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Liu J, Li D, Wang J, Wang Q, Guo X, Fu Q, Kear P, Zhu G, Yang X. Genome-wide characterization of the CPA gene family in potato and a preliminary functional analysis of its role in NaCl tolerance. BMC Genomics 2024; 25:144. [PMID: 38317113 PMCID: PMC10840148 DOI: 10.1186/s12864-024-10000-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The cation/proton antiporter (CPA) superfamily plays a crucial role in regulating ion homeostasis and pH in plant cells, contributing to stress resistance. However, in potato (Solanum tuberosum L.), systematic identification and analysis of CPA genes are lacking. RESULTS A total of 33 StCPA members were identified and classified into StNHX (n = 7), StKEA (n = 6), and StCHX (n = 20) subfamilies. StCHX owned the highest number of conserved motifs, followed by StKEA and StNHX. The StNHX and StKEA subfamilies owned more exons than StCHX. NaCl stress induced the differentially expression of 19 genes in roots or leaves, among which StCHX14 and StCHX16 were specifically induced in leaves, while StCHX2 and StCHX19 were specifically expressed in the roots. A total of 11 strongly responded genes were further verified by qPCR. Six CPA family members, StNHX1, StNHX2, StNHX3, StNHX5, StNHX6 and StCHX19, were proved to transport Na+ through yeast complementation experiments. CONCLUSIONS This study provides comprehensive insights into StCPAs and their response to NaCl stress, facilitating further functional characterization.
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Affiliation(s)
- Jintao Liu
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
- Southwest United Graduate School, Kunming, 650500, China
| | - Dianjue Li
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Jing Wang
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Qian Wang
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Xiao Guo
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan, 250100, China
| | - Qi Fu
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific, Beijing, 100081, China
| | - Guangtao Zhu
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China.
- Southwest United Graduate School, Kunming, 650500, China.
| | - Xiaohui Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan, 250100, China.
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Zhu Z, Wei L, Guo L, Bao H, Wang X, Kear P, Wang Z, Zhu G. Integrated Full-Length Transcriptome and Metabolome Profiling Reveals Flavonoid Regulation in Response to Freezing Stress in Potato. Plants (Basel) 2023; 12:2054. [PMID: 37653971 PMCID: PMC10223400 DOI: 10.3390/plants12102054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/10/2023] [Accepted: 05/14/2023] [Indexed: 09/02/2023]
Abstract
Cold stress impairs plant growth and development, resulting in crop failure. Cultivated potato (Solanum tuberosum L.) is sensitive to freezing, while its wild relative, S. commersonii, has a strong freezing tolerance. To decipher the anti-freezing mechanism of CM, we carried out a transcriptomic and metabolomic analysis of an anti-freezing variety of CM (a type of S. commersonii) and a freeze-sensitive variety of DM (a type of Solanum tuberosum L.). A total of 49,232 high-quality transcripts from 12,811 gene loci, including 46,772 coding sequences and 2018 non-coding RNAs, were identified. KEEG enrichment analysis of differentially expressed genes (DEGs) between the two varieties showed that the flavonoid biosynthesis pathway was strongly induced by freezing stress, which was proven by flavonoid metabolome analysis. Consistent with the accumulation of more flavonoids, nearly all the pathway genes were significantly upregulated in CM than those in DM. The transcript levels of two chalcone synthase (CHS-1) isoforms and four isoforms of flavonoid 3'-hydroxylase (F3'H-1) were confirmed by qRT-PCR. Co-expression analysis identified one Myb-related and three UGTs (UDP-glycosyltransferase) that were significantly upregulated in CM during freezing stress. Our findings support that the flavonoid pathway was significantly enhanced by freezing stress and the greater accumulation ofglycosylatedflavonoids in resistant types than that of sensitive types, maybe accounting for the increased freezing tolerance of freeze-resistant potato varieties.
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Affiliation(s)
- Zhiguo Zhu
- Yunnan Key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Lingling Wei
- Yunnan Key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Lei Guo
- Yunnan Key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Huihui Bao
- Yunnan Key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Xuemei Wang
- Yunnan Key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming 650500, China
| | - Philip Kear
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Zhen Wang
- International Potato Center (CIP), CIP China Center for Asia Pacific, Beijing 100081, China
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, School of Life Sciences, Yunnan Normal University, Kunming 650500, China
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Zhao X, Guo Y, Kang L, Yin C, Bi A, Xu D, Zhang Z, Zhang J, Yang X, Xu J, Xu S, Song X, Zhang M, Li Y, Kear P, Wang J, Liu Z, Fu X, Lu F. Population genomics unravels the Holocene history of bread wheat and its relatives. Nat Plants 2023; 9:403-419. [PMID: 36928772 DOI: 10.1038/s41477-023-01367-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 02/08/2023] [Indexed: 05/06/2023]
Abstract
Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.
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Affiliation(s)
- Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yafei Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lipeng Kang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Aoyue Bi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daxing Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiliang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jijin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohan Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Song Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyue Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Ming Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Philip Kear
- International Potato Center-China Center for Asia and the Pacific, Beijing, China
| | - Jing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
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Sun C, Liang W, Yan K, Xu D, Qin T, Fiaz S, Kear P, Bi Z, Liu Y, Liu Z, Zhang J, Bai J. Expression of Potato StDRO1 in Arabidopsis Alters Root Architecture and Drought Tolerance. Front Plant Sci 2022; 13:836063. [PMID: 35665176 PMCID: PMC9161210 DOI: 10.3389/fpls.2022.836063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Potato (Solanum tuberosum L) is the third important crop for providing calories to a large human population, and is considered sensitive to moderately sensitive to drought stress conditions. The development of drought-tolerant, elite varieties of potato is a challenging task, which can be achieved through molecular breeding. Recently, the DEEPER ROOTING 1 (DRO1) gene has been identified in rice, which influences plant root system and regulates grain yield under drought stress conditions. The potato StDRO1 protein is mainly localized in the plasma membrane of tobacco leaf cells, and overexpression analysis of StDRO1 in Arabidopsis resulted in an increased lateral root number, but decreased lateral root angle, lateral branch angle, and silique angle. Additionally, the drought treatment analysis indicated that StDRO1 regulated drought tolerance and rescued the defective root architecture and drought-tolerant phenotypes of Atdro1, an Arabidopsis AtDRO1 null mutant. Furthermore, StDRO1 expression was significantly higher in the drought-tolerant potato cultivar "Unica" compared to the drought-sensitive cultivar "Atlantic." The transcriptional response of StDRO1 under drought stress occurred significantly earlier in Unica than in Atlantic. Collectively, the outcome of the present investigation elucidated the role of DRO1 function in the alternation of root architecture, which potentially acts as a key gene in the development of a drought stress-tolerant cultivar. Furthermore, these findings will provide the theoretical basis for molecular breeding of drought-tolerant potato cultivars for the farming community.
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Affiliation(s)
- Chao Sun
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wenjun Liang
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Derong Xu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Tianyuan Qin
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing, China
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhen Liu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Junlian Zhang
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
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Whitt L, Ricachenevsky FK, Ziegler GZ, Clemens S, Walker E, Maathuis FJM, Kear P, Baxter I. A curated list of genes that affect the plant ionome. Plant Direct 2020; 4:e00272. [PMID: 33103043 PMCID: PMC7576880 DOI: 10.1002/pld3.272] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 05/07/2023]
Abstract
Understanding the mechanisms underlying plants' adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements, and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.
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Affiliation(s)
- Lauren Whitt
- Donald Danforth Plant Science CenterSaint LouisMOUSA
| | - Felipe Klein Ricachenevsky
- Departamento de Botânica Programa de Pós‐Graduação em Biologia Celular e MolecularUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | | | | | | | | | | | - Ivan Baxter
- Donald Danforth Plant Science CenterSaint LouisMOUSA
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Yang Z, Feng S, Tang D, Zhang L, Li Y, Kear P, Huang S, Zhang C. The mutation of a PECTATE LYASE-LIKE gene is responsible for the Yellow Margin phenotype in potato. Theor Appl Genet 2020; 133:1123-1131. [PMID: 31970451 DOI: 10.1007/s00122-020-03536-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
The yellow margin (ym) gene was mapped to a 30-kb genomic region in potato and the mutation of a pectate lyase gene led to this phenotype. The practice of clonally propagating potato (Solanum tuberosum L.), which has been lasted for thousands of years, has caused the accumulation of deleterious alleles. Despite yellow margin (ym) being a common cause of a detrimental weak-vigor phenotype and reduced yield in diploid potato, the underlying gene has eluded discovery to date. In this paper, we mapped the ym gene to a 30-kb region containing four annotated genes. Among them, PGSC0003DMG402023481 encodes a pectate lyase-like gene (StPLL) with lower expression in ym plants than in the wild-type plants. PCR amplification confirmed a 4.1-kb deletion in the mutant allele of StPLL. Knockout of StPLL in diploid potato resulted in a similar phenotype with the ym plants. This study not only characterizes the ym allele but also provides the molecular tools to select and purge it from populations, while also deepening our understanding of the morphogenesis in potato.
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Affiliation(s)
- Zhongmin Yang
- College of Horticulture, Northwest Agriculture and Forest University, Yangling, 712100, Shaanxi, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, Guangdong, China
| | - Shuangshuang Feng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210000, Jiangsu, China
| | - Die Tang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, Guangdong, China
| | - Lidong Zhang
- The AGIS-CAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Yumei Li
- The AGIS-CAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Philip Kear
- International Potato Center (CIP), CIP China Center Asia Pacific, Beijing, 100081, China
| | - Sanwen Huang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, Guangdong, China.
| | - Chunzhi Zhang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, Guangdong, China.
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