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Ding T, Cai L, He Y, Li Y, Tian E, Zhou Q, Zhou X, Wang X, Yu K, Shen X. BnPLP1 Positively Regulates Flowering Time, Plant Height, and Main Inflorescence Length in Brassica napus. Genes (Basel) 2023; 14:2206. [PMID: 38137028 PMCID: PMC10743044 DOI: 10.3390/genes14122206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein prenylation mediated by the Arabidopsis thaliana PLURIPETALA (AtPLP) gene plays a crucial role in plant growth, development, and environmental response by adding a 15-carbon farnesyl group or one to two 20-carbon geranylgeranyl groups onto one to two cysteine residues at the C-terminus of the target protein. However, the homologous genes and their functions of AtPLP in rapeseed are unclear. In this study, bioinformatics analysis and gene cloning demonstrated the existence of two homologous genes of AtPLP in the Brassica napus L. genome, namely, BnPLP1 and BnPLP2. Evolutionary analysis revealed that BnPLP1 originated from the B. rapa L. genome, while BnPLP2 originated from the B. oleracea L. genome. Genetic transformation analysis revealed that the overexpression of BnPLP1 in Arabidopsis plants exhibited earlier flowering initiation, a prolonged flowering period, increased plant height, and longer main inflorescence length compared to the wild type. Contrarily, the downregulation of BnPLP1 expression in B. napus plants led to delayed flowering initiation, shortened flowering period, decreased plant height, and reduced main inflorescence length compared to the wild type. These findings indicate that the BnPLP1 gene positively regulates flowering time, plant height, and main inflorescence length. This provides a new gene for the genetic improvement of flowering time and plant architecture in rapeseed.
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Affiliation(s)
- Ting Ding
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Lei Cai
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Yuqi He
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Yuanhong Li
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Entang Tian
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Qianhui Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xufan Zhou
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China;
| | - Kunjiang Yu
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
- Center for Research and Development of Fine Chemical of Guizhou University, Guiyang 550025, China
| | - Xinjie Shen
- College of Agriculture, Guizhou University, Guiyang 550025, China; (T.D.); (L.C.); (Y.H.); (Y.L.); (E.T.); (Q.Z.); (X.Z.)
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Feng H, Guo C, Li Z, Gao Y, Zhang Q, Geng Z, Wang J, Chen G, Liu K, Li H, Yang W. Machine learning assisted dynamic phenotypes and genomic variants help understand the ecotype divergence in rapeseed. FRONTIERS IN PLANT SCIENCE 2022; 13:1028779. [PMID: 36457523 PMCID: PMC9705987 DOI: 10.3389/fpls.2022.1028779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Three ecotypes of rapeseed, winter, spring, and semi-winter, have been formed to enable the plant to adapt to different geographic areas. Although several major loci had been found to contribute to the flowering divergence, the genomic footprints and associated dynamic plant architecture in the vegetative growth stage underlying the ecotype divergence remain largely unknown in rapeseed. Here, a set of 41 dynamic i-traits and 30 growth-related traits were obtained by high-throughput phenotyping of 171 diverse rapeseed accessions. Large phenotypic variation and high broad-sense heritability were observed for these i-traits across all developmental stages. Of these, 19 i-traits were identified to contribute to the divergence of three ecotypes using random forest model of machine learning approach, and could serve as biomarkers to predict the ecotype. Furthermore, we analyzed genomic variations of the population, QTL information of all dynamic i-traits, and genomic basis of the ecotype differentiation. It was found that 213, 237, and 184 QTLs responsible for the differentiated i-traits overlapped with the signals of ecotype divergence between winter and spring, winter and semi-winter, and spring and semi-winter, respectively. Of which, there were four common divergent regions between winter and spring/semi-winter and the strongest divergent regions between spring and semi-winter were found to overlap with the dynamic QTLs responsible for the differentiated i-traits at multiple growth stages. Our study provides important insights into the divergence of plant architecture in the vegetative growth stage among the three ecotypes, which was contributed to by the genetic differentiation, and might contribute to environmental adaption and yield improvement.
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Affiliation(s)
- Hui Feng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zongyi Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yuan Gao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Zedong Geng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoxing Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Haitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Jin Q, Gao G, Guo C, Yang T, Li G, Song J, Zheng N, Yin S, Yi L, Li Z, Ge X, King GJ, Wang J, Zhou G. Transposon insertions within alleles of BnaFT.A2 are associated with seasonal crop type in rapeseed. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3469-3483. [PMID: 35997786 DOI: 10.1007/s00122-022-04193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
We identified two new transposon insertions within the promoter of BnaFT.A2 in addition to an existing 288 bp MITE within the second intron. Each insertion event corresponds to a distinct BnaFT.A2 haplotype and is closely associated with established crop seasonal ecotypes. Florigen, encoded by FLOWERING LOCUS T (FT), plays key roles not only as a flowering hormone, but also a universal growth factor affecting several aspects of plant architecture. In rapeseed, BnaFT.A2 has been revealed as one of the major loci associated with flowering time and different ecotypes. However, it is unclear how allelic variations of BnaFT.A2 affect its function in flowering time regulation and beyond. In this study, we confirmed an existing 288 bp miniature inverted-repeat transposable element (MITE) insertion within the second intron and identified two new insertions within the promoter of BnaFT.A2-a 3971 bp CACTA and a 1079 bp Helitron. Each insertion event corresponds to a distinct BnaFT.A2 haplotype and is closely associated with established crop seasonal ecotypes. These alleles have similar tissue-specific expression patterns but discrete transcriptional patterns tightly associated with rapeseed flowering time and ecotype. RNAi lines and mutants of BnaFT.A2 flowered significantly later than controls. Differentially expressed genes (DEGs), identified in transcriptomic profiling of seedling leaves from two loss-of-function mutants (Bnaft.a2-L1 and Bnaft.a2-L2) compared with controls, indicated significant enrichment for hormone metabolic genes and roles related to plant cell wall synthesis and photosynthesis. Plants with loss-of-function BnaFT.A2 had smaller leaves and lower net photosynthetic rate compared to controls. These findings not only further clarify the genetic basis of flowering time variation and ecotype formation in B. napus, but also provide an additional toolbox for genetic improvement of seasonal adaptation and production.
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Affiliation(s)
- Qingdong Jin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gengdong Gao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaocheng Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Taihua Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ge Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jurong Song
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Na Zheng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuai Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Licong Yi
- Cash Crops Institute, Hubei Academy of Agricultural Science, Wuhan, 430064, China
| | - Zhen Li
- School of Agriculture, Jinhua Polytechnic, Jinhua, 321007, China
| | - Xianhong Ge
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Jing Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guangsheng Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Jin Q, Yin S, Li G, Guo T, Wan M, Li H, Li J, Ge X, King GJ, Li Z, Wang J, Zhou G. Functional homoeologous alleles of CONSTANS contribute to seasonal crop type in rapeseed. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3287-3303. [PMID: 34410456 DOI: 10.1007/s00122-021-03896-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Two CO paralogs in Brassica napus were confirmed and shown distinct expression pattern and function in promoting flowering and allelic variation s within BnaCO.A10 were found closely associated with ecotype divergence. CONSTANS (CO) is a key gene that responds to photoperiod and in Arabidopsis can promote flowering under long-day (LD) conditions. Brassica napus L. is a major oil crop and close relative of Arabidopsis, and arose via allopolyploidization from the diploids B. rapa (A genome) and B. oleracea (C genome). In this study, we confirmed that B. napus has two CO genes located on the A10 (BnaCO.A10) and C9 (BnaCO.C9) chromosomes. Significant differences in level and temporal pattern of transcription, as well as in protein function, of these homoeologous may have resulted from sequence variation in the promoter as well as in the coding region. Apart from two insertions of 527 bp and 2002 bp in the promoter of BnaCO.C9 that function as transcriptional enhancers, this gene is otherwise highly conserved in both promoter and coding region. However, BnaCO.A10 was classified into two haplotypes and transgene analysis in Arabidopsis and backcross analysis in rapeseed indicated that the winter-type haplotype had a greater effect in promoting flowering than the spring type. We discuss the contribution of CO alleles to species evolution, and for eco-geographic radiation following crop domestication, alongside scope for managing this locus in future breeding.
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Affiliation(s)
- Qingdong Jin
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuai Yin
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ge Li
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tao Guo
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ming Wan
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haitao Li
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Juanjuan Li
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianhong Ge
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wang
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guangsheng Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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Wang J, Sheng J, Zhu J, Hu Z, Diao Y. Comparative transcriptome analysis and identification of candidate adaptive evolution genes of Miscanthus lutarioriparius and Miscanthus sacchariflorus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1499-1512. [PMID: 34366592 PMCID: PMC8295449 DOI: 10.1007/s12298-021-01030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Miscanthus species are perennial C4 grasses that are considered promising energy crops because of their high biomass yields, excellent adaptability and low management costs. Miscanthus lutarioriparius and Miscanthus sacchariflorus are closely related subspecies that are distributed in different habitats. However, there are only a few reports on the mechanisms by which Miscanthus adapts to different environments. Here, comparative transcriptomic and morphological analyses were used to study the evolutionary adaptation of M. lutarioriparius and M. sacchariflorus to different habitats. In total, among 7586 identified orthologs, 2060 orthologs involved in phenylpropanoid biosynthesis and plant hormones were differentially expressed between the two species. Through an analysis of the Ka/Ks ratios of the orthologs, we estimated that the divergence time between the two species was approximately 4.37 Mya. In addition, 37 candidate positively selected orthologs (PSGs) that played important roles in the adaptation of these species to different habitats were identified. Then, the expression levels of 20 PSGs in response to flooding and drought stress were analyzed, and the analysis revealed significant changes in their expression levels. These results facilitate our understanding of the evolutionary adaptation to habitats and the speciation of M. lutarioriparius and M. sacchariflorus. We hypothesise that lignin synthesis genes are the main cause of the morphological differences between the two species. In summary, the plant nonspecific phospholipase C gene family and the receptor-like protein kinase gene family played important roles in the evolution of these two species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01030-1.
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Affiliation(s)
- Jia Wang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001 People’s Republic of China
| | - Jiajing Sheng
- College of Life Sciences, Nantong University, Nantong, 226019 People’s Republic of China
| | - Jianyong Zhu
- College of Forestry and Life Sciences, Chongqing University of Arts and Sciences, Chongqing, 402160 People’s Republic of China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Ying Diao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
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Zhou FY, Yu Q, Zhang Y, Han YJ, Yao CC. Overexpression of AGAMOUS-like gene PfAG5 promotes early flowering in Polypogon fugax. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:793-801. [PMID: 33820601 DOI: 10.1071/fp21047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Herbicides are the major tool for controlling large populations of yield depleting weeds. However, over-reliance on herbicides has resulted in weed adaptation and herbicide resistance. In recent years, early flowering weed species related to herbicide resistance is emerging, which may cause seed loss before crop harvest, creating a new problem for non-chemical weed management. In this study, a homologue gene of AGAMOUS sub-family (referred to as PfAG5) of the MADS-box family was cloned from plants of an early flowering Polypogon fugax Nees ex Steud. population resistant to the ACCase inhibitor herbicide (clodinafop-propargyl). The PfAG5 gene was functionally characterised in Arabidopsis thaliana L. Overexpression of the PfAG5 gene in Arabidopsis resulted in early flowering, abnormal flowers (e.g. small petals), short plants and reduced seed set, compared with the wild type. The expression of the PfAG5 gene was high in leaves and flowers, but low in pods in transgenic Arabidopsis. The PfAG5 gene was expressed earlier and higher in the resistant (R) than the susceptible (S) P. fugax plants. Furthermore, one protein (FRIGIDA-like) with relevance to flowering time regulation and interacts with PfAG5 in resistant (R) P. fugax was identified by the yeast two-hybrid and pull-down assays. These results suggest that the PfAG5 gene is involved in modulating early flowering in P. fugax.
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Affiliation(s)
- Feng-Yan Zhou
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230001, China; and Corresponding author.
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI), School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia
| | - Yong Zhang
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Yun-Jing Han
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Chuan-Chun Yao
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230001, China
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Zheng Y, Gao Z, Luo L, Wang Y, Chen Q, Yang Y, Kong X, Yang Y. Divergence of the genetic contribution of FRIGIDA homologues in regulating the flowering time in Brassica rapa ssp. rapa. Gene 2021; 796-797:145790. [PMID: 34175395 DOI: 10.1016/j.gene.2021.145790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/04/2021] [Accepted: 06/22/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Yan Zheng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zean Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Landi Luo
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yonggang Wang
- Agricultural Technology Extension Center of Zhaoyang District, Zhaotong 657000, China
| | - Qian Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Ya Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiangxiang Kong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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Tudor EH, Jones DM, He Z, Bancroft I, Trick M, Wells R, Irwin JA, Dean C. QTL-seq identifies BnaFT.A02 and BnaFLC.A02 as candidates for variation in vernalization requirement and response in winter oilseed rape (Brassica napus). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2466-2481. [PMID: 32452611 PMCID: PMC7680531 DOI: 10.1111/pbi.13421] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 05/11/2020] [Indexed: 05/05/2023]
Abstract
Winter, spring and biennial varieties of Brassica napus that vary in vernalization requirement are grown for vegetable and oil production. Here, we show that the obligate or facultative nature of the vernalization requirement in European winter oilseed rape is determined by allelic variation at a 10 Mbp region on chromosome A02. This region includes orthologues of the key floral regulators FLOWERING LOCUS C (BnaFLC.A02) and FLOWERING LOCUS T (BnaFT.A02). Polymorphism at BnaFLC.A02 and BnaFT.A02, mostly in cis-regulatory regions, results in distinct gene expression dynamics in response to vernalization treatment. Our data suggest allelic variation at BnaFT.A02 is associated with flowering time in the absence of vernalization, while variation at BnaFLC.A02 is associated with flowering time under vernalizing conditions. We hypothesize selection for BnaFLC.A02 and BnaFT.A02 gene expression variation has facilitated the generation of European winter oilseed rape varieties that are adapted to different winter climates. This knowledge will allow for the selection of alleles of flowering time regulators that alter the vernalization requirement of oilseed rape, informing the generation of new varieties with adapted flowering times and improved yields.
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Affiliation(s)
| | | | - Zhesi He
- Department of BiologyUniversity of YorkYorkUK
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Linden KJ, Callis J. The ubiquitin system affects agronomic plant traits. J Biol Chem 2020; 295:13940-13955. [PMID: 32796036 DOI: 10.1074/jbc.rev120.011303] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
In a single vascular plant species, the ubiquitin system consists of thousands of different proteins involved in attaching ubiquitin to substrates, recognizing or processing ubiquitinated proteins, or constituting or regulating the 26S proteasome. The ubiquitin system affects plant health, reproduction, and responses to the environment, processes that impact important agronomic traits. Here we summarize three agronomic traits influenced by ubiquitination: induction of flowering, seed size, and pathogen responses. Specifically, we review how the ubiquitin system affects expression of genes or abundance of proteins important for determining when a plant flowers (focusing on FLOWERING LOCUS C, FRIGIDA, and CONSTANS), highlight some recent studies on how seed size is affected by the ubiquitin system, and discuss how the ubiquitin system affects proteins involved in pathogen or effector recognition with details of recent studies on FLAGELLIN SENSING 2 and SUPPRESSOR OF NPR CONSTITUTIVE 1, respectively, as examples. Finally, we discuss the effects of pathogen-derived proteins on plant host ubiquitin system proteins. Further understanding of the molecular basis of the above processes could identify possible genes for modification or selection for crop improvement.
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Affiliation(s)
- Katrina J Linden
- Department of Molecular and Cellular Biology and the Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA
| | - Judy Callis
- Department of Molecular and Cellular Biology and the Integrative Genetics and Genomics Graduate Group, University of California, Davis, California, USA.
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Yin S, Wan M, Guo C, Wang B, Li H, Li G, Tian Y, Ge X, King GJ, Liu K, Li Z, Wang J. Transposon insertions within alleles of BnaFLC.A10 and BnaFLC.A2 are associated with seasonal crop type in rapeseed. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4729-4741. [PMID: 32417916 DOI: 10.1093/jxb/eraa237] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/10/2020] [Indexed: 05/08/2023]
Abstract
In Brassicaceae, the requirement for vernalization is conferred by high expression of FLOWERING LOCUS C (FLC). The expression of FLC is known to be repressed by prolonged exposure to cold. Rapeseed (Brassica napus L.) cultivars can be classified into spring, winter, and semi-winter crop types, depending on their respective vernalization requirements. In addition to two known distinct transposon insertion events, here we identified a 4.422 kb hAT and a 5.625 kb long interspersed nuclear element transposon insertion within BnaFLC.A10, and a 810 bp miniature inverted-repeat transposable element (MITE) in BnaFLC.A2. Quantitative PCR demonstrated that these insertions lead to distinct gene expression patterns and contribute differentially to the vernalization response. Transgenic and haplotype analysis indicated that the known 621 bp MITE in the promoter region of BnaFLC.A10 is a transcriptional enhancer that appears to be the main determinant of rapeseed vernalization, and has contributed to the adaptation of rapeseed in winter cultivation environments. In the absence of this transposon insertion, the functional allele of BnaFLC.A2 is a major determinant of vernalization demand. Thus, the combination of BnaFLC.A10 carrying the 621 bp MITE insertion and a functional BnaFLC.A2 appears necessary to establish the winter rapeseed crop phenotype.
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Affiliation(s)
- Shuai Yin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ming Wan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Haitao Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ge Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanyong Tian
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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11
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Akter A, Itabashi E, Kakizaki T, Okazaki K, Dennis ES, Fujimoto R. Genome Triplication Leads to Transcriptional Divergence of FLOWERING LOCUS C Genes During Vernalization in the Genus Brassica. FRONTIERS IN PLANT SCIENCE 2020; 11:619417. [PMID: 33633752 PMCID: PMC7900002 DOI: 10.3389/fpls.2020.619417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/29/2020] [Indexed: 05/17/2023]
Abstract
The genus Brassica includes oil crops, vegetables, condiments, fodder crops, and ornamental plants. Brassica species underwent a whole genome triplication event after speciation between ancestral species of Brassica and closely related genera including Arabidopsis thaliana. Diploid species such as Brassica rapa and Brassica oleracea have three copies of genes orthologous to each A. thaliana gene, although deletion in one or two of the three homologs has occurred in some genes. The floral transition is one of the crucial events in a plant's life history, and time of flowering is an important agricultural trait. There is a variation in flowering time within species of the genus Brassica, and this variation is largely dependent on a difference in vernalization requirements. In Brassica, like in A. thaliana, the key gene of vernalization is FLOWERING LOCUS C (FLC). In Brassica species, the vernalization response including the repression of FLC expression by cold treatment and the enrichment of the repressive histone modification tri-methylated histone H3 lysine 27 (H3K27me3) at the FLC locus is similar to A. thaliana. B. rapa and B. oleracea each have four paralogs of FLC, and the allotetraploid species, Brassica napus, has nine paralogs. The increased number of paralogs makes the role of FLC in vernalization more complicated; in a single plant, paralogs vary in the expression level of FLC before and after vernalization. There is also variation in FLC expression levels between accessions. In this review, we focus on the regulatory circuits of the vernalization response of FLC expression in the genus Brassica.
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Affiliation(s)
- Ayasha Akter
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Department of Horticulture, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsu, Japan
| | - Tomohiro Kakizaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsu, Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Elizabeth S. Dennis
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science, University of Technology, Sydney, Broadway, NSW, Australia
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- *Correspondence: Ryo Fujimoto,
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12
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Song JM, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie WZ, Cheng Y, Zhang Y, Liu K, Yang QY, Chen LL, Guo L. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. NATURE PLANTS 2020; 6:34-45. [PMID: 31932676 PMCID: PMC6965005 DOI: 10.1038/s41477-019-0577-7] [Citation(s) in RCA: 361] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/29/2019] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2-149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianlin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhiquan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Run Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wen-Zhao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuanfang Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
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13
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Raman H, Raman R, Qiu Y, Yadav AS, Sureshkumar S, Borg L, Rohan M, Wheeler D, Owen O, Menz I, Balasubramanian S. GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola. BMC Genomics 2019; 20:636. [PMID: 31387521 PMCID: PMC6685183 DOI: 10.1186/s12864-019-5964-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. However, our understanding of underlying genes and their role in canola productivity is limited. Results We report our analyses of a diverse GWAS panel (300–368 accessions) of canola and identify SNPs that are significantly associated with variation in flowering time and response to photoperiod across multiple locations. We show that several of these associations map in the vicinity of FLOWERING LOCUS T (FT) paralogs and its known transcriptional regulators. Complementary QTL and eQTL mapping studies, conducted in an Australian doubled haploid population, also detected consistent genomic regions close to the FT paralogs associated with flowering time and yield-related traits. FT sequences vary between accessions. Expression levels of FT in plants grown in field (or under controlled environment cabinets) correlated with flowering time. We show that markers linked to the FT paralogs display association with variation in multiple traits including flowering time, plant emergence, shoot biomass and grain yield. Conclusions Our findings suggest that FT paralogs not only control flowering time but also modulate yield-related productivity traits in canola. Electronic supplementary material The online version of this article (10.1186/s12864-019-5964-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Yu Qiu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Avilash Singh Yadav
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Sridevi Sureshkumar
- School of Biological Sciences, Monash University, Clayton, VIC3800, Australia
| | - Lauren Borg
- Centre for Bioinformatics and Biometrics, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Maheswaran Rohan
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Oliver Owen
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Ian Menz
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
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14
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Zhao B, Wang B, Li Z, Guo T, Zhao J, Guan Z, Liu K. Identification and characterization of a new dwarf locus DS-4 encoding an Aux/IAA7 protein in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1435-1449. [PMID: 30688990 DOI: 10.1007/s00122-019-03290-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 01/12/2019] [Indexed: 05/20/2023]
Abstract
A dominant dwarfing gene, ds - 4 , encodes an Aux/IAA protein that negatively regulates plant stature through an auxin signaling pathway. Dwarfism is an important agronomic trait affecting yield in many crop species. The molecular mechanisms underlying dwarfism in oilseed rape (Brassica napus) are poorly understood, restricting the progress of breeding dwarf varieties in this species. Here, we identified and characterized a new dwarf locus, DS-4, in B. napus. Next-generation sequencing-assisted genetic mapping and candidate gene analysis found that DS-4 encodes a nucleus-targeted auxin/indole-3-acetic acid (Aux/IAA) protein. A substitution (P87L) was found in the highly conserved degron motif of the Aux/IAA7 protein in the ds-4 mutant. This mutation co-segregated with the phenotype of individuals in the BC1F2 population. The P87L substitution was confirmed as the cause of the extreme dwarf phenotype by ectopic expression of the mutant allele BnaC05.iaa7 (equivalent to ds-4) in Arabidopsis. The P87L substitution blocked the interaction of BnaC05.iaa7 with TRANSPORT INHIBITOR RESPONSE 1 in the presence of auxin. The BnaC05.IAA7 gene is highly expressed in the cotyledons, hypocotyls, stems and leaves, but weakly in the roots and seeds of B. napus. Our findings provide new insights into the molecular mechanisms underlying dominant (gain-of-function) dwarfism in B. napus. Our identification of a distinct gene locus controlling plant height may help to improve lodging resistance in oilseed rape.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhaohong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tao Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junwei Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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15
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Leijten W, Koes R, Roobeek I, Frugis G. Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species. PLANTS 2018; 7:plants7040111. [PMID: 30558374 PMCID: PMC6313873 DOI: 10.3390/plants7040111] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/07/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Flowering and seed set are essential for plant species to survive, hence plants need to adapt to highly variable environments to flower in the most favorable conditions. Endogenous cues such as plant age and hormones coordinate with the environmental cues like temperature and day length to determine optimal time for the transition from vegetative to reproductive growth. In a breeding context, controlling flowering time would help to speed up the production of new hybrids and produce high yield throughout the year. The flowering time genetic network is extensively studied in the plant model species Arabidopsis thaliana, however this knowledge is still limited in most crops. This article reviews evidence of conservation and divergence of flowering time regulation in A. thaliana with its related crop species in the Brassicaceae and with more distant vegetable crops within the Asteraceae family. Despite the overall conservation of most flowering time pathways in these families, many genes controlling this trait remain elusive, and the function of most Arabidopsis homologs in these crops are yet to be determined. However, the knowledge gathered so far in both model and crop species can be already exploited in vegetable crop breeding for flowering time control.
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Affiliation(s)
- Willeke Leijten
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Ronald Koes
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Ilja Roobeek
- ENZA Zaden Research & Development B.V., Haling 1E, 1602 DB Enkhuizen, The Netherlands.
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria (IBBA), Operative Unit of Rome, Consiglio Nazionale delle Ricerche (CNR), Via Salaria Km. 29,300 ⁻ 00015, Monterotondo Scalo, Roma, Italy.
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16
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Su T, Wang W, Li P, Zhang B, Li P, Xin X, Sun H, Yu Y, Zhang D, Zhao X, Wen C, Zhou G, Wang Y, Zheng H, Yu S, Zhang F. A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp. pekinensis) Selection. MOLECULAR PLANT 2018; 11:1360-1376. [PMID: 30217779 DOI: 10.1016/j.molp.2018.08.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 05/08/2023]
Abstract
Chinese cabbage is the most consumed leafy crop in East Asian countries. However, premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution. In the past 40 years, spring Chinese cabbage with strong winterness has been selected to meet the market demand. Here, we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes. In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China. We identified 23 genomic loci that underwent intensive selection, and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1 (BrVIN3.1) and FLOWER LOCUS C 1 (BrFLC1) is a determinant genetic source of variation during selection. Moreover, we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVIN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage. Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant varieties by molecular-marker-assisted selection, transgenic or gene editing approaches.
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Affiliation(s)
- Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Bin Zhang
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Pan Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
| | - Honghe Sun
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing, China
| | - Yuntong Wang
- Biomarker Technologies Corporation, Beijing, China
| | | | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China.
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