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Chen Q, Gao K, Xu Y, Sun Y, Pan B, Chen D, Luo C, Cheng X, Liu H, Huang C. Research advance on cold tolerance in chrysanthemum. FRONTIERS IN PLANT SCIENCE 2023; 14:1259229. [PMID: 37828931 PMCID: PMC10565118 DOI: 10.3389/fpls.2023.1259229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
Abstract
Chrysanthemums are one of the top ten most well-known traditional famous flowers in China and one of the top four cut flowers worldwide, holding a significant position in landscape gardening. The cold temperatures of winter restrict the cultivation, introduction, and application of chrysanthemum, resulting in high costs for year-round production. This severely impacts the ornamental and economic value of chrysanthemum. Therefore, research on cold tolerance is of vital importance for guiding chrysanthemum production and application. With the development of genomics, transcriptomics, metabolomics, and other omics approaches, along with high-throughput molecular marker technologies, research on chrysanthemum cold tolerance has been continuously advancing. This article provides a comprehensive overview of the progress in cold tolerance research from various aspects, including chrysanthemum phenotype, physiological mechanisms, the forward genetics, molecular mechanisms, and breeding. The aim is to offer insights into the mechanisms of cold tolerance in chrysanthemum and provide reference for in-depth research and the development of new cold tolerance chrysanthemum varieties.
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Affiliation(s)
- Qingbing Chen
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - Kang Gao
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - YuRan Xu
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - YaHui Sun
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - Bo Pan
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Architecture, North China University of Water Resources and Electric Power, Zhengzhou, China
| | - Dongliang Chen
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chang Luo
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xi Cheng
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hua Liu
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Conglin Huang
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Ouyang Q, Zhang Y, Yang X, Yang C, Hou D, Liu H, Xu H. Overexpression of OsPIN9 Impairs Chilling Tolerance via Disturbing ROS Homeostasis in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2809. [PMID: 37570963 PMCID: PMC10421329 DOI: 10.3390/plants12152809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]
Abstract
The auxin efflux transporter PIN-FORMED (PIN) family is one of the major protein families that facilitates polar auxin transport in plants. Here, we report that overexpression of OsPIN9 leads to altered plant architecture and chilling tolerance in rice. The expression profile analysis indicated that OsPIN9 was gradually suppressed by chilling stress. The shoot height and adventitious root number of OsPIN9-overexpressing (OE) plants were significantly reduced at the seedling stage. The roots of OE plants were more tolerant to N-1-naphthylphthalamic acid (NPA) treatment than WT plants, indicating the disturbance of auxin homeostasis in OE lines. The chilling tolerance assay showed that the survival rate of OE plants was markedly lower than that of wild-type (WT) plants. Consistently, more dead cells, increased electrolyte leakage, and increased malondialdehyde (MDA) content were observed in OE plants compared to those in WT plants under chilling conditions. Notably, OE plants accumulated more hydrogen peroxide (H2O2) and less superoxide anion radicals (O2-) than WT plants under chilling conditions. In contrast, catalase (CAT) and superoxide dismutase (SOD) activities in OE lines decreased significantly compared to those in WT plants at the early chilling stage, implying that the impaired chilling tolerance of transgenic plants is probably attributed to the sharp induction of H2O2 and the delayed induction of antioxidant enzyme activities at this stage. In addition, several OsRboh genes, which play a crucial role in ROS production under abiotic stress, showed an obvious increase after chilling stress in OE plants compared to that in WT plants, which probably at least in part contributes to the production of ROS under chilling stress in OE plants. Together, our results reveal that OsPIN9 plays a vital role in regulating plant architecture and, more importantly, is involved in regulating rice chilling tolerance by influencing auxin and ROS homeostasis.
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Affiliation(s)
| | | | | | | | | | | | - Huawei Xu
- College of Agriculture, Henan University of Science and Technology, Luoyang 471000, China; (Q.O.); (Y.Z.); (X.Y.); (C.Y.); (D.H.); (H.L.)
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Yan W, Yuan S, Zu Y, Chang Z, Li Y, Chen Z, Xie G, Chen L, Lu C, Deng XW, Yang C, Xu C, Tang X. Ornithine δ-aminotransferase OsOAT is critical for male fertility and cold tolerance during rice plant development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1301-1318. [PMID: 36932862 DOI: 10.1111/tpj.16194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/11/2023] [Indexed: 06/17/2023]
Abstract
Cold stress is a major factor limiting the production and geographical distribution of rice (Oryza sativa) varieties. However, the molecular mechanisms underlying cold tolerance remain to be elucidated. Here, we report that ornithine δ-aminotransferase (OsOAT) contributes to cold tolerance during the vegetative and reproductive development of rice. osoat mutant was identified as a temperature-sensitive male sterile mutant with deformed floral organs and seedlings sensitive to cold stress. Comparative transcriptome analysis showed that OsOAT mutation and cold treatment of the wild-type plant led to similar changes in the global gene expression profiles in anthers. OsOAT genes in indica rice Huanghuazhan (HHZ) and japonica rice Wuyungeng (WYG) are different in gene structure and response to cold. OsOAT is cold-inducible in WYG but cold-irresponsive in HHZ. Further studies showed that indica varieties carry both WYG-type and HHZ-type OsOAT, whereas japonica varieties mostly carry WYG-type OsOAT. Cultivars carrying HHZ-type OsOAT are mainly distributed in low-latitude regions, whereas varieties carrying WYG-type OsOAT are distributed in both low- and high-latitude regions. Moreover, indica varieties carrying WYG-type OsOAT generally have higher seed-setting rates than those carrying HHZ-type OsOAT under cold stress at reproductive stage, highlighting the favorable selection for WYG-type OsOAT during domestication and breeding to cope with low temperatures.
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Affiliation(s)
- Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Shuting Yuan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Yazhou Zu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Zhenyi Chang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yiqi Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Gang Xie
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Lei Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Changqing Lu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Xing Wang Deng
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
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Yongbin Q, Summat P, Panyawut N, Sikaewtung K, Ditthab K, Tongmark K, Chakhonkaen S, Sangarwut N, Wasinanon T, Kaewmungkun K, Muangprom A. Identification of Rice Accessions Having Cold Tolerance at the Seedling Stage and Development of Novel Genotypic Assays for Predicting Cold Tolerance. PLANTS (BASEL, SWITZERLAND) 2023; 12:215. [PMID: 36616346 PMCID: PMC9823403 DOI: 10.3390/plants12010215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Rice is susceptible to cold stress at the seedling stage, which can delay growth and decrease yield. We evaluated 187 rice accessions for cold tolerance at the seedling stage and developed genotypic assays for three markers. All japonica (20/20) and 20/140 indica accessions were highly cold tolerant. Two SNP markers specific for COLD1 and LOC_Os10g34840 were practical to use by normal agarose gel. The SNP marker specific for COLD1 was highly specific for predicting cold tolerance. However, the sensitivity of this marker was low as several cold-tolerant indica accessions lacked the cold-tolerant allele. The LOC_Os10g34840 marker was slightly more sensitive than the COLD1 marker for predicting highly cold-tolerant accessions. An insertion/deletion variant in the NAC6 gene was identified as a novel cold tolerance marker. The NAC6 marker predicted more highly cold-tolerant accessions compared with the other two markers. The SNP marker specific for LOC_Os10g34840 and the NAC6 marker were present in several tested subgroups, suggesting their wide effects and distribution. The three markers combined predicted the most highly cold-tolerant accessions, indicating that the marker combination is superior for applications such as marker-assisted breeding. The cold-tolerant accessions and the genotypic marker assays will be useful for future rice breeding.
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Affiliation(s)
- Qi Yongbin
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Patcharaporn Summat
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Centre, Khlong Luang, Pathum Thani 12120, Thailand
| | - Natjaree Panyawut
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
- Nadi District Agricultural Extension Office, Chamanan Road, Nadi Subdistrict, Nadi District, Prachinburi 25220, Thailand
| | - Kannika Sikaewtung
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Khanittha Ditthab
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Keasinee Tongmark
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sriprapai Chakhonkaen
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Numphet Sangarwut
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Thiwawan Wasinanon
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kanokwan Kaewmungkun
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Amorntip Muangprom
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
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Li J, Feng B, Yu P, Fu W, Wang W, Lin J, Qin Y, Li H, Chen T, Xu C, Tao L, Wu Z, Fu G. Oligomeric Proanthocyanidins Confer Cold Tolerance in Rice through Maintaining Energy Homeostasis. Antioxidants (Basel) 2022; 12:antiox12010079. [PMID: 36670941 PMCID: PMC9854629 DOI: 10.3390/antiox12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Oligomeric proanthocyanidins (OPCs) are abundant polyphenols found in foods and botanicals that benefit human health, but our understanding of the functions of OPCs in rice plants is limited, particularly under cold stress. Two rice genotypes, named Zhongzao39 (ZZ39) and its recombinant inbred line RIL82, were subjected to cold stress. More damage was caused to RIL82 by cold stress than to ZZ39 plants. Transcriptome analysis suggested that OPCs were involved in regulating cold tolerance in the two genotypes. A greater increase in OPCs content was detected in ZZ39 than in RIL82 plants under cold stress compared to their respective controls. Exogenous OPCs alleviated cold damage of rice plants by increasing antioxidant capacity. ATPase activity was higher and poly (ADP-ribose) polymerase (PARP) activity was lower under cold stress in ZZ39 than in RIL82 plants. Importantly, improvements in cold tolerance were observed in plants treated with the OPCs and 3-aminobenzamide (PARP inhibitor, 3ab) combination compared to the seedling plants treated with H2O, OPCs, or 3ab alone. Therefore, OPCs increased ATPase activity and inhibited PARP activity to provide sufficient energy for rice seedling plants to develop antioxidant capacity against cold stress.
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Affiliation(s)
- Juncai Li
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Baohua Feng
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Pinghui Yu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Weimeng Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Wenting Wang
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jie Lin
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yebo Qin
- Zhejiang Agricultural Technology Extension Center, Hangzhou 310020, China
| | - Hubo Li
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Tingting Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Chunmei Xu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Longxing Tao
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhihai Wu
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (Z.W.); (G.F.)
| | - Guanfu Fu
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
- Correspondence: (Z.W.); (G.F.)
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Nie Y, Guo L, Cui F, Shen Y, Ye X, Deng D, Wang S, Zhu J, Wu W. Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2111-2125. [PMID: 36070250 DOI: 10.1111/jipb.13357] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) have been identified as major regulators of cold acclimation in many angiosperm plants. However, their origin and evolutionary process associated to cold responsiveness are still lacking. By integrating multi-omics data of genomes, transcriptomes, and CBFs/DREB1s genome-wide binding profiles, we unveil the origin and evolution of CBFs/DREB1s and their regulatory network. Gene collinearity and phylogeny analyses show that CBF/DREB1 is an innovation evolved from tandem duplication-derived DREB III gene. A subsequent event of ε-whole genome duplication led to two CBF/DREB1 archetypes (Clades I and II) in ancient angiosperms. In contrast to cold-insensitivity of Clade I and their parent DREB III genes, Clade II evolved a further innovation in cold-sensitive response and was stepwise expanded in eudicots and monocots by independent duplications. In geological time, the duplication events were mainly enriched around the Cretaceous-Paleogene (K-Pg) boundary and/or in the Late Cenozoic Ice Age, when the global average temperature significantly decreased. Consequently, the duplicated CBF/DREB1 genes contributed to the rewiring of CBFs/DREB1s-regulatory network for cold tolerance. Altogether, our results highlight an origin and convergent evolution of CBFs/DREB1s and their regulatory network probably for angiosperms adaptation to global cooling.
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Affiliation(s)
- Yuqi Nie
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Fuqiang Cui
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
| | - Jianhua Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, 20742, USA
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
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Li J, Khatab AA, Hu L, Zhao L, Yang J, Wang L, Xie G. Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms232113208. [PMID: 36361995 PMCID: PMC9655271 DOI: 10.3390/ijms232113208] [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: 09/19/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.
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Affiliation(s)
- Jianguo Li
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ahmed Adel Khatab
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihua Hu
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science & Technology, Guangxi University, Nanning 530004, China
| | - Liyan Zhao
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiangyi Yang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science & Technology, Guangxi University, Nanning 530004, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation & Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
| | - Guosheng Xie
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, China
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Khatab AA, Li J, Hu L, Yang J, Fan C, Wang L, Xie G. Global identification of quantitative trait loci and candidate genes for cold stress and chilling acclimation in rice through GWAS and RNA-seq. PLANTA 2022; 256:82. [PMID: 36103054 DOI: 10.1007/s00425-022-03995-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: 08/16/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
Associated analysis of GWAS with RNA-seq had detected candidate genes responsible for cold stress and chilling acclimation in rice. Haplotypes of two candidate genes and geographic distribution were analyzed. To explore new candidate genes and genetic resources for cold tolerance improvement in rice, genome-wide association study (GWAS) mapping experiments with 351 rice core germplasms was performed for three traits (survival rate, shoot length and chlorophyll content) under three temperature conditions (normal temperature, cold stress and chilling acclimation), yielding a total of 134 QTLs, of which 54, 59 and 21 QTLs were responsible for normal temperature, cold stress and chilling acclimation conditions, respectively. Integrated analysis of significant SNPs in 134 QTLs further identified 116 QTLs for three temperature treatments, 53, 43 and 18 QTLs responsible for normal temperature, cold stress and chilling acclimation, respectively, and 2 QTLs were responsible for both cold stress and chilling acclimation. Matching differentially expressed genes from RNA-seq to 43 and 18 QTLs for cold stress and chilling acclimation, we identified 69 and 44 trait-associated candidate genes, respectively, to be classified into six and five groups, particularly involved in metabolisms, reactive oxygen species scavenging and hormone signaling. Interestingly, two candidate genes LOC_Os01g04814, encoding a vacuolar protein sorting-associating protein 4B, and LOC_Os01g48440, encoding glycosyltransferase family 43 protein, showed the highest expression levels under chilling acclimation. Haplotype analysis revealed that both genes had a distinctive differentiation with subpopulation. Haplotypes of both genes with more japonica accessions have higher latitude distribution and higher chilling tolerance than the chilling sensitive indica accessions. These findings reveal the new insight into the molecular mechanism and candidate genes for cold stress and chilling acclimation in rice.
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Affiliation(s)
- Ahmed Adel Khatab
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jiangyi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Chuchuan Fan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingqiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China.
| | - Guosheng Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice. PLANTS 2022; 11:plants11182329. [PMID: 36145730 PMCID: PMC9506393 DOI: 10.3390/plants11182329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022]
Abstract
Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.
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10
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Mao F, Wu D, Lu F, Yi X, Gu Y, Liu B, Liu F, Tang T, Shi J, Zhao X, Liu L, Ji L. QTL mapping and candidate gene analysis of low temperature germination in rice ( Oryza sativa L.) using a genome wide association study. PeerJ 2022; 10:e13407. [PMID: 35578671 PMCID: PMC9107303 DOI: 10.7717/peerj.13407] [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: 12/20/2021] [Accepted: 04/18/2022] [Indexed: 01/14/2023] Open
Abstract
Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.
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Affiliation(s)
- Feng Mao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China,Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Depeng Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fangfang Lu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Xin Yi
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Bin Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Jianxin Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lilian Ji
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China
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11
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Qing D, Deng G, Pan Y, Gao L, Liang H, Zhou W, Chen W, Li J, Huang J, Gao J, Lu C, Wu H, Liu K, Dai G. ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress. BREEDING SCIENCE 2022; 72:150-168. [PMID: 36275934 PMCID: PMC9522529 DOI: 10.1270/jsbbs.21081] [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: 09/16/2021] [Accepted: 11/11/2021] [Indexed: 06/16/2023]
Abstract
Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for a relative and absolute quantification (iTRAQ) labeling-based quantitative proteomics approach was used to detected changes in protein levels. Two-week-old seedlings of the cold tolerant rice variety Kongyu131 were treated at 8°C for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to the control group. Functional analysis revealed that most of the regulated proteins are involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulated proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is that it provides new insights into cold stress responses in rice with respect to proteomics and provides candidate genes for cold-tolerance rice breeding.
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Affiliation(s)
- Dongjin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Lijun Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Weiwei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Jingcheng Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Ju Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Chunju Lu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Hao Wu
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Kaiqiang Liu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Gaoxing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
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Pan X, Guan L, Lei K, Li J, Zhang X. Transcriptional and physiological data revealed cold tolerance in a photo-thermo sensitive genic male sterile line Yu17S. BMC PLANT BIOLOGY 2022; 22:44. [PMID: 35062884 PMCID: PMC8781465 DOI: 10.1186/s12870-022-03437-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Rice is highly sensitive to chilling stress during the seedling stage. However, the adaptable photo-thermo sensitive genic male sterile (PTGMS) rice line, Yu17S, exhibits tolerance to low temperatures. Currently, the molecular characteristics of Yu17S are unclear. RESULTS To evaluate the molecular mechanisms behind cold responses in rice seedlings, a comparative transcriptome analysis was performed in Yu17S during seedling development under normal temperature and low temperature conditions. In total, 9317 differentially expressed genes were detected. Gene ontology and pathway analyses revealed that these genes were involved mostly in photosynthesis, carotenoid biosynthesis, carbohydrate metabolism and plant hormone signal transduction. An integrated analysis of specific pathways combined with physiological data indicated that rice seedlings improved the performance of photosystem II when exposed to cold conditions. Genes involved in starch degradation and sucrose metabolism were activated in rice plants exposed to cold stress treatments, which was accompanied by the accumulation of soluble sugar, trehalose, raffinose and galactinol. Furthermore, chilling stress induced the expression of phytoene desaturase, 15-cis-ζ-carotene isomerase, ζ-carotene desaturase, carotenoid isomerase and β-carotene hydroxylase; this was coupled with the activation of carotenoid synthase activity and increases in abscisic acid (ABA) levels in rice seedlings. CONCLUSIONS Our results suggest that Yu17S exhibited better tolerance to cold stress with the activation of carotenoid synthase activity and increasing of ABA levels, and as well as the expression of photosynthesis-related genes under cold condition in rice seedlings.
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Affiliation(s)
- Xiaoxue Pan
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences/Chongqing Key Laboratory of Adversity Agriculture, Chongqing, 401329, China
| | - Ling Guan
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences/Chongqing Key Laboratory of Adversity Agriculture, Chongqing, 401329, China
| | - Kairong Lei
- Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences/Chongqing Key Laboratory of Adversity Agriculture, Chongqing, 401329, China
| | - Jingyong Li
- Chongqing Rationing Rice Research Center, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, China
| | - Xianwei Zhang
- Chongqing Rationing Rice Research Center, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, China.
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Li J, Zhang Z, Chong K, Xu Y. Chilling tolerance in rice: Past and present. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153576. [PMID: 34875419 DOI: 10.1016/j.jplph.2021.153576] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.
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Affiliation(s)
- Junhua Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Zeyong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yunyuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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14
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Wang D, Liu Z, Xiao Y, Liu X, Chen Y, Zhang Z, Kang H, Wang X, Jiang S, Peng S, Tan X, Zhang D, Liu Y, Wang GL, Li C. Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage. RICE (NEW YORK, N.Y.) 2021; 14:98. [PMID: 34825994 PMCID: PMC8626552 DOI: 10.1186/s12284-021-00538-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1-3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.
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Affiliation(s)
- Dan Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Zhuo Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yinghui Xiao
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xionglun Liu
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yue Chen
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zhuo Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Su Jiang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shasha Peng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, 43210, USA.
| | - Chenggang Li
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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15
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Li C, Liu J, Bian J, Jin T, Zou B, Liu S, Zhang X, Wang P, Tan J, Wu G, Chen Q, Wang Y, Zhong Q, Huang S, Yang M, Huang T, He H, Bian J. Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS. BMC PLANT BIOLOGY 2021; 21:542. [PMID: 34800993 PMCID: PMC8605578 DOI: 10.1186/s12870-021-03317-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage. RESULTS In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2-2, qSR3-1, qSR3-2, qSR3-3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2-1, qSR3-4, qSR3-5, qSR3-6, qSR3-7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9. CONCLUSION This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.
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Affiliation(s)
- Caijing Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Jindong Liu
- Agricultural Genomics Institute in Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000 Guangdong Province China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong Province China
| | - Tao Jin
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Baoli Zou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Shilei Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Xiangyu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Peng Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Jingai Tan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Guangliang Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Qin Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Yanning Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Qi Zhong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Shiying Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Mengmeng Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Tao Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Nanchang, 330045 Jiangxi Province China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Nanchang, 330045 Jiangxi Province China
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Phan H, Schläppi M. Low Temperature Antioxidant Activity QTL Associate with Genomic Regions Involved in Physiological Cold Stress Tolerance Responses in Rice ( Oryza sativa L.). Genes (Basel) 2021; 12:genes12111700. [PMID: 34828305 PMCID: PMC8618774 DOI: 10.3390/genes12111700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023] Open
Abstract
Boosting cold stress tolerance in crop plants can minimize stress-mediated yield losses. Asian rice (Oryza sativa L.), one of the most consumed cereal crops, originated from subtropical regions and is generally sensitive to low temperature environments. Within the two subspecies of rice, JAPONICA, and INDICA, the cold tolerance potential of its accessions is highly variable and depends on their genetic background. Yet, cold stress tolerance response mechanisms are complex and not well understood. This study utilized 370 accessions from the Rice Diversity Panel 1 (RDP1) to investigate and correlate four cold stress tolerance response phenotypes: membrane damage, seedling survivability, and catalase and anthocyanin antioxidative activity. Most JAPONICA accessions, and admixed accessions within JAPONICA, had lower membrane damage, higher antioxidative activity, and overall, higher seedling survivability compared to INDICA accessions. Genome-wide association study (GWAS) mapping was done using the four traits to find novel quantitative trait loci (QTL), and to validate and fine-map previously identified QTL. A total of 20 QTL associated to two or more traits were uncovered by our study. Gene Ontology (GO) term enrichment analyses satisfying four layers of filtering retrieved three potential pathways: signal transduction, maintenance of plasma membrane and cell wall integrity, and nucleic acids metabolism as general mechanisms of cold stress tolerance responses involving antioxidant activity.
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17
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Martinez-Seidel F, Suwanchaikasem P, Nie S, Leeming MG, Pereira Firmino AA, Williamson NA, Kopka J, Roessner U, Boughton BA. Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root Meristems. FRONTIERS IN PLANT SCIENCE 2021; 12:656683. [PMID: 33995454 PMCID: PMC8121087 DOI: 10.3389/fpls.2021.656683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Due to their sessile nature, plants rely on root systems to mediate many biotic and abiotic cues. To overcome these challenges, the root proteome is shaped to specific responses. Proteome-wide reprogramming events are magnified in meristems due to their active protein production. Using meristems as a test system, here, we study the major rewiring that plants undergo during cold acclimation. We performed tandem mass tag-based bottom-up quantitative proteomics of two consecutive segments of barley seminal root apexes subjected to suboptimal temperatures. After comparing changes in total and ribosomal protein (RP) fraction-enriched contents with shifts in individual protein abundances, we report ribosome accumulation accompanied by an intricate translational reprogramming in the distal apex zone. Reprogramming ranges from increases in ribosome biogenesis to protein folding factors and suggests roles for cold-specific RP paralogs. Ribosome biogenesis is the largest cellular investment; thus, the vast accumulation of ribosomes and specific translation-related proteins during cold acclimation could imply a divergent ribosomal population that would lead to a proteome shift across the root. Consequently, beyond the translational reprogramming, we report a proteome rewiring. First, triggered protein accumulation includes spliceosome activity in the root tip and a ubiquitous upregulation of glutathione production and S-glutathionylation (S-GSH) assemblage machineries in both root zones. Second, triggered protein depletion includes intrinsically enriched proteins in the tip-adjacent zone, which comprise the plant immune system. In summary, ribosome and translation-related protein accumulation happens concomitantly to a proteome reprogramming in barley root meristems during cold acclimation. The cold-accumulated proteome is functionally implicated in feedbacking transcript to protein translation at both ends and could guide cold acclimation.
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Affiliation(s)
- Federico Martinez-Seidel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
- School of Chemistry, The University of Melbourne, Parkville, VIC, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Berin A. Boughton
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian National Phenome Centre, Murdoch University, Murdoch, WA, Australia
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Bai LWD, Liu J, Dai LF, Deng QW, Chen YL, Xie JK, Luo XD. Identification and characterisation of cold stress-related proteins in Oryza rufipogon at the seedling stage using label-free quantitative proteomic analysis. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:542-555. [PMID: 33487217 DOI: 10.1071/fp20046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
In this study, label-free quantitative proteomics were used to study cold stress-related proteins in Dongxiang wild rice (Oryza rufipogon Griff., DWR) and cold sensitive cultivated rice 'Xieqingzao B'(Oryza sativa L. ssp. indica cv., XB). The results demonstrated the presence of 101 and 216 differentially expressed proteins (DEPs) were detected in DWR and XB, respectively, after cold stress. Bioinformatics analysis showed that DWR and XB differed significantly in their ability to scavenge reactive oxygen species (ROS) and regulate energy metabolism. Of the 101 DEPs of DWR, 46 DEPs related to differential expressed genes were also detected by transcriptome analysis. And 13 out of 101 DEPs were located in previous cold related quantitative trait loci (QTL). Quantitative real-time PCR analysis indicated that protein expression and transcription patterns were not similar in XB and DWR. Protein-protein interaction (PPI) network was constituted using the DEPs of DWR and XB, and the following three centre proteins were identified: Q8H3I3, Q9LDN2, and Q2QXR8. Next, we selected a centre protein and two of the 37 DEPs with high levels of differential expression (fold change ≥ 2) were used for cloning and prokaryotic expression. We found that Q5Z9Q8 could significantly improve the cold tolerance of Escherichia coli.
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Affiliation(s)
- Li-Wei-Dan Bai
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Jian Liu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Liang-Fang Dai
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Qian-Wen Deng
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Ya-Ling Chen
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China
| | - Jian-Kun Xie
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China; and Corresponding authors. ;
| | - Xiang-Dong Luo
- College of Life Science, Jiangxi Normal University, Nanchang 330022, PR China; and Corresponding authors. ;
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Al-Tamimi N, Oakey H, Tester M, Negrão S. Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping. Methods Mol Biol 2021; 2238:339-375. [PMID: 33471343 DOI: 10.1007/978-1-0716-1068-8_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.
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Affiliation(s)
- Nadia Al-Tamimi
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Oakey
- School of Agriculture Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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20
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Yang J, Yang M, Su L, Zhou D, Huang C, Wang H, Guo T, Chen Z. Genome-wide association study reveals novel genetic loci contributing to cold tolerance at the germination stage in indica rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110669. [PMID: 33218635 DOI: 10.1016/j.plantsci.2020.110669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 08/13/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
Low temperature at the germination stage is one of the major abiotic stresses limiting rice (Oryza sativa L.) production, especially in regions where rice seeds are sown directly. However, few relevant genetic loci and genes have been identified. In this study, we report the phenotypic analysis of low temperature germination (LTG) in 200 indica rice varieties and a genome-wide association study (GWAS) of LTG in this collection using 161,657 high-quality SNPs, which were identified via genotyping-by-sequencing (GBS) of all the rice varieties. A total of 159 genetic loci were detected, and they were evenly distributed on all 12 chromosomes. Among them, 51 loci were detected more than twice; in particular, 23 loci were detected repeatedly in both the wet and dry seasons, and 569 genes were predicted in the 200-kb genomic region harbouring these 23 loci. Furthermore, 14,742 differentially expressed genes (DEGs) were identified using RNA sequencing. By integrating GWAS and RNA sequencing, 179 candidate DEGs were obtained. Sequence variation in the region of loci 95 was analyzed using 20 varieties with extreme phenotype. The polymorphisms of three DEGs (Os07g0585500, Os07g0585700, Os07g0585900) were associated with their phenotypes. Haplotype analysis of the three genes demonstrated that almost all the varieties with the same haplotype as japonica Nipponbare on the three DEGs showed high LTG ability. These findings provide valuable information for understanding the genetic control of LTG and performing molecular breeding with marker-assisted selection in indica rice.
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Affiliation(s)
- Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Meng Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Ling Su
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Danhua Zhou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
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Shimoyama N, Johnson M, Beaumont A, Schläppi M. Multiple Cold Tolerance Trait Phenotyping Reveals Shared Quantitative Trait Loci in Oryza sativa. RICE (NEW YORK, N.Y.) 2020; 13:57. [PMID: 32797316 PMCID: PMC7427827 DOI: 10.1186/s12284-020-00414-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/29/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species. RESULTS The Rice Diversity Panel 1 (RDP1) was used to investigate a core set of Oryza sativa accessions. The tools available for this panel allowed for a comprehensive analysis of two chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches using all 354 accessions yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL covering 25% of the rice genome, while 40 QTL were identified by multiple traits. QTL mappings using subsets of rice accession clusters yielded another 255 QTL, for a total of 500 QTL. The genes within these multiple trait QTL were analyzed for Gene Ontology (GO) term and potential pathway enrichments. Terms related to "carbohydrate biosynthesis", "carbohydrate transmembrane transport", "small molecule protein modification", and "plasma membrane" were enriched from this list. Filtering was done to identify more likely candidate pathways involved in conferring chilling tolerance, resulting in enrichment of terms related to "Golgi apparatus", "stress response", "transmembrane transport", and "signal transduction". CONCLUSIONS Taken together, these GO term clusters revealed a likely involvement of Golgi-mediated subcellular and extracellular vesicle and intracellular carbohydrate transport as a general cold stress tolerance response mechanism to achieve cell and metabolic homeostasis under chilling stress.
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Affiliation(s)
- Naoki Shimoyama
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Melineeh Johnson
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - André Beaumont
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Michael Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
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22
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Fang C, Zhang P, Li L, Yang L, Mu D, Yan X, Li Z, Lin W. Serine hydroxymethyltransferase localised in the endoplasmic reticulum plays a role in scavenging H 2O 2 to enhance rice chilling tolerance. BMC PLANT BIOLOGY 2020; 20:236. [PMID: 32456700 PMCID: PMC7249644 DOI: 10.1186/s12870-020-02446-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 05/14/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice is a chilling-sensitive crop that would suffer serious damage from low temperatures. Overexpression of the Lsi1 gene (Lsi1-OX) in rice enhances its chilling tolerance. This study revealed that a serine hydroxymethyltransferase (OsSHMT) mainly localised in the endoplasmic reticulum (ER) is involved in increasing tolerance to chilling. RESULTS A higher transcription level of OsSHMT was detected in Lsi1-OX rice than in the wild type. Histone H1 and nucleic acid binding protein were found to bind to the promoter region of OsSHMT and regulate its expression, and the transcription levels of these proteins were also up-regulated in the Lsi1-OX rice. Moreover, OsSHMT interacts with ATP synthase subunit α, heat shock protein Hsp70, mitochondrial substrate carrier family protein, ascorbate peroxidase 1 and ATP synthase subunit β. Lsi1-encoded protein OsNIP2;1 also interacts with ATP synthase subunit β, and the coordination of these proteins appears to function in reducing reactive oxygen species, as the H2O2 content of transgenic OsSHMT Arabidopsis thaliana was lower than that of the non-transgenic line under chilling treatment. CONCLUSIONS Our results indicate that ER-localised OsSHMT plays a role in scavenging H2O2 to enhance the chilling tolerance of Lsi1-OX rice and that ATP synthase subunit β is an intermediate junction between OsNIP2;1 and OsSHMT.
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Affiliation(s)
- Changxun Fang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China
| | - Pengli Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China
| | - Lanlan Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China
| | - Luke Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China
| | - Dan Mu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China
| | - Xue Yan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China
| | - Zhong Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, P. R. China.
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China.
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23
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Shi Y, Phan H, Liu Y, Cao S, Zhang Z, Chu C, Schläppi MR. Glycosyltransferase OsUGT90A1 helps protect the plasma membrane during chilling stress in rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2723-2739. [PMID: 31974553 PMCID: PMC7210772 DOI: 10.1093/jxb/eraa025] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 05/09/2023]
Abstract
Due to its subtropical origins, rice (Oryza sativa) is sensitive to low-temperature stress. In this study, we identify LOC_Os04g24110, annotated to encode the UDP-glycosyltransferase enzyme UGT90A1, as a gene associated with the low-temperature seedling survivability (LTSS) quantitative trait locus qLTSS4-1. Differences between haplotypes in the control region of OsUGT90A1 correlate with chilling tolerance phenotypes, and reflect differential expression between tolerant and sensitive accessions rather than differences in protein sequences. Expression of OsUGT90A1 is initially enhanced by low temperature, and its overexpression helps to maintain membrane integrity during cold stress and promotes leaf growth during stress recovery, which are correlated with reduced levels of reactive oxygen species due to increased activities of antioxidant enzymes. In addition, overexpression of OsUGT90A1 in Arabidopsis improves freezing survival and tolerance to salt stress, again correlated with enhanced activities of antioxidant enzymes. Overexpression of OsUGT90A1 in rice decreases root lengths in 3-week-old seedlings while gene-knockout increases the length, indicating that its differential expression may affect phytohormone activities. We conclude that higher OsUGT90A1 expression in chilling-tolerant accessions helps to maintain cell membrane integrity as an abiotic stress-tolerance mechanism that prepares plants for the resumption of growth and development during subsequent stress recovery.
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Affiliation(s)
- Yao Shi
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Present address: The University of Pennsylvania School of Dental Medicine, Levy Building, Biochemistry Department, Rm538, 240 S 40th St, Philadelphia, PA 19104, USA
| | - Huy Phan
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Yaju Liu
- National Sweet Potato Improvement Center, Sweet Potato Research Institute, Xuzhou, P.R. China
| | - Shouyun Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhihua Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Michael R Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Correspondence:
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24
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Thapa R, Tabien RE, Thomson MJ, Septiningsih EM. Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice. Front Genet 2020; 11:22. [PMID: 32153631 PMCID: PMC7047875 DOI: 10.3389/fgene.2020.00022] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.
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Affiliation(s)
- Ranjita Thapa
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
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25
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Najeeb S, Ali J, Mahender A, Pang Y, Zilhas J, Murugaiyan V, Vemireddy LR, Li Z. Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2020; 40:10. [PMID: 31975784 PMCID: PMC6944268 DOI: 10.1007/s11032-019-1090-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7 ) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT 1 , qLTT 2 , qLTT 3 , qLTT 5 , qLTT 6 , qLTT 8 , qLTT 9 , and qLTT 11 . A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.
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Affiliation(s)
- S. Najeeb
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Science & Technology (SKAUST), Khudwani, Kashmir 190025 India
| | - J. Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - A. Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Y.L. Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 People’s Republic of China
| | - J. Zilhas
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - V. Murugaiyan
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
- Plant Nutrition, Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, 53012 Bonn, Germany
| | - Lakshminarayana R. Vemireddy
- Department of Genetics and Plant Breeding, Sri Venkateswara Agricultural College, Acharya NG Ranga Agricultural University, Tirupati, Andhra Pradesh 517502 India
| | - Z. Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 People’s Republic of China
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26
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Tareke Woldegiorgis S, Wang S, He Y, Xu Z, Chen L, Tao H, Zhang Y, Zou Y, Harrison A, Zhang L, Ai Y, Liu W, He H. Rice Stress-Resistant SNP Database. RICE (NEW YORK, N.Y.) 2019; 12:97. [PMID: 31872320 PMCID: PMC6928182 DOI: 10.1186/s12284-019-0356-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/06/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) yield is limited inherently by environmental stresses, including biotic and abiotic stresses. Thus, it is of great importance to perform in-depth explorations on the genes that are closely associated with the stress-resistant traits in rice. The existing rice SNP databases have made considerable contributions to rice genomic variation information but none of them have a particular focus on integrating stress-resistant variation and related phenotype data into one web resource. RESULTS Rice Stress-Resistant SNP database (http://bioinformatics.fafu.edu.cn/RSRS) mainly focuses on SNPs specific to biotic and abiotic stress-resistant ability in rice, and presents them in a unified web resource platform. The Rice Stress-Resistant SNP (RSRS) database contains over 9.5 million stress-resistant SNPs and 797 stress-resistant candidate genes in rice, which were detected from more than 400 stress-resistant rice varieties. We incorporated the SNPs function, genome annotation and phenotype information into this database. Besides, the database has a user-friendly web interface for users to query, browse and visualize a specific SNP efficiently. RSRS database allows users to query the SNP information and their relevant annotations for individual variety or more varieties. The search results can be visualized graphically in a genome browser or displayed in formatted tables. Users can also align SNPs between two or more rice accessions. CONCLUSION RSRS database shows great utility for scientists to further characterize the function of variants related to environmental stress-resistant ability in rice.
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Affiliation(s)
| | - Shaobo Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yiruo He
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Zhenhua Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lijuan Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huan Tao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yu Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yang Zou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, Colchester, UK
| | - Lina Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yufang Ai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Li C, Wang D, Peng S, Chen Y, Su P, Chen J, Zheng L, Tan X, Liu J, Xiao Y, Kang H, Zhang D, Wang GL, Liu Y. Genome-wide association mapping of resistance against rice blast strains in South China and identification of a new Pik allele. RICE (NEW YORK, N.Y.) 2019; 12:47. [PMID: 31309315 PMCID: PMC6629727 DOI: 10.1186/s12284-019-0309-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/30/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Effective management of rice blast, caused by the fungus Magnaporthe oryzae, requires an understanding of the genetic architecture of the resistance to the disease in rice. Rice resistance varies with M. oryzae strains, and many quantitative trait loci (QTLs) affecting rice blast resistance have been mapped using different strains of M. oryzae from different areas. However, little is known about the genetic architecture of rice resistance against the M. oryzae population in Hunan Province, which is a main rice production area in South China. RESULTS In this study, we used three isolates from Hunan Province and the rice diversity panel 1 to perform a genome-wide association study (GWAS) of blast resistance in rice. A total of 56 QTLs were identified. One of the QTLs is localized with the resistance gene Pik locus which confers resistance to all three isolates. Genomic sequence analysis of the resistant cultivars led to the identification of a new Pik allele, which we named Pikx. Yeast two-hybrid and co-immunoprecipitation assays between AvrPiks and Pikx confirmed that Pikx is a new allele at the Pik locus. CONCLUSIONS Our GWAS has identified many new blast resistance QTLs. The identified new Pik allele Pikx will be useful for breeding cultivars with high resistance to blast in Hunan and other South China provinces. Further research on the relationship between AvrPiks and Pikx will provide new insights into the molecular mechanism of rice resistance to M. oryzae.
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Affiliation(s)
- Chenggang Li
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Dan Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shasha Peng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yue Chen
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Pin Su
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jianbin Chen
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Limin Zheng
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jinling Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yinghui Xiao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Houxiang Kang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Guo-Liang Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China and College of Agronomy, Hunan Agricultural University, Changsha, 410128, Hunan, China.
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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Schubert M, Grønvold L, Sandve SR, Hvidsten TR, Fjellheim S. Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae. PLANT PHYSIOLOGY 2019; 180:404-419. [PMID: 30850470 PMCID: PMC6501083 DOI: 10.1104/pp.18.01448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/25/2019] [Indexed: 05/24/2023]
Abstract
The grass subfamily Pooideae dominates the grass floras in cold temperate regions and has evolved complex physiological adaptations to cope with extreme environmental conditions like frost, winter, and seasonality. One such adaptation is cold acclimation, wherein plants increase their frost tolerance in response to gradually falling temperatures and shorter days in the autumn. However, understanding how complex traits like cold acclimation evolve remains a major challenge in evolutionary biology. Here, we investigated the evolution of cold acclimation in Pooideae and found that a phylogenetically diverse set of Pooideae species displayed cold acclimation capacity. However, comparing differential gene expression after cold treatment in transcriptomes of five phylogenetically diverse species revealed widespread species-specific responses of genes with conserved sequences. Furthermore, we studied the correlation between gene family size and number of cold-responsive genes as well as between selection pressure on coding sequences of genes and their cold responsiveness. We saw evidence of protein-coding and regulatory sequence evolution as well as the origin of novel genes and functions contributing toward evolution of a cold response in Pooideae. Our results reflect that selection pressure resulting from global cooling must have acted on already diverged lineages. Nevertheless, conservation of cold-induced gene expression of certain genes indicates that the Pooideae ancestor may have possessed some molecular machinery to mitigate cold stress. Evolution of adaptations to seasonally cold climates is regarded as particularly difficult. How Pooideae evolved to transition from tropical to temperate biomes sheds light on how complex traits evolve in the light of climate changes.
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Affiliation(s)
- Marian Schubert
- Department of Plant Sciences, Norwegian University of Life Sciences, NO-1432 As, Norway
| | - Lars Grønvold
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, NO-1432 As, Norway
| | - Simen R Sandve
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 As, Norway
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, NO-1432 As, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umea, Sweden
| | - Siri Fjellheim
- Department of Plant Sciences, Norwegian University of Life Sciences, NO-1432 As, Norway
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Li N, Zheng H, Cui J, Wang J, Liu H, Sun J, Liu T, Zhao H, Lai Y, Zou D. Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage. RICE (NEW YORK, N.Y.) 2019; 12:24. [PMID: 30976929 PMCID: PMC6459459 DOI: 10.1186/s12284-019-0285-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Salinity-alkalinity stress is one of the major factors limiting rice production. The damage caused by alkaline salt stress to rice growth is more severe than that caused by neutral salt stress. At present, the genetic resources (quantitative trait loci (QTLs) and genes) that can be used by rice breeders to improve alkalinity tolerance are limited. Here, we assessed the alkalinity tolerance of rice at the seedling stage and performed a genome-wide association study (GWAS) based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 295 japonica rice varieties. RESULTS We used the score of alkalinity tolerance (SAT), the concentrations of Na+ and K+ in the shoots (SNC and SKC, respectively) and the Na+/K+ ratio of shoots (SNK) as indices to assess alkalinity tolerance at the seedling stage in rice. Based on population structure analysis, the japonica rice panel was divided into three subgroups. Linkage disequilibrium (LD) analysis showed that LD decay occurred at 109.77 kb for the whole genome and varied between 13.79 kb and 415.77 kb across the 12 chromosomes, at which point the pairwise squared correlation coefficient (r2) decreased to half of its maximum value. A total of eight QTLs significantly associated with the SAT, SNC and SNK were identified by genome-wide association mapping. A common QTL associated with the SAT, SNC and SNK on chromosome 3 at the position of 15.0 Mb, which explaining 13.36~13.64% of phenotypic variation, was selected for further analysis. The candidate genes were filtered based on LD decay, Gene Ontology (GO) enrichment, RNA sequencing data, and quantitative real-time PCR (qRT-PCR) analysis. Moreover, sequence analysis revealed one 7-bp insertion/deletion (indel) difference in LOC_Os03g26210 (OsIRO3) between the alkalinity-tolerant and alkalinity-sensitive rice varieties. OsIRO3 encodes a bHLH-type transcription factor and has been shown to be a negative regulator of the Fe-deficiency response in rice. CONCLUSION Based on these results, OsIRO3 maybe a novel functional gene associated with alkalinity tolerance in japonica rice. This study provides resources for improving alkalinity tolerance in rice, and the functional molecular marker could be verified to breed new rice varieties with alkalinity tolerance via marker-assisted selection (MAS).
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Affiliation(s)
- Ning Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Jingnan Cui
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jian Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Tongtong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Yongcai Lai
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China.
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30
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Early selection of bZIP73 facilitated adaptation of japonica rice to cold climates. Nat Commun 2018; 9:3302. [PMID: 30120236 PMCID: PMC6098049 DOI: 10.1038/s41467-018-05753-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/08/2018] [Indexed: 12/17/2022] Open
Abstract
Cold stress is a major factor limiting production and geographic distribution of rice (Oryza sativa). Although the growth range of japonica subspecies has expanded northward compared to modern wild rice (O. rufipogon), the molecular basis of the adaptation remains unclear. Here we report bZIP73, a bZIP transcription factor-coding gene with only one functional polymorphism (+511 G>A) between the two subspecies japonica and indica, may have facilitated japonica adaptation to cold climates. We show the japonica version of bZIP73 (bZIP73Jap) interacts with bZIP71 and modulates ABA levels and ROS homeostasis. Evolutionary and population genetic analyses suggest bZIP73 has undergone balancing selection; the bZIP73Jap allele has firstly selected from standing variations in wild rice and likely facilitated cold climate adaptation during initial japonica domestication, while the indica allele bZIP73Ind was subsequently selected for reasons that remain unclear. Our findings reveal early selection of bZIP73Jap may have facilitated climate adaptation of primitive rice germplasms. Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.
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31
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Xiao N, Gao Y, Qian H, Gao Q, Wu Y, Zhang D, Zhang X, Yu L, Li Y, Pan C, Liu G, Zhou C, Jiang M, Huang N, Dai Z, Liang C, Chen Z, Chen J, Li A. Identification of Genes Related to Cold Tolerance and a Functional Allele That Confers Cold Tolerance. PLANT PHYSIOLOGY 2018; 177:1108-1123. [PMID: 29764927 PMCID: PMC6052991 DOI: 10.1104/pp.18.00209] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/05/2018] [Indexed: 05/22/2023]
Abstract
Cold stress is a major factor limiting rice (Oryza sativa) production worldwide, especially at the seedling and booting stages. The identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed-setting rate than did accessions that had no cold-tolerant alleles or carried a single allele. At the seedling stage, eight genetic loci related to CT have been identified. Among these, LOC_Os10g34840 was identified as the candidate gene for the qPSR10 genetic locus that is associated with CT in rice seedlings. A single-nucleotide polymorphism (SNP), SNP2G, at position 343 in LOC_Os10g34840 is responsible for conferring CT at the seedling stage in rice. Further analysis of the haplotype network revealed that SNP2G was present in 80.08% of the temperate japonica accessions but only 3.8% of the indica ones. We used marker-assisted selection to construct a series of BC4F3 near-isogenic lines possessing the cold-tolerant allele SNP2G When subjected to cold stress, plants carrying SNP2G survived better as seedlings and showed higher grain weight than plants carrying the SNP2A allele. The CT-related loci identified here and the functional verification of LOC_Os10g34840 will provide genetic resources for breeding cold-tolerant varieties and for studying the molecular basis of CT in rice.
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Affiliation(s)
- Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Yong Gao
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Huangjun Qian
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Qiang Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunyu Wu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Dongping Zhang
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Xiaoxiang Zhang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Ling Yu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Yuhong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Cunhong Pan
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Guangqing Liu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Changhai Zhou
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
| | - Min Jiang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Niansheng Huang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Zhengyuan Dai
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
| | - Chengzhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhou Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianmin Chen
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu, Yangzhou University, Yangzhou 225009, China
| | - Aihong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou 225009, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
- National Rice Industry Technology System of Yangzhou Comprehensive Experimental Station, Yangzhou, Jiangsu Province, 225009, China
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Song J, Li J, Sun J, Hu T, Wu A, Liu S, Wang W, Ma D, Zhao M. Genome-Wide Association Mapping for Cold Tolerance in a Core Collection of Rice ( Oryza sativa L.) Landraces by Using High-Density Single Nucleotide Polymorphism Markers From Specific-Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:875. [PMID: 30013584 PMCID: PMC6036282 DOI: 10.3389/fpls.2018.00875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/05/2018] [Indexed: 05/02/2023]
Abstract
Understanding the genetic mechanism of cold tolerance in rice is important to mine elite genes from rice landraces and breed excellent cultivars for this trait. In this study, a genome-wide association study (GWAS) was performed using high-density single nucleotide polymorphisms (SNPs) obtained using specific-locus amplified fragment sequencing (SLAF-seq) technology from a core collection of landraces of rice. A total of 67,511 SNPs obtained from 116,643 SLAF tags were used for genotyping the 150 accessions of rice landraces in the Ting's rice core collection. A compressed mixed liner model was used to perform GWAS by using the high-density SNPs for cold tolerance in rice landraces at the seedling stage. A total of 26 SNPs were found to be significantly (P < 1.48 × 10-7) associated with cold tolerance, which could explained phenotypic variations ranging from 26 to 33%. Among them, two quantitative trait loci (QTLs) were mapped closely to the previously cloned/mapped genes or QTLs for cold tolerance. A newly identified QTL for cold tolerance in rice was further characterized by sequencing, real time-polymerase chain reaction, and bioinformatics analyses. One candidate gene, i.e., Os01g0620100, showed different gene expression levels between the cold tolerant and sensitive landraces under cold stress. We found the difference of coding amino acid in Os01g0620100 between cold tolerant and sensitive landraces caused by polymorphism within the coding domain sequence. In addition, the prediction of Os01g0620100 protein revealed a WD40 domain that was frequently found in cold tolerant landraces. Therefore, we speculated that Os01g0620100 was highly important for the response to cold stress in rice. These results indicated that rice landraces are important sources for investigating rice cold tolerance, and the mapping results might provide important information to breed cold-tolerant rice cultivars by using marker-assisted selection.
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Affiliation(s)
- Jiayu Song
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jinqun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Tao Hu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Aiting Wu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Sitong Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenjia Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Minghui Zhao
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
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Wang J, Wang J, Wang X, Li R, Chen B. Proteomic response of hybrid wild rice to cold stress at the seedling stage. PLoS One 2018; 13:e0198675. [PMID: 29879216 PMCID: PMC5991693 DOI: 10.1371/journal.pone.0198675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022] Open
Abstract
Low temperature at the seedling stage is a major damaging factor for rice production in southern China. To better understand the cold response of cultivated and wild rice, cold-sensitive cultivar 93–11 (Oryza sativa L. ssp. Indica) and cold-resistant hybrid wild rice DC907 with a 93–11 genetic background were used for a quantitative proteomic analysis with tandem mass tags (TMT) in parallel. Rice seedlings grown for four weeks at a normal temperature (25°C) were treated at 8–10°C for 24, 72 and 120 h. The number of differentially expressed proteins increased gradually over time in the cold-exposed rice in comparison with the untreated rice. A total of 366 unique proteins involved in ATP synthesis, photosystem, reactive oxygen species, stress response, cell growth and integrity were identified as responding to cold stress in DC907. While both DC907 and 93–11 underwent similar alterations in proteomic profiles in response to cold stress, DC907 responded in a prompter manner in terms of expressing cold-responding proteins, maintained a higher level of photosynthesis to power the cells, and possessed a stable and higher level of DIR proteins to prevent the plant from obtaining irreversible cell structure damage. The observations made in this study may lay a new foundation for further investigation of cold sensitivity or tolerance mechanisms in rice.
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Affiliation(s)
- Jinzi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
| | - Jun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Xin Wang
- College of Agriculture, Guangxi University, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
- * E-mail: (BC); (RL)
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
- * E-mail: (BC); (RL)
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Buti M, Pasquariello M, Ronga D, Milc JA, Pecchioni N, Ho VT, Pucciariello C, Perata P, Francia E. Transcriptome profiling of short-term response to chilling stress in tolerant and sensitive Oryza sativa ssp. Japonica seedlings. Funct Integr Genomics 2018; 18:627-644. [PMID: 29876699 DOI: 10.1007/s10142-018-0615-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/07/2018] [Accepted: 05/23/2018] [Indexed: 12/26/2022]
Abstract
Low temperature is a major factor limiting rice growth and yield, and seedling is one of the developmental stages at which sensitivity to chilling stress is higher. Tolerance to chilling is a complex quantitative trait, so one of the most effective approaches to identify genes and pathways involved is to compare the stress-induced expression changes between tolerant and sensitive genotypes. Phenotypic responses to chilling of 13 Japonica cultivars were evaluated, and Thaibonnet and Volano were selected as sensitive and tolerant genotypes, respectively. To thoroughly profile the short-term response of the two cultivars to chilling, RNA-Seq was performed on Thaibonnet and Volano seedlings after 0 (not stressed), 2, and 10 h at 10 °C. Differential expression analysis revealed that the ICE-DREB1/CBF pathway plays a primary role in chilling tolerance, mainly due to some important transcription factors involved (some of which had never been reported before). Moreover, the expression trends of some genes that were radically different between Thaibonnet and Volano (i.e., calcium-dependent protein kinases OsCDPK21 and OsCDPK23, cytochrome P450 monooxygenase CYP76M8, etc.) suggest their involvement in low temperature tolerance too. Density of differentially expressed genes along rice genome was determined and linked to the position of known QTLs: remarkable co-locations were reported, delivering an overview of genomic regions determinant for low temperature response at seedling stage. Our study contributes to a better understanding of the molecular mechanisms underlying rice response to chilling and provides a solid background for development of low temperature-tolerant germplasm.
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Affiliation(s)
- Matteo Buti
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy.
| | | | - Domenico Ronga
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy
| | - Justyna Anna Milc
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Nicola Pecchioni
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
- Cereal Research Centre, Council for Agricultural Research and Economics, Foggia, Italy
| | - Viet The Ho
- PlantLab, Scuola Superiore Sant'Anna, Pisa, Italy
- Ho Chi Minh City University of Food Industry, Ho Chi Minh, Vietnam
| | | | | | - Enrico Francia
- BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola, 2 - Pad. Besta, 42122, Reggio Emilia, Italy
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
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35
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Wang H, Lee AR, Park SY, Jin SH, Lee J, Ham TH, Park Y, Zhao WG, Kwon SW. Genome-wide association study reveals candidate genes related to low temperature tolerance in rice ( Oryza sativa) during germination. 3 Biotech 2018; 8:235. [PMID: 29725574 DOI: 10.1007/s13205-018-1252-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/23/2018] [Indexed: 01/05/2023] Open
Abstract
In this study, relative germination percentage (RGP) and delayed mean germination time (DMGT) were measured in various rice accessions at the germination stage and carried out association analysis to identify candidate genes related to low temperature germination (LTG) using a natural population comprising 137 rice cultivars and inbred lines selected from the Korean rice core set. Genome-wide association study using ~ 1.44 million high-quality SNPs, which were identified by re-sequencing all rice collections, revealed 48 candidate genes on chromosome 10 and 55 candidate genes on chromosome 11 in the high peak SNP sites of associated loci for RGP and DMGT, respectively. By detecting highly associated variations located inside genic regions and performing functional annotation of the genes, we detected 23 candidate genes for RGP and 18 genes for DMGT for LTG. In addition, the haplotype and sequence analysis of the candidate gene (Os10g0371100) with RGP trait and the candidate gene (Os11t0104240-00) with DMGT revealed correlation between sequences of functional variations and phenotypes. Several novel LTG-related candidate genes previously were known for the function during rice germination and uncovered their substantial natural variations. These candidate genes represent valuable resources for molecular breeding and genetic improvement of cold tolerance during rice germination.
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Affiliation(s)
- Heng Wang
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Ah-Rim Lee
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - So-Yeon Park
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Sang-Hyeon Jin
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
| | - Joohyun Lee
- 2Department of Applied Bioscience, Konkuk University, Seoul, 05029 Republic of Korea
| | - Tae-Ho Ham
- 2Department of Applied Bioscience, Konkuk University, Seoul, 05029 Republic of Korea
- 3Department of Agricultural Science, Korea National Open University, Seoul, 03087 Republic of Korea
| | - Yongjin Park
- 4Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439 Republic of Korea
| | - Wei-Guo Zhao
- 5School of Biology and Technology, Jiangsu University of Science and Technology, Zhenjiang, 212018 Jiangsu People's Republic of China
| | - Soon-Wook Kwon
- 1Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463 Republic of Korea
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36
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Sun J, Yang L, Wang J, Liu H, Zheng H, Xie D, Zhang M, Feng M, Jia Y, Zhao H, Zou D. Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy. RICE (NEW YORK, N.Y.) 2018; 11:24. [PMID: 29671148 PMCID: PMC5906412 DOI: 10.1186/s12284-018-0218-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 04/04/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield under cold stress. The cold tolerance of rice is controlled by quantitative trait loci (QTLs). Based on the complex genetic basis of cold tolerance in rice, additional efforts are needed to detect reliable QTLs and identify candidate genes. In this study, recombinant inbred lines (RILs) derived from a cross between a cold sensitive variety, Dongnong422, and strongly cold-tolerant variety, Kongyu131, were used to screen for cold-tolerant loci at the booting stage of rice. RESULTS A novel major QTL, qPSST6, controlling the percent seed set under cold water treatment (PSST) under the field conditions of 17 °C cold water irrigation was located on the 28.4 cM interval on chromosome 6. Using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) technology (Seq-BSA), a 1.81 Mb region that contains 269 predicted genes on chromosome 6 was identified as the candidate region of qPSST6. Two genes, LOC_Os06g39740 and LOC_Os06g39750, were annotated as "response to cold" by gene ontology (GO) analysis. qRT-PCR analysis revealed that LOC_Os06g39750 was strongly induced by cold stress. Haplotype analysis also demonstrate a key role of LOC_Os06g39750 in regulating the PSST of rice, suggesting that it was the candidate gene of qPSST6. CONCLUSIONS The information obtained in this study is useful for gene cloning of qPSST6 and for breeding cold-tolerant varieties of rice using marker assisted selection (MAS).
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Affiliation(s)
- Jian Sun
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Luomiao Yang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Jingguo Wang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Hualong Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Hongliang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Dongwei Xie
- The Institute of Industrial Crops of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Minghui Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030 China
| | - Mingfang Feng
- College of Life Science, Northeast Agricultural University, Harbin, 150030 China
| | - Yan Jia
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Hongwei Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Detang Zou
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
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37
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Zhang M, Ye J, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Wei X, Yang Y. Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage. PLANT CELL REPORTS 2018; 37:529-539. [PMID: 29322237 DOI: 10.1007/s00299-017-2247-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/28/2017] [Indexed: 05/14/2023]
Abstract
A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China. We improved the method to assess cold tolerance at the bud burst stage in indica rice, and used severity of damage (SD) and seed survival rate (SR) as the cold-tolerant indices. Population structure analysis demonstrated that the Chinese indica panel was divided into three subgroups. In total, 47 significant single-nucleotide polymorphism (SNP) loci associated with SD and SR, were detected by association mapping based on mixed linear model. Because some loci overlapped between SD and SR, the loci contained 13 genome intervals and most of them have been reported previously. A major QTL for cold tolerance on chromosome 1 at the position of 31.6 Mb, explaining 13.2% of phenotypic variation, was selected for further analysis. Through LD decay, GO enrichment, RNA-seq data, and gene expression pattern analyses, we identified three genes (LOC_Os01g55510, LOC_Os01g55350 and LOC_Os01g55560) that were differentially expressed between cold-tolerant and cold-sensitive varieties, suggesting they may be candidate genes for cold tolerance. Together, our results provide a new method to assess cold tolerance in indica rice, and establish the foundation for isolating genes related to cold tolerance that could be used in rice breeding.
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Affiliation(s)
- Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jing Ye
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.
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38
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Wang X, Zou B, Shao Q, Cui Y, Lu S, Zhang Y, Huang Q, Huang J, Hua J. Natural variation reveals that OsSAP16 controls low-temperature germination in rice. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:413-421. [PMID: 29237030 PMCID: PMC5853544 DOI: 10.1093/jxb/erx413] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/25/2017] [Indexed: 05/06/2023]
Abstract
Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs. We further identified Stress-Associated Protein 16 (OsSAP16), coding for a zinc-finger domain protein, as a causal gene for one of the major LTG QTLs. Loss of OsSAP16 function reduces germination while greater expression of OsSAP16 enhances germination at low temperature. In addition, accessions with extremely high and low LTG values have correspondingly high and low OsSAP16 expression at low temperatures, suggesting that variation in expression of the OsSAP16 gene contributes to LTG variation. As the first case of identification of an LTG gene through GWAS, this study indicates that GWAS of natural accessions is an effective strategy in genetically dissecting LTG processes and gaining molecular understanding of low-temperature response and germination.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Baohong Zou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Qiaolin Shao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yongmei Cui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shan Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Quansheng Huang
- Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Correspondence: ,
| | - Jian Hua
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY, USA
- Correspondence: ,
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39
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Biswas PS, Khatun H, Das N, Sarker MM, Anisuzzaman M. Mapping and validation of QTLs for cold tolerance at seedling stage in rice from an indica cultivar Habiganj Boro VI (Hbj.BVI). 3 Biotech 2017; 7:359. [PMID: 28979832 PMCID: PMC5626667 DOI: 10.1007/s13205-017-0993-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/23/2017] [Indexed: 10/18/2022] Open
Abstract
Yellowing, stunting, and seedling death associated with cold stress is a common problem in many Asian countries for winter rice cultivation. Improvement of cultivars through marker-assisted selection of QTLs for cold tolerance at seedling stage from locally adapted germplasm/cultivar is the most effective and sustainable strategy to resolve this problem. A study was undertaken to map QTLs from 151 F2:3 progenies of a cross between a cold susceptible variety, BR1 and a locally adapted traditional indica cultivar, Hbj.BVI. A total of six significant QTLs were identified for two cold tolerance indices-cold-induced leaf discoloration and survival rate after a recovery period of seven days on chromosomes 6, 8, 11, and 12. Among these QTLs, qCTSL-8-1 and qCTSS-8-1 being co-localized into RM7027-RM339 on chromosome 8 and qCTSL-12-1 and qCTSS-12-1 into RM247-RM2529 on chromosome 12 showed 12.78 and 14.96% contribution, respectively, to the total phenotypic variation for cold tolerance. Validation of QTL effect in BC1F3 population derived a cross between a cold susceptible BRRI dhan28 and Hbj.BVI showed dominating effect of qCTSL-12-1 on cold tolerance at seedling stage and it became stronger when one or more other QTLs were co-segregated with it. These results suggest that the QTLs identified in this study are stable and effective on other genetic background also, which warrant the use of these QTLs for further study aiming to cultivar development for seedling stage cold tolerance.
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Affiliation(s)
- Partha S. Biswas
- International Rice Research Institute, Philippines, Los Baños, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701 Bangladesh
| | - Hasina Khatun
- International Rice Research Institute, Philippines, Los Baños, Philippines
- Bangladesh Rice Research Institute, Gazipur, 1701 Bangladesh
| | - Nomita Das
- Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md. Mahathir Sarker
- Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur, 1706 Bangladesh
| | - M. Anisuzzaman
- Bangladesh Rice Research Institute, Gazipur, 1701 Bangladesh
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40
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Zhang T, Huang L, Wang Y, Wang W, Zhao X, Zhang S, Zhang J, Hu F, Fu B, Li Z. Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing. PLoS One 2017; 12:e0188625. [PMID: 29190752 PMCID: PMC5708648 DOI: 10.1371/journal.pone.0188625] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 11/11/2017] [Indexed: 11/18/2022] Open
Abstract
Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O. longistaminata should thus provide a basis for rice CT improvement through molecular breeding. In this study, high-throughput RNA sequencing was performed to profile global transcriptome alterations and crucial genes involved in response to long-term low temperature in O. longistaminata shoots and rhizomes subjected to 7 days of chilling stress. A total of 605 and 403 genes were respectively identified as up- and down-regulated in O. longistaminata under 7 days of chilling stress, with 354 and 371 differentially expressed genes (DEGs) found exclusively in shoots and rhizomes, respectively. GO enrichment and KEGG pathway analyses revealed that multiple transcriptional regulatory pathways were enriched in commonly induced genes in both tissues; in contrast, only the photosynthesis pathway was prevalent in genes uniquely induced in shoots, whereas several key metabolic pathways and the programmed cell death process were enriched in genes induced only in rhizomes. Further analysis of these tissue-specific DEGs showed that the CBF/DREB1 regulon and other transcription factors (TFs), including AP2/EREBPs, MYBs, and WRKYs, were synergistically involved in transcriptional regulation of chilling stress response in shoots. Different sets of TFs, such as OsERF922, OsNAC9, OsWRKY25, and WRKY74, and eight genes encoding antioxidant enzymes were exclusively activated in rhizomes under long-term low-temperature treatment. Furthermore, several cis-regulatory elements, including the ICE1-binding site, the GATA element for phytochrome regulation, and the W-box for WRKY binding, were highly abundant in both tissues, confirming the involvement of multiple regulatory genes and complex networks in the transcriptional regulation of CT in O. longistaminata. Finally, most chilling-induced genes with alternative splicing exclusive to shoots were associated with photosynthesis and regulation of gene expression, while those enriched in rhizomes were primarily related to stress signal transduction; this indicates that tissue-specific transcriptional and post-transcriptional regulation mechanisms synergistically contribute to O. longistaminata long-term CT. Our findings provide an overview of the complex regulatory networks of CT in O. longistaminata.
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Affiliation(s)
- Ting Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyu Huang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agriculture, Yunnan University, Yunnan, China
- Research Center for Perennial Rice Engineering and Technology, Yunnan University, Yunnan, China
| | - Yinxiao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shilai Zhang
- School of Agriculture, Yunnan University, Yunnan, China
- Research Center for Perennial Rice Engineering and Technology, Yunnan University, Yunnan, China
| | - Jing Zhang
- School of Agriculture, Yunnan University, Yunnan, China
- Research Center for Perennial Rice Engineering and Technology, Yunnan University, Yunnan, China
| | - Fengyi Hu
- School of Agriculture, Yunnan University, Yunnan, China
- Research Center for Perennial Rice Engineering and Technology, Yunnan University, Yunnan, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
- * E-mail:
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural Sciences, Shenzhen, China
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41
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Zhang Z, Li J, Pan Y, Li J, Zhou L, Shi H, Zeng Y, Guo H, Yang S, Zheng W, Yu J, Sun X, Li G, Ding Y, Ma L, Shen S, Dai L, Zhang H, Yang S, Guo Y, Li Z. Natural variation in CTB4a enhances rice adaptation to cold habitats. Nat Commun 2017; 8:14788. [PMID: 28332574 PMCID: PMC5376651 DOI: 10.1038/ncomms14788] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/26/2017] [Indexed: 12/26/2022] Open
Abstract
Low temperature is a major factor limiting rice productivity and geographical distribution. Improved cold tolerance and expanded cultivation to high-altitude or high-latitude regions would help meet growing rice demand. Here we explored a QTL for cold tolerance and cloned the gene, CTB4a (cold tolerance at booting stage), encoding a conserved leucine-rich repeat receptor-like kinase. We show that different CTB4a alleles confer distinct levels of cold tolerance and selection for variation in the CTB4a promoter region has occurred on the basis of environmental temperature. The newly generated cold-tolerant haplotype Tej-Hap-KMXBG was retained by artificial selection during temperate japonica evolution in cold habitats for low-temperature acclimation. Moreover, CTB4a interacts with AtpB, a beta subunit of ATP synthase. Upregulation of CTB4a correlates with increased ATP synthase activity, ATP content, enhanced seed setting and improved yield under cold stress conditions. These findings suggest strategies to improve cold tolerance in crop plants. Low temperature is a major factor limiting productivity in rice. Here the authors show that the CTB4a gene confers cold tolerance to japonica varieties adapted to cold habitats at the booting stage of development, and propose that CTB4a acts via an interaction with the beta subunit of ATP synthase.
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Affiliation(s)
- Zhanying Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jinjie Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yinghua Pan
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.,Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Jilong Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Lei Zhou
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.,Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Hongli Shi
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yawen Zeng
- Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Haifeng Guo
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Shuming Yang
- Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Weiwei Zheng
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jianping Yu
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xingming Sun
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Gangling Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shiquan Shen
- Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Luyuan Dai
- Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Hongliang Zhang
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zichao Li
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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42
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Shakiba E, Edwards JD, Jodari F, Duke SE, Baldo AM, Korniliev P, McCouch SR, Eizenga GC. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PLoS One 2017; 12:e0172133. [PMID: 28282385 PMCID: PMC5345765 DOI: 10.1371/journal.pone.0172133] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/31/2017] [Indexed: 01/11/2023] Open
Abstract
Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.
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Affiliation(s)
- Ehsan Shakiba
- University of Arkansas, Rice Research and Extension Center, Stuttgart, Arkansas, United States of America
| | - Jeremy D. Edwards
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Farman Jodari
- Rice Experiment Station (RES), Biggs, California, United States of America
| | - Sara E. Duke
- USDA/ARS Plains Area, College Station, Texas, United States of America
| | - Angela M. Baldo
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Pavel Korniliev
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Susan R. McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, United States of America
| | - Georgia C. Eizenga
- USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
- * E-mail:
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43
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Schläppi MR, Jackson AK, Eizenga GC, Wang A, Chu C, Shi Y, Shimoyama N, Boykin DL. Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection. FRONTIERS IN PLANT SCIENCE 2017; 8:957. [PMID: 28642772 PMCID: PMC5463297 DOI: 10.3389/fpls.2017.00957] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 05/21/2023]
Abstract
Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)-QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.
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Affiliation(s)
- Michael R. Schläppi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
- *Correspondence: Michael R. Schläppi,
| | - Aaron K. Jackson
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, United States Department of Agriculture – Agricultural Research Service, StuttgartAR, United States
| | - Aiju Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yao Shi
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Naoki Shimoyama
- Department of Biological Sciences, Marquette University, MilwaukeeWI, United States
| | - Debbie L. Boykin
- United States Department of Agriculture – Agricultural Research Service, StonevilleMS, United States
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Kumar M, Gho YS, Jung KH, Kim SR. Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage. FRONTIERS IN PLANT SCIENCE 2017; 8:1120. [PMID: 28713404 PMCID: PMC5491850 DOI: 10.3389/fpls.2017.01120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/09/2017] [Indexed: 05/14/2023]
Abstract
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.
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Affiliation(s)
- Manu Kumar
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
| | - Yun-Shil Gho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
| | - Seong-Ryong Kim
- Department of Life Sciences, Sogang UniversitySeoul, South Korea
- *Correspondence: Seong-Ryong Kim, Ki-Hong Jung,
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