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Cheng J, Jia Y, Hill C, He T, Wang K, Guo G, Shabala S, Zhou M, Han Y, Li C. Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement. J Adv Res 2024:S2090-1232(23)00408-3. [PMID: 38199453 DOI: 10.1016/j.jare.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known. OBJECTIVES This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits. METHODS Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes. RESULTS There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed. CONCLUSION Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate.
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Affiliation(s)
- Jingye Cheng
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia; Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jia
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Camilla Hill
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Tianhua He
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
| | - Chengdao Li
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
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Slafer GA, Casas AM, Igartua E. Sense in sensitivity: difference in the meaning of photoperiod-insensitivity between wheat and barley. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad128. [PMID: 37021554 DOI: 10.1093/jxb/erad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Indexed: 06/19/2023]
Abstract
The description of long photoperiod sensitivity in wheat and barley is a cause of confusion for researchers working in these crops, usually accustomed to free exchange of physiological and genetic knowledge of such similar crops. Indeed, wheat and barley scientists customarily quote studies of either crop species when researching one of them. Among their numerous similarities the main gene controlling that response is the same in both crops (PPD1; PPD-H1 in barley and PPD-D1 in hexaploid wheat). However, the photoperiod responses are different: (i) the main dominant allele inducing shorter time to anthesis is the insensitive allele in wheat (Ppd-D1a) but the sensitive allele in barley (Ppd-H1) (i.e. sensitivity to photoperiod produces opposite effects on time to heading in wheat and barley), (ii) the main "insensitive" allele in wheat, Ppd-D1a, does confer insensitivity, whilst that of barley reduces the sensitivity but still responds to photoperiod. The different behaviour of PPD1 genes in wheat and barley is put in a common framework based on the similarities and differences of the molecular bases of their mutations, which include polymorphism at gene expression levels, copy number variation, and sequence of coding regions. This common perspective sheds light on a source on confusion for cereal researchers, and prompts us to recommend accounting for the photoperiod sensitivity status of the plant materials when doing research on genetic control of phenology. Finally, we provide advice to facilitate the management of natural PPD1 diversity in breeding programs and suggest targets for further modification through gene editing, based on mutual knowledge on the two crops.
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Affiliation(s)
- Gustavo A Slafer
- Department of Crop and Forest Sciences University of Lleida and AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25198 Lleida, Spain
- ICREA, Catalonian Institution for Research and Advanced Studies, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD, CSIC, Avda. Montañana 1005, E-50059 Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD, CSIC, Avda. Montañana 1005, E-50059 Zaragoza, Spain
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Cheng J, Hill C, Han Y, He T, Ye X, Shabala S, Guo G, Zhou M, Wang K, Li C. New semi-dwarfing alleles with increased coleoptile length by gene editing of gibberellin 3-oxidase 1 using CRISPR-Cas9 in barley (Hordeum vulgare L.). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:806-818. [PMID: 36587283 PMCID: PMC10037138 DOI: 10.1111/pbi.13998] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/15/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
The green revolution was based on genetic modification of the gibberellin (GA) hormone system with "dwarfing" gene mutations that reduces GA signals, conferring shorter stature, thus enabling plant adaptation to modern farming conditions. Strong GA-related mutants with shorter stature often have reduced coleoptile length, discounting yield gain due to their unsatisfactory seedling emergence under drought conditions. Here we present gibberellin (GA) 3-oxidase1 (GA3ox1) as an alternative semi-dwarfing gene in barley that combines an optimal reduction in plant height without restricting coleoptile and seedling growth. Using large-scale field trials with an extensive collection of barley accessions, we showed that a natural GA3ox1 haplotype moderately reduced plant height by 5-10 cm. We used CRISPR/Cas9 technology, generated several novel GA3ox1 mutants and validated the function of GA3ox1. We showed that altered GA3ox1 activities changed the level of active GA isoforms and consequently increased coleoptile length by an average of 8.2 mm, which could provide essential adaptation to maintain yield under climate change. We revealed that CRISPR/Cas9-induced GA3ox1 mutations increased seed dormancy to an ideal level that could benefit the malting industry. We conclude that selecting HvGA3ox1 alleles offers a new opportunity for developing barley varieties with optimal stature, longer coleoptile and additional agronomic traits.
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Affiliation(s)
- Jingye Cheng
- Tasmanian Institute of AgricultureUniversity of TasmaniaHobartTASAustralia
- Western Crop Genetics Alliance, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWAAustralia
| | - Camilla Hill
- Western Crop Genetics Alliance, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWAAustralia
| | - Yong Han
- Agriculture and Food, Department of Primary Industries and Regional DevelopmentSouth PerthWAAustralia
| | - Tianhua He
- Western Crop Genetics Alliance, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWAAustralia
| | - Xingguo Ye
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Sergey Shabala
- Tasmanian Institute of AgricultureUniversity of TasmaniaHobartTASAustralia
- School of Biological ScienceUniversity of Western AustraliaPerthWAAustralia
| | - Ganggang Guo
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Meixue Zhou
- Tasmanian Institute of AgricultureUniversity of TasmaniaHobartTASAustralia
| | - Ke Wang
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWAAustralia
- Agriculture and Food, Department of Primary Industries and Regional DevelopmentSouth PerthWAAustralia
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Revolinski SR, Maughan PJ, Coleman CE, Burke IC. Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome. Commun Biol 2023; 6:326. [PMID: 36973344 PMCID: PMC10042881 DOI: 10.1038/s42003-023-04620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Bromus tectorum L. is arguably the most successful invasive weed in the world. It has fundamentally altered arid ecosystems of the western United States, where it now found on an excess of 20 million hectares. Invasion success is related to avoidance of abiotic stress and human management. Early flowering is a heritable trait utilized by B. tectorum, enabling the species to temporally monopolize limited resources and outcompete the native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies. To study flowering time traits in B. tectorum, we assembled a chromosome scale reference genome for B. tectorum. To assess the utility of the assembled genome, 121 diverse B. tectorum accessions are phenotyped and subjected to a genome wide association study (GWAS). Candidate genes, representing homologs of genes that have been previously associated with plant height or flowering phenology traits in related species are located near QTLs we identified. This study uses a high-resolution GWAS to identify reproductive phenology genes in a weedy species and represents a considerable step forward in understanding the mechanisms underlying genetic plasticity in one of the most successful invasive weed species.
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Affiliation(s)
- Samuel R Revolinski
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Peter J Maughan
- Department of Plant & Wildlife Science, Brigham Young University, Provo, UT, USA
| | - Craig E Coleman
- Department of Plant & Wildlife Science, Brigham Young University, Provo, UT, USA
| | - Ian C Burke
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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Zhang W, Tan C, Hu H, Pan R, Xiao Y, Ouyang K, Zhou G, Jia Y, Zhang X, Hill CB, Wang P, Chapman B, Han Y, Xu L, Xu Y, Angessa T, Luo H, Westcott S, Sharma D, Nevo E, Barrero RA, Bellgard MI, He T, Tian X, Li C. Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:46-62. [PMID: 36054248 PMCID: PMC9829399 DOI: 10.1111/pbi.13917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.
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Affiliation(s)
- Wenying Zhang
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Cong Tan
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Haifei Hu
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rui Pan
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Yuhui Xiao
- Grandomics Biotechnology Co., LtdWuhanChina
| | - Kai Ouyang
- Grandomics Biotechnology Co., LtdWuhanChina
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yong Jia
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiao‐Qi Zhang
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Camilla Beate Hill
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Penghao Wang
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Brett Chapman
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Yong Han
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Le Xu
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Tefera Angessa
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Hao Luo
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Sharon Westcott
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Darshan Sharma
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | - Roberto A. Barrero
- eResearch OfficeQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Matthew I. Bellgard
- eResearch OfficeQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Tianhua He
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Future Food Institute, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
- Department of Primary Industries and Regional DevelopmentSouth PerthWestern AustraliaAustralia
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Dang VH, Hill CB, Zhang XQ, Angessa TT, McFawn LA, Li C. Multi-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3087-3102. [PMID: 35879467 PMCID: PMC9482607 DOI: 10.1007/s00122-022-04169-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Key genes controlling flowering and interactions of different photoperiod alleles with various environments were identified in a barley MAGIC population. A new candidate gene for vernalisation requirements was also detected. Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions.
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Affiliation(s)
- Viet Hoang Dang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
- Department of Primary Industries and Regional Development, Perth, WA, Australia
| | - Camilla Beate Hill
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia
| | - Lee-Anne McFawn
- Department of Primary Industries and Regional Development, Perth, WA, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Perth, WA, Australia.
- Department of Primary Industries and Regional Development, Perth, WA, Australia.
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Li B, Yang C, An B, Wang H, Albaqami M, Abou-Elwafa SF, Xu L, Xu Y. Comparative transcriptomic and epigenetic analyses reveal conserved and divergent regulatory pathways in barley response to temperature stresses. PHYSIOLOGIA PLANTARUM 2022; 174:e13727. [PMID: 35657636 DOI: 10.1111/ppl.13727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/29/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation and histone modification enable plants to rapidly adapt to adverse temperature stresses, including low temperature (LT) and high temperature (HT) stress. In this study, we conducted physiological, epigenetic, and transcriptomic analyses of barley seedlings grown under control (22°C), mild low temperature (MLT, 14°C) and HT (38°C) conditions to elucidate the underlying molecular mechanisms. Compared to MLT, HT implies greater deleterious effects on barley seedlings' growth. The methylation-sensitive amplification polymorphism analysis showed that MLT induced more DNA methylation and HT more DNA demethylation compared to control. Besides, the higher levels of H3K9ac and H3K4me3 under HT compared to MLT stresses might lead to the loosening of chromatin and, subsequently, the activation of gene expression. Consistently, the transcriptome analysis revealed that there were more differentially expressed genes (DEGs) in plants subjected to HT stress than MLT stress compared to control. The common and unique pathways of these DEGs between MLT and HT were also analyzed. Transcription factors, such as ERF, bHLH, NAC, HSF, and MYB, were most involved in MLT and HT stress. The underlying gene regulation networks of epigenetic modulation-related genes were further explored by weight gene co-expression network analysis. Our study provides new insights into the understanding of epigenetic regulation responses to temperature stress in barley, which will lead to improved strategies for the development of cold- and heat-tolerant barley varieties for sustainable barley production in a climate-changing world.
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Affiliation(s)
- Bo Li
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Caixian Yang
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Bingzhuang An
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Hongpan Wang
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Mohammed Albaqami
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Le Xu
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
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Zhu F, Ahchige MW, Brotman Y, Alseekh S, Zsögön A, Fernie AR. Bringing more players into play: Leveraging stress in genome wide association studies. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153657. [PMID: 35231821 DOI: 10.1016/j.jplph.2022.153657] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
In order to meet the demand of the burgeoning human population as well as to adapt crops to the enhanced abiotic and biotic stress caused by the global climatic change, breeders focus on identifying valuable genes to improve both crop stress tolerance and crop quality. Recently, with the development of next-generation sequencing methods, millions of high quality single-nucleotide polymorphisms (SNPs) have been made available and genome-wide association studies (GWAS) are widely used in crop improvement studies to identify the associations between genetic variants of genomes and relevant crop agronomic traits. Here, we review classic cases of use of GWAS to identify genetic variants associated with valuable traits such as geographic adaptation, crop quality and metabolites. We discuss the power of stress GWAS to identify further associations including those with genes that are not, or only lowly, expressed during optimal growth conditions. Finally, we emphasize recent demonstrations of the efficiency and accuracy of time-resolved dynamic stress GWAS and GWAS based on genomic gene expression and structural variations, which can be applied to resolve more comprehensively the genetic regulation mechanisms of complex traits.
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Affiliation(s)
- Feng Zhu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Micha Wijesingha Ahchige
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Agustin Zsögön
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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Ochagavía H, Kiss T, Karsai I, Casas AM, Igartua E. Responses of Barley to High Ambient Temperature Are Modulated by Vernalization. FRONTIERS IN PLANT SCIENCE 2022; 12:776982. [PMID: 35145529 PMCID: PMC8822234 DOI: 10.3389/fpls.2021.776982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/15/2021] [Indexed: 06/06/2023]
Abstract
Ambient temperatures are increasing due to climate change. Cereal crops development and production will be affected consequently. Flowering time is a key factor for adaptation of small grain cereals and, therefore, exploring developmental responses of barley to rising temperatures is required. In this work, we studied phasic growth, and inflorescence traits related to yield, in eight near isogenic lines of barley (Hordeum vulgare L.) differing at the VRN-H1, VRN-H2 and PPD-H1 genes, representing different growth habits. The lines were grown in contrasting vernalization treatments, under two temperature regimes (18 and 25°C), in long days. Lines with recessive ppd-H1 presented delayed development compared to lines with the sensitive PPD-H1 allele, across the two growth phases considered. High temperature delayed flowering in all unvernalized plants, and in vernalized spring barleys carrying the insensitive ppd-H1 allele, whilst it accelerated flowering in spring barleys with the sensitive PPD-H1 allele. This finding evidenced an interaction between PPD-H1, temperature and vernalization. At the high temperature, PPD-H1 lines in spring backgrounds (VRN-H1-7) yielded more, whereas lines with ppd-H1 were best in vrn-H1 background. Our study revealed new information that will support breeding high-yielding cultivars with specific combinations of major adaptation genes tailored to future climatic conditions.
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Affiliation(s)
| | - Tibor Kiss
- Agricultural Institute, Centre for Agricultural Research, ELKH, Martonvásár, Hungary
- Center for Research and Development, Food and Wine Center of Excellence, Eszterházy Károly Catholic University, Eger, Hungary
| | - Ildikó Karsai
- Agricultural Institute, Centre for Agricultural Research, ELKH, Martonvásár, Hungary
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Zaragoza, Spain
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10
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de Aquino SO, Kiwuka C, Tournebize R, Gain C, Marraccini P, Mariac C, Bethune K, Couderc M, Cubry P, Andrade AC, Lepelley M, Darracq O, Crouzillat D, Anten N, Musoli P, Vigouroux Y, de Kochko A, Manel S, François O, Poncet V. Adaptive potential of
Coffea canephora
from Uganda in response to climate change. Mol Ecol 2022; 31:1800-1819. [DOI: 10.1111/mec.16360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
| | - Catherine Kiwuka
- NARO Kampala Uganda
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | - Clément Gain
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
| | | | - Cédric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Kévin Bethune
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Marie Couderc
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | | | | | | | | | | | - Niels Anten
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD Montpellier France
| | - Olivier François
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
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11
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Keeble-Gagnère G, Pasam R, Forrest KL, Wong D, Robinson H, Godoy J, Rattey A, Moody D, Mullan D, Walmsley T, Daetwyler HD, Tibbits J, Hayden MJ. Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization. FRONTIERS IN PLANT SCIENCE 2021; 12:756877. [PMID: 35003156 PMCID: PMC8728019 DOI: 10.3389/fpls.2021.756877] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/27/2021] [Indexed: 05/26/2023]
Abstract
Array-based single nucleotide polymorphism (SNP) genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Illumina Infinium Wheat Barley 40K SNP array Version 1.0. We show that the approach delivers high quality and high resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimizing ascertainment bias. Comprising mostly biallelic markers that were designed to be species-specific and single-copy, the array permits highly accurate imputation in diverse germplasm to improve the statistical power of genome-wide association studies (GWAS) and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Aegilops tauschii Coss. (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheat, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley, as well as direct connections to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool, Pretzel (https://plantinformatics.io/) which enables the content of the array to be visualized and interrogated interactively in the context of numerous genetic and genomic resources to be connected more seamlessly to research and breeding. The array is available for use by the international wheat and barley community.
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Affiliation(s)
| | - Raj Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Kerrie L. Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Debbie Wong
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | | | | | | | | | | | | | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew J. Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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12
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Chen L, He F, Long R, Zhang F, Li M, Wang Z, Kang J, Yang Q. A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1937-1951. [PMID: 34487430 DOI: 10.1111/jipb.13172] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/03/2021] [Indexed: 05/04/2023]
Abstract
Alfalfa (Medicago sativa L.) is an important forage crop worldwide. However, little is known about the effects of breeding status and different geographical populations on alfalfa improvement. Here, we sequenced 220 alfalfa core germplasms and determined that Chinese alfalfa cultivars form an independent group, as evidenced by comparisons of FST values between different subgroups, suggesting that geographical origin plays an important role in group differentiation. By tracing the influence of geographical regions on the genetic diversity of alfalfa varieties in China, we identified 350 common candidate genetic regions and 548 genes under selection. We also defined 165 loci associated with 24 important traits from genome-wide association studies. Of those, 17 genomic regions closely associated with a given phenotype were under selection, with the underlying haplotypes showing significant differences between subgroups of distinct geographical origins. Based on results from expression analysis and association mapping, we propose that 6-phosphogluconolactonase (MsPGL) and a gene encoding a protein with NHL domains (MsNHL) are critical candidate genes for root growth. In conclusion, our results provide valuable information for alfalfa improvement via molecular breeding.
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Affiliation(s)
- Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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13
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He T, Angessa TT, Hill CB, Zhang XQ, Chen K, Luo H, Wang Y, Karunarathne SD, Zhou G, Tan C, Wang P, Westcott S, Li C. Genomic structural equation modelling provides a whole-system approach for the future crop breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2875-2889. [PMID: 34059938 DOI: 10.1007/s00122-021-03865-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/15/2021] [Indexed: 06/12/2023]
Abstract
Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For example, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content; we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding.
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Affiliation(s)
- Tianhua He
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Camilla Beate Hill
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Kefei Chen
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
- Faculty of Science and Engineering, SAGI West, Curtin University, Bentley, WA, Australia
| | - Hao Luo
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Yonggang Wang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Sakura D Karunarathne
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Cong Tan
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Penghao Wang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia.
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, Hubei, China.
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14
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Fernández-Calleja M, Casas AM, Igartua E. Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1867-1897. [PMID: 33969431 PMCID: PMC8263424 DOI: 10.1007/s00122-021-03824-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/24/2021] [Indexed: 05/10/2023]
Abstract
This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.
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Affiliation(s)
- Miriam Fernández-Calleja
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain.
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15
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Hill CB, Angessa TT, Zhang XQ, Chen K, Zhou G, Tan C, Wang P, Westcott S, Li C. A global barley panel revealing genomic signatures of breeding in modern Australian cultivars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:419-434. [PMID: 33506596 DOI: 10.1111/tpj.15173] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today's gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.
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Affiliation(s)
- Camilla Beate Hill
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Kefei Chen
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
- Statistics for the Australian Grains Industry (SAGI) West, Faculty of Science and Engineering, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Cong Tan
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Penghao Wang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
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16
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Han Y, Broughton S, Liu L, Zhang XQ, Zeng J, He X, Li C. Highly efficient and genotype-independent barley gene editing based on anther culture. PLANT COMMUNICATIONS 2021; 2:100082. [PMID: 33898972 PMCID: PMC8060703 DOI: 10.1016/j.xplc.2020.100082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/14/2020] [Accepted: 06/03/2020] [Indexed: 05/05/2023]
Abstract
Recalcitrance to tissue culture and genetic transformation is the major bottleneck for gene manipulation in crops. In barley, immature embryos of Golden Promise have typically been used as explants for transformation. However, the genotype dependence of this approach limits the genetic modification of commercial varieties. Here, we developed an anther culture-based system that permits the effective creation of transgenic and gene-edited plants from commercial barley varieties. The protocol was tested in Golden Promise and four Australian varieties, which differed in phenology, callus induction, and green plant regeneration responses. Agrobacterium-mediated transformation was performed on microspore-derived callus to target the HvPDS gene, and T0 albinos with targeted mutations were successfully obtained from commercial varieties. Further editing of three targets was achieved with an average mutation rate of 53% in the five varieties. In 51 analyzed T0 individuals, Cas9 induced a large proportion (69%) of single-base indels and two-base deletions in the target sites, with variable mutation rates among targets and varieties. Both on-target and off-target activities were detected in T1 progenies. Compared with immature embryo protocols, this genotype-independent platform can deliver a high editing efficiency and more regenerant plants within a similar time frame. It shows promise for functional genomics and the application of CRISPR technologies for the precise improvement of commercial varieties.
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Affiliation(s)
- Yong Han
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
| | - Sue Broughton
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA 6151, Australia
| | - Li Liu
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA 6151, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
| | - Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Xiaoyan He
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA 6151, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
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17
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Jayakodi M, Padmarasu S, Haberer G, Bonthala VS, Gundlach H, Monat C, Lux T, Kamal N, Lang D, Himmelbach A, Ens J, Zhang XQ, Angessa TT, Zhou G, Tan C, Hill C, Wang P, Schreiber M, Boston LB, Plott C, Jenkins J, Guo Y, Fiebig A, Budak H, Xu D, Zhang J, Wang C, Grimwood J, Schmutz J, Guo G, Zhang G, Mochida K, Hirayama T, Sato K, Chalmers KJ, Langridge P, Waugh R, Pozniak CJ, Scholz U, Mayer KFX, Spannagl M, Li C, Mascher M, Stein N. The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 2020; 588:284-289. [PMID: 33239781 PMCID: PMC7759462 DOI: 10.1038/s41586-020-2947-8] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
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Affiliation(s)
- Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Venkata Suresh Bonthala
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cécile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Thomas Lux
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nadia Kamal
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Lang
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jennifer Ens
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Tefera T Angessa
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Camilla Hill
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Penghao Wang
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Lori B Boston
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | | | - Jerry Jenkins
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Dongdong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Chunchao Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jane Grimwood
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha, Institute for Biotechnology, Huntsville, AL, USA
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kenneth J Chalmers
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Robbie Waugh
- The James Hutton Institute, Dundee, UK
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chengdao Li
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia.
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
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18
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Karunarathne SD, Han Y, Zhang XQ, Zhou G, Hill CB, Chen K, Angessa T, Li C. Genome-Wide Association Study and Identification of Candidate Genes for Nitrogen Use Efficiency in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2020; 11:571912. [PMID: 33013994 PMCID: PMC7500209 DOI: 10.3389/fpls.2020.571912] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/18/2020] [Indexed: 05/05/2023]
Abstract
Nitrogen (N) fertilizer is largely responsible for barley grain yield potential and quality, yet excessive application leads to environmental pollution and high production costs. Therefore, efficient use of N is fundamental for sustainable agriculture. In the present study, we investigated the performance of 282 barley accessions through hydroponic screening using optimal and low NH4NO3 treatments. Low-N treatment led to an average shoot dry weight reduction of 50%, but there were significant genotypic differences among the accessions. Approximately 20% of the genotypes showed high (>75%) relative shoot dry weight under low-N treatment and were classified as low-N tolerant, whereas 20% were low-N sensitive (≤55%). Low-N tolerant accessions exhibited well-developed root systems with an average increase of 60% in relative root dry weight to facilitate more N absorption. A genome-wide association study (GWAS) identified 66 significant marker trait associations (MTAs) conferring high nitrogen use efficiency, four of which were stable across experiments. These four MTAs were located on chromosomes 1H(1), 3H(1), and 7H(2) and were associated with relative shoot length, relative shoot and root dry weight. Genes corresponding to the significant MTAs were retrieved as candidate genes, including members of the asparagine synthetase gene family, several transcription factor families, protein kinases, and nitrate transporters. Most importantly, the high-affinity nitrate transporter 2.7 (HvNRT2.7) was identified as a promising candidate on 7H for root and shoot dry weight. The identified candidate genes provide new insights into our understanding of the molecular mechanisms driving nitrogen use efficiency in barley and represent potential targets for genetic improvement.
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Affiliation(s)
- Sakura D Karunarathne
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Yong Han
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development, Government of Western Australia, Perth, WA, Australia
| | - Camilla B Hill
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Kefei Chen
- SAGI West, Faculty of Science and Engineering, Curtin University, Perth, WA, Australia
| | - Tefera Angessa
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development, Government of Western Australia, Perth, WA, Australia
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19
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Luo H, Hill CB, Zhou G, Zhang XQ, Li C. Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley. BMC PLANT BIOLOGY 2020; 20:346. [PMID: 32698771 PMCID: PMC7374919 DOI: 10.1186/s12870-020-02547-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/08/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Drought is projected to become more frequent and severe in a changing climate, which requires deep sowing of crop seeds to reach soil moisture. Coleoptile length is a key agronomic trait in cereal crops such as barley, as long coleoptiles are linked to drought tolerance and improved seedling establishment under early water-limited growing conditions. RESULTS In this study, we detected large genetic variation in a panel of 328 diverse barley (Hordeum vulgare L.) accessions. To understand the overall genetic basis of barley coleoptile length, all accessions were germinated in the dark and phenotyped for coleoptile length after 2 weeks. The investigated barleys had significant variation for coleoptile length. We then conducted genome-wide association studies (GWASs) with more than 30,000 molecular markers and identified 8 genes and 12 intergenic loci significantly associated with coleoptile length in our barley panel. The Squamosa promoter-binding-like protein 3 gene (SPL3) on chromosome 6H was identified as a major candidate gene. The missense variant on the second exon changed serine to alanine in the conserved SBP domain, which likely impacted its DNA-binding activity. CONCLUSION This study provides genetic loci for seedling coleoptile length along with candidate genes for future potential incorporation in breeding programmes to enhance early vigour and yield potential in water-limited environments.
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Affiliation(s)
- Hao Luo
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Gaofeng Zhou
- Department of Primary Industries and Regional Development, Agriculture and Food, South Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
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20
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Li Z, Lhundrup N, Guo G, Dol K, Chen P, Gao L, Chemi W, Zhang J, Wang J, Nyema T, Dawa D, Li H. Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley ( Hordeum Vulgare L.) in the Qinghai-Tibet Plateau. Front Genet 2020; 11:638. [PMID: 32719715 PMCID: PMC7351530 DOI: 10.3389/fgene.2020.00638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022] Open
Abstract
Barley (Hordeum vulgare L.) is one of the most important cereal crops worldwide. In the Qinghai-Tibet Plateau, six-rowed hulless (or naked) barley, called “qingke” in Chinese or “nas” in Tibetan, is produced mainly in Tibet. The complexity of the environment in the Qinghai-Tibet Plateau has provided unique opportunities for research on the breeding and adaptability of qingke barley. However, the genetic architecture of many important agronomic traits for qingke barley remains elusive. Heading date (HD), plant height (PH), and spike length (SL) are three prominent agronomic traits in barley. Here, we used genome-wide association (GWAS) mapping and GWAS with eigenvector decomposition (EigenGWAS) to detect quantitative trait loci (QTL) and selective signatures for HD, PH, and SL in a collection of 308 qingke barley accessions. The accessions were genotyped using a newly-developed, proprietary genotyping-by-sequencing (tGBS) technology, that yielded 14,970 high quality single nucleotide polymorphisms (SNPs). We found that the number of SNPs was higher in the varieties than in the landraces, which suggested that Tibetan varieties and varieties in the Tibetan area may have originated from different landraces in different areas. We have identified 62 QTLs associated with three important traits, and the observed phenotypic variation is well-explained by the identified QTLs. We mapped 114 known genes that include, but are not limited to, vernalization, and photoperiod genes. We found that 83.87% of the identified QTLs are located in the non-coding regulatory regions of annotated barley genes. Forty-eight of the QTLs are first reported here, 28 QTLs have pleotropic effects, and three QTL are located in the regions of the well-characterized genes HvVRN1, HvVRN3, and PpD-H2. EigenGWAS analysis revealed that multiple heading-date-related loci bear signatures of selection. Our results confirm that the barley panel used in this study is highly diverse, and showed a great promise for identifying the genetic basis of adaptive traits. This study should increase our understanding of complex traits in qingke barley, and should facilitate genome-assisted breeding for qingke barley improvement.
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Affiliation(s)
- Zhiyong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Namgyal Lhundrup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kar Dol
- Tibet Agricultural and Animal Husbandry College, Nyingchi, China
| | - Panpan Chen
- Tibet Agricultural and Animal Husbandry College, Nyingchi, China
| | - Liyun Gao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Wangmo Chemi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tashi Nyema
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Dondrup Dawa
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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21
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Mwando E, Han Y, Angessa TT, Zhou G, Hill CB, Zhang XQ, Li C. Genome-Wide Association Study of Salinity Tolerance During Germination in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2020; 11:118. [PMID: 32153619 PMCID: PMC7047234 DOI: 10.3389/fpls.2020.00118] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/27/2020] [Indexed: 05/21/2023]
Abstract
Barley seeds need to be able to germinate and establish seedlings in saline soils in Mediterranean-type climates. Despite being a major cereal crop, barley has few reported quantitative trait loci (QTL) and candidate genes underlying salt tolerance at the germination stage. Breeding programs targeting salinity tolerance at germination require an understanding of genetic loci and alleles in the current germplasm. In this study, we investigated seed-germination-related traits under control and salt stress conditions in 350 diverse barley accessions. A genome-wide association study, using ~24,000 genetic markers, was undertaken to detect marker-trait associations (MTA) and the underlying candidate genes for salinity tolerance during germination. We detected 19 loci containing 52 significant salt-tolerance-associated markers across all chromosomes, and 4 genes belonging to 4 family functions underlying the predicted MTAs. Our results provide new genetic resources and information to improve salt tolerance at germination in future barley varieties via genomic and marker-assisted selection and to open up avenues for further functional characterization of the identified candidate genes.
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Affiliation(s)
- Edward Mwando
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Yong Han
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Tefera Tolera Angessa
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development Government of Western Australia, Perth, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development Government of Western Australia, Perth, WA, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development Government of Western Australia, Perth, WA, Australia
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22
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He T, Hill CB, Angessa TT, Zhang XQ, Chen K, Moody D, Telfer P, Westcott S, Li C. Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5603-5616. [PMID: 31504706 PMCID: PMC6812734 DOI: 10.1093/jxb/erz332] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/13/2019] [Indexed: 05/10/2023]
Abstract
Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene-phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene-phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.
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Affiliation(s)
- Tianhua He
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Tefera Tolera Angessa
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Kefei Chen
- SAGI-WEST, Faculty of Science and Engineering, Curtin University, Bentley, WA, Australia
| | | | - Paul Telfer
- Australian Grain Technologies Pty Ltd (AGT), SA, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Hubei Jingzhou, China
- Correspondence:
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23
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Monteagudo A, Casas AM, Cantalapiedra CP, Contreras-Moreira B, Gracia MP, Igartua E. Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety. FRONTIERS IN PLANT SCIENCE 2019; 10:434. [PMID: 31031782 PMCID: PMC6470277 DOI: 10.3389/fpls.2019.00434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/22/2019] [Indexed: 05/20/2023]
Abstract
The Spanish Barley Core Collection (SBCC) is a source of genetic variability of potential interest for breeding, particularly for adaptation to Mediterranean environments. Two backcross populations (BC2F5) were developed using the elite cultivar Cierzo as the recurrent parent. The donor parents, namely SBCC042 and SBCC073, were selected from the SBCC lines due to their outstanding yield in drought environments. Flowering time, yield and drought-related traits were evaluated in two field trials in Zaragoza (Spain) during the 2014-15 and 2015-16 seasons and validated in the 2017-18 season. Two hundred sixty-four lines of each population were genotyped with the Barley Illumina iSelect 50k SNP chip. Genetic maps for each population were generated. The map for SBCC042 × Cierzo contains 12,893 SNPs distributed in 9 linkage groups. The map for SBCC073 × Cierzo includes 12,026 SNPs in 7 linkage groups. Both populations shared two QTL hotspots. There are QTLs for flowering time, thousand-kernel weight (TKW), and hectoliter weight on a segment of 23 Mb at ~515 Mb on chromosome 1H, which encompasses the HvFT3 gene. In both populations, flowering was accelerated by the landrace allele, which also increased the TKW. In the same region, better soil coverage was contributed by SBCC042 but coincident with a lower hectoliter weight. The second large hotspot was on chromosome 6H and contained QTLs with wide intervals for grain yield, plant height and TKW. Landrace alleles contributed to increased plant height and TKW and reduced grain yield. Only SBCC042 contributed favorable alleles for "green area," with three significant QTLs that increased ground coverage after winter, which might be exploited as an adaptive trait of this landrace. Some genes of interest found in or very close to the peaks of the QTLs are highlighted. Strategies to deploy the QTLs found for breeding and pre-breeding are proposed.
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Affiliation(s)
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Zaragoza, Spain
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24
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Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley. Sci Data 2019; 6:12. [PMID: 30931948 PMCID: PMC6472358 DOI: 10.1038/s41597-019-0011-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 11/24/2022] Open
Abstract
In barley and other cereal crops, phenological diversity drives adaptation to different cultivation areas. Improvement of barley yield and quality traits requires adaptation to specific production areas with introgression of favorable alleles dependent upon precise identification of the underlying genes. Combining targeted sequence capture systems with next-generation sequencing provides an efficient approach to explore target genetic regions at high resolution, and allows rapid discovery of thousands of genetic polymorphisms. Here, we apply a versatile target-capture method to detect genome-wide polymorphisms in 174 flowering time-related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Sequences were generated across a phenologically diverse panel of 895 barley varieties, resulting a high mean depth coverage of ~25x allowing reliable discovery and calling of insertion-deletion (InDel) and single nucleotide polymorphisms (SNPs). Sequences of InDel and SNPs from the targeted enrichment were utilized to develop 67 Kompetitive Allele Specific PCR (KASP) markers for validation. This work provides researchers and breeders a comprehensive molecular toolkit for the selection of phenology-related traits in barley. Design Type(s) | genetic polymorphism analysis objective • strain comparison design | Measurement Type(s) | genetic variation | Technology Type(s) | DNA sequencing | Factor Type(s) | cultivar | Sample Characteristic(s) | Hordeum vulgare subsp. vulgare • leaf |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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