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Guo N, Wang S, Wang T, Duan M, Zong M, Miao L, Han S, Wang G, Liu X, Zhang D, Jiao C, Xu H, Chen L, Fei Z, Li J, Liu F. A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification. PLANT COMMUNICATIONS 2024; 5:100791. [PMID: 38168637 PMCID: PMC10873912 DOI: 10.1016/j.xplc.2023.100791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/08/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.
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Affiliation(s)
- Ning Guo
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shenyun Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
| | - Tianyi Wang
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Mengmeng Duan
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Mei Zong
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Liming Miao
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Shuo Han
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Guixiang Wang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Deshuang Zhang
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Chengzhi Jiao
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Hongwei Xu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin 301700, China.
| | | | - Jianbin Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Vegetable Research Institute, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China.
| | - Fan Liu
- State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China.
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Ahn JY, Subburaj S, Yan F, Yao J, Chandrasekaran A, Ahn KG, Lee GJ. Molecular Evaluation of the Effects of FLC Homologs and Coordinating Regulators on the Flowering Responses to Vernalization in Cabbage ( Brassica oleracea var. capitata) Genotypes. Genes (Basel) 2024; 15:154. [PMID: 38397144 PMCID: PMC10887945 DOI: 10.3390/genes15020154] [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: 11/15/2023] [Revised: 01/08/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The flowering loci of cabbage must be understood to boost their productivity. In this study, to clarify the flowering mechanisms of cabbage, we examined the three flowering repressors BoFLC1, 2 and 3, and the flowering regulators BoGI, BoCOOLAIR, and BoVIN3 of early (CAB1), middle (CAB3), and late (CAB5) flowering cabbage genotypes. Analysis of allele-specifically amplified genomic DNA and various sequence alignments demonstrated that maximal insertions and deletions influenced cabbage flowering behavior, notably in CAB3 and CAB5. Phylogenetic studies showed that BoFLC1, 2, and 3 in the CAB1, 3, and 5 genotypes had the highest homologies to other Brassica species, with CAB3 and 5 the most similar. Although CAB3 and CAB5 have comparable genetic patterns, flowering repressors and flowering regulators were investigated individually with and without vernalization to determine their minor flowering differences. The expression investigation revealed that vernalized CAB5 downregulated all BoFLC genes compared to CAB3 and, in contrast, CAB3 exhibited upregulated BoCOOLAIR. We hypothesized that the CAB3 BoFLC locus' additional insertions may have led to BoCOOLAIR overexpression and BoFLC downregulation. This study sheds light on cabbage genotypes-particularly those of CAB1 and CAB5-and suggests that structural variations in BoFLC2 and 3 bind flowering regulators, such as COOLAIR, which may affect cabbage flowering time.
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Affiliation(s)
- Ju-Young Ahn
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Saminathan Subburaj
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Fanzhuang Yan
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Jian Yao
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Ajithan Chandrasekaran
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Kyoung-Gu Ahn
- Joen Seed Co., Ltd., Goesan 28051, Republic of Korea;
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
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Shuang LS, Cuevas H, Lemke C, Kim C, Shehzad T, Paterson AH. Genetic dissection of morphological variation between cauliflower and a rapid cycling Brassica oleracea line. G3 (BETHESDA, MD.) 2023; 13:jkad163. [PMID: 37506262 PMCID: PMC10627287 DOI: 10.1093/g3journal/jkad163] [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: 10/08/2022] [Revised: 08/10/2022] [Accepted: 03/14/2023] [Indexed: 07/30/2023]
Abstract
To improve resolution to small genomic regions and sensitivity to small-effect loci in the identification of genetic factors conferring the enlarged inflorescence and other traits of cauliflower while also expediting further genetic dissection, 104 near-isogenic introgression lines (NIILs) covering 78.56% of the cauliflower genome, were selected from an advanced backcross population using cauliflower [Brassica oleracea var. botrytis L., mutant for Orange gene (ORG)] as the donor parent and a rapid cycling line (TO1434) as recurrent parent. Subsets of the advanced backcross population and NIILs were planted in the field for 8 seasons, finding 141 marker-trait associations for 15 leaf-, stem-, and flower-traits. Exemplifying the usefulness of these lines, we delineated the previously known flower color gene to a 4.5 MB interval on C3; a gene for small plant size to a 3.4 MB region on C8; and a gene for large plant size and flowering time to a 6.1 MB region on C9. This approach unmasked closely linked QTL alleles with opposing effects (on chr. 8) and revealed both alleles with expected phenotypic effects and effects opposite the parental phenotypes. Selected B. oleracea NIILs with short generation time add new value to widely used research and teaching materials.
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Affiliation(s)
- Lan Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Hugo Cuevas
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
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Qi Y, Chen C, Li X, Liu Y, Qi H, Xue Y, Yang F. Silencing ApoC3 alleviates LPS-induced acute lung injury by inhibiting TLR signaling pathway. Immunol Res 2023; 71:687-697. [PMID: 37036635 DOI: 10.1007/s12026-023-09379-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/31/2023] [Indexed: 04/11/2023]
Abstract
This study aims to confirm whether apolipoprotein C3 (ApoC3) can regulate the inflammatory response and tissue damage in acute lung injury (ALI) and explore its regulatory pathway. ALI mouse model was established by intraperitoneal injection of lipopolysaccharide (LPS). ApoC3 levels were detected by real-time quantitative polymerase chain reaction, immunohistochemistry, and western blot assays. The levels of various inflammatory factors were detected by enzyme-linked immunosorbent assay and western blot analysis. Finally, the expression of toll-like receptor (TLR)/nuclear factor kappa B (NF-κB) signaling pathway-related protein [TLR2, myeloid differentiation primary response protein 88 (MyD88), IL-1 receptor-associated kinase 1 (IRAK1), NF-κB p65, and inhibitor of kappa B alpha (IκBα)], SLP adaptor and CSK interacting membrane protein (SCIMP), spleen tyrosine kinase (Syk), and phosphorylated (p)-Syk was detected by western blot analysis. ApoC3 was overexpressed in ALI mouse lung tissue and cell inflammation model. Silencing ApoC3 reduced inflammatory factors and alleviated lung tissue damage in ALI mice. Silencing ApoC3 reduced inflammatory factors and downregulated the expression of TLR2, MyD88, IRAK1, NF-κB p65, and increased IκBα expression in LPS-treated RAW264.7 cells. Moreover, co-transfection of si-TLR2 and shApoC3 further enhanced the inhibitory effects on the levels of inflammatory factors induced by silencing ApoC3. ApoC3 overexpression increased the levels of inflammatory factors and protein expression of SCIMP and p-Syk, while silencing TLR2 reversed the promotive effects of ApoC3 overexpression on above factors. In LPS-induced ALI mouse model and inflammatory cell model, downregulation of ApoC3 reduced inflammatory factors and relieved tissue damage. This process might be achieved through the TLR pathway.
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Affiliation(s)
- Yongjie Qi
- Pulmonary and Critical Care Medicine, Jinan People's Hospital, Jinan, Shandong, 271199, People's Republic of China
| | - Chen Chen
- Pulmonary and Critical Care Medicine, Jinan People's Hospital, Jinan, Shandong, 271199, People's Republic of China
| | - Xuejun Li
- Pulmonary and Critical Care Medicine, Jinan People's Hospital, Jinan, Shandong, 271199, People's Republic of China
| | - Yi Liu
- Pulmonary and Critical Care Medicine, Jinan People's Hospital, Jinan, Shandong, 271199, People's Republic of China
| | - Huiqin Qi
- Pulmonary and Critical Care Medicine, Jinan People's Hospital, Jinan, Shandong, 271199, People's Republic of China
| | - Yingchang Xue
- Pulmonary and Critical Care Medicine, Jinan People's Hospital, Jinan, Shandong, 271199, People's Republic of China
| | - Fengyong Yang
- Department of Emergency, Jinan Key Laboratory of Acute Lung Injury Prevention and Treatment, Jinan Clinical Research Center of Respiratory Medicine, Jinan Clinical Research Center of Critical Care Medicine, Jinan People's Hospital, Jinan, 271199, Shandong, People's Republic of China.
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Kinoshita Y, Motoki K, Hosokawa M. Upregulation of tandem duplicated BoFLC1 genes is associated with the non-flowering trait in Brassica oleracea var. capitata. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:41. [PMID: 36897379 DOI: 10.1007/s00122-023-04311-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Tandem duplicated BoFLC1 genes (BoFLC1a and BoFLC1b), which were identified as the candidate causal genes for the non-flowering trait in the cabbage mutant 'nfc', were upregulated during winter in 'nfc'. The non-flowering natural cabbage mutant 'nfc' was discovered from the breeding line 'T15' with normal flowering characteristics. In this study, we investigated the molecular basis underlying the non-flowering trait of 'nfc'. First, 'nfc' was induced to flower using the grafting floral induction method, and three F2 populations were generated. The flowering phenotype of each F2 population was widely distributed with non-flowering individuals appearing in two populations. QTL-seq analysis detected a genomic region associated with flowering date at approximately 51 Mb on chromosome 9 in two of the three F2 populations. Subsequent validation and fine mapping of the candidate genomic region using QTL analysis identified the quantitative trait loci (QTL) at 50,177,696-51,474,818 bp on chromosome 9 covering 241 genes. Additionally, RNA-seq analysis in leaves and shoot apices of 'nfc' and 'T15' plants identified 19 and 15 differentially expressed genes related to flowering time, respectively. Based on these results, we identified tandem duplicated BoFLC1 genes, which are homologs of the floral repressor FLOWERING LOCUS C, as the candidate genes responsible for the non-flowering trait of 'nfc'. We designated the tandem duplicated BoFLC1 genes as BoFLC1a and BoFLC1b. Expression analysis revealed that the expression levels of BoFLC1a and BoFLC1b were downregulated during winter in 'T15' but were upregulated and maintained during winter in 'nfc'. Additionally, the expression level of the floral integrator BoFT was upregulated in the spring in 'T15' but hardly upregulated in 'nfc'. These results suggest that the upregulated levels of BoFLC1a and BoFLC1b contributed to the non-flowering trait of 'nfc'.
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Affiliation(s)
- Yu Kinoshita
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto 619-0218, Japan
| | - Munetaka Hosokawa
- Faculty of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, Nara, Nara 631-8505, Japan.
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Pisias MT, Bakala HS, McAlvay AC, Mabry ME, Birchler JA, Yang B, Pires JC. Prospects of Feral Crop De Novo Redomestication. PLANT & CELL PHYSIOLOGY 2022; 63:1641-1653. [PMID: 35639623 DOI: 10.1093/pcp/pcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.
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Affiliation(s)
- Michael T Pisias
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Harmeet Singh Bakala
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO 63132, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Tucker Hall, Columbia, MO 65211, USA
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Li Q, Peng A, Yang J, Zheng S, Li Z, Mu Y, Chen L, Si J, Ren X, Song H. A 215-bp indel at intron I of BoFLC2 affects flowering time in Brassica oleracea var. capitata during vernalization. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2785-2797. [PMID: 35760921 DOI: 10.1007/s00122-022-04149-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
In response to cold, a 215-bp deletion at intron I of BoFLC2 slows its silencing activity by feedback to the core genes of the PHD-PRC2 complex, resulting in late flowering in cabbage. Cabbage is a plant-vernalization-responsive flowering type. In response to cold, BoFLC2 is an important transcription factor, which allows cabbage plants to remain in the vegetative phase. However, there have been few reports on the detailed and functional effects of genetic variation in BoFLC2 on flowering time in cabbage. Herein, BoFLC2E and BoFLC2L, cloned from extremely early and extremely late flowering cabbages, respectively, exhibited a 215-bp indel at intron I, three non-synonymous SNPs and a 3-bp indel at exon II. BoFLC2L was found to be related to late flowering, as verified in 40 extremely early/late flowering accessions, a diverse set of cabbage inbred lines and two F2 generations by using indel-FLC2 marker. Among the genetic variation of BoFLC2, the 215-bp deletion at intron I was the main reason for the delayed flowering time, as verified in the transgenic progenies of seed-vernalization-responsive Arabidopsis thaliana (Col) and rapid cycler B. oleracea (TO1000, boflc2). This is the first report to show that the intron I indel of BoFLC2 affects the flowering time of cabbage. Although the intron I 215-bp indel between BoFLC2E and BoFLC2L did not cause alternative splicing, it slowed BoFLC2L silencing during vernalization and feedback to the core genes of the PHD-PRC2 complex, resulting in their lower transcription levels. Our study not only provides an effective molecular marker-assisted selective strategy for identifying bolting-resistant resources and breeding improved varieties in cabbage, but also provides an entry point for exploring the mechanisms of flowering time in plant-vernalization-responsive plants.
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Affiliation(s)
- Qinfei Li
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Ao Peng
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Jiaqin Yang
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Sidi Zheng
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Zhangping Li
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Yinhui Mu
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Lei Chen
- Chongqing Academy of Agricultural Sciences, Chongqing Sanqian Seed Industry Co., Ltd, Chongqing, 400060, China
| | - Jun Si
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Xuesong Ren
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
| | - Hongyuan Song
- Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
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Jiang L, Chi C, Yuan F, Lu M, Hu D, Wang L, Liu X. Anti-inflammatory effects of anemonin on acute ulcerative colitis via targeted regulation of protein kinase C-θ. Chin Med 2022; 17:39. [PMID: 35346284 PMCID: PMC8962473 DOI: 10.1186/s13020-022-00599-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Ulcerative colitis (UC) is an inflammatory bowel disease that causes continuous mucosal inflammation. Anemonin is a natural molecule from the Ranunculaceae and Gramineae plants that exerts anti-inflammatory properties. This study aimed to explore the effects and mechanisms of anemonin on UC. Methods C57BL/6 mice were administered dextran sulphate sodium (DSS; 3% [w/v]) to establish an animal model of UC. Mice were treated with an intraperitoneal injection of anemonin. Body weight and the disease activity index (DAI) were recorded. Haematoxylin and eosin staining, RT-qPCR, ELISA, and western blotting were performed to evaluate the histopathological changes and tissue inflammation. HT-29 cells were treated with lipopolysaccharide (LPS) and anemonin. Cell inflammation was evaluated using RT-qPCR and western blotting. The target proteins of anemonin were predicted using bioinformatics analysis and confirmed in vitro and in vivo. Results Anemonin improved DSS-induced body weight loss, shortened colon length, increased DAI, and induced pathological changes in the colon tissue of mice. Anemonin inhibited DSS-induced colon tissue inflammation as the release of IL-1β, TNF-α, and IL-6 was significantly suppressed. Additionally, anemonin attenuated LPS-induced cytokine production in HT-29 cells. PKC-θ was predicted as a target protein of anemonin. Anemonin did not affect PRKCQ gene transcription, but inhibited its translation. PRKCQ overexpression partially reversed the protective effects of anemonin on HT-29 cells. Adeno-associated virus delivery of the PRKCQ vector significantly reversed the protective effects of anemonin on the mouse colon. Conclusions Anemonin has the potential to treat UC. The anti-inflammatory effects of anemonin may be mediated through targeting PKC-θ.
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Affiliation(s)
- Lu Jiang
- Department of Gastroenterology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No.42 Wenhua west road, Jinan, 250011, Shandong, China.
| | - Chunhua Chi
- Department of Anorectal Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, Shandong, China
| | - Fang Yuan
- Department of Gastrology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, Shandong, China
| | - Meiqi Lu
- Department of Gastroenterology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No.42 Wenhua west road, Jinan, 250011, Shandong, China
| | - Dongqing Hu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, Shandong, China
| | - Lin Wang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, Shandong, China
| | - Xiaoming Liu
- Department of Geriatrics, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No.42 Wenhua west road, Jinan, 250011, Shandong, China.
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9
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Fulgione A, Neto C, Elfarargi AF, Tergemina E, Ansari S, Göktay M, Dinis H, Döring N, Flood PJ, Rodriguez-Pacheco S, Walden N, Koch MA, Roux F, Hermisson J, Hancock AM. Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages. Nat Commun 2022; 13:1461. [PMID: 35304466 PMCID: PMC8933414 DOI: 10.1038/s41467-022-28800-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
Understanding how populations adapt to abrupt environmental change is necessary to predict responses to future challenges, but identifying specific adaptive variants, quantifying their responses to selection and reconstructing their detailed histories is challenging in natural populations. Here, we use Arabidopsis from the Cape Verde Islands as a model to investigate the mechanisms of adaptation after a sudden shift to a more arid climate. We find genome-wide evidence of adaptation after a multivariate change in selection pressures. In particular, time to flowering is reduced in parallel across islands, substantially increasing fitness. This change is mediated by convergent de novo loss of function of two core flowering time genes: FRI on one island and FLC on the other. Evolutionary reconstructions reveal a case where expansion of the new populations coincided with the emergence and proliferation of these variants, consistent with models of rapid adaptation and evolutionary rescue. Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.
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Affiliation(s)
- Andrea Fulgione
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria.,Vienna Graduate School for Population Genetics, Vienna, Austria
| | - Célia Neto
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Shifa Ansari
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mehmet Göktay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Herculano Dinis
- Parque Natural do Fogo, Direção Nacional do Ambiente, Praia, Santiago, Cabo Verde.,Associação Projecto Vitó, São Filipe, Fogo, Cabo Verde
| | - Nina Döring
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pádraic J Flood
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Nora Walden
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany.,Biosystematics, Wageningen University, Wageningen, The Netherlands
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - Fabrice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Joachim Hermisson
- Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria
| | - Angela M Hancock
- Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria.
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10
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Wang T, Chai Z, Wang L, Liu B, Zhao J, Ren J, Yang B, Wei X, Jiang L, Liu F. IL-9 blockade attenuates inflammation in a murine model of mechanical ventilation-induced lung injury by inhibiting the NLRP3 inflammasome pathway. Inflammopharmacology 2022; 30:1395-1406. [PMID: 35296962 DOI: 10.1007/s10787-022-00947-7] [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: 11/25/2021] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Ventilation-induced lung injury (VILI) causes a huge economic and social burden, and its prevention and treatment have gained increasing attention in recent years. IL-9 is an important inflammatory factor, but its potential role in VILI remains unclear. This study intended to explore whether blocking IL-9 could alleviate VILI and explore its underlying mechanism. METHODS Lung injury was induced by mechanical ventilation (MV) in C57BL/6 mice. Changes in inflammatory factors and NLRP3-related proteins were assessed using quantitative reverse transcription-polymerase chain reaction, western blotting, and enzyme-linked immunosorbent assay. Subsequently, Nlrp3-/- mice were used to further elucidate the underlying mechanism. RESULTS The percentage of Th9 cells in the peripheral blood, bronchoalveolar lavage fluid (BALF), and lung tissues of MV mice was increased compared to those of control mice. Treatment with anti-IL-9 mAb significantly alleviated the changes in lung histopathology, wet/dry lung proportion, total protein content, and neutrophil content in BALF induced by VILI. Additionally, administering anti-IL-9 mAb significantly downregulated the expression levels of inflammatory factors in BALF and lung tissues of mice with VILI. In addition, administering anti-IL-9 mAb inhibited NLRP3 inflammasome activation, as evidenced by the observed downregulation of NLRP3, ASC, cleaved caspase-1, and GSDMD-N. Additionally, NLRP3-deficient mice had lower lung injury induced by VILI than wild-type mice. Furthermore, the anti-IL-9 mAb only partially inhibited VILI in Nlrp3-/- mice. CONCLUSIONS In MV mice, the anti-IL-9 mAb alleviated lung injury and reduced the secretion and expression of inflammatory factors partly by inhibiting the NLRP3 inflammasome pathway.
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Affiliation(s)
- Tao Wang
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ziqi Chai
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Lijuan Wang
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Bo Liu
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Junbo Zhao
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jie Ren
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Bo Yang
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xiaoyong Wei
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Lihua Jiang
- Department of Anesthesiology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Fuyun Liu
- Department of Pediatric Orthopaedics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Zhengzhou Kangfufront Street, Zhengzhou, 450052, Henan, China.
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11
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Zanini SF, Bayer PE, Wells R, Snowdon RJ, Batley J, Varshney RK, Nguyen HT, Edwards D, Golicz AA. Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs. THE PLANT GENOME 2022; 15:e20177. [PMID: 34904403 DOI: 10.1002/tpg2.20177] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/07/2021] [Indexed: 05/15/2023]
Abstract
Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.], rice (Oryza sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.). Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic diversity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.
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Affiliation(s)
- Silvia F Zanini
- Dep. of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig Univ. Giessen, Giessen, 35392, Germany
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Rachel Wells
- Dep. of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR47UH, UK
| | - Rod J Snowdon
- Dep. of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig Univ. Giessen, Giessen, 35392, Germany
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- State Agricultural Biotechnology Centre, Centre for Crop Food Innovation, Food Futures Institute, Murdoch Univ., Murdoch, WA, Australia
| | - Henry T Nguyen
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, USA
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Agnieszka A Golicz
- Dep. of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig Univ. Giessen, Giessen, 35392, Germany
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12
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Tang Q, Kuang H, Yu C, An G, Tao R, Zhang W, Jia Y. Non-vernalization requirement in Chinese kale caused by loss of BoFLC and low expressions of its paralogs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:473-483. [PMID: 34716468 PMCID: PMC8866342 DOI: 10.1007/s00122-021-03977-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/13/2021] [Indexed: 05/03/2023]
Abstract
We identified the loss of BoFLC gene as the cause of non-vernalization requirement in B. oleracea. Our developed codominant marker of BoFLC gene can be used for breeding program of B. oleracea crops. Many species of the Brassicaceae family, including some Brassica crops, require vernalization to avoid pre-winter flowering. Vernalization is an unfavorable trait for Chinese kale (Brassica oleracea var. chinensis Lei), a stem vegetable, and therefore it has been lost during its domestication/breeding process. To reveal the genetics of vernalization variation, we constructed an F2 population through crossing a Chinese kale (a non-vernalization crop) with a kale (a vernalization crop). Using bulked segregant analysis (BSA) and RNA-seq, we identified one major quantitative trait locus (QTL) controlling vernalization and fine-mapped it to a region spanning 80 kb. Synteny analysis and PCR-based sequencing results revealed that compared to that of the kale parent, the candidate region of the Chinese kale parent lost a 9,325-bp fragment containing FLC homolog (BoFLC). In addition to the BoFLC gene, there are four other FLC homologs in the genome of B. oleracea, including Bo3g005470, Bo3g024250, Bo9g173370, and Bo9g173400. The qPCR analysis showed that the BoFLC had the highest expression among the five members of the FLC family. Considering the low expression levels of the four paralogs of BoFLC, we speculate that its paralogs cannot compensate the function of the lost BoFLC, therefore the presence/absence (PA) polymorphism of BoFLC determines the vernalization variation. Based on the PA polymorphism of BoFLC, we designed a codominant marker for the vernalization trait, which can be used for breeding programs of B. oleracea crops.
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Affiliation(s)
- Qiwei Tang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changchun Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanghui An
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rong Tao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China.
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13
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Guo P, Ma Y, Deng G, Li L, Gong Y, Yang F, You Y. CYR61, regulated by miR-22-3p and MALAT1, promotes autophagy in HK-2 cell inflammatory model. Transl Androl Urol 2021; 10:3486-3500. [PMID: 34532273 PMCID: PMC8421830 DOI: 10.21037/tau-21-623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background Renal tubular epithelial cells play an important role in renal function and are a major site of injury from inflammation. Emerging evidence suggests that CYR61 is involved in the regulation of autophagy. However, there are few studies on CYR61 in nephropathy and associated inflammation. This study aimed to clarify how CYR61 regulates autophagy in human renal epithelial cells while in an inflammatory state and regulates the upstream pathway of CYR61 levels. Methods The human renal tubular epithelial cells (HK-2) cell line treated by lipopolysaccharide (LPS) was used as an inflammatory model of human epithelial cells. Short hairpin RNA (shRNA) was used to down-regulate CYR61, and the changes in the transcription and expression levels of related molecules, as well as the morphological changes of HK-2 cells, were detected by quantitative real time-PCR (qRT-PCR), western blot (WB), and transmission electron microscopy. Either CYR61 or MALAT1 were up-regulated by overexpression vectors, or MALAT1 was down-regulated by miR-22-3p mimics. Subsequently, the levels of CYR61, MALAT1, related inflammatory factors, and autophagy factors were measured by qPCR, WB, and enzyme-linked immunosorbent assay (ELISA). Cell apoptosis was detected by flow cytometry and acridine-orange assay. Results We observed that down-regulation of CYR61 could down-regulate 1B-light chain 3 (LC3) level and inhibit autophagy in the LPS-induced inflammation model of HK-2 cells. The expression levels of CYR61, Beclin1, Atg5, LC3, interleukin 6 (IL-6), and tumor necrosis factor-α (TNF-α) were significantly increased by upregulating CYR61 or MALAT1 by overexpression vector, while the expression level of p62 was significantly decreased, intracellular reactive oxygen species (ROS) content was increased, and the proportion of autophagy and apoptosis was increased. The use of miR-22-3p mimics significantly reversed the changes induced by up-regulation of CYR61 or MALAT1 at the molecular and cellular levels. Conclusions Our data indicated that CYR61 positively regulates autophagy of HK-2 cells under an inflammatory state, and was negatively regulated by miR-22-3p, while miR-22-3p and MALAT1 were negatively regulated by each other.
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Affiliation(s)
- Pengwei Guo
- Department of Nephrology, Jinan University, Guangzhou, China.,Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yanfei Ma
- Department of Gland Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Gao Deng
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Lingling Li
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yunxia Gong
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Fafen Yang
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yanwu You
- Department of Nephrology, Jinan University, Guangzhou, China.,Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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14
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Hao Y, Wang Z, Wang X, Zhan W, Wu D. OGDH is involved in sepsis induced acute lung injury through the MAPK pathway. J Thorac Dis 2021; 13:5042-5054. [PMID: 34527342 PMCID: PMC8411135 DOI: 10.21037/jtd-21-948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/02/2021] [Indexed: 11/06/2022]
Abstract
Background Acute lung injury (ALI) induced by sepsis is a common cause of death in clinical practice, and there remains a lack of clinical effective treatment. Cecal ligation and puncture (CLP) is a classic animal model of sepsis, which can induce ALI. Studies have shown that in the lung injury cell model, OGDH (oxoglutarate dehydrogenase) transcription is up-regulated, which is a potential therapeutic target for acute pneumonia. The purpose of this study was to confirm the effects of OGDH on lung injury and inflammation in animal and cell models, and to explore its mechanism. Methods By analyzing the GSE16650 gene set, the upregulated OGDH gene was detected in the lung injury cell model. In a sepsis animal model established by CLP and a lung injury cell model, RT-PCR, immunohistochemistry, WB, and other techniques were used to verify the upregulation of OGDH expression, which was then was down-regulated with shRNA to confirm its relationship with ALI. Further, ELISA, RT-PCR, and WB were used to detect the effect of OGDH on the expression of pro-inflammatory factors including IL-1β, IL-6, IL-18, and TNF-α. The downstream pathway of OGDH was predicted using KEGG and GSEA tools and verified by WB and immunofluorescence. Results The results showed OGDH was highly expressed in a lung injury cell model and the lung tissue of ALI mice induced by CLP, and downregulation of OGDH alleviated sepsis induced ALI. In animal models and cell models, the expression of OGDH was positively correlated with the expression of pro-inflammatory factors. OGDH may act through the MAPK pathway. Conclusions Under the pathological condition of sepsis, OGDH amplifies the inflammatory response through the MAPK pathway, releases pro-inflammatory factors, and induces ALI.
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Affiliation(s)
- Yuewei Hao
- Department of Emergency, Shandong Second Provincial General Hospital, Jinan, China
| | - Zheng Wang
- Prehospital Emergency, Shandong Second Provincial General Hospital, Jinan, China
| | - Xinfang Wang
- Neonatal Intensive Care Unit, Shandong Second Provincial General Hospital, Jinan, China
| | - Wenming Zhan
- Department of Internal Medicine-Cardiovascular, Xishui People's Hospital, Xishui, China
| | - Dianshui Wu
- Department of Clinical Laboratory, Shandong Second Provincial General Hospital, Jinan, China
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15
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Abstract
Broccoli (Brassica oleracea L. var. italica) is one of the most important vegetable crops cultivated worldwide. The market demand for broccoli is still increasing due to its richness in vitamins, anthocyanins, mineral substances, fiber, secondary metabolites and other nutrients. The famous secondary metabolites, glucosinolates, sulforaphane and selenium have protective effects against cancer. Significant progress has been made in fine-mapping and cloning genes that are responsible for important traits; this progress provides a foundation for marker-assisted selection (MAS) in broccoli breeding. Genetic engineering by the well-developed Agrobacterium tumefaciens-mediated transformation in broccoli has contributed to the improvement of quality; postharvest life; glucosinolate and sulforaphane content; and resistance to insects, pathogens and abiotic stresses. Here, we review recent progress in the genetics and molecular breeding of broccoli. Future perspectives for improving broccoli are also briefly discussed.
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16
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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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17
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Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification. BMC Biol 2021; 19:93. [PMID: 33952264 PMCID: PMC8097969 DOI: 10.1186/s12915-021-01031-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
Background Brassica oleracea includes several morphologically diverse, economically important vegetable crops, such as the cauliflower and cabbage. However, genetic variants, especially large structural variants (SVs), that underlie the extreme morphological diversity of B. oleracea remain largely unexplored. Results Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~ 120 K high-confidence SVs. Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development. Conclusions This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01031-2.
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18
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Arias T, Niederhuth CE, McSteen P, Pires JC. The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype. FRONTIERS IN PLANT SCIENCE 2021; 12:637115. [PMID: 33747016 PMCID: PMC7973465 DOI: 10.3389/fpls.2021.637115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by humans during domestication. We used a combination of developmental studies and transcriptomics to understand the vegetative domestication syndrome of kale. To identify candidate genes that are responsible for the evolution of domestic kale, we searched for transcriptome-wide differences among three vegetative B. oleracea morphotypes. RNA-seq experiments were used to understand the global pattern of expressed genes during a mixture of stages at one time in kale, cabbage, and the rapid cycling kale line TO1000. We identified gene expression patterns that differ among morphotypes and estimate the contribution of morphotype-specific gene expression that sets kale apart (3958 differentially expressed genes). Differentially expressed genes that regulate the vegetative to reproductive transition were abundant in all morphotypes. Genes involved in leaf morphology, plant architecture, defense, and nutrition were differentially expressed in kale. This allowed us to identify a set of candidate genes we suggest may be important in the kale domestication syndrome. Understanding candidate genes responsible for kale domestication is of importance to ultimately improve Cole crop production.
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19
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Ma X, Zhang L, Pei Z, Zhang L, Liu Z, Liu D, Hao X, Jin Z, Pei Y. Hydrogen sulfide promotes flowering in heading Chinese cabbage by S-sulfhydration of BraFLCs. HORTICULTURE RESEARCH 2021; 8:19. [PMID: 33518701 PMCID: PMC7848000 DOI: 10.1038/s41438-020-00453-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/03/2020] [Accepted: 11/20/2020] [Indexed: 05/07/2023]
Abstract
Heading Chinese cabbage (Brassica rapa L. syn. B. campestris L. ssp. chinensis Makino var. pekinensis (Rupr.) J. Cao et Sh. Cao) is a cruciferous Brassica vegetable that has a triplicate genome, owing to an ancient genome duplication event. It is unclear whether the duplicated homologs have conserved or diversified functions. Hydrogen sulfide (H2S) is a plant gasotransmitter that plays important physiological roles in growth, development, and responses to environmental stresses. The modification of cysteines through S-sulfhydration is an important mechanism of H2S, which regulates protein functions. H2S promotes flowering in Arabidopsis and heading Chinese cabbage. Here we investigated the molecular mechanisms of H2S used to promote flowering in the latter. Four, five, and four BraFLC, BraSOC I, and BraFT homologs were identified in heading Chinese cabbage. Different BraFLC proteins were bound to different CArG boxes in the promoter regions of the BraSOC I and BraFT homologs, producing different binding patterns. Thus, there may be functionally diverse BraFLC homologs in heading Chinese cabbage. Exogenous H2S at 100 μmol L-1 significantly promoted flowering by compensating for insufficient vernalization. BraFLC 1 and BraFLC 3 underwent S-sulfhydration by H2S, after which their abilities to bind most BraSOC I or BraFT promoter probes weakened or even disappeared. These changes in binding ability were consistent with the expression pattern of the BraFT and BraSOC I homologs in seedlings treated with H2S. These results indicated that H2S signaling regulates flowering time. In summary, H2S signaling promoted plant flowering by weakening or eliminating the binding abilities of BraFLCs to downstream promoters through S-sulfhydration.
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Affiliation(s)
- Xiaoli Ma
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
- Department of Biological Science and Technology, Jinzhong University, Jinzhong, Shanxi Province, 030619, China
| | - Liping Zhang
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Zhuoya Pei
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Linlin Zhang
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Zhiqiang Liu
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Danmei Liu
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Xuefeng Hao
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
- Department of Biology, Taiyuan Normal University, Jinzhong, Shanxi Province, 030619, China
| | - Zhuping Jin
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China.
| | - Yanxi Pei
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China.
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Stansell Z, Björkman T. From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection. HORTICULTURE RESEARCH 2020; 7:159. [PMID: 33082966 PMCID: PMC7528014 DOI: 10.1038/s41438-020-00375-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/12/2020] [Accepted: 08/01/2020] [Indexed: 05/03/2023]
Abstract
Worldwide, broccoli (Brassica oleracea var. italica) is among the most economically important, nutritionally rich, and widely-grown vegetable crops. To explore the genomic basis of the dramatic changes in broccoli morphology in the last century, we evaluated 109 broccoli or broccoli/cauliflower intermediates for 24 horticultural traits. Genotype-by-sequencing markers were used to determine four subpopulations within italica: Calabrese broccoli landraces and hybrids, sprouting broccoli, and violet cauliflower, and to evaluate between and within group relatedness and diversity. While overall horticultural quality and harvest index of improved hybrid broccoli germplasm has increased by year of cultivar release, this improvement has been accompanied by a considerable reduction in allelic diversity when compared to the larger pool of germplasm. Two landraces are the most likely founding source of modern broccoli hybrids, and within these modern hybrids, we identified 13 reduction-in-diversity genomic regions, 53 selective sweeps, and 30 (>1 Mbp) runs of homozygosity. Landrace accessions collected in southern Italy contained 4.8-fold greater unique alleles per accessions compared to modern hybrids and provide a valuable resource in subsequent improvement efforts. This work broadens the understanding of broccoli germplasm, informs conservation efforts, and enables breeding for complex quality traits and regionally adapted cultivars.
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Affiliation(s)
- Zachary Stansell
- Cornell University, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
- Cornell AgriTech, Cornell University, Geneva, NY 14456 USA
| | - Thomas Björkman
- Cornell University, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
- Cornell AgriTech, Cornell University, Geneva, NY 14456 USA
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21
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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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22
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The vernalisation regulator FLOWERING LOCUS C is differentially expressed in biennial and annual Brassica napus. Sci Rep 2019; 9:14911. [PMID: 31624282 PMCID: PMC6797750 DOI: 10.1038/s41598-019-51212-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 09/26/2019] [Indexed: 11/11/2022] Open
Abstract
Plants in temperate areas evolved vernalisation requirement to avoid pre-winter flowering. In Brassicaceae, a period of extended cold reduces the expression of the flowering inhibitor FLOWERING LOCUS C (FLC) and paves the way for the expression of downstream flowering regulators. As with all polyploid species of the Brassicaceae, the model allotetraploid Brassica napus (rapeseed, canola) is highly duplicated and carries 9 annotated copies of Bna.FLC. To investigate whether these multiple homeologs and paralogs have retained their original function in vernalisation or undergone subfunctionalisation, we compared the expression patterns of all 9 copies between vernalisation-dependent (biennial, winter type) and vernalisation-independent (annual, spring type) accessions, using RT-qPCR with copy-specific primers and RNAseq data from a diversity set. Our results show that only 3 copies – Bna.FLC.A03b, Bna.FLC.A10 and to some extent Bna.FLC.C02 – are differentially expressed between the two growth types, showing that expression of the other 6 copies does not correlate with growth type. One of those 6 copies, Bna.FLC.C03b, was not expressed at all, indicating a pseudogene, while three further copies, Bna.FLC.C03a and Bna.FLC.C09ab, did not respond to cold treatment. Sequence variation at the COOLAIR binding site of Bna.FLC.A10 was found to explain most of the variation in gene expression. However, we also found that Bna.FLC.A10 expression is not fully predictive of growth type.
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23
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Schiessl S, Williams N, Specht P, Staiger D, Johansson M. Different copies of SENSITIVITY TO RED LIGHT REDUCED 1 show strong subfunctionalization in Brassica napus. BMC PLANT BIOLOGY 2019; 19:372. [PMID: 31438864 PMCID: PMC6704554 DOI: 10.1186/s12870-019-1973-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Correct timing of flowering is critical for plants to produce enough viable offspring. In Arabidopsis thaliana (Arabidopsis), flowering time is regulated by an intricate network of molecular signaling pathways. Arabidopsis srr1-1 mutants lacking SENSITIVITY TO RED LIGHT REDUCED 1 (SRR1) expression flower early, particularly under short day (SD) conditions (1). SRR1 ensures that plants do not flower prematurely in such non-inductive conditions by controlling repression of the key florigen FT. Here, we have examined the role of SRR1 in the closely related crop species Brassica napus. RESULTS Arabidopsis SRR1 has five homologs in Brassica napus. They can be divided into two groups, where the A02 and C02 copies show high similarity to AtSRR1 on the protein level. The other group, including the A03, A10 and C09 copies all carry a larger deletion in the amino acid sequence. Three of the homologs are expressed at detectable levels: A02, C02 and C09. Notably, the gene copies show a differential expression pattern between spring and winter type accessions of B. napus. When the three expressed gene copies were introduced into the srr1-1 background, only A02 and C02 were able to complement the srr1-1 early flowering phenotype, while C09 could not. Transcriptional analysis of known SRR1 targets in Bna.SRR1-transformed lines showed that CYCLING DOF FACTOR 1 (CDF1) expression is key for flowering time control via SRR1. CONCLUSIONS We observed subfunctionalization of the B. napus SRR1 gene copies, with differential expression between early and late flowering accessions of some Bna.SRR1 copies. This suggests involvement of Bna.SRR1 in regulation of seasonal flowering in B. napus. The C09 gene copy was unable to complement srr1-1 plants, but is highly expressed in B. napus, suggesting specialization of a particular function. Furthermore, the C09 protein carries a deletion which may pinpoint a key region of the SRR1 protein potentially important for its molecular function. This is important evidence of functional domain annotation in the highly conserved but unique SRR1 amino acid sequence.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Giessen, Germany
| | - Natalie Williams
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Pascal Specht
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, 35392 Giessen, Giessen, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Mikael Johansson
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
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24
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Woodhouse MR, Hufford MB. Parallelism and convergence in post-domestication adaptation in cereal grasses. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180245. [PMID: 31154975 DOI: 10.1098/rstb.2018.0245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- M R Woodhouse
- Iowa State University, Ecology, Evolution, and Organismal Biology , Ames, IA 50011 , USA
| | - M B Hufford
- Iowa State University, Ecology, Evolution, and Organismal Biology , Ames, IA 50011 , USA
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25
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Huang K, Zhu A, Chen X, Shi Y, Tang Q, Wang X, Sun Z, Luan M, Chen J. Comparative transcriptomics reveals the selection patterns of domesticated ramie. Ecol Evol 2019; 9:7057-7068. [PMID: 31380033 PMCID: PMC6662332 DOI: 10.1002/ece3.5271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 04/08/2019] [Accepted: 04/29/2019] [Indexed: 11/20/2022] Open
Abstract
Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern and genetic relationships among a cultivated variety of ramie (BNZ: B. nivea, ZZ1) and four wild species, BNT (B. nivea var. tenacissima), BNN (B. nivea var. nipononivea), BNW (B. nivea var. nivea), and BAN (B. nivea var. viridula), in the section Tilocnide, we performed an RNA sequencing analysis of these ramie species. The de novo assembly of the "all-ramie" transcriptome yielded 119,114 unigenes with an average length of 633 bp, and a total of 7,084 orthologous gene pairs were identified. The phylogenetic tree showed that the cultivar BNZ clustered with BAN in one group, BNW was closely related to BNT, and BNN formed a separate group. Introgression analysis indicated that gene flow occurred from BNZ to BNN and BAN, and between BAN and BNN. Among these orthologs, 2,425 and 269 genes underwent significant purifying and positive selection, respectively. For these positively selected genes, oxidation-reduction process (GO:0055114) and stress response pathways (GO:0006950) were enriched, indicating that modulation of the cellular redox status was important during both ramie fiber evolution and improvement. Two genes related to the suppression of flowering and one gene annotated as a flowering-promoting factor were subjected to positive selection, probably caused by human manipulation. Additionally, five genes were homologs of those involved in abiotic stress tolerance and disease resistance, with higher expression levels in the cultivar BNZ than in the wild species. Collectively, the results of this study indicated that domestication has resulted in the upregulation of many genes involved in the abiotic and biotic stress responses, fiber yield, and plant growth of ramie.
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Affiliation(s)
- Kun‐Yong Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Ai‐Guo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | | | - Ya‐Liang Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Xiao‐Fei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Zhi‐Min Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Ming‐Bao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
| | - Jian‐Hua Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering MicrobiologyMinistry of AgricultureChangshaChina
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26
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Abuyusuf M, Nath UK, Kim HT, Islam MR, Park JI, Nou IS. Molecular markers based on sequence variation in BoFLC1.C9 for characterizing early- and late-flowering cabbage genotypes. BMC Genet 2019; 20:42. [PMID: 31029104 PMCID: PMC6487051 DOI: 10.1186/s12863-019-0740-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cabbage (Brassica oleracea var. capitata) is popular worldwide for consumption as a leafy vegetable. Premature flowering is triggered by low temperature, and deteriorates quality of cabbage as vegetable. In general, growers prefer late-flowering varieties to assure good quality compact head. Here, we report BoFLC1.C9 as a gene with clear sequence variation between cabbage lines with different flowering times, and proposed as molecular marker to characterize early- and late-flowering cabbage lines. RESULTS We identified sequence variation of 67 bp insertions in intron 2, which were contributed in flowering time variation between two inbred lines through rapid down-regulation of the BoFLC1.C9 gene in early-flowering line compared to late-flowering one upon vernalization. One set of primer 'F7R7' proposed as marker, of which was explained with 83 and 80% of flowering time variation in 141 F2 individuals and 20 commercial lines, respectively. CONCLUSIONS This F7R7 marker could be used as genetic tools to characterize flowering time variation and to select as well to develop early- and late-flowering cabbage cultivars.
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Affiliation(s)
- Md Abuyusuf
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Agronomy, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Md Rafiqul Islam
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
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27
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Xiao D, Shen HR, Zhao JJ, Wei YP, Liu DR, Hou XL, Bonnema G. Genetic dissection of flowering time in Brassica rapa responses to temperature and photoperiod. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:110-119. [PMID: 30823988 DOI: 10.1016/j.plantsci.2018.10.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/19/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
The Brassica rapa (B. rapa) species displays enormous phenotypic diversity, with leafy vegetables, storage root vegetables and oil crops. These different crops all have different flowering time, which determine their growing season and cultivation area. Little is known about the effects of diverse temperature and day-lengths on flowering time QTL associated with FLC paralogues. We phenotyped the flowering time of a doubled haploid population, established from a cross between Yellow sarson and Pak choi under diverse environmental conditions. We identified flowering-time QTL (fQTL) in different photoperiod and temperature regimes in the greenhouse, and studied their colocation with known flowering time genes. As several fQTL colocalized with FLC paralogues, we studied the expression patterns of four FLC paralogues during the course of vernalization in parental lines. Under all environmental conditions tested the major fQTL that mapped to the BrFLC2_A02 locus was detected, however its effect decreased when plants were grown at low temperatures. Another fQTL that mapped to the FLC paralogue, BrFLC5_A03 was also identified under all tested environments, while no fQTL colocated with BrFLC1_A10 or BrFLC3_A03. Furthermore, the vernalization treatment decreased expression of all BrFLC paralogues in the parental lines, and showed the lowest transcript level after 28 days of vernalization. Transcript abundance stayed low after returning the plants for seven days to normal growth temperature. Interestingly, transcript abundance of BrFLC3_A03 and BrFLC5_A03 was repressed much stronger and already reached lowest levels after 14d in the early-flowering type YS-143. This study improves understanding of the effects of daylength and vernalization on flowering time in B. rapa and the role of the different BrFLC paralogues therein.
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Affiliation(s)
- Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China; Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao-Ran Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Jun Zhao
- Horticultural College, Agricultural University of Hebei, Baoding, 071001, China
| | - Yan-Ping Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong-Rang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, the Netherlands.
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28
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Motoki K, Kinoshita Y, Hosokawa M. Non-vernalization Flowering and Seed Set of Cabbage Induced by Grafting Onto Radish Rootstocks. FRONTIERS IN PLANT SCIENCE 2019; 9:1967. [PMID: 30687362 PMCID: PMC6335391 DOI: 10.3389/fpls.2018.01967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Cabbage (Brassica oleracea var. capitata) requires a long-term low-temperature exposure for floral induction, causing a delay in the breeding cycle. The objective of this study is to develop a method to induce flowering in cabbage without low-temperature treatment, using a grafting method. We conducted grafting experiments using two flower-induced Chinese kale cultivars (B. oleracea var. alboglabra) and seven radish cultivars/accessions as rootstocks and investigated the flowering response of grafted cabbage scions without low-temperature treatment. "Watanabe-seiko No.1" cabbage, when grafted onto the two Chinese kale cultivars, did not formed flower buds. Flowering was successfully induced in "Watanabe-seiko No.1" by grafting onto three out of the seven tested radish cultivars, and in "Kinkei No.201" and "Red cabbage" by grafting onto one tested radish cultivar. In "Watanabe-seiko No.1," the earliest flower bud appearance was observed at 29 days after grafting. Seeds were also obtained from the three cabbage cultivars that flowered by grafting. Gene expression analysis of "Watanabe-seiko No.1" cabbage scions which formed flower buds by grafting, revealed high expression of the homolog of the floral integrator, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (BoSOC1), at the time of flower bud appearance. However, in the same leaf samples, we observed low expression of two homologs of florigen, FLOWERING LOCUS T (BoFT.C2 and BoFT.C6). In addition, two homologs of the floral repressor FLOWERING LOCUS C (BoFLC3 and BoFLC4), which are known to be down-regulated before flower bud differentiation in the vernalization pathway, were highly expressed, indicating that grafting onto radish induces cabbage flowering independently of the vernalization pathway. The expression level of the radish FT homolog (RsFT) in "Rat's tail-G2," which had highly induced flowering in the grafted cabbage scion, was higher than in the other radish cultivars. However, although "Rat's tail-CH" effectively induced flowering in the cabbage scion, the expression of RsFT was low in this cultivar. In this study, floral induction of non-vernalized cabbage cannot be explained by the expression levels of RsFT in rootstock plants, alone. The flowering of non-vernalized cabbage would be induced by transmissible agents from rootstocks and not by the expression of cabbage FT, BoFT, from the scion itself.
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Affiliation(s)
- Ko Motoki
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yu Kinoshita
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Munetaka Hosokawa
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Laboratory of Floriculture, Department of Agriculture, Kindai University, Nara, Japan
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29
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Jian H, Zhang A, Ma J, Wang T, Yang B, Shuang LS, Liu M, Li J, Xu X, Paterson AH, Liu L. Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L. BMC Genomics 2019; 20:21. [PMID: 30626329 PMCID: PMC6325782 DOI: 10.1186/s12864-018-5356-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/09/2018] [Indexed: 01/10/2023] Open
Abstract
Background Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QTL) analysis of flowering time in a recombinant inbred line (RIL) population, including lines with extreme differences in flowering time, in six environments, along with RNA-Seq analysis. Results We detected 27 QTLs distributed on eight chromosomes among six environments, including one major QTL on chromosome C02 that explained 11–25% of the phenotypic variation and was stably detected in all six environments. RNA-Seq analysis revealed 105 flowering time-related differentially expressed genes (DEGs) that play roles in the circadian clock/photoperiod, autonomous pathway, and hormone and vernalization pathways. We focused on DEGs related to the regulation of flowering time, especially DEGs in QTL regions. Conclusions We identified 45 flowering time-related genes in these QTL regions, eight of which are DEGs, including key flowering time genes PSEUDO RESPONSE REGULATOR 7 (PRR7) and FY (located in a major QTL region on C02). These findings provide insights into the genetic architecture of flowering time in B. napus. Electronic supplementary material The online version of this article (10.1186/s12864-018-5356-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.,Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Jinqi Ma
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Tengyue Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Lan Shuan Shuang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Min Liu
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Academy of Agricultural Sciences, Chongqing, 400715, China.
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30
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Lin CW, Fu SF, Liu YJ, Chen CC, Chang CH, Yang YW, Huang HJ. Analysis of ambient temperature-responsive transcriptome in shoot apical meristem of heat-tolerant and heat-sensitive broccoli inbred lines during floral head formation. BMC PLANT BIOLOGY 2019; 19:3. [PMID: 30606114 PMCID: PMC6318969 DOI: 10.1186/s12870-018-1613-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/20/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Head formation of broccoli (Brassica oleracea var. italica) is greatly reduced under high temperature (22 °C and 27 °C). Broccoli inbred lines that are capable of producing heads at high temperatures in summer are varieties that are unique to Taiwan. However, knowledge of the early-activated pathways of broccoli head formation under high temperature is limited. RESULTS We compared heat-tolerant (HT) and heat-sensitive (HS) transcriptome of broccoli under different temperatures. Weighted gene correlation network analysis (WGCNA) revealed that genes involved in calcium signaling pathways, mitogen-activated protein kinase (MAPK) cascades, leucine-rich repeat receptor-like kinases (LRR-RLKs), and genes coding for heat-shock proteins and reactive oxygen species homeostasis shared a similar expression pattern to BoFLC1, which was highly expressed at high temperature (27 °C). Of note, these genes were less expressed in HT than HS broccoli at 22 °C. Co-expression analysis identified a model for LRR-RLKs in survival-reproduction tradeoffs by modulating MAPK- versus phytohormones-signaling during head formation. The difference in head-forming ability in response to heat stress between HT and HS broccoli may result from their differential transcriptome profiles of LRR-RLK genes. High temperature induced JA- as well as suppressed auxin- and cytokinin-related pathways may facilitate a balancing act to ensure fitness at 27 °C. BoFLC1 was less expressed in HT than HS at 22 °C, whereas other FLC homologues were not. Promoter analysis of BoFLC1 showed fewer AT dinucleotide repeats in HT broccoli. These results provide insight into the early activation of stress- or development-related pathways during head formation in broccoli. The identification of the BoFLC1 DNA biomarker may facilitate breeding of HT broccoli. CONCLUSIONS In this study, HT and HS broccoli genotypes were used to determine the effect of temperature on head formation by transcriptome profiling. On the basis of the expression pattern of high temperature-associated signaling genes, the HS transcriptome may be involved in stress defense instead of transition to the reproductive phase in response to heat stress. Transcriptome profiling of HT and HS broccoli helps in understanding the molecular mechanisms underlying head-forming capacity and in promoting functional marker-assisted breeding.
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Affiliation(s)
- Chung-Wen Lin
- Department of Life Sciences, National Cheng Kung University, No. 1, University Rd, Tainan City, 701 Taiwan
| | - Shih-Feng Fu
- Department of Biology, National Changhua University of Education, Changhua, 500 Taiwan
| | - Yu-Ju Liu
- Department of Life Sciences, National Cheng Kung University, No. 1, University Rd, Tainan City, 701 Taiwan
| | - Chi-Chien Chen
- Department of Life Sciences, National Cheng Kung University, No. 1, University Rd, Tainan City, 701 Taiwan
| | - Ching-Han Chang
- Department of Life Sciences, National Cheng Kung University, No. 1, University Rd, Tainan City, 701 Taiwan
| | - Yau-Wen Yang
- Kale Biotech. Co, No.218, Fudong St., East Dist, Tainan City, 701 Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, No. 1, University Rd, Tainan City, 701 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, No. 1, University Rd, Tainan City, 701 Taiwan
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31
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Stansell Z, Farnham M, Björkman T. Complex Horticultural Quality Traits in Broccoli Are Illuminated by Evaluation of the Immortal BolTBDH Mapping Population. FRONTIERS IN PLANT SCIENCE 2019; 10:1104. [PMID: 31620146 PMCID: PMC6759917 DOI: 10.3389/fpls.2019.01104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/12/2019] [Indexed: 05/19/2023]
Abstract
Improving horticultural quality in regionally adapted broccoli (Brassica oleracea var. italica) and other B. oleracea crops is challenging due to complex genetic control of traits affecting morphology, development, and yield. Mapping horticultural quality traits to genomic loci is an essential step in these improvement efforts. Understanding the mechanisms underlying horticultural quality enables multi-trait marker-assisted selection for improved, resilient, and regionally adapted B. oleracea germplasm. The publicly-available biparental double-haploid BolTBDH mapping population (Chinese kale × broccoli; N = 175) was evaluated for 25 horticultural traits in six trait classes (architecture, biomass, phenology, leaf morphology, floral morphology, and head quality) by multiple quantitative trait loci mapping using 1,881 genotype-by-sequencing derived single nucleotide polymorphisms. The physical locations of 56 single and 41 epistatic quantitative trait locus (QTL) were identified. Four head quality QTL (OQ_C03@57.0, OQ_C04@33.3, OQ_CC08@25.5, and OQ_C09@49.7) explain a cumulative 81.9% of phenotypic variance in the broccoli heading phenotype, contain the FLOWERING LOCUS C (FLC) homologs Bo9g173400 and Bo9g173370, and exhibit epistatic effects. Three key genomic hotspots associated with pleiotropic control of the broccoli heading phenotype were identified. One phenology hotspot reduces days to flowering by 7.0 days and includes an additional FLC homolog Bo3g024250 that does not exhibit epistatic effects with the three horticultural quality hotspots. Strong candidates for other horticultural traits were identified: BoLMI1 (Bo3g002560) associated with serrated leaf margins and leaf apex shape, BoCCD4 (Bo3g158650) implicated in flower color, and BoAP2 (Bo1g004960) implicated in the hooked sepal horticultural trait. The BolTBDH population provides a framework for B. oleracea improvement by targeting key genomic loci contributing to high horticultural quality broccoli and enabling de novo mapping of currently unexplored traits.
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Affiliation(s)
- Zachary Stansell
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Cornell Agritech, Cornell University, Geneva, NY, United States
- *Correspondence: Zachary Stansell,
| | - Mark Farnham
- USDA-ARS Vegetable Laboratory, Department of Horticulture, Charleston, SC, United States
| | - Thomas Björkman
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Cornell Agritech, Cornell University, Geneva, NY, United States
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32
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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: 38] [Impact Index Per Article: 6.3] [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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33
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Li B, Zhao W, Li D, Chao H, Zhao X, Ta N, Li Y, Guan Z, Guo L, Zhang L, Li S, Wang H, Li M. Genetic dissection of the mechanism of flowering time based on an environmentally stable and specific QTL in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:296-310. [PMID: 30466595 DOI: 10.1016/j.plantsci.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 05/02/2023]
Abstract
Flowering time is an important agronomic trait that is highly influenced by the environment. To elucidate the genetic mechanism of flowering time in rapeseed (Brassica napus L.), a genome-wide QTL analysis was performed in a doubled haploid population grown in winter, semi-winter and spring ecological conditions. Fifty-five consensus QTLs were identified after combining phenotype and genomic data, including 12 environment-stable QTLs and 43 environment-specific QTLs. Importantly, six major QTLs for flowering time were identified, of which two were considered environment-specific QTLs in spring ecological condition and four were considered environment-stable QTLs in winter and semi-winter ecological conditions. Through QTL comparison, 18 QTLs were colocalized with QTLs from six other published studies. Combining the candidate genes with their functional annotation, in 49 of 55 consensus QTLs, 151 candidate genes in B. napus corresponding to 95 homologous genes in Arabidopsis thaliana related to flowering were identified, including BnaC03g32910D (CO), BnaA02g12130D (FT) and BnaA03g13630D (FLC). Most of the candidate genes were involved in different flowering regulatory pathways. Based on re-sequencing and differences in sequence annotation between the two parents, we found that regions containing some candidate genes have numerous non-frameshift InDels and many non- synonymous mutations, which might directly lead to gene functional variation. Flowering time was negativly correlated with seed yield and thousand seed weight based on a QTL comparison of flowering time and seed yield traits, which has implications in breeding new early-maturing varieties of B. napus. Moreover, a putative flowering regulatory network was constructed, including the photoperiod, circadian clock, vernalization, autonomous and gibberellin pathways. Multiple copies of genes led to functional difference among the different copies of homologous genes, which also increased the complexity of the flowering regulatory networks. Taken together, the present results not only provide new insights into the genetic regulatory network underlying the control of flowering time but also improve our understanding of flowering time regulatory pathways in rapeseed.
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Affiliation(s)
- Baojun Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Weiguo Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China; Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Dianrong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Zhao
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Na Ta
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Yonghong Li
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Zhoubo Guan
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Lina Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Shisheng Li
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
| | - Hao Wang
- Hybrid Rape Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, China.
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34
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Li H, Fan Y, Yu J, Chai L, Zhang J, Jiang J, Cui C, Zheng B, Jiang L, Lu K. Genome-Wide Identification of Flowering-Time Genes in Brassica Species and Reveals a Correlation between Selective Pressure and Expression Patterns of Vernalization-Pathway Genes in Brassica napus. Int J Mol Sci 2018; 19:E3632. [PMID: 30453667 PMCID: PMC6274771 DOI: 10.3390/ijms19113632] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/11/2018] [Accepted: 11/14/2018] [Indexed: 12/28/2022] Open
Abstract
Flowering time is a key agronomic trait, directly influencing crop yield and quality. Many flowering-time genes have been identified and characterized in the model plant Arabidopsis thaliana; however, these genes remain uncharacterized in many agronomically important Brassica crops. In this study, we identified 1064, 510, and 524 putative orthologs of A. thaliana flowering-time genes from Brassica napus, Brassica rapa, and Brassica oleracea, respectively, and found that genes involved in the aging and ambient temperature pathways were fewer than those in other flowering pathways. Flowering-time genes were distributed mostly on chromosome C03 in B. napus and B. oleracea, and on chromosome A09 in B. rapa. Calculation of non-synonymous (Ka)/synonymous substitution (Ks) ratios suggested that flowering-time genes in vernalization pathways experienced higher selection pressure than those in other pathways. Expression analysis showed that most vernalization-pathway genes were expressed in flowering organs. Approximately 40% of these genes were highly expressed in the anther, whereas flowering-time integrator genes were expressed in a highly organ-specific manner. Evolutionary selection pressures were negatively correlated with the breadth and expression levels of vernalization-pathway genes. These findings provide an integrated framework of flowering-time genes in these three Brassica crops and provide a foundation for deciphering the relationship between gene expression patterns and their evolutionary selection pressures in Brassica napus.
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Affiliation(s)
- Haojie Li
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Liang Chai
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Jingfang Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Jun Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Benchuan Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Liangcai Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
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35
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Xi X, Wei K, Gao B, Liu J, Liang J, Cheng F, Wang X, Wu J. BrFLC5: a weak regulator of flowering time in Brassica rapa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2107-2116. [PMID: 30008108 DOI: 10.1007/s00122-018-3139-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/28/2018] [Indexed: 05/08/2023]
Abstract
A splicing site mutation in BrFLC5, a non-syntenic paralogue of FLOWERING LOCUS C, was demonstrated to be related to flowering time variation in Brassica rapa. Flowering time regulation in Brassica rapa is more complex than in Arabidopsis, as there are multiple paralogues of flowering time genes in B. rapa. Brassica rapa contains four FLOWERING LOCUS C (FLC) genes, three of which are syntenic orthologues of AtFLC, while BrFLC5 is not. BrFLC1, BrFLC2, and BrFLC3 have been reported to be involved in flowering time regulation. However, BrFLC5 has thus far been deemed a pseudogene. We detected two alternative splicing patterns of BrFLC5 resulting from a nucleotide mutation (G/A) at the first nucleotide of intron 3 (named as Pi3+1(G/A)). Genotyping of BrFLC5Pi3 + 1(G/A) for 301 B. rapa accessions showed that this single nucleotide polymorphism was significantly related to flowering time variation (p < 0.001). In the collection, the frequency of the functional G allele (35.2%) was much lower than that of the nonfunctional A allele (59.1%); however, the frequency of the G allele was very high among the turnips (83.6%). An F2 population segregating at this locus was developed to analyze the genetic effect of BrFLC5. The result showed that the G allele individuals began to bolt two days later than the A allele individuals, indicating that BrFLC5 is a weak regulator of flowering time. BrFLC5 was expressed at the lowest level among the three analyzed BrFLCs. The late allele (G allele) was dominant to the early allele (A allele) at the BrFLC5 locus, which was in contrast to that of BrFLC1 and BrFLC2. This characteristic suggests that BrFLC5 would be more efficient for breeding premature bolting resistance in B. rapa.
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Affiliation(s)
- Xi Xi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China
| | - Keyun Wei
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China
| | - Baozhen Gao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China
| | - Jiahe Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, Beijing, 100081, China.
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36
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Subtropical adaptation of a temperate plant (Brassica oleracea var. italica) utilizes non-vernalization-responsive QTLs. Sci Rep 2018; 8:13609. [PMID: 30206285 PMCID: PMC6134136 DOI: 10.1038/s41598-018-31987-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/28/2018] [Indexed: 11/08/2022] Open
Abstract
While many tropical plants have been adapted to temperate cultivation, few temperate plants have been adapted to the tropics. Originating in Western Europe, Brassica oleracea vernalization requires a period of low temperature and BoFLC2 regulates the transition to floral development. In B. oleracea germplasm selected in Taiwan, a non-vernalization pathway involving BoFLC3 rather than BoFLC2 regulates curd induction. In 112 subtropical breeding lines, specific haplotype combinations of BoFLC3 and PAN (involved in floral organ identity and a positional candidate for additional curd induction variation) adapt B. oleracea to high ambient temperature and short daylength. Duplicated genes permitted evolution of alternative pathways for control of flowering in temperate and tropical environments, a principle that might be utilized via natural or engineered approaches in other plants. New insight into regulation of Brassica flowering exemplifies translational agriculture, tapping knowledge of botanical models to improve food security under projected climate change scenarios.
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37
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Shah S, Weinholdt C, Jedrusik N, Molina C, Zou J, Große I, Schiessl S, Jung C, Emrani N. Whole-transcriptome analysis reveals genetic factors underlying flowering time regulation in rapeseed (Brassica napus L.). PLANT, CELL & ENVIRONMENT 2018; 41:1935-1947. [PMID: 29813173 DOI: 10.1111/pce.13353] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/20/2018] [Accepted: 05/19/2018] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus L.), one of the most important sources of vegetable oil and protein-rich meals worldwide, is adapted to different geographical regions by modification of flowering time. Rapeseed cultivars have different day length and vernalization requirements, which categorize them into winter, spring, and semiwinter ecotypes. To gain a deeper insight into genetic factors controlling floral transition in B. napus, we performed RNA sequencing (RNA-seq) in the semiwinter doubled haploid line, Ningyou7, at different developmental stages and temperature regimes. The expression profiles of more than 54,000 gene models were compared between different treatments and developmental stages, and the differentially expressed genes were considered as targets for association analysis and genetic mapping to confirm their role in floral transition. Consequently, 36 genes with association to flowering time, seed yield, or both were identified. We found novel indications for neofunctionalization in homologs of known flowering time regulators like VIN3 and FUL. Our study proved the potential of RNA-seq along with association analysis and genetic mapping to identify candidate genes for floral transition in rapeseed. The candidate genes identified in this study could be subjected to genetic modification or targeted mutagenesis and genotype building to breed rapeseed adapted to certain environments.
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Affiliation(s)
- Smit Shah
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Claus Weinholdt
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Nicole Jedrusik
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Carlos Molina
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ivo Große
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sarah Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Nazgol Emrani
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
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38
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Shea DJ, Tomaru Y, Itabashi E, Nakamura Y, Miyazaki T, Kakizaki T, Naher TN, Shimizu M, Fujimoto R, Fukai E, Okazaki K. The production and characterization of a BoFLC2 introgressed Brassica rapa by repeated backcrossing to an F 1. BREEDING SCIENCE 2018; 68:316-325. [PMID: 30100798 PMCID: PMC6081295 DOI: 10.1270/jsbbs.17115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/13/2018] [Indexed: 05/25/2023]
Abstract
Flowering time is an important agronomic trait for Brassica rapa crops, and previous breeding work in Brassica has successfully transmitted other important agronomic traits from donor species. However, there has been no previous attempts to produce hybrids replacing the original Brassica FLC alleles with alien FLC alleles. In this paper, we introduce the creation of a chromosome substitution line (CSSL) containing a homozygous introgression of Flowering Locus C from Brassica oleracea (BoFLC2) into a B. rapa genomic background, and characterize the CSSL line with respect to the parental cultivars. The preferential transmission of alien chromosome inheritance and the pattern of transmission observed during the production of the CSSLs are also discussed.
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Affiliation(s)
- Daniel J. Shea
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Yuki Tomaru
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Etsuko Itabashi
- National Institute of Vegetable and Tea Science,
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Yuri Nakamura
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Toshio Miyazaki
- Nippon Norin Seed Co.,
6-6-5 Takinogawa, Kita-ku, Tokyo 114-0023,
Japan
| | - Tomohiro Kakizaki
- National Institute of Vegetable and Tea Science,
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | | | - Motoki Shimizu
- Iwate Biotechnology Research Center,
22-174-4 Narita, Kitakami, Iwate 024-0003,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Eigo Fukai
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Keiichi Okazaki
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
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Jiang L, Li D, Jin L, Ruan Y, Shen WH, Liu C. Histone lysine methyltransferases BnaSDG8.A and BnaSDG8.C are involved in the floral transition in Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:672-685. [PMID: 29797624 DOI: 10.1111/tpj.13978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 05/22/2023]
Abstract
Although increasing experimental evidence demonstrates that histone methylations play important roles in Arabidopsis plant growth and development, little information is available regarding Brassica napus. In this study, we characterized two genes encoding homologues of the Arabidopsis histone 3 lysine 36 (H3K36) methyltransferase SDG8, namely, BnaSDG8.A and BnaSDG8.C. Although no duplication of SDG8 homologous genes had been previously reported to occur during the evolution of any sequenced species, a domain-duplication was uncovered in BnaSDG8.C. This duplication led to the identification of a previously unknown NNH domain in the SDG8 homologues, providing a useful reference for future studies and revealing the finer mechanism of SDG8 function. One NNH domain is present in BnaSDG8.A, while two adjacent NNH domains are present in BnaSDG8.C. Reverse transcriptase-quantitative polymerase chain reaction analysis revealed similar patterns but with varied levels of expression of BnaSDG8.A/C in different plant organs/tissues. To directly investigate their function, BnaSDG8.A/C cDNA was ectopically expressed to complement the Arabidopsis mutant. We observed that the expression of either BnaSDG8.A or BnaSDG8.C could rescue the Arabidopsis sdg8 mutant to the wild-type phenotype. Using RNAi and CRISPR/Cas9-mediated gene editing, we obtained BnaSDG8.A/C knockdown and knockout mutants with the early flowering phenotype as compared with the control. Further analysis of two types of the mutants revealed that BnaSDG8.A/C are required for H3K36 m2/3 deposition and prevent the floral transition of B. napus by directly enhancing the H3K36 m2/3 levels at the BnaFLC chromatin loci. This observation on the floral transition by epigenetic modification in B. napus provides useful information for breeding early-flowering varieties.
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Affiliation(s)
- Ling Jiang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Donghao Li
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lu Jin
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Ying Ruan
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cedex, 67084, France
| | - Chunlin Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
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40
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Liu D, Dong X, Liu Z, Tang J, Zhuang M, Zhang Y, Lv H, Liu Y, Li Z, Fang Z, Yang L. Fine Mapping and Candidate Gene Identification for Wax Biosynthesis Locus, BoWax1 in Brassica oleracea L. var. capitata. FRONTIERS IN PLANT SCIENCE 2018; 9:309. [PMID: 29760714 PMCID: PMC5937124 DOI: 10.3389/fpls.2018.00309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 02/22/2018] [Indexed: 06/08/2023]
Abstract
Cuticular waxes play important roles in plant protection against various biotic and abiotic environmental stresses. The cuticular wax covering gives normal cabbage a glaucous appearance, but the appearance of waxless mutant is glossy green. Based on the present study, inheritance of the glossy green character of mutant HUAYOU2 follows a simple recessive pattern. Genetic analysis of an F2 population comprising 808 recessive individuals derived from HUAYOU2 (P1, maternal parent) and M36 (P2, paternal parent) revealed that a single recessive locus, BoWax1 (Brassica oleracea Wax 1), controls glossy green trait in B. oleracea. This locus was mapped to a region of 158.5 kb on chromosome C01. Based on nucleotide sequence analysis, Bol013612 was identified as the candidate gene for BoWax1. Sequencing results demonstrated that there is a deletion mutation of two nucleotides in the cDNA of Bol013612 of HUAYOU2, which may account for its glossy green trait. These results lay the foundation for functional analysis of BoWax1 and may accelerate research on wax metabolism in cabbage.
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Affiliation(s)
- Dongming Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Open Key Laboratory of Horticultural Plant Physiology and Genetic Improvement, High School of Henan Province, College of Horticulture, Henan Agricultural University, Zhengzhou, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xin Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zezhou Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Tang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yumei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhansheng Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Zheng Y, Luo L, Liu Y, Yang Y, Wang C, Kong X, Yang Y. Effect of vernalization on tuberization and flowering in the Tibetan turnip is associated with changes in the expression of FLC homologues. PLANT DIVERSITY 2018; 40:50-56. [PMID: 30159542 PMCID: PMC6091928 DOI: 10.1016/j.pld.2018.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 05/18/2023]
Abstract
The turnip (Brassica rapa var. rapa) is a biennial crop that is planted in late summer/early fall and forms fleshy tubers for food in temperate regions. The harvested tubers then overwinter and are planted again the next spring for flowering and seeds. FLOWERING LOCUS C (FLC) is a MADS-box transcription factor that acts as a major repressor of floral transition by suppressing the flowering promoters FT and SOC1. Here we show that vernalization effectively represses tuber formation and promotes flowering in Tibetan turnip. We functionally characterized four FLC homologues (BrrFLC1, FLC2, FLC3, and FLC5), and found that BrrFLC2 and BrrFLC1 play a major role in repressing flowering in turnip and in transgenic Arabidopsis. In contrast, tuber formation was correlated with BrrFLC1 expression in the hypocotyl and was repressed under cold treatment following the quantitative downregulation of BrrFLC1. Grafting experiments of non-vernalized and vernalized turnips revealed that vernalization independently suppressed tuberization in the tuber or hypocotyl of the rootstock or scion, which occurred in parallel with the reduction in BrrFLC1 activity. Together, our results demonstrate that the Tibetan turnip is highly responsive to cold exposure, which is associated with the expression levels of BrrFLC genes.
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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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Landi Luo
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yuanyuan Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yunqiang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Chuntao Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, 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
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Corresponding author. Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China. Fax: +86 871 65230873.
| | - Yongping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Corresponding author. Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China. Fax: +86 871 65230873.
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Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
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43
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Rosen A, Hasan Y, Briggs W, Uptmoor R. Genome-Based Prediction of Time to Curd Induction in Cauliflower. FRONTIERS IN PLANT SCIENCE 2018; 9:78. [PMID: 29467774 PMCID: PMC5807883 DOI: 10.3389/fpls.2018.00078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
The development of cauliflower (Brassica oleracea var. botrytis) is highly dependent on temperature due to vernalization requirements, which often causes delay and unevenness in maturity during months with warm temperatures. Integrating quantitative genetic analyses with phenology modeling was suggested to accelerate breeding strategies toward wide-adaptation cauliflower. The present study aims at establishing a genome-based model simulating the development of doubled haploid (DH) cauliflower lines to predict time to curd induction of DH lines not used for model parameterization and test hybrids derived from the bi-parental cross. Leaf appearance rate and the relation between temperature and thermal time to curd induction were examined in greenhouse trials on 180 DH lines at seven temperatures. Quantitative trait loci (QTL) analyses carried out on model parameters revealed ten QTL for leaf appearance rate (LAR), five for the slope and two for the intercept of linear temperature-response functions. Results of the QTL-based phenology model were compared to a genomic selection (GS) model. Model validation was carried out on data comprising four field trials with 72 independent DH lines, 160 hybrids derived from the parameterization set, and 34 hybrids derived from independent lines of the population. The QTL model resulted in a moderately accurate prediction of time to curd induction (R2 = 0.42-0.51) while the GS model generated slightly better results (R2 = 0.52-0.61). Predictions of time to curd induction of test hybrids from independent DH lines were less precise with R2 = 0.40 for the QTL and R2 = 0.48 for the GS model. Implementation of juvenile-to-adult phase transition is proposed for model improvement.
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Affiliation(s)
- Arne Rosen
- Faculty of Agriculture and Environmental Science, University of Rostock, Rostock, Germany
| | - Yaser Hasan
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hannover, Germany
| | | | - Ralf Uptmoor
- Faculty of Agriculture and Environmental Science, University of Rostock, Rostock, Germany
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Thorwarth P, Yousef EAA, Schmid KJ. Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower. G3 (BETHESDA, MD.) 2018; 8:707-718. [PMID: 29255118 PMCID: PMC5919744 DOI: 10.1534/g3.117.300199] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/13/2017] [Indexed: 02/06/2023]
Abstract
Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower (Brassica oleracea var. botrytis) by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS) and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding.
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Affiliation(s)
- Patrick Thorwarth
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Eltohamy A A Yousef
- Department of Horticulture, Faculty of Agriculture, University of Suez Canal, Ismailia 41522, Egypt
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
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45
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Rahman H, Bennett RA, Kebede B. Molecular mapping of QTL alleles of Brassica oleracea affecting days to flowering and photosensitivity in spring Brassica napus. PLoS One 2018; 13:e0189723. [PMID: 29320498 PMCID: PMC5761838 DOI: 10.1371/journal.pone.0189723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/30/2017] [Indexed: 12/29/2022] Open
Abstract
Earliness of flowering and maturity are important traits in spring Brassica napus canola–whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B. napus were introgressed from the late flowering species B. oleracea. Additive effect of the C1 QTL allele at 14 to18 h photoperiod was 1.1 to 2.9 days; however, the same QTL allele exerted an additive effect of 6.2 days at 10 h photoperiod. Additive effect of the C9 QTL at 10 h photoperiod was 2.8 days. These two QTL also showed significant interaction in the control of flowering only under a short-day (10 h photoperiod) condition with an effect of 2.3 days. A few additional QTL were also detected on the chromosomes C2 and C8; however, none of these QTL could be detected under all photoperiod and temperature conditions. BLASTn search identified several putative flowering time genes on the chromosomes C1 and C9 and located the physical position of the QTL markers in the Brassica genome; however, only a few of these genes were found within the QTL region. Thus, the molecular markers and the genomic regions identified in this research could potentially be used in breeding for the development of early flowering photoinsensitive B. napus canola cultivars, as well as for identification of candidate genes involved in flowering time variation and photosensitivity.
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Affiliation(s)
- Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
- * E-mail:
| | - Rick A. Bennett
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
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Lee CR, Hsieh JW, Schranz ME, Mitchell-Olds T. The Functional Change and Deletion of FLC Homologs Contribute to the Evolution of Rapid Flowering in Boechera stricta. FRONTIERS IN PLANT SCIENCE 2018; 9:1078. [PMID: 30108602 PMCID: PMC6080596 DOI: 10.3389/fpls.2018.01078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/03/2018] [Indexed: 05/04/2023]
Abstract
Differences in the timing of vegetative-to-reproductive phase transition have evolved independently and repeatedly in different plant species. Due to their specific biological functions and positions in pathways, some genes are important targets of repeated evolution - independent mutations on these genes caused the evolution of similar phenotypes in distantly related organisms. While many studies have investigated these genes, it remains unclear how gene duplications influence repeated phenotypic evolution. Here we characterized the genetic architecture underlying a novel rapid-flowering phenotype in Boechera stricta and investigated the candidate genes BsFLC1 and BsFLC2. The expression patterns of BsFLC1 suggested its function in flowering time suppression, and the deletion of BsFLC1 is associated with rapid flowering and loss of vernalization requirement. In contrast, BsFLC2 did not appear to be associated with flowering and had accumulated multiple amino acid substitutions in the relatively short evolutionary timeframe after gene duplication. These non-synonymous substitutions greatly changed the physicochemical properties of the original amino acids, concentrated non-randomly near a protein-interacting domain, and had greater substitution rate than synonymous changes. Here we suggested that, after recent gene duplication of the FLC gene, the evolution of rapid phenology was made possible by the change of BsFLC2 expression pattern or protein sequences and the deletion of BsFLC1.
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Affiliation(s)
- Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- *Correspondence: Cheng-Ruei Lee,
| | - Jo-Wei Hsieh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - M. E. Schranz
- Biosystematics Group, Wageningen University & Research, Wageningen, Netherlands
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47
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Itabashi E, Osabe K, Fujimoto R, Kakizaki T. Epigenetic regulation of agronomical traits in Brassicaceae. PLANT CELL REPORTS 2018; 37:87-101. [PMID: 29058037 DOI: 10.1007/s00299-017-2223-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/05/2017] [Indexed: 05/08/2023]
Abstract
Epigenetic regulation, covalent modification of DNA and changes in histone proteins are closely linked to plant development and stress response through flexibly altering the chromatin structure to regulate gene expression. In this review, we will illustrate the importance of epigenetic influences by discussing three agriculturally important traits of Brassicaceae. (1) Vernalization, an acceleration of flowering by prolonged cold exposure regulated through epigenetic silencing of a central floral repressor, FLOWERING LOCUS C. This is associated with cold-dependent repressive histone mark accumulation, which confers competency of consequence vegetative-to-reproductive phase transition. (2) Hybrid vigor, in which an F1 hybrid shows superior performance to the parental lines. Combination of distinct epigenomes with different DNA methylation states between parental lines is important for increase in growth rate in a hybrid progeny. This is independent of siRNA-directed DNA methylation but dependent on the chromatin remodeler DDM1. (3) Self-incompatibility, a reproductive mating system to prevent self-fertilization. This is controlled by the S-locus consisting of SP11 and SRK which are responsible for self/non-self recognition. Because self-incompatibility in Brassicaceae is sporophytically controlled, there are dominance relationships between S haplotypes in the stigma and pollen. The dominance relationships in the pollen rely on de novo DNA methylation at the promoter region of a recessive allele, which is triggered by siRNA production from a flanking region of a dominant allele.
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Affiliation(s)
- Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie, 514-2392, Japan.
| | - Kenji Osabe
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Kunigami, Okinawa, 904-0495, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Tomohiro Kakizaki
- Institute of Vegetable and Floriculture Science, NARO, Kusawa, Ano, Tsu, Mie, 514-2392, Japan
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48
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Bloomer RH, Dean C. Fine-tuning timing: natural variation informs the mechanistic basis of the switch to flowering in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5439-5452. [PMID: 28992087 DOI: 10.1093/jxb/erx270] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The evolution of diverse life history strategies has allowed Arabidopsis thaliana to adapt to worldwide locations, spanning a range of latitudinal and environmental conditions. Arabidopsis thaliana accessions are either vernalization-requiring winter annuals or rapid cyclers, with extensive natural variation in vernalization requirement and response. Genetic and molecular analysis of this variation has enhanced our understanding of the mechanisms involved in life history determination, with translation to both natural and crop systems in the Brassicaceae and beyond.
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Affiliation(s)
- R H Bloomer
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - C Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Schiessl SV, Huettel B, Kuehn D, Reinhardt R, Snowdon RJ. Flowering Time Gene Variation in Brassica Species Shows Evolutionary Principles. FRONTIERS IN PLANT SCIENCE 2017; 8:1742. [PMID: 29089948 PMCID: PMC5651034 DOI: 10.3389/fpls.2017.01742] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/25/2017] [Indexed: 05/02/2023]
Abstract
Flowering time genes have a strong influence on successful reproduction and life cycle adaptation. However, their regulation is highly complex and only well understood in diploid model systems. For crops with a polyploid background from the genus Brassica, data on flowering time gene variation are scarce, although indispensable for modern breeding techniques like marker-assisted breeding. We have deep-sequenced all paralogs of 35 Arabidopsis thaliana flowering regulators using Sequence Capture followed by Illumina sequencing in two selected accessions of the vegetable species Brassica rapa and Brassica oleracea, respectively. Using these data, we were able to call SNPs, InDels and copy number variations (CNVs) for genes from the total flowering time network including central flowering regulators, but also genes from the vernalisation pathway, the photoperiod pathway, temperature regulation, the circadian clock and the downstream effectors. Comparing the results to a complementary data set from the allotetraploid species Brassica napus, we detected rearrangements in B. napus which probably occurred early after the allopolyploidisation event. Those data are both a valuable resource for flowering time research in those vegetable species, as well as a contribution to speciation genetics.
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Affiliation(s)
- Sarah V. Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
- *Correspondence: Sarah V. Schiessl
| | - Bruno Huettel
- Max Planck Institute for Breeding Research, Cologne, Germany
| | - Diana Kuehn
- Max Planck Institute for Breeding Research, Cologne, Germany
| | | | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 2016; 7:13390. [PMID: 27834372 PMCID: PMC5114598 DOI: 10.1038/ncomms13390] [Citation(s) in RCA: 248] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023] Open
Abstract
There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis. Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleracea reference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits
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