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Scossa F, Alseekh S, Fernie AR. Integrating multi-omics data for crop improvement. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153352. [PMID: 33360148 DOI: 10.1016/j.jplph.2020.153352] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/26/2023]
Abstract
Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178, Rome, Italy.
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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Li K, Wen W, Alseekh S, Yang X, Guo H, Li W, Wang L, Pan Q, Zhan W, Liu J, Li Y, Wu X, Brotman Y, Willmitzer L, Li J, Fernie AR, Yan J. Large-scale metabolite quantitative trait locus analysis provides new insights for high-quality maize improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:216-230. [PMID: 30888713 DOI: 10.1111/tpj.14317] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/27/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
It is generally recognized that many favorable genes which were lost during domestication, including those related to both nutritional value and stress resistance, remain hidden in wild relatives. To uncover such genes in teosinte, an ancestor of maize, we conducted metabolite profiling in a BC2 F7 population generated from a cross between the maize wild relative (Zea mays ssp. mexicana) and maize inbred line Mo17. In total, 65 primary metabolites were quantified in four tissues (seedling-stage leaf, grouting-stage leaf, young kernel and mature kernel) with clear tissue-specific patterns emerging. Three hundred and fifty quantitative trait loci (QTLs) for these metabolites were obtained, which were distributed unevenly across the genome and included two QTL hotspots. Metabolite concentrations frequently increased in the presence of alleles from the teosinte genome while the opposite was observed for grain yield and shape trait QTLs. Combination of the multi-tissue transcriptome and metabolome data provided considerable insight into the metabolic variations between maize and its wild relatives. This study thus identifies favorable genes hidden in the wild relative which should allow us to balance high yield and quality in future modern crop breeding programs.
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Affiliation(s)
- Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Centre of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Xiaohong Yang
- Beijing Key Laboratory of Crop Genetic Improvement, National Maize Improvement Center of China, China Agricultural University, West Yuanmingyuan Lu 2, 100193, Haidian, Beijing, China
| | - Huan Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Luxi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Wei Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Xiao Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Lothar Willmitzer
- Centre of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Jiansheng Li
- Beijing Key Laboratory of Crop Genetic Improvement, National Maize Improvement Center of China, China Agricultural University, West Yuanmingyuan Lu 2, 100193, Haidian, Beijing, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Centre of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
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Lu R, Xu W, Lu Q, Li P, Losh J, Hina F, Li E, Qiu Y. Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae. PLANT DIVERSITY 2018; 40:253-264. [PMID: 30740572 PMCID: PMC6317509 DOI: 10.1016/j.pld.2018.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/21/2023]
Abstract
The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA)-Eastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered C roomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (EST-SSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.
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Affiliation(s)
- Ruisen Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wuqin Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qixiang Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jocelyn Losh
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Faiza Hina
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Enxiang Li
- College of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Yingxiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Corresponding author.
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