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Wang R, Li Y, Xu S, Huang Q, Tu M, Zhu Y, Cen H, Dong J, Jiang L, Yao X. Genome-wide association study reveals the genetic basis for petal-size formation in rapeseed (Brassica napus) and CRISPR-Cas9-mediated mutagenesis of BnFHY3 for petal-size reduction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:373-387. [PMID: 38159103 DOI: 10.1111/tpj.16609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Petals in rapeseed (Brassica napus) serve multiple functions, including protection of reproductive organs, nutrient acquisition, and attraction of pollinators. However, they also cluster densely at the top, forming a thick layer that absorbs and reflects a considerable amount of photosynthetically active radiation. Breeding genotypes with large, small, or even petal-less varieties, requires knowledge of primary genes for allelic selection and manipulation. However, our current understanding of petal-size regulation is limited, and the lack of markers and pre-breeding materials hinders targeted petal-size breeding. Here, we conducted a genome-wide association study on petal size using 295 diverse accessions. We identified 20 significant single nucleotide polymorphisms and 236 genes associated with petal-size variation. Through a cross-analysis of genomic and transcriptomic data, we focused on 14 specific genes, from which molecular markers for diverging petal-size features can be developed. Leveraging CRISPR-Cas9 technology, we successfully generated a quadruple mutant of Far-Red Elongated Hypocotyl 3 (q-bnfhy3), which exhibited smaller petals compared to the wild type. Our study provides insights into the genetic basis of petal-size regulation in rapeseed and offers abundant potential molecular markers for breeding. The q-bnfhy3 mutant unveiled a novel role of FHY3 orthologues in regulating petal size in addition to previously reported functions.
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Affiliation(s)
- Ruisen Wang
- Jaixing Academy of Agricultural Sciences, Jiaxing, 314000, China
| | - Yafei Li
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Shiqi Xu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Qi Huang
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Mengxin Tu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Yang Zhu
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Haiyan Cen
- College of Food Science and Bioengineering, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, 866 Yu-Hang-Tang Road, Hangzhou, 310058, China
| | - Xiangtan Yao
- Jaixing Academy of Agricultural Sciences, Jiaxing, 314000, China
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Tang Y, Zhang G, Jiang X, Shen S, Guan M, Tang Y, Sun F, Hu R, Chen S, Zhao H, Li J, Lu K, Yin N, Qu C. Genome-Wide Association Study of Glucosinolate Metabolites (mGWAS) in Brassica napus L. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030639. [PMID: 36771722 PMCID: PMC9921834 DOI: 10.3390/plants12030639] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 06/12/2023]
Abstract
Glucosinolates (GSLs) are secondary plant metabolites that are enriched in rapeseed and related Brassica species, and they play important roles in defense due to their anti-nutritive and toxic properties. Here, we conducted a genome-wide association study of six glucosinolate metabolites (mGWAS) in rapeseed, including three aliphatic glucosinolates (m145 gluconapin, m150 glucobrassicanapin and m151 progoitrin), one aromatic glucosinolate (m157 gluconasturtiin) and two indole glucosinolates (m165 indolylmethyl glucosinolate and m172 4-hydroxyglucobrassicin), respectively. We identified 113 candidate intervals significantly associated with these six glucosinolate metabolites. In the genomic regions linked to the mGWAS peaks, 187 candidate genes involved in glucosinolate biosynthesis (e.g., BnaMAM1, BnaGGP1, BnaSUR1 and BnaMYB51) and novel genes (e.g., BnaMYB44, BnaERF025, BnaE2FC, BnaNAC102 and BnaDREB1D) were predicted based on the mGWAS, combined with analysis of differentially expressed genes. Our results provide insight into the genetic basis of glucosinolate biosynthesis in rapeseed and should facilitate marker-based breeding for improved seed quality in Brassica species.
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Affiliation(s)
- Yunshan Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Guorui Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Xinyue Jiang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Shulin Shen
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Mingwei Guan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Yuhan Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Fujun Sun
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Ran Hu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Si Chen
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Nengwen Yin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Gao Z, Liang Y, Wang Y, Xiao Y, Chen J, Yang X, Shi T. Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations. FRONTIERS IN PLANT SCIENCE 2022; 13:973347. [PMID: 36212363 PMCID: PMC9539442 DOI: 10.3389/fpls.2022.973347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Understanding the genetic variants responsible for floral trait diversity is important for the molecular breeding of ornamental flowers. Widely used in water gardening for thousands of years, the sacred lotus exhibits a wide range of diversity in floral organs. Nevertheless, the genetic variations underlying various morphological characteristics in lotus remain largely unclear. Here, we performed a genome-wide association study of sacred lotus for 12 well-recorded ornamental traits. Given a moderate linkage disequilibrium level of 32.9 kb, we successfully identified 149 candidate genes responsible for seven flower traits and plant size variations, including many pleiotropic genes affecting multiple floral-organ-related traits, such as NnKUP2. Notably, we found a 2.75-kb presence-and-absence genomic fragment significantly associated with stamen petaloid and petal number variations, which was further confirmed by re-examining another independent population dataset with petal number records. Intriguingly, this fragment carries MITE transposons bound by siRNAs and is related to the expression differentiation of a nearby candidate gene between few-petalled and double-petalled lotuses. Overall, these genetic variations and candidate genes responsible for diverse lotus traits revealed by our GWAS highlight the role of transposon variations, particularly MITEs, in shaping floral trait diversity.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuting Liang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Yuhan Wang
- Wuhan Institute of Design and Sciences, Wuhan, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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Jacobs SJ, Grundler MC, Henriquez CL, Zapata F. An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae). Sci Rep 2021; 11:24013. [PMID: 34907249 PMCID: PMC8671583 DOI: 10.1038/s41598-021-03419-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species (\documentclass[12pt]{minimal}
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\begin{document}$$< 20\%$$\end{document}<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.
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Affiliation(s)
- Sarah J Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.,Department of Botany, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
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