR compared with PMS. These results highlighted the pivotal role of CmoAP2/ERF in conferring resistance to PM and identifies it as a valuable molecular entity for breeding resistant pumpkin cultivars.
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Zhang Y, Wang Y, Sun X, Yuan J, Zhao Z, Gao J, Wen X, Tang F, Kang M, Abliz B, Zhang Z, Zhang H, Wang F, Li Z. Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice. PLANTS 2022; 11:plants11111498. [PMID: 35684271 PMCID: PMC9182821 DOI: 10.3390/plants11111498] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022]
Abstract
Malate dehydrogenase (MDH) is widely present in nature and regulates plant growth and development, as well as playing essential roles, especially in abiotic stress responses. Nevertheless, there is no comprehensive knowledge to date on MDH family members in rice. In this study, a total of 12 MDH members in rice were identified through genome-wide analysis and divided into three groups on the basis of their phylogenetic relationship and protein-conserved motifs. Evolutionary analysis showed that MDH proteins from rice, maize and wheat shared a close phylogenetic relationship, and the MDH family was conserved in the long-term process of domestication. We identified two segmental duplication events involving four genes, which could be the major force driving the expansion of the OsMDH family. The expression profile, cis-regulatory elements and qRT-PCR results of these genes revealed that a few OsMDH showed high tissue specificity, almost all of which had stress response elements in the promoter region, and ten MDH members were significantly induced by salt stress. Through gene-based association analysis, we found a significant correlation between salt tolerance at the seedling stage and the genetic variation of OsMDH8.1 and OsMDH12.1. Additionally, we found that the polymorphism in the promoter region of OsMDH8.1 might be related to the salt tolerance of rice. This study aimed to provide valuable information on the functional study of the rice MDH gene family related to salt stress response and revealed that OsMDH8.1 might be an important gene for the cultivar improvement of salt tolerance in rice.
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Affiliation(s)
- Yanhong Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Yulong Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xingming Sun
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Yuan
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Zhiqiang Zhao
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
| | - Jie Gao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaorong Wen
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Fusen Tang
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Mintai Kang
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
| | - Buhaliqem Abliz
- Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (J.Y.); (Z.Z.); (B.A.)
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fengbin Wang
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Saline-Alkali Land in Arid and Semi-Arid Regions), Ministry of Agriculture and Rural Affairs, Urumqi 830091, China
- Rice Experiment Station in Wensu, Xinjiang Academy of Agricultural Sciences, Wensu, Aksu 843100, China; (X.W.); (F.T.); (M.K.)
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Correspondence: (F.W.); (Z.L.)
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China; (Y.Z.); (Y.W.); (X.S.); (J.G.); (Z.Z.); (H.Z.)
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Correspondence: (F.W.); (Z.L.)
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He Y, Wei M, Yan Y, Yu C, Cheng S, Sun Y, Zhu X, Wei L, Wang H, Miao L. Research Advances in Genetic Mechanisms of Major Cucumber Diseases Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:862486. [PMID: 35665153 PMCID: PMC9161162 DOI: 10.3389/fpls.2022.862486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 06/15/2023]
Abstract
Cucumber (Cucumis sativus L.) is an important economic vegetable crop worldwide that is susceptible to various common pathogens, including powdery mildew (PM), downy mildew (DM), and Fusarium wilt (FM). In cucumber breeding programs, identifying disease resistance and related molecular markers is generally a top priority. PM, DM, and FW are the major diseases of cucumber in China that cause severe yield losses and the genetic-based cucumber resistance against these diseases has been developed over the last decade. Still, the molecular mechanisms of cucumber disease resistance remain unclear. In this review, we summarize recent findings on the inheritance, molecular markers, and quantitative trait locus mapping of cucumber PM, DM, and FM resistance. In addition, several candidate genes, such as PM, DM, and FM resistance genes, with or without functional verification are reviewed. The data help to reveal the molecular mechanisms of cucumber disease resistance and provide exciting new opportunities for further resistance breeding.
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Affiliation(s)
- Yujin He
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Mingming Wei
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resource Utilization of Rubber Tree, State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Yanyan Yan
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Chao Yu
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Siqi Cheng
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yihan Sun
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xiangtao Zhu
- College of Jiyang, Zhejiang Agriculture and Forestry University, Zhuji, China
| | - Lingling Wei
- Institute of Ecological Civilization, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Huasen Wang
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resource Utilization of Rubber Tree, State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Li Miao
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
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9
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Meng X, Yu Y, Song T, Yu Y, Cui N, Ma Z, Chen L, Fan H. Transcriptome Sequence Analysis of the Defense Responses of Resistant and Susceptible Cucumber Strains to Podosphaera xanthii. FRONTIERS IN PLANT SCIENCE 2022; 13:872218. [PMID: 35645993 PMCID: PMC9134894 DOI: 10.3389/fpls.2022.872218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew (PM) caused by Podosphaera xanthii poses a continuous threat to the performance and yield of the cucumber (Cucumis sativus L.). Control in the initial stages of infection is particularly important. Here, we studied the differential physiological and transcriptomic changes between PM-resistant strain B21-a-2-1-2 and PM-susceptible strain B21-a-2-2-2 at the early stage of P. xanthii attack. When challenged with P. xanthii, the tolerant line can postpone the formation of the pathogen primary germ. Comparative transcriptomic analysis suggested that DEGs related to the cell wall and to pathogen and hormone responses were similar enriched in both cucumber lines under P. xanthii infection. Notably, the number of DEGs triggered by P. xanthii in B21-a-2-1-2 was quintuple that in B21-a-2-2-2, revealing that the success of defense of resistant cucumber is due to rapidly mobilizing multiple responses. The unique responses detected were genes related to SA signaling, MAPK signaling, and Dof and WRKY transcription factors. Furthermore, 5 P. xanthii -inducible hub genes were identified, including GLPK, ILK1, EIN2, BCDHβ1, and RGGA, which are considered to be key candidate genes for disease control. This study combined multiple analytical approaches to capture potential molecular players and will provide key resources for developing cucumber cultivars resistant to pathogen stress.
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Affiliation(s)
- Xiangnan Meng
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yongbo Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Tiefeng Song
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yang Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Na Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Zhangtong Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Lijie Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, China
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10
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Alkemade JA, Nazzicari N, Messmer MM, Annicchiarico P, Ferrari B, Voegele RT, Finckh MR, Arncken C, Hohmann P. Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1011-1024. [PMID: 34988630 PMCID: PMC8942938 DOI: 10.1007/s00122-021-04014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/06/2021] [Indexed: 05/11/2023]
Abstract
GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland.
| | | | - Barbara Ferrari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Ralf T Voegele
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Maria R Finckh
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Christine Arncken
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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