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Wang H, Feng M, Zhong X, Yu Q, Que Y, Xu L, Guo J. Identification of Saccharum CaM gene family and function characterization of ScCaM1 during cold and oxidant exposure in Pichia pastoris. Genes Genomics 2023; 45:103-122. [PMID: 35608775 DOI: 10.1007/s13258-022-01263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/03/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Calmodulin (CaM) plays an essential role in binding calcium ions and mediating the interpretation of Ca2+ signals in plants under various stresses. However, the evolutionary relationship of CaM family proteins in Saccharum has not been elucidated. OBJECTIVE To deduce and explore the evolution and function of Saccharum CaM family. METHODS A total of 104 typical CaMs were obtained from Saccharum spontaneum and other 18 plant species. The molecular characteristics and evolution of those CaM proteins were analyzed. A typical CaM gene, ScCaM1, was subsequently cloned from sugarcane (Saccharum spp. hybrid). Its expression patterns in different tissues and under various abiotic stresses were assessed by quantitative real-time PCR. Then the green fluorescent protein was used to determine the subcellular localization of ScCaM1. Finally, the function of ScCaM1 was evaluated via heterologous yeast expression systems. RESULTS Three typical CaM members (SsCaM1, SsCaM2, and SsCaM3) were identified from the S. spontaneum genome database. CaMs were originated from the two last common ancestors before the origin of angiosperms. The number of CaM family members did not correlate to the genome size but correlated with allopolyploidization events. The ScCaM1 was more highly expressed in buds and roots than in other tissues. The expression patterns of ScCaM1 suggested that it was involved in responses to various abiotic stresses in sugarcane via different hormonal signaling pathways. Noteworthily, its expression levels appeared relatively stable during the cold exposure in the cold-tolerant variety but significantly suppressed in the cold-susceptible variety. Moreover, the recombinant yeast (Pichia pastoris) overexpressing ScCaM1 grew better than the wild-type yeast strain under cold and oxidative stresses. It was revealed that the ScCaM1 played a positive role in reactive oxygen species scavenging and conferred enhanced cold and oxidative stress tolerance to cells. CONCLUSION This study provided comprehensive information on the CaM gene family in Saccharum and would facilitate further investigation of their functional characterization.
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Affiliation(s)
- Hengbo Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meichang Feng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoqiang Zhong
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing Yu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Correr FH, Furtado A, Franco Garcia AA, Henry RJ, Rodrigues Alves Margarido G. Allele expression biases in mixed-ploid sugarcane accessions. Sci Rep 2022; 12:8778. [PMID: 35610293 PMCID: PMC9130122 DOI: 10.1038/s41598-022-12725-0] [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: 12/21/2021] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, genes showing ASE (ASEGs) were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.
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Affiliation(s)
- Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Antonio Augusto Franco Garcia
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
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Rody HVS, Bombardelli RGH, Creste S, Camargo LEA, Van Sluys MA, Monteiro-Vitorello CB. Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype. BMC Genomics 2019; 20:809. [PMID: 31694536 PMCID: PMC6836459 DOI: 10.1186/s12864-019-6207-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging. RESULTS We predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes. S. spontaneum chromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs. CONCLUSIONS Most of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestral S. spontaneum genotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.
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Affiliation(s)
- Hugo V S Rody
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Renato G H Bombardelli
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Silvana Creste
- Centro de Cana, IAC-Apta, Ribeirão Preto, Av. Pádua Dias n11, CEP 13418-900, Piracicaba, São Paulo, Brazil
| | - Luís E A Camargo
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânia, Universidade de São Paulo, Instituto de Biociências, São Paulo, Brazil
| | - Claudia B Monteiro-Vitorello
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.
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Zhang J, Zhang Q, Li L, Tang H, Zhang Q, Chen Y, Arrow J, Zhang X, Wang A, Miao C, Ming R. Recent polyploidization events in three Saccharum founding species. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:264-274. [PMID: 29878497 PMCID: PMC6330536 DOI: 10.1111/pbi.12962] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/21/2018] [Accepted: 06/04/2018] [Indexed: 05/07/2023]
Abstract
The complexity of polyploid Saccharum genomes hindered progress of genome research and crop improvement in sugarcane. To understand their genome structure, transcriptomes of 59 F1 individuals derived from S. officinarumLA Purple and S. robustum Molokai 5829 (2n = 80, x = 10 for both) were sequenced, yielding 11 157 and 8998 SNPs and 83 and 105 linkage groups, respectively. Most markers in each linkage group aligned to single sorghum chromosome. However, 71 interchromosomal rearrangements were detected between sorghum and S. officinarum or S. robustum, and 24 (33.8%) of them were shared between S. officinarum and S. robustum, indicating their occurrence before the speciation event that separated these two species. More than 2000 gene pairs from S. spontaneum, S. officinarum and S. robustum were analysed to estimate their divergence time. Saccharum officinarum and S. robustum diverged about 385 thousand years ago, and the whole-genome duplication events occurred after the speciation event because of shared interchromosomal rearrangements. The ancestor of these two species diverged from S. spontaneum about 769 thousand years ago, and the reduction in basic chromosome number from 10 to 8 in S. spontaneum occurred after the speciation event but before the two rounds of whole-genome duplication. Our results proved that S. officinarum is a legitimate species in its own right and not a selection from S. robustum during the domestication process in the past 10 000 years. Our findings rejected a long-standing hypothesis and clarified the timing of speciation and whole-genome duplication events in Saccharum.
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Affiliation(s)
- Jisen Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of Life SciencesFujian Normal UniversityFuzhouChina
| | - Qing Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Leiting Li
- College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Haibao Tang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenChinese Academy of SciencesWuhanChina
| | - Yang Chen
- College of Life SciencesFujian Normal UniversityFuzhouChina
| | - Jie Arrow
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Xingtan Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Aiqin Wang
- State Key Lab for Conservation and Utilization of Subtropical Agro‐biological ResourcesGuangxi UniversityNanningChina
| | - Chenyong Miao
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Ray Ming
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
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Wang HB, Chen PH, Yang YQ, D'Hont A, Lu YH. Molecular insights into the origin of the brown rust resistance gene Bru1 among Saccharum species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2431-2443. [PMID: 28821913 DOI: 10.1007/s00122-017-2968-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
Analysis of 387 sugarcane clones using Bru 1 diagnostic markers revealed two possible sources of Bru 1 in Chinese cultivars: one from Saccharum spontaneum and another from Saccharum robustum of New Guinea. Sugarcane brown rust (SBR) is an important fungal disease in many sugarcane production areas around the world, and can cause considerable yield losses in susceptible sugarcane cultivars. One major SBR resistance gene, named Bru1, initially identified from cultivar R570, was shown to be a major SBR resistance source in most of the sugarcane producing areas of the world. In this study, by using the two Bru1-associated markers, R12H16 and 9O20-F4, we surveyed the presence of Bru1 in a Chinese sugarcane germplasm collection of 387 clones, consisting of 228 hybrid cultivars bred by different Chinese sugarcane breeding establishments, 54 exotic hybrid cultivars introduced from other countries and 105 clones of sugarcane ancestral species. The Bru1-bearing haplotype was detected in 43.4% of Chinese sugarcane cultivars, 20.4% of exotic hybrid cultivars, and only 3.8% of ancestral species. Among the 33 Chinese cultivars for which phenotypes of resistance to SBR were available, Bru1 was present in 69.2% (18/26) of the resistant clones. Analyses of the allelic sequence variations of R12H16 and 9O20-F4 suggested two possible sources of Bru1 in Chinese cultivars: one from S. spontaneum and another from S. robustum of New Guinea. In addition, we developed an improved Bru1 diagnostic marker, 9O20-F4-HaeIII, which can eliminate all the false results of 9O20-F4-RsaI observed among S. spontaneum, as well as a new dominant Bru1 diagnostic marker, R12E03-2, from the BAC ShCIR12E03. Our results provide valuable information for further efforts of breeding SBR-resistant varieties, searching new SBR resistance sources and cloning of Bru1 in sugarcane.
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Affiliation(s)
- Heng-Bo Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China
| | - Ping-Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China
| | - Yan-Qing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China
| | | | - Yun-Hai Lu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China.
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