Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley
Introduction: Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-07-01
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| Series: | Journal of Advanced Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2090123222002107 |
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| author | Cheng-Wei Qiu Yue Ma Wenxing Liu Shuo Zhang Yizhou Wang Shengguan Cai Guoping Zhang Caspar C.C. Chater Zhong-Hua Chen Feibo Wu |
| author_facet | Cheng-Wei Qiu Yue Ma Wenxing Liu Shuo Zhang Yizhou Wang Shengguan Cai Guoping Zhang Caspar C.C. Chater Zhong-Hua Chen Feibo Wu |
| author_sort | Cheng-Wei Qiu |
| collection | DOAJ |
| description | Introduction: Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. Objectives: To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. Methods: Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. Results: Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. Conclusion: Our findings reveal functional genes that have been selected across barley’s complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops. |
| first_indexed | 2024-03-13T02:36:45Z |
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| id | doaj.art-d3ba9af722ee4738a2f3527a19393d98 |
| institution | Directory Open Access Journal |
| issn | 2090-1232 |
| language | English |
| last_indexed | 2024-03-13T02:36:45Z |
| publishDate | 2023-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Advanced Research |
| spelling | doaj.art-d3ba9af722ee4738a2f3527a19393d982023-06-29T04:14:16ZengElsevierJournal of Advanced Research2090-12322023-07-01493145Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barleyCheng-Wei Qiu0Yue Ma1Wenxing Liu2Shuo Zhang3Yizhou Wang4Shengguan Cai5Guoping Zhang6Caspar C.C. Chater7Zhong-Hua Chen8Feibo Wu9Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, ChinaDepartment of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, ChinaDepartment of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, ChinaDepartment of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, ChinaDepartment of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, ChinaDepartment of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, ChinaDepartment of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, ChinaRoyal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UKSchool of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia; Corresponding authors at: School of Science, Western Sydney University, Penrith, NSW, Australia (Z.-H. Chen); College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China (F. Wu).Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Corresponding authors at: School of Science, Western Sydney University, Penrith, NSW, Australia (Z.-H. Chen); College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China (F. Wu).Introduction: Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance. Objectives: To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley. Methods: Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes. Results: Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley. Conclusion: Our findings reveal functional genes that have been selected across barley’s complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.http://www.sciencedirect.com/science/article/pii/S2090123222002107Ecological adaptationMolecular evolutionPopulation geneticsDrought tolerance-associated genesTibetan wild barley (Hordeum vulgare ssp. agriocrithon) |
| spellingShingle | Cheng-Wei Qiu Yue Ma Wenxing Liu Shuo Zhang Yizhou Wang Shengguan Cai Guoping Zhang Caspar C.C. Chater Zhong-Hua Chen Feibo Wu Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley Journal of Advanced Research Ecological adaptation Molecular evolution Population genetics Drought tolerance-associated genes Tibetan wild barley (Hordeum vulgare ssp. agriocrithon) |
| title | Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley |
| title_full | Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley |
| title_fullStr | Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley |
| title_full_unstemmed | Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley |
| title_short | Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley |
| title_sort | genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley |
| topic | Ecological adaptation Molecular evolution Population genetics Drought tolerance-associated genes Tibetan wild barley (Hordeum vulgare ssp. agriocrithon) |
| url | http://www.sciencedirect.com/science/article/pii/S2090123222002107 |
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