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Nampei M, Ogi H, Sreewongchai T, Nishida S, Ueda A. Potassium transporter OsHAK17 may contribute to saline-alkaline tolerant mechanisms in rice (Oryza sativa). JOURNAL OF PLANT RESEARCH 2024; 137:505-520. [PMID: 38427146 PMCID: PMC11082038 DOI: 10.1007/s10265-024-01529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/28/2024] [Indexed: 03/02/2024]
Abstract
Rice production is seriously affected by saline-alkaline stress worldwide. To elucidate the saline-alkaline tolerance mechanisms in a novel tolerant rice variety, Shwe Nang Gyi (SNG), we investigated ion accumulation in SNG and Koshihikari (KSH), which is a saline-alkaline sensitive rice variety, and the candidates for saline-alkaline inducible genes in SNG using RNA-seq. SNG had superior ion accumulation capacity, such as K and Zn, compared to KSH. In contrast, SNG accumulated the same level of Na content in its leaf blades as KSH despite the higher dry weight of the SNG leaf blades. We further found that the expression of numerous genes, including several K+ transporter/high-affinity K+ transporter/K+ uptake protein/K+ transporter (HAK/KUP/KT) family members, were upregulated in SNG, and that OsHAK17 and OsHAK21 expression levels in the roots were significantly higher in SNG than in KSH. Moreover, yeast complementation analysis revealed that OsHAK17 was involved in K+ uptake under high-Na conditions. These results suggested that SNG has an effective K+ acquisition system supported by OsHAK17 functioning in saline-alkaline environments.
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Affiliation(s)
- Mami Nampei
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8528, Japan
| | - Hiromu Ogi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8528, Japan
| | - Tanee Sreewongchai
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Road, Lat Yao, Chatuchak, 10900, Bangkok, Thailand
| | - Sho Nishida
- Faculty of Agriculture, Saga University, 1Honjo-Machi, Saga City, Saga, 840-8502, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Korimoto, Kagoshima City, Kagoshima, 890-0065, Japan
| | - Akihiro Ueda
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8528, Japan.
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Sahito JH, Zhang H, Gishkori ZGN, Ma C, Wang Z, Ding D, Zhang X, Tang J. Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize. Int J Mol Sci 2024; 25:1918. [PMID: 38339196 PMCID: PMC10855973 DOI: 10.3390/ijms25031918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.
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Affiliation(s)
- Javed Hussain Sahito
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zeeshan Ghulam Nabi Gishkori
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhui Ma
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhihao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
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Hu Y, Li C, Zhou R, Song Y, Lv Z, Wang Q, Dong X, Liu S, Feng C, Zhou Y, Zeng X, Zhang L, Wang Z, Di H. The Transcription Factor ZmNAC89 Gene Is Involved in Salt Tolerance in Maize ( Zea mays L.). Int J Mol Sci 2023; 24:15099. [PMID: 37894780 PMCID: PMC10606073 DOI: 10.3390/ijms242015099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The NAC gene family has transcription factors specific to plants, which are involved in development and stress response and adaptation. In this study, ZmNAC89, an NAC gene in maize that plays a role in saline-alkaline tolerance, was isolated and characterized. ZmNAC89 was localized in the nucleus and had transcriptional activation activity during in vitro experiments. The expression of ZmNAC89 was strongly upregulated under saline-alkaline, drought and ABA treatments. Overexpression of the ZmNAC89 gene in transgenic Arabidopsis and maize enhanced salt tolerance at the seedling stage. Differentially expressed genes (DEGs) were then confirmed via RNA-sequencing analysis with the transgenic maize line. GO analyses showed that oxidation-reduction process-regulated genes were involved in ZmNAC89-mediated salt-alkaline stress. ZmNAC89 may regulate maize saline-alkali tolerance through the REDOX pathway and ABA signal transduction pathway. From 140 inbred maize lines, 20 haplotypes and 16 SNPs were found in the coding region of the ZmNAC89 gene, including the excellent haplotype HAP20. These results contribute to a better understanding of the response mechanism of maize to salt-alkali stress and marker-assisted selection during maize breeding.
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Affiliation(s)
- Yingying Hu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chunxiang Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Runyu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yongfeng Song
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhichao Lv
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Qi Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xiaojie Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
- Institute of Crop Resources Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Shan Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chenchen Feng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
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Xu N, Chen B, Cheng Y, Su Y, Song M, Guo R, Wang M, Deng K, Lan T, Bao S, Wang G, Guo Z, Yu L. Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean. Genes (Basel) 2023; 14:1294. [PMID: 37372474 DOI: 10.3390/genes14061294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132-346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean.
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Affiliation(s)
- Ning Xu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Bingru Chen
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yuxin Cheng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yufei Su
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Mengyuan Song
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Rongqiu Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Minghai Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Kunpeng Deng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Tianjiao Lan
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Shuying Bao
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Guifang Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Zhongxiao Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Lihe Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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Wang X, Hu Y, Wang Y, Wang Y, Gao S, Zhang T, Guo J, Shi L. Integrated metabolomic and transcriptomic strategies to reveal alkali-resistance mechanisms in wild soybean during post-germination growth stage. PLANTA 2023; 257:95. [PMID: 37036535 DOI: 10.1007/s00425-023-04129-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
The keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced reutilization of reserves in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. Soil alkalization of farmlands is increasingly serious, adversely restricting crop growth and endangering food security. Here, based on integrated analysis of transcriptomics and metabolomics, we systematically investigated changes in cotyledon weight and young root growth in response to alkali stress in two ecotypes of wild soybean after germination to reveal alkali-resistance mechanisms in barren-tolerant wild soybean. Compared with barren-tolerant wild soybean, the dry weight of common wild soybean cotyledons under alkali stress decreased slowly and the length of young roots shortened. In barren-tolerant wild soybean, nitrogen-transport amino acids asparagine and glutamate decreased in cotyledons but increased in young roots, and nitrogen-compound transporter genes and genes involved in asparagine metabolism were significantly up-regulated in both cotyledons and young roots. Moreover, isocitric, succinic, and L-malic acids involved in the glyoxylate cycle significantly accumulated and the malate synthetase gene was up-regulated in barren-tolerant wild soybean cotyledons. In barren-tolerant wild soybean young roots, glutamate and glycine related to glutathione metabolism increased significantly and the glutathione reductase gene was up-regulated. Pyruvic acid and citric acid involved in pyruvate-citrate metabolism increased distinctly and genes encoding pyruvate decarboxylase and citrate synthetase were up-regulated. Integrated analysis showed that the keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced protein decomposition, amino acid transport, and lipolysis in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. This study provides new ideas for the exploitation and utilization of wild soybean resources.
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Affiliation(s)
- Xiaoning Wang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yunan Hu
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yuming Wang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Yida Wang
- College of Physical Education, Northeast Normal University, Changchun, 130024, China
| | - Shujuan Gao
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Tao Zhang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Jixun Guo
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Lianxuan Shi
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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