1
|
Laitinen RAE, Nikoloski Z. Strategies to identify and dissect trade-offs in plants. Mol Ecol 2024; 33:e16780. [PMID: 36380694 DOI: 10.1111/mec.16780] [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: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022]
Abstract
Trade-offs between traits arise and reflect constraints imposed by the environment and physicochemical laws. Trade-off situations are expected to be highly relevant for sessile plants, which have to respond to changes in the environment to ensure survival. Despite increasing interest in determining the genetic and molecular basis of plant trade-offs, there are still gaps and differences with respect to how trade-offs are defined, how they are measured, and how their genetic architecture is dissected. The first step to fill these gaps is to establish what is meant by trade-offs. In this review we provide a classification of the existing definitions of trade-offs according to: (1) the measures used for their quantification, (2) the dependence of trade-offs on environment, and (3) experimental designed used (i.e. a single individual across different environments or a population of individuals in single or multiple environments). We then compare the approaches for quantification of trade-offs based on phenotypic, between-individual, and genetic correlations, and stress the need for developing further quantification indices particularly for trade-offs between multiple traits. Lastly, we highlight the genetic mechanisms underpinning trade-offs and experimental designs that facilitate their discovery in plants, with focus on usage of natural variability. This review also offers a perspective for future research aimed at identification of plant trade-offs, dissection of their genetic architecture, and development of strategies to overcome trade-offs, with applications in crop breeding.
Collapse
Affiliation(s)
- Roosa A E Laitinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| |
Collapse
|
2
|
Zhang B, Su T, Xin X, Li P, Wang J, Wang W, Yu Y, Zhao X, Zhang D, Li D, Zhang F, Yu S. Wall-associated kinase BrWAK1 confers resistance to downy mildew in Brassica rapa. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2125-2139. [PMID: 37402218 PMCID: PMC10502744 DOI: 10.1111/pbi.14118] [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: 12/26/2022] [Revised: 05/16/2023] [Accepted: 06/15/2023] [Indexed: 07/06/2023]
Abstract
The plant cell wall is the first line of defence against physical damage and pathogen attack. Wall-associated kinase (WAK) has the ability to perceive the changes in the cell wall matrix and transform signals into the cytoplasm, being involved in plant development and the defence response. Downy mildew, caused by Hyaloperonospora brassicae, can result in a massive loss in Chinese cabbage (Brassica rapa L. ssp. pekinensis) production. Herein, we identified a candidate resistant WAK gene, BrWAK1, in a major resistant quantitative trait locus, using a double haploid population derived from resistant inbred line T12-19 and the susceptible line 91-112. The expression of BrWAK1 could be induced by salicylic acid and pathogen inoculation. Expression of BrWAK1 in 91-112 could significantly enhance resistance to the pathogen, while truncating BrWAK1 in T12-19 increased disease susceptibility. Variation in the extracellular galacturonan binding (GUB) domain of BrWAK1 was found to mainly confer resistance to downy mildew in T12-19. Moreover, BrWAK1 was proved to interact with BrBAK1 (brassinosteroid insensitive 1 associated kinase), resulting in the activation of the downstream mitogen-activated protein kinase (MAPK) cascade to trigger the defence response. BrWAK1 is the first identified and thoroughly characterized WAK gene conferring disease resistance in Chinese cabbage, and the plant biomass is not significantly influenced by BrWAK1, which will greatly accelerate Chinese cabbage breeding for downy mildew resistance.
Collapse
Affiliation(s)
- Bin Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Tongbing Su
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Xiaoyun Xin
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Peirong Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Jiao Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Weihong Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Yangjun Yu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Xiuyun Zhao
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Deshuang Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Dayong Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| | - Shuancang Yu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
- State Key Laboratory of Vegetable BiobreedingBeijingChina
| |
Collapse
|
3
|
Su T, Wang W, Wang Z, Li P, Xin X, Yu Y, Zhang D, Zhao X, Wang J, Sun L, Jin G, Zhang F, Yu S. BrMYB108 confers resistance to Verticillium wilt by activating ROS generation in Brassica rapa. Cell Rep 2023; 42:112938. [PMID: 37552600 DOI: 10.1016/j.celrep.2023.112938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/12/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
Increasing plant resistance to Verticillium wilt (VW), which causes massive losses of Brassica rapa crops, is a challenge worldwide. However, few causal genes for VW resistance have been identified by forward genetic approaches, resulting in limited application in breeding. We combine a genome-wide association study in a natural population and quantitative trait locus mapping in an F2 population and identify that the MYB transcription factor BrMYB108 regulates plant resistance to VW. A 179 bp insertion in the BrMYB108 promoter alters its expression pattern during Verticillium longisporum (VL) infection. High BrMYB108 expression leads to high VL resistance, which is confirmed by disease resistance tests using BrMYB108 overexpression and loss-of-function mutants. Furthermore, we verify that BrMYB108 confers VL resistance by regulating reactive oxygen species (ROS) generation through binding to the promoters of respiratory burst oxidase genes (Rboh). A loss-of-function mutant of AtRbohF in Arabidopsis shows significant susceptibility to VL. Thus, BrMYB108 and its target ROS genes could be used as targets for genetic engineering for VL resistance of B. rapa.
Collapse
Affiliation(s)
- Tongbing Su
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Weihong Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Zheng Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Peirong Li
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Xiaoyun Xin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Yangjun Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Deshuang Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Xiuyun Zhao
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Jiao Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Liling Sun
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Guihua Jin
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Fenglan Zhang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China.
| | - Shuancang Yu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China; Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China.
| |
Collapse
|
4
|
Qu G, Gao Y, Wang X, Fu W, Sun Y, Gao X, Wang W, Hao C, Feng H, Wang Y. Fine mapping and analysis of candidate genes for qFT7.1, a major quantitative trait locus controlling flowering time in Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2233-2246. [PMID: 35532733 DOI: 10.1007/s00122-022-04108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
qFT7.1, a major QTL for flowering time in Brassica rapa was fine-mapped to chromosome A07 in a 56.4-kb interval, in which the most likely candidate gene is BraA07g018240.3C. In Brassica rapa, flowering time (FT) is an important agronomic trait that affects the yield, quality, and adaption. FT is a complicated trait that is regulated by many genes and is affected greatly by the environment. In this study, a chromosome segment substitution line (CSSL), CSSL16, was selected that showed later flowering than the recurrent parent, a rapid-cycling inbred line of B. rapa (RcBr). Using Bulked Segregant RNA sequencing, we identified a late flowering quantitative trait locus (QTL), designated as qFT7.1, on chromosome A07, based on a secondary-F2 population derived from the cross between CSSL16 and RcBr. qFT7.1 was further validated by conventional QTL mapping. This QTL explained 39.9% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 56.4-kb interval using recombinant analysis. Expression analysis suggested that BraA07g018240.3C, which is homologous to ATC (encoding Arabidopsis thaliana CENTRORADIALIS homologue), a gene for delayed flowering in Arabidopsis, as the most promising candidate gene. Sequence analysis demonstrated that two synonymous mutations existed in the coding region and numerous bases replacements existed in promoter region between BraA07g018240.3C from CSSL16 and RcBr. The results will increase our knowledge related to the molecular mechanism of late flowering in B. rapa and lays a solid foundation for the breeding of late bolting B. rapa.
Collapse
Affiliation(s)
- Gaoyang Qu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yue Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xian Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Fu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yunxia Sun
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xu Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Chunming Hao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
| |
Collapse
|
5
|
Yue X, Su T, Xin X, Li P, Wang W, Yu Y, Zhang D, Zhao X, Wang J, Sun L, Jin G, Yu S, Zhang F. The Adaxial/Abaxial Patterning of Auxin and Auxin Gene in Leaf Veins Functions in Leafy Head Formation of Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2022; 13:918112. [PMID: 35755702 PMCID: PMC9224592 DOI: 10.3389/fpls.2022.918112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Leaf curling is an essential prerequisite for the formation of leafy heads in Chinese cabbage. However, the part or tissue that determines leaf curvature remains largely unclear. In this study, we first introduced the auxin-responsive marker DR5::GUS into the Chinese cabbage genome and visualized its expression during the farming season. We demonstrated that auxin response is adaxially/abaxially distributed in leaf veins. Together with the fact that leaf veins occupy considerable proportions of the Chinese cabbage leaf, we propose that leaf veins play a crucial supporting role as a framework for heading. Then, by combining analyses of QTL mapping and a time-course transcriptome from heading Chinese cabbage and non-heading pak choi during the farming season, we identified the auxin-related gene BrPIN5 as a strong candidate for leafy head formation. PIN5 displays an adaxial/abaxial expression pattern in leaf veins, similar to that of DR5::GUS, revealing an involvement of BrPIN5 in leafy head development. The association of BrPIN5 function with heading was further confirmed by its haplo-specificity to heading individuals in both a natural population and two segregating populations. We thus conclude that the adaxial/abaxial patterning of auxin and auxin genes in leaf veins functions in the formation of the leafy head in Chinese cabbage.
Collapse
Affiliation(s)
- Xiaozhen Yue
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jiao Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Liling Sun
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Guihua Jin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- National Engineering Research Center for Vegetables, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| |
Collapse
|
6
|
Li J, Yu X, Zhang C, Li N, Zhao J. The application of CRISPR/Cas technologies to Brassica crops: current progress and future perspectives. ABIOTECH 2022; 3:146-161. [PMID: 36304520 PMCID: PMC9590542 DOI: 10.1007/s42994-022-00076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022]
Abstract
Brassica species are a global source of nutrients and edible vegetable oil for humans. However, all commercially important Brassica crops underwent a whole-genome triplication event, hindering the development of functional genomics and breeding programs. Fortunately, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) technologies, by allowing multiplex and precise genome engineering, have become valuable genome-editing tools and opened up new avenues for biotechnology. Here, we review current progress in the use of CRISPR/Cas technologies with an emphasis on the latest breakthroughs in precise genome editing. We also summarize the application of CRISPR/Cas technologies to Brassica crops for trait improvements. Finally, we discuss the challenges and future directions of these technologies for comprehensive application in Brassica crops. Ongoing advancement in CRISPR/Cas technologies, in combination with other achievements, will play a significant role in the genetic improvement and molecular breeding of Brassica crops.
Collapse
Affiliation(s)
- Jun Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Xiaoxiao Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Chao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
| | - Na Li
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life Sciences, Hebei Agricultural University, Baoding, 071001 China
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| |
Collapse
|
7
|
Wang Z, Yang J, Cheng F, Li P, Xin X, Wang W, Yu Y, Zhang D, Zhao X, Yu S, Zhang F, Dong Y, Su T. Subgenome dominance and its evolutionary implications in crop domestication and breeding. HORTICULTURE RESEARCH 2022; 9:uhac090. [PMID: 35873727 PMCID: PMC9297153 DOI: 10.1093/hr/uhac090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 05/29/2023]
Abstract
Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the 'two-step theory', B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.
Collapse
Affiliation(s)
| | | | | | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | | | | |
Collapse
|
8
|
Yuan L, Zhang L, Wu Y, Zheng Y, Nie L, Zhang S, Lan T, Zhao Y, Zhu S, Hou J, Chen G, Tang X, Wang C. Comparative transcriptome analysis reveals that chlorophyll metabolism contributes to leaf color changes in wucai (Brassica campestris L.) in response to cold. BMC PLANT BIOLOGY 2021; 21:438. [PMID: 34583634 PMCID: PMC8477495 DOI: 10.1186/s12870-021-03218-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 09/20/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Chlorophyll (Chl) is a vital photosynthetic pigment involved in capturing light energy and energy conversion. In this study, the color conversion of inner-leaves from green to yellow in the new wucai (Brassica campestris L.) cultivar W7-2 was detected under low temperature. The W7-2 displayed a normal green leaf phenotype at the seedling stage, but the inner leaves gradually turned yellow when the temperature was decreased to 10 °C/2 °C (day/night), This study facilitates us to understand the physiological and molecular mechanisms underlying leaf color changes in response to low temperature. RESULTS A comparative leaf transcriptome analysis of W7-2 under low temperature treatment was performed on three stages (before, during and after leaf color change) with leaves that did not change color under normal temperature at the same period as a control. A total of 67,826 differentially expressed genes (DEGs) were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis revealed that the DEGs were mainly enriched in porphyrin and Chl metabolism, carotenoids metabolism, photosynthesis, and circadian rhythm. In the porphyrin and chlorophyll metabolic pathways, the expression of several genes was reduced [i.e. magnesium chelatase subunit H (CHLH)] under low temperature. Almost all genes [i.e. phytoene synthase (PSY)] in the carotenoids (Car) biosynthesis pathway were downregulated under low temperature. The genes associated with photosynthesis [i.e. photosystem II oxygen-evolving enhancer protein 1 (PsbO)] were also downregulated under LT. Our study also showed that elongated hypocotyl5 (HY5), which participates in circadian rhythm, and the metabolism of Chl and Car, is responsible for the regulation of leaf color change and cold tolerance in W7-2. CONCLUSIONS The color of inner-leaves was changed from green to yellow under low temperature in temperature-sensitive mutant W7-2. Physiological, biochemical and transcriptomic studies showed that HY5 transcription factor and the downstream genes such as CHLH and PSY, which regulate the accumulation of different pigments, are required for the modulation of leaf color change in wucai under low temperature.
Collapse
Affiliation(s)
- Lingyun Yuan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200 Anhui China
| | - Liting Zhang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
| | - Ying Wu
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
| | - Yushan Zheng
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
| | - Libing Nie
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
| | - Shengnan Zhang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
| | - Tian Lan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
| | - Yang Zhao
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
| | - Shidong Zhu
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200 Anhui China
| | - Jinfeng Hou
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200 Anhui China
| | - Guohu Chen
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200 Anhui China
| | - Xiaoyan Tang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200 Anhui China
| | - Chenggang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei, 230036 Anhui China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei, 230036 Anhui China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan, 238200 Anhui China
| |
Collapse
|