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Liu L, Zhan J, Yan J. Engineering the future cereal crops with big biological data: toward intelligence-driven breeding by design. J Genet Genomics 2024; 51:781-789. [PMID: 38531485 DOI: 10.1016/j.jgg.2024.03.005] [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: 10/30/2023] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.
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Affiliation(s)
- Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jimin Zhan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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Bai Y, He J, Yao Y, An L, Cui Y, Li X, Yao X, Xiao S, Wu K. Identification and functional analysis of long non-coding RNA (lncRNA) and metabolites response to mowing in hulless barley (Hordeum vulgare L. var. nudum hook. f.). BMC PLANT BIOLOGY 2024; 24:666. [PMID: 38997634 PMCID: PMC11241897 DOI: 10.1186/s12870-024-05334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Hulless barley (Hordeum vulgare L. var. nudum Hook. f.) is a significant cereal crop and a substantial source of forage for livestock. Long non-coding RNAs (lncRNAs) and metabolites play crucial roles in the nutrient accumulation and regeneration of hulless barley plants following mowing. The study aimed to identify differentially expressed lncRNAs and metabolites in hulless barley plants by analyzing transcriptomic and metabolomic datasets at 2 h, 24 h, and 72 h following mowing. RESULTS The study revealed that 190, 90, and 438 lncRNA genes were differentially expressed at the 2 h, 24 h, and 72 h time points compared to the non-mowing control. We identified 14 lncRNA genes-11 downregulated and 3 upregulated-showing consistently significant differential expression across all time points after mowing. These differentially expressed lncRNAs target genes involved in critical processes such as cytokinin signaling, cell wall degradation, storage protein accumulation, and biomass increase. In addition, we identified ten differentially expressed metabolites targeting diverse metabolic pathways, including plant hormones, alkaloids, and flavonoids, before and after mowing at various time points. Endogenous hormone analysis revealed that cytokinin most likely played a crucial role in the regeneration of hulless barley after mowing. CONCLUSIONS This study created a comprehensive dataset of lncRNAs, metabolites, and hormones in hulless barley after mowing, revealing valuable insights into the functional characteristics of lncRNAs, metabolites, and hormones in regulating plant regeneration. The results indicated that cytokinin plays a significant role in facilitating the regeneration process of hulless barley after mowing. This comprehensive dataset is an invaluable resource for better understanding the complex mechanisms that underlie plant regeneration, with significant implications for crop improvement.
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Affiliation(s)
- Yixiong Bai
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Jiaqi He
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Youhua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Likun An
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Yongmei Cui
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Xin Li
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Xiaohua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Shanshan Xiao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Kunlun Wu
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China.
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Shen C, Zhang Y, Li G, Shi J, Wang D, Zhu W, Yang X, Dreni L, Tucker MR, Zhang D. MADS8 is indispensable for female reproductive development at high ambient temperatures in cereal crops. THE PLANT CELL 2023; 36:65-84. [PMID: 37738656 PMCID: PMC10734617 DOI: 10.1093/plcell/koad246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 09/24/2023]
Abstract
Temperature is a major factor that regulates plant growth and phenotypic diversity. To ensure reproductive success at a range of temperatures, plants must maintain developmental stability of their sexual organs when exposed to temperature fluctuations. However, the mechanisms integrating plant floral organ development and temperature responses are largely unknown. Here, we generated barley and rice loss-of-function mutants in the SEPALLATA-like MADS-box gene MADS8. The mutants in both species form multiple carpels that lack ovules at high ambient temperatures. Tissue-specific markers revealed that HvMADS8 is required to maintain floral meristem determinacy and ovule initiation at high temperatures, and transcriptome analyses confirmed that temperature-dependent differentially expressed genes in Hvmads8 mutants predominantly associate with floral organ and meristem regulation. HvMADS8 temperature-responsive activity relies on increased binding to promoters of downstream targets, as revealed by a cleavage under targets and tagmentation (CUT&Tag) analysis. We also demonstrate that HvMADS8 directly binds to 2 orthologs of D-class floral homeotic genes to activate their expression. Overall, our findings revealed a new, conserved role for MADS8 in maintaining pistil number and ovule initiation in cereal crops, extending the known function of plant MADS-box proteins in floral organ regulation.
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Affiliation(s)
- Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Gang Li
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Duoxiang Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Wanwan Zhu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xiujuan Yang
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Ludovico Dreni
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Matthew R Tucker
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Waite campus, Adelaide, South Australia 5064, Australia
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Qiu CW, Ma Y, Liu W, Zhang S, Wang Y, Cai S, Zhang G, Chater CCC, Chen ZH, Wu F. Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley. J Adv Res 2023; 49:31-45. [PMID: 36170948 PMCID: PMC10334146 DOI: 10.1016/j.jare.2022.09.008] [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: 05/26/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
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.
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Affiliation(s)
- Cheng-Wei Qiu
- Department 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, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuo Zhang
- Department 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, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK; School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Rajendran NR, Qureshi N, Pourkheirandish M. Genotyping by Sequencing Advancements in Barley. FRONTIERS IN PLANT SCIENCE 2022; 13:931423. [PMID: 36003814 PMCID: PMC9394214 DOI: 10.3389/fpls.2022.931423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.
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Affiliation(s)
- Nirmal Raj Rajendran
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Naeela Qureshi
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Estado de Mexico, Mexico
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
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Chen W, Chen L, Zhang X, Yang N, Guo J, Wang M, Ji S, Zhao X, Yin P, Cai L, Xu J, Zhang L, Han Y, Xiao Y, Xu G, Wang Y, Wang S, Wu S, Yang F, Jackson D, Cheng J, Chen S, Sun C, Qin F, Tian F, Fernie AR, Li J, Yan J, Yang X. Convergent selection of a WD40 protein that enhances grain yield in maize and rice. Science 2022; 375:eabg7985. [PMID: 35324310 DOI: 10.1126/science.abg7985] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A better understanding of the extent of convergent selection among crops could greatly improve breeding programs. We found that the quantitative trait locus KRN2 in maize and its rice ortholog, OsKRN2, experienced convergent selection. These orthologs encode WD40 proteins and interact with a gene of unknown function, DUF1644, to negatively regulate grain number in both crops. Knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-offs in other agronomic traits. Furthermore, genome-wide scans identified 490 pairs of orthologous genes that underwent convergent selection during maize and rice evolution, and these were enriched for two shared molecular pathways. KRN2, together with other convergently selected genes, provides an excellent target for future crop improvement.
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Affiliation(s)
- Wenkang Chen
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.,Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jianghua Guo
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Min Wang
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Shenghui Ji
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Xiangyu Zhao
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Pengfei Yin
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Lichun Cai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Jing Xu
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Lili Zhang
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Yingjia Han
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Yingni Xiao
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Gen Xu
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuhui Wang
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Sheng Wu
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.,Hubei Hongshan Laboratory, Wuhan 430070, China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China.,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Saihua Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China.,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China.,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jiansheng Li
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China.,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.,Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China.,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
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Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China. PLANTS 2022; 11:plants11020209. [PMID: 35050097 PMCID: PMC8779797 DOI: 10.3390/plants11020209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
The domestication process of cultivated barley in China remains under debate because of the controversial origins of barley. Here, we analyzed transcriptomic and non-targeted metabolic data from 29 accessions together with public resequencing data from 124 accessions to explore the domestication process of cultivated barley in China (Cb-C). These analyses revealed that both Cb-C and Tibetan wild barley (Wb-T) were the descendants of wild barley from the Near East Fertile Crescent (Wb-NE), yielding little support for a local origin of Wb-T. Wb-T was more likely an intermediate in the domestication process from Wb-NE to Cb-C. Wb-T contributed more genetically to Cb-C than Wb-NE, and was domesticated into Cb-C about 3300 years ago. These results together seem to support that Wb-T may be a feralized or hybrid form of cultivated barley from the Near East Fertile Crescent or central Asia. Additionally, the metabolite analysis revealed divergent metabolites of alkaloids and phenylpropanoids and these metabolites were specifically targeted for selection in the evolutionary stages from Wb-NE to Wb-T and from Wb-T to Cb-C. The key missense SNPs in the genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be responsible for the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Our findings allow for a better understanding of the domestication process of cultivated barley in China.
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Baiakhmetov E, Nowak A, Gudkova PD, Nobis M. Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae). Sci Rep 2020; 10:13803. [PMID: 32796878 PMCID: PMC7427808 DOI: 10.1038/s41598-020-70582-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022] Open
Abstract
Hybridisation in the wild between closely related species is a common mechanism of speciation in the plant kingdom and, in particular, in the grass family. Here we explore the potential for natural hybridisation in Stipa (one of the largest genera in Poaceae) between genetically distant species at their distribution edges in Mountains of Central Asia using integrative taxonomy. Our research highlights the applicability of classical morphological and genome reduction approaches in studies on wild plant species. The obtained results revealed a new nothospecies, Stipa × lazkovii, which exhibits intermediate characters to S. krylovii and S. bungeana. A high-density DArTseq assay disclosed that S. × lazkovii is an F1 hybrid, and established that the plastid and mitochondrial DNA was inherited from S. bungeana. In addition, molecular markers detected a hybridisation event between morphologically and genetically distant species S. bungeana and probably S. glareosa. Moreover, our findings demonstrated an uncertainty on the taxonomic status of S. bungeana that currently belongs to the section Leiostipa, but it is genetically closer to S. breviflora from the section Barbatae. Finally, we noticed a discrepancy between the current molecular data with the previous findings on S. capillata and S. sareptana.
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Affiliation(s)
- Evgenii Baiakhmetov
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.
| | - Arkadiusz Nowak
- Botanical Garden-Centre for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973, Warszawa, Poland.,Institute of Biology, Opole University, Oleska 22, 45-052, Opole, Poland
| | - Polina D Gudkova
- Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.,Department of Biology, Altai State University, Lenin 61 Ave, 656049, Barnaul, Russia
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
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Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3836172. [PMID: 32318238 PMCID: PMC7149453 DOI: 10.1155/2020/3836172] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.
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Siniauskaya MG, Makarevich AM, Goloenko IM, Pankratov VS, Liaudanski AD, Danilenko NG, Lukhanina NV, Shimkevich AM, Davydenko OG. The study of organelle DNA variability in alloplasmic barley lines in the NGS era. Vavilovskii Zhurnal Genet Selektsii 2020; 24:12-19. [PMID: 33659776 PMCID: PMC7716555 DOI: 10.18699/vj19.589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Alloplasmic lines are a suitable model for studying molecular coevolution and interrelations between genetic systems of plant cells. Whole chloroplast (cp) and mitochondrial (mt) genome sequences were obtained by the MiSeq System (Illumina). Organelle DNA samples were prepared from a set of 12 alloplasmic barley lines with different cytoplasms of Hordeum vulgare ssp. spontaneum and H. vulgare ssp. vulgare, as well as from their paternal varieties. A bioinformatic approach for analysis of NGS data obtained on an organellar DNA mix has been developed and verified. A comparative study of Hordeum organelle genomes’ variability and disposition of polymorphic loci was conducted. Eight types of chloroplast DNA and 5 types of mitochondrial DNA were distinguished for the barley sample set examined. These results were compared with the previous data of a restriction fragment length polymorphism (RFLP) study of organelle DNAs for the same material. Formerly established data about a field evaluation of alloplasmic barley lines were revised in the light of information about organelle genomes gained after NGS. Totally 17 polymorphic loci were found at exons of chloroplast genomes. Seven of the SNPs were located in the genes of the Ndh complex. The nonsynonymous changes of nucleotides were detected in the matK, rpoC1, ndhK, ndhG and infA genes. Some of the SNPs detected are very similar in codon position and in the type of amino acid substitution to the places where RNA editing can occur. Thus, these results outline new perspectives for the future study of nuclear-cytoplasmic interactions in alloplasmic lines.
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Affiliation(s)
- M G Siniauskaya
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - A M Makarevich
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - I M Goloenko
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - V S Pankratov
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - A D Liaudanski
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - N G Danilenko
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - N V Lukhanina
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - A M Shimkevich
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - O G Davydenko
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
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Hughes A, Oliveira HR, Fradgley N, Corke FMK, Cockram J, Doonan JH, Nibau C. μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:98-111. [PMID: 30868647 PMCID: PMC6618119 DOI: 10.1111/tpj.14312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/22/2019] [Accepted: 03/05/2019] [Indexed: 05/29/2023]
Abstract
Wheat and barley are two of the founder crops domesticated in the Fertile Crescent, and currently represent crops of major economic importance in temperate regions. Due to impacts on yield, quality and end-use, grain morphometric traits remain an important goal for modern breeding programmes and are believed to have been selected for by human populations. To directly and accurately assess the three-dimensional (3D) characteristics of grains, we combine X-ray microcomputed tomography (μCT) imaging techniques with bespoke image analysis tools and mathematical modelling to investigate how grain size and shape vary across wild and domesticated wheat and barley. We find that grain depth and, to a lesser extent, width are major drivers of shape change and that these traits are still relatively plastic in modern bread wheat varieties. Significant changes in grain depth are also observed to be associated with differences in ploidy. Finally, we present a model that can accurately predict the wild or domesticated status of a grain from a given taxa based on the relationship between three morphometric parameters (length, width and depth) and suggest its general applicability to both archaeological identification studies and breeding programmes.
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Affiliation(s)
- Aoife Hughes
- The National Plant Phenomics CentreInstitute of Biological, Rural and Environmental Sciences (IBERS)Aberystwyth UniversityGogerddan, AberystwythSY23 3EEUK
- Present address:
Computational and Systems Biology and Crop GeneticsJohn Innes CentreNorwichNR4 7 UHUK
| | - Hugo R. Oliveira
- School of Earth and Environmental SciencesManchester Institute of BiotechnologyUniversity of ManchesterManchesterM1 7DNUK
- Present address:
Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB)Faculdade das Ciências Humanas e SociaisUniversidade do AlgarveCampus de GambelasFaro8005‐139Portugal
| | - Nick Fradgley
- John Bingham LaboratoryNIABHuntingdon RoadCambridgeCB3 0LEUK
| | - Fiona M. K. Corke
- The National Plant Phenomics CentreInstitute of Biological, Rural and Environmental Sciences (IBERS)Aberystwyth UniversityGogerddan, AberystwythSY23 3EEUK
| | - James Cockram
- John Bingham LaboratoryNIABHuntingdon RoadCambridgeCB3 0LEUK
| | - John H. Doonan
- The National Plant Phenomics CentreInstitute of Biological, Rural and Environmental Sciences (IBERS)Aberystwyth UniversityGogerddan, AberystwythSY23 3EEUK
| | - Candida Nibau
- The National Plant Phenomics CentreInstitute of Biological, Rural and Environmental Sciences (IBERS)Aberystwyth UniversityGogerddan, AberystwythSY23 3EEUK
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12
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Schmidt SB, George TS, Brown LK, Booth A, Wishart J, Hedley PE, Martin P, Russell J, Husted S. Ancient barley landraces adapted to marginal soils demonstrate exceptional tolerance to manganese limitation. ANNALS OF BOTANY 2019; 123:831-843. [PMID: 30561497 PMCID: PMC6526322 DOI: 10.1093/aob/mcy215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/05/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Micronutrient deficiency in cereals is a problem of global significance, severely reducing grain yield and quality in marginal soils. Ancient landraces represent, through hundreds of years of local adaptation to adverse soil conditions, a unique reservoir of genes and unexplored traits for enhancing yield and abiotic stress tolerance. Here we explored and compared the genetic variation in a population of Northern European barley landraces and modern elite varieties, and their tolerance to manganese (Mn) limitation. METHODS A total of 135 barley accessions were genotyped and the genetic diversity was explored using Neighbor-Joining clustering. Based on this analysis, a sub-population of genetically diverse landraces and modern elite control lines were evaluated phenotypically for their ability to cope with Mn-deficient conditions, across three different environments increasing in complexity from hydroponics through pot experiments to regional field trials. KEY RESULTS Genetically a group of Scottish barley landraces (Bere barley) were found to cluster according to their island of origin, and accessions adapted to distinct biogeographical zones with reduced soil fertility had particularly larger Mn, but also zinc (Zn) and copper (Cu) concentrations in the shoot. Strikingly, when grown in an alkaline sandy soil in the field, the locally adapted landraces demonstrated an exceptional ability to acquire and translocate Mn to developing leaves, maintain photosynthesis and generate robust grain yields, whereas modern elite varieties totally failed to complete their life cycle. CONCLUSIONS Our results highlight the importance of gene pools of local adaptation and the value of ancient landrace material to identify and characterize genes that control nutrient use efficiency traits in adverse environments to raise future crop production and improve agricultural sustainability in marginal soils. We propose and discuss a model summarizing the physiological mechanisms involved in the complex trait of tolerance to Mn limitation.
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Affiliation(s)
- Sidsel Birkelund Schmidt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C., Denmark
| | | | | | - Allan Booth
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - John Wishart
- The Agronomy Institute, Orkney College, University of the Highlands and Islands, Orkney, UK
| | | | - Peter Martin
- The Agronomy Institute, Orkney College, University of the Highlands and Islands, Orkney, UK
| | | | - Søren Husted
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C., Denmark
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13
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The complex geography of domestication of the African rice Oryza glaberrima. PLoS Genet 2019; 15:e1007414. [PMID: 30845217 PMCID: PMC6424484 DOI: 10.1371/journal.pgen.1007414] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 03/19/2019] [Accepted: 02/08/2019] [Indexed: 11/19/2022] Open
Abstract
While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remain elusive. The inner Niger delta has been suggested as the center of origin but molecular data to support this hypothesis is lacking. Here, we present a comprehensive analysis of the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals of domesticated African rice Oryza glaberrima and its progenitor O. barthii, we hypothesize a non-centric (i.e. multiregional) domestication origin for African rice. Our analyses showed genetic structure within O. glaberrima that has a geographical association. Furthermore, we have evidence that the previously hypothesized O. barthii progenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors were either mislabeled or may actually represent feral wild-domesticated hybrids. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. In addition, measurements of panicle threshability, a key early domestication trait for seed shattering, were consistent with the gene phylogeographic results. We suggest seed non-shattering was selected from multiple genotypes, possibly arising from different geographical regions. Based on our evidence, O. glaberrima was not domesticated from a single centric location but was a result of diffuse process where multiple regions contributed key alleles for different domestication traits. For many crops it is not clear how they were domesticated from their wild progenitors. Transition from a wild to domesticated state required a series of genetic changes, and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop. Moreover, population comparisons provide insight into the relationship between wild and cultivated populations and the evolutionary history of domestication. In this study, we investigated the domestication history of Oryza glaberrima, a rice species that was domesticated in West Africa independent from the Asian rice species O. sativa. Using genome-wide data from a large sample of domesticated and wild African rice samples we did not find evidence that supported the established domestication model for O. glaberrima—a single domestication origin. Rather, our evidence suggests the domestication process for African rice was initiated in multiple regions of West Africa, caused potentially by the local environments and cultivation preference of people. Hence domestication of African rice was a multi-regional process.
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14
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Haas M, Schreiber M, Mascher M. Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:204-225. [PMID: 30414305 DOI: 10.1111/jipb.12737] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/27/2018] [Indexed: 05/02/2023]
Abstract
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
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Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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15
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Shaaf S, Bretani G, Biswas A, Fontana IM, Rossini L. Genetics of barley tiller and leaf development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:226-256. [PMID: 30548413 DOI: 10.1111/jipb.12757] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
In cereals, tillering and leaf development are key factors in the concept of crop ideotype, introduced in the 1960s to enhance crop yield, via manipulation of plant architecture. In the present review, we discuss advances in genetic analysis of barley shoot architecture, focusing on tillering, leaf size and angle. We also discuss novel phenotyping techniques, such as 2D and 3D imaging, that have been introduced in the era of phenomics, facilitating reliable trait measurement. We discuss the identification of genes and pathways that are involved in barley tillering and leaf development, highlighting key hormones involved in the control of plant architecture in barley and rice. Knowledge on genetic control of traits related to plant architecture provides useful resources for designing ideotypes for enhanced barley yield and performance.
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Affiliation(s)
- Salar Shaaf
- University of Milan, DiSAA, Via Celoria 2, 20133 Milan, Italy
| | | | - Abhisek Biswas
- University of Milan, DiSAA, Via Celoria 2, 20133 Milan, Italy
| | | | - Laura Rossini
- University of Milan, DiSAA, Via Celoria 2, 20133 Milan, Italy
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16
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Burgarella C, Barnaud A, Kane NA, Jankowski F, Scarcelli N, Billot C, Vigouroux Y, Berthouly-Salazar C. Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation. FRONTIERS IN PLANT SCIENCE 2019; 10:4. [PMID: 30774638 PMCID: PMC6367218 DOI: 10.3389/fpls.2019.00004] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 01/04/2019] [Indexed: 05/18/2023]
Abstract
Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.
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Affiliation(s)
- Concetta Burgarella
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
- *Correspondence: Concetta Burgarella, Cécile Berthouly-Salazar,
| | - Adeline Barnaud
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Ndjido Ardo Kane
- Laboratoire National de Recherches sur les Productions Végétales, Institut Sénégalais de Recherches Agricoles, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Dakar, Senegal
| | - Frédérique Jankowski
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UPR GREEN, Montpellier, France
- GREEN, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Université de Montpellier, Montpellier, France
- Bureau d’Analyses Macro-Economiques, Institut Sénégalais de Recherches Agricoles, Dakar, Senegal
| | - Nora Scarcelli
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Claire Billot
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Cécile Berthouly-Salazar
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Dakar, Senegal
- *Correspondence: Concetta Burgarella, Cécile Berthouly-Salazar,
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17
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Romero CC, Vels A, Niks RE. Identification of a large-effect QTL associated with kernel discoloration in barley. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2018.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Abstract
Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools has made it possible to conduct genetic mapping and population genetic studies to unravel the molecular underpinnings of domestication and crop evolution in diverse crop species. We propose three future avenues for the study of crop evolution: establishment of high-quality reference genomes for crops and their wild relatives; genomic characterization of germplasm collections; and the adoption of novel methodologies such as archaeogenetics, epigenomics, and genome editing.
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Affiliation(s)
- Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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19
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Djemal R, Mila I, Bouzayen M, Pirrello J, Khoudi H. Molecular cloning and characterization of novel WIN1/SHN1 ethylene responsive transcription factor HvSHN1 in barley (Hordeum vulgare L.). JOURNAL OF PLANT PHYSIOLOGY 2018; 228:39-46. [PMID: 29852333 DOI: 10.1016/j.jplph.2018.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/11/2018] [Accepted: 04/08/2018] [Indexed: 05/23/2023]
Abstract
Barley (Hordeum vulgare L.) is the fourth major cereal crop and shows high adaptive capabilities to diverse environments. Thus, it might represent a potential reservoir of novel genes to improve abiotic stress tolerance. In this study, a novel AP2/ERF transcription factor gene designated as HvSHN1 was isolated from barley. Protein sequence analysis showed that the HvSHN1 protein contained a nuclear localization signal and the conserved AP2/ERF domain. Phylogenetic analysis showed that HvSHN1 belongs to the group Va protein in the ERF subfamily which contains the Arabidopsis genes (SHN1, 2 and 3) and the wheat gene TdSHN1 with which it has 94.7% protein sequence identity. Expression profile analysis revealed that HvSHN1 is strongly induced by heat, cold, salt and drought. Transient expression using tobacco BY-2 protoplast coupled to confocal microscopy analysis revealed that HvSHN1 is exclusively targeted to the nucleus. Interestingly, when constitutively expressed in transgenic tobacco, HvSHN1 up-regulated stress responsive genes known to harbor GCC or DRE motif in their promoter regions. Therefore, HvSHN1 might represent a potential candidate for improvement of abiotic stress tolerance in economically important crops.
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Affiliation(s)
- Rania Djemal
- Laboratory of Plant Biotechnology and Improvement, University of Sfax, Center of Biotechnology of Sfax, Route Sidi Mansour, Km 6 B.P' 1177, 3018, Sfax, Tunisia
| | - Isabelle Mila
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Julien Pirrello
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan, F-31326, France; INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Habib Khoudi
- Laboratory of Plant Biotechnology and Improvement, University of Sfax, Center of Biotechnology of Sfax, Route Sidi Mansour, Km 6 B.P' 1177, 3018, Sfax, Tunisia.
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20
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Pankin A, Altmüller J, Becker C, von Korff M. Targeted resequencing reveals genomic signatures of barley domestication. THE NEW PHYTOLOGIST 2018; 218:1247-1259. [PMID: 29528492 PMCID: PMC5947139 DOI: 10.1111/nph.15077] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear. To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci. We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts. These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.
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Affiliation(s)
- Artem Pankin
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Christian Becker
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Maria von Korff
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’Heinrich‐Heine‐University40225DüsseldorfGermany
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21
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Al-Abdallat AM, Karadsheh A, Hadadd NI, Akash MW, Ceccarelli S, Baum M, Hasan M, Jighly A, Abu Elenein JM. Assessment of genetic diversity and yield performance in Jordanian barley (Hordeum vulgare L.) landraces grown under Rainfed conditions. BMC PLANT BIOLOGY 2017; 17:191. [PMID: 29096621 PMCID: PMC5668982 DOI: 10.1186/s12870-017-1140-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/25/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Barley (Hordeum vulgare L.) is a major cereal crop, which is cultivated under variable environmental conditions and abiotic stresses in marginal areas around the globe. In this study, we evaluated 150 Jordanian landraces obtained from ICARDA Gene Bank and four local checks for yield and yield components related-traits in two locations across Jordan for three growing seasons under rainfed conditions. The study aims to identify superior Jordanian barley genotypes under dry conditions, to understand the genotype × environment (G × E) interactions, to analyze stability parameters and to identify markers associated with yield and yield components under rainfed conditions. RESULTS The barley accessions exhibited significant variation for all traits studied. Three accessions with high yield, cultivar superiority and stability under specific environments were identified with accession G69 is the highest yielding and superior for Madaba and overall environments and G144 is the highest yielding at Ramtha. Accession G123 was high yielding in all environments and was stable across different environments. At the genetic level, the Jordanian landraces were found to be diverse with a clustering that was based on row-type. The GWAS analysis identified 77 significant markers-traits associations for multiple traits including grain yield (GY) with three significant QTLs located at 1H, 2H and 7H, which seem important for dry environments. CONCLUSION Utilizing Jordanian barley landraces can effectively improve and adapt the current barley cultivars for cultivation under environmental stresses in dry regions. Utilization of markers associated with important agronomical traits and their incorporation in breeding using marker assisted selection can improve barley tolerance to drought stress.
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Affiliation(s)
- A. M. Al-Abdallat
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, 11942 Jordan
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 950764, Amman, 11195 Jordan
| | - A. Karadsheh
- Al-Mushaqer Regional Center, NCARE, Madaba, Jordan
| | - N. I. Hadadd
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, 11942 Jordan
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 950764, Amman, 11195 Jordan
| | - M. W. Akash
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, 11942 Jordan
| | - S. Ceccarelli
- Consultant, Rete Semi Rurali, Via di Casignano 25, 50018 Scandicci, FI Italy
| | - M. Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 950764, Amman, 11195 Jordan
| | - M. Hasan
- Department of Plant Production and Protection, Faculty of Agricultural Technology, Al-Balqa’ Applied University, Al-Salt, 19117 Jordan
| | - A. Jighly
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 950764, Amman, 11195 Jordan
- Agriculture Victoria, Bioscience Research, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083 Australia
- School of Applied Systems Biology, La Trobe University, Vic, Bundoora, 3083 Australia
| | - J. M. Abu Elenein
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, 11942 Jordan
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