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Tabusam J, Liu M, Luo L, Zulfiqar S, Shen S, Ma W, Zhao J. Physiological Control and Genetic Basis of Leaf Curvature and Heading in Brassica rapa L. J Adv Res 2023; 53:49-59. [PMID: 36581197 PMCID: PMC10658314 DOI: 10.1016/j.jare.2022.12.010] [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: 10/11/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Heading is an important agronomic feature for Chinese cabbage, cabbage, and lettuce. The heading leaves function as nutrition storage organs, which contribute to the high quality and economic worth of leafy heads. Leaf development is crucial during the heading stage, most genes previously predicted to be involved in the heading process are based on Arabidopsis leaf development studies. AIM OF REVIEW Till date, there is no published review article that demonstrated a complete layout of all the identified regulators of leaf curvature and heading. In this review, we have summarized all the identified physiological and genetic regulators that are directly or indirectly involved in leaf curvature and heading in Brassica crops. By integrating all identified regulators that provide a coherent logic of leaf incurvature and heading, we proposed a molecular mechanism in Brassica crops with graphical illustrations. This review adds value to future breeding of distinct heading kinds of cabbage and Chinese cabbage by providing unique insights into leaf development. KEY SCIENTIFIC CONCEPTS OF REVIEW Leaf curvature and heading are established by synergistic interactions among genes, transcription factors, microRNAs, phytohormones, and environmental stimuli that regulate primary and secondary morphogenesis. Various genes have been identified using transformation and genome editing that are responsible for the formation of leaf curvature and heading in Brassica crops. A range of leaf morphologies have been observed in Brassica, which are established because of the mutated determinants that are responsible for cell division and leaf polarity.
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Affiliation(s)
- Javaria Tabusam
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Lei Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China
| | - Sumer Zulfiqar
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Wei Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000 Baoding, China.
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Zhao Y, Huang S, Zhang Y, Tan C, Feng H. Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:170. [PMID: 37420138 DOI: 10.1007/s00122-023-04411-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
Brassica orphan gene BrFLM, identified by two allelic mutants, was involved in leafy head formation in Chinese cabbage. Leafy head formation is a unique agronomic trait of Chinese cabbage that determines its yield and quality. In our previous study, an EMS mutagenesis Chinese cabbage mutant library was constructed using the heading Chinese cabbage double haploid (DH) line FT as the wild-type. Here, we screened two extremely similar leafy head deficiency mutants lfm-1 and lfm-2 with geotropic growth leaves from the library to investigate the gene(s) related to leafy head formation. Reciprocal crossing results showed that these two mutants were allelic. We utilized lfm-1 to identify the mutant gene(s). Genetic analysis showed that the mutated trait was controlled by a single nuclear gene Brlfm. Mutmap analysis showed that Brlfm was located on chromosome A05, and BraA05g012440.3C or BraA05g021450.3C were the candidate gene. Kompetitive allele-specific PCR analysis eliminated BraA05g012440.3C from the candidates. Sanger sequencing identified an SNP from G to A at the 271st nucleotide on BraA05g021450.3C. The sequencing of lfm-2 detected another non-synonymous SNP (G to A) located at the 266st nucleotide on BraA05g021450.3C, which verified its function on leafy head formation. We blasted BraA05g021450.3C on database and found that it belongs to a Brassica orphan gene encoding an unknown 13.74 kDa protein, named BrLFM. Subcellular localization showed that BrLFM was located in the nucleus. These findings reveal that BrLFM is involved in leafy head formation in Chinese cabbage.
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Affiliation(s)
- Yonghui Zhao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shengnan Huang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yun Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chong Tan
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, 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.
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Ritonga FN, Zhou D, Zhang Y, Song R, Li C, Li J, Gao J. The Roles of Gibberellins in Regulating Leaf Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:1243. [PMID: 36986931 PMCID: PMC10051486 DOI: 10.3390/plants12061243] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/11/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Plant growth and development are correlated with many aspects, including phytohormones, which have specific functions. However, the mechanism underlying the process has not been well elucidated. Gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development, including cell elongation, leaf expansion, leaf senescence, seed germination, and leafy head formation. The central genes involved in GA biosynthesis include GA20 oxidase genes (GA20oxs), GA3oxs, and GA2oxs, which correlate with bioactive GAs. The GA content and GA biosynthesis genes are affected by light, carbon availability, stresses, phytohormone crosstalk, and transcription factors (TFs) as well. However, GA is the main hormone associated with BR, ABA, SA, JA, cytokinin, and auxin, regulating a wide range of growth and developmental processes. DELLA proteins act as plant growth suppressors by inhibiting the elongation and proliferation of cells. GAs induce DELLA repressor protein degradation during the GA biosynthesis process to control several critical developmental processes by interacting with F-box, PIFS, ROS, SCLl3, and other proteins. Bioactive GA levels are inversely related to DELLA proteins, and a lack of DELLA function consequently activates GA responses. In this review, we summarized the diverse roles of GAs in plant development stages, with a focus on GA biosynthesis and signal transduction, to develop new insight and an understanding of the mechanisms underlying plant development.
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Affiliation(s)
- Faujiah Nurhasanah Ritonga
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
- Graduate School, Padjadjaran University, Bandung 40132, West Java, Indonesia
| | - Dandan Zhou
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
| | - Yihui Zhang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Runxian Song
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Cheng Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Jingjuan Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
| | - Jianwei Gao
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Science, Jinan 250100, China
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Hao N, Cao J, Wang C, Zhu Y, Du Y, Wu T. Understanding the molecular mechanism of leaf morphogenesis in vegetable crops conduces to breeding process. FRONTIERS IN PLANT SCIENCE 2022; 13:971453. [PMID: 36570936 PMCID: PMC9773389 DOI: 10.3389/fpls.2022.971453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Leaf morphology can affect the development and yield of plants by regulating plant architecture and photosynthesis. Several factors can determine the final leaf morphology, including the leaf complexity, size, shape, and margin type, which suggests that leaf morphogenesis is a complex regulation network. The formation of diverse leaf morphology is precisely controlled by gene regulation on translation and transcription levels. To further reveal this, more and more genome data has been published for different kinds of vegetable crops and advanced genotyping approaches have also been applied to identify the causal genes for the target traits. Therefore, the studies on the molecular regulation of leaf morphogenesis in vegetable crops have also been largely improved. This review will summarize the progress on identified genes or regulatory mechanisms of leaf morphogenesis and development in vegetable crops. These identified markers can be applied for further molecular-assisted selection (MAS) in vegetable crops. Overall, the review will contribute to understanding the leaf morphology of different crops from the perspective of molecular regulation and shortening the breeding cycle for vegetable crops.
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Affiliation(s)
- Ning Hao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Chunhua Wang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Yipeng Zhu
- Guiyang Productivity Promotion Center, Guiyang Science and Technology Bureau, Guiyang, China
| | - Yalin Du
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
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Rushworth CA, Wagner MR, Mitchell-Olds T, Anderson JT. The Boechera model system for evolutionary ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1939-1961. [PMID: 36371714 DOI: 10.1002/ajb2.16090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.
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Affiliation(s)
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
| | | | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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An G, Yu C, Yan C, Wang M, Zhang W, Jia Y, Shi C, Larkin RM, Chen J, Lavelle D, Michelmore RW, Kuang H. Loss-of-function of SAWTOOTH 1 affects leaf dorsiventrality genes to promote leafy heads in lettuce. THE PLANT CELL 2022; 34:4329-4347. [PMID: 35916734 PMCID: PMC9614500 DOI: 10.1093/plcell/koac234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The mechanisms underlying leafy heads in vegetables are poorly understood. Here, we cloned a quantitative trait locus (QTL) controlling leafy heads in lettuce (Lactuca sativa). The QTL encodes a transcription factor, SAWTOOTH 1 (LsSAW1), which has a BEL1-like homeodomain and is a homolog of Arabidopsis thaliana. A 1-bp deletion in Lssaw1 contributes to the development of leafy heads. Laser-capture microdissection and RNA-sequencing showed that LsSAW1 regulates leaf dorsiventrality and loss-of-function of Lssaw1 downregulates the expression of many adaxial genes but upregulates abaxial genes. LsSAW1 binds to the promoter region of the adaxial gene ASYMMETRIC LEAVES 1 (LsAS1) to upregulate its expression. Overexpression of LsAS1 compromised the effects of Lssaw1 on heading. LsSAW1 also binds to the promoter region of the abaxial gene YABBY 1 (LsYAB1), but downregulates its expression. Overexpression of LsYAB1 led to bending leaves in LsSAW1 genotypes. LsSAW1 directly interacts with KNOTTED 1 (LsKN1), which is necessary for leafy heads in lettuce. RNA-seq data showed that LsSAW1 and LsKN1 exert antagonistic effects on the expression of thousands of genes. LsSAW1 compromises the ability of LsKN1 to repress LsAS1. Our results suggest that downregulation or loss-of-function of adaxial genes and upregulation of abaxial genes allow for the development of leafy heads.
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Affiliation(s)
- Guanghui An
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changchun Yu
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenghuan Yan
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Menglu Wang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Shi
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dean Lavelle
- Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology and Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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Li J, Wang H, Zhou D, Li C, Ding Q, Yang X, Wang F, Zheng H, Gao J. Genetic and Transcriptome Analysis of Leaf Trichome Development in Chinese Cabbage ( Brassica rapa L. subsp. pekinensis) and Molecular Marker Development. Int J Mol Sci 2022; 23:ijms232112721. [PMID: 36361510 PMCID: PMC9659260 DOI: 10.3390/ijms232112721] [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: 09/04/2022] [Revised: 10/13/2022] [Accepted: 10/19/2022] [Indexed: 01/25/2023] Open
Abstract
Chinese cabbage (Brassica rapa L. subsp. pekinensis) is one of the vegetables with the largest cultivated area in China and has been a great addition to the daily diet of Chinese people. A genetic map has been constructed in our previous study using the F2 population of two inbred lines of Chinese cabbage, namely "G291" (a hairy line) and "ZHB" (a hairless line), based on which a candidate gene related to trichome traits was identified on chromosome A06 with a phenotypic variance of 47%. A molecular marker was found to co-segregate with the trichome traits of the F2 population, which is in the 5'-flanking region of BrGL1, and a corresponding patent has been granted (NO. CN 108545775 B). Transcriptome analysis was carried out on the cotyledon, the first true leaf and the leaf closest to each inflorescence of F2 individuals of "G291 × ZHB" with or without trichomes, respectively. Ten pathways, including 189 DEGs, were identified to be involved in the development of trichomes in Chinese cabbage, which may be specifically related to the development of leaf trichomes. Most of the pathways were related to the biosynthesis of the secondary metabolites, which may help plants to adapt to the ever-changing external environment. DEGs also enriched the "plant-pathogen interaction" pathway, which is consistent with the conclusion that trichomes are related to the disease resistance of plants. Our study provides a basis for future research on the occurrence and development of trichomes in Chinese cabbage.
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Affiliation(s)
- Jingjuan Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hongxia Wang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dandan Zhou
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
| | - Cheng Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Qian Ding
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaogang Yang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fengde Wang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
| | - Han Zheng
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Correspondence: (H.Z.); (J.G.)
| | - Jianwei Gao
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Life Science, Shandong Normal University, Jinan 250100, China
- Correspondence: (H.Z.); (J.G.)
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Alemán-Báez J, Qin J, Cai C, Zou C, Bucher J, Paulo MJ, Voorrips RE, Bonnema G. Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3611-3628. [PMID: 36057748 PMCID: PMC9519658 DOI: 10.1007/s00122-022-04205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.
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Affiliation(s)
- Jorge Alemán-Báez
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Jian Qin
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Chengcheng Cai
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Chunmei Zou
- Centre for Crop Systems Analysis, Wageningen University and Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Roeland E. Voorrips
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
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OCTOPUS regulates BIN2 to control leaf curvature in Chinese cabbage. Proc Natl Acad Sci U S A 2022; 119:e2208978119. [PMID: 35969746 PMCID: PMC9407555 DOI: 10.1073/pnas.2208978119] [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] [Indexed: 11/18/2022] Open
Abstract
Heading is one of the most important agronomic traits for Chinese cabbage crops. During the heading stage, leaf axial growth is an essential process. In the past, most genes predicted to be involved in the heading process have been based on leaf development studies in Arabidopsis. No genes that control leaf axial growth have been mapped and cloned via forward genetics in Chinese cabbage. In this study, we characterize the inward curling mutant ic1 in Brassica rapa ssp. pekinensis and identify a mutation in the OCTOPUS (BrOPS) gene by map-based cloning. OPS is involved in phloem differentiation in Arabidopsis, a functionalization of regulating leaf curvature that is differentiated in Chinese cabbage. In the presence of brassinosteroid (BR) at the early heading stage in ic1, the mutation of BrOPS fails to sequester brassinosteroid insensitive 2 (BrBIN2) from the nucleus, allowing BrBIN2 to phosphorylate and inactivate BrBES1, which in turn relieves the repression of BrAS1 and results in leaf inward curving. Taken together, the results of our findings indicate that BrOPS positively regulates BR signaling by antagonizing BrBIN2 to promote leaf epinastic growth at the early heading stage in Chinese cabbage.
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Huang S, Gao Y, Xue M, Xu J, Liao R, Shang S, Yang X, Zhao Y, Li C, Liu Z, Feng H. BrKAO2 mutations disrupt leafy head formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2453-2468. [PMID: 35726066 DOI: 10.1007/s00122-022-04126-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The role of BrKAO2 in leafy head formation was confirmed by using two allelic Chinese cabbage mutants. Chinese cabbage yield and quality are determined by leafy head formation. Cloning and characterising the key genes regulating leafy head formation are essential for its varietal improvement. We used an EMS-mutagenised population of the heading type 'FT' Chinese cabbage line and identified two allelic non-heading mutants, i.e. nhm3-1 and nhm3-2. Genetic analysis showed that the mutant trait was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping revealed that BraA05g012440.3C was the candidate gene, which encodes ent-kaurenoic acid oxidase 2 in gibberellin (GA) biosynthetic pathway. It was named BrKAO2. Two non-synonymous mutations in the second BrKAO2 exon, respectively, accounted for the mutant phenotypes of nhm3-1 and nhm3-2. BrKAO2 was expressed during all leaf development stages, and there were no significant differences between the wild type and mutants in terms of BrKAO2 expression. The mutant phenotypes were restored to the wild type via exogenous GA3 application. RNA-Seq was performed on wild-type 'FT', nhm3-1, and nhm3-1 + GA3 rosette leaves, and several key genes involved in GA biosynthesis, signal transduction, and leafy head development were identified. These findings indicate that BrKAO2 is responsible for the leafy head formation in nhm3 mutants.
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Affiliation(s)
- Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yue Gao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Meihui Xue
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Junjie Xu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Ruiqi Liao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shayu Shang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Xiaofei Yang
- Integrated Department, Wafangdian Agriculture Technology and Popularization Center, Dalian, 116300, China
| | - Yonghui Zhao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chengyu Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road Shenhe District, Shenyang, 110866, People's Republic of China.
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11
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Construction of an Intragenic SSR-Based Linkage Map and QTL Mapping for Agronomic Traits in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most widely cultivated and economically important vegetables in China. Constructing an effective genetic linkage map and mapping quantitative trait loci (QTLs) related to yield and leafy head morphology is of great importance for molecular breeding of Chinese cabbage. Using two diverse Chinese cabbage inbred lines, ZHB and G291, as parents, an F2 segregating population consisting of 240 individuals was prepared for genetic map construction and phenotype investigation in this study. The two parents are significantly different in both shape and size. Sixteen important agronomic traits of F2 individuals were investigated. A genetic map of 105 intragenic simple sequence repeat (SSR) markers distributed across 10 linkage groups (LGs) was constructed, which was 2034.1 cM in length and had an average inter-locus distance of 21.75 cM. We identified 48 QTLs for the tested important agronomic traits on the studied LGs, with LOD scores of 2.51–12.49, which explained the phenotypic variance of 3.41–26.66%. The QTLs identified in this study will facilitate further genetic analysis and marker-assisted genetic improvement of Chinese cabbage.
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12
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Guo X, Liang J, Lin R, Zhang L, Wu J, Wang X. Series-Spatial Transcriptome Profiling of Leafy Head Reveals the Key Transition Leaves for Head Formation in Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2022; 12:787826. [PMID: 35069646 PMCID: PMC8770947 DOI: 10.3389/fpls.2021.787826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/08/2021] [Indexed: 05/12/2023]
Abstract
Chinese cabbage is an important leaf heading vegetable crop. At the heading stage, its leaves across inner to outer show significant morphological differentiation. However, the genetic control of this complex leaf morphological differentiation remains unclear. Here, we reported the transcriptome profiling of Chinese cabbage plant at the heading stage using 24 spatially dissected tissues representing different regions of the inner to outer leaves. Genome-wide transcriptome analysis clearly separated the inner leaf tissues from the outer leaf tissues. In particular, we identified the key transition leaf by the spatial expression analysis of key genes for leaf development and sugar metabolism. We observed that the key transition leaves were the first inwardly curved ones. Surprisingly, most of the heading candidate genes identified by domestication selection analysis obviously showed a corresponding expression transition, supporting that key transition leaves are related to leafy head formation. The key transition leaves were controlled by a complex signal network, including not only internal hormones and protein kinases but also external light and other stimuli. Our findings provide new insights and the rich resource to unravel the genetic control of heading traits.
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13
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Xie H, Hou J, Fu N, Wei M, Li Y, Yu K, Song H, Li S, Liu J. Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica. BMC Genomics 2021; 22:556. [PMID: 34281524 PMCID: PMC8290542 DOI: 10.1186/s12864-021-07882-x] [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: 04/18/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C4 grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet. Results Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F6 and F7 recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes (Seita.6G228600.v2.2 and Seita.6G228700.v2.2) and a cinnamyl alcohol dehydrogenase (CAD) gene (Seita.1G057300.v2.2) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively. Conclusions This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the CAD gene (Seita.1G057300.v2.2) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07882-x.
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Affiliation(s)
- Huifang Xie
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Junliang Hou
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Nan Fu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Menghan Wei
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Yunfei Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Hui Song
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China.
| | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China.
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14
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Soundararajan P, Park SG, Won SY, Moon MS, Park HW, Ku KM, Kim JS. Influence of Genotype on High Glucosinolate Synthesis Lines of Brassica rapa. Int J Mol Sci 2021; 22:ijms22147301. [PMID: 34298919 PMCID: PMC8305852 DOI: 10.3390/ijms22147301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/03/2022] Open
Abstract
This study was conducted to investigate doubled haploid (DH) lines produced between high GSL (HGSL) Brassica rapa ssp. trilocularis (yellow sarson) and low GSL (LGSL) B. rapa ssp. chinensis (pak choi) parents. In total, 161 DH lines were generated. GSL content of HGSL DH lines ranged from 44.12 to 57.04 μmol·g−1·dry weight (dw), which is within the level of high GSL B. rapa ssp. trilocularis (47.46 to 59.56 μmol g−1 dw). We resequenced five of the HGSL DH lines and three of the LGSL DH lines. Recombination blocks were formed between the parental and DH lines with 108,328 single-nucleotide polymorphisms in all chromosomes. In the measured GSL, gluconapin occurred as the major substrate in HGSL DH lines. Among the HGSL DH lines, BrYSP_DH005 had glucoraphanin levels approximately 12-fold higher than those of the HGSL mother plant. The hydrolysis capacity of GSL was analyzed in HGSL DH lines with a Korean pak choi cultivar as a control. Bioactive compounds, such as 3-butenyl isothiocyanate, 4-pentenyl isothiocyanate, 2-phenethyl isothiocyanate, and sulforaphane, were present in the HGSL DH lines at 3-fold to 6.3-fold higher levels compared to the commercial cultivar. The selected HGSL DH lines, resequencing data, and SNP identification were utilized for genome-assisted selection to develop elite GSL-enriched cultivars and the industrial production of potential anti-cancerous metabolites such as gluconapin and glucoraphanin.
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Affiliation(s)
- Prabhakaran Soundararajan
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea; (P.S.); (S.Y.W.); (M.-S.M.); (H.W.P.)
| | - Sin-Gi Park
- Bioinformatics Team of Theragen Etex Institute, Suwon 16229, Korea;
| | - So Youn Won
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea; (P.S.); (S.Y.W.); (M.-S.M.); (H.W.P.)
| | - Mi-Sun Moon
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea; (P.S.); (S.Y.W.); (M.-S.M.); (H.W.P.)
| | - Hyun Woo Park
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea; (P.S.); (S.Y.W.); (M.-S.M.); (H.W.P.)
| | - Kang-Mo Ku
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Korea;
- Department of Horticulture, Chonnam National University, Gwangju 61186, Korea
| | - Jung Sun Kim
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea; (P.S.); (S.Y.W.); (M.-S.M.); (H.W.P.)
- Correspondence:
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15
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Bhatia N, Runions A, Tsiantis M. Leaf Shape Diversity: From Genetic Modules to Computational Models. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:325-356. [PMID: 34143649 DOI: 10.1146/annurev-arplant-080720-101613] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plant leaves display considerable variation in shape. Here, we introduce key aspects of leaf development, focusing on the morphogenetic basis of leaf shape diversity. We discuss the importance of the genetic control of the amount, duration, and direction of cellular growth for the emergence of leaf form. We highlight how the combined use of live imaging and computational frameworks can help conceptualize how regulated cellular growth is translated into different leaf shapes. In particular, we focus on the morphogenetic differences between simple and complex leaves and how carnivorous plants form three-dimensional insect traps. We discuss how evolution has shaped leaf diversity in the case of complex leaves, by tinkering with organ-wide growth and local growth repression, and in carnivorous plants, by modifying the relative growth of the lower and upper sides of the leaf primordium to create insect-digesting traps.
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Affiliation(s)
- Neha Bhatia
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Adam Runions
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Current affiliation: Department of Computer Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
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16
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Kawakatsu Y, Sakamoto T, Nakayama H, Kaminoyama K, Igarashi K, Yasugi M, Kudoh H, Nagano AJ, Yano K, Kubo N, Notaguchi M, Kimura S. Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan. HORTICULTURE RESEARCH 2021; 8:132. [PMID: 34059655 PMCID: PMC8167115 DOI: 10.1038/s41438-021-00569-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/09/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna.
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Affiliation(s)
- Yaichi Kawakatsu
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Tomoaki Sakamoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Hokuto Nakayama
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kaori Kaminoyama
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Kaori Igarashi
- School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Masaki Yasugi
- Faculty of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi, 321-8585, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, 606-8522, Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 74 Oji, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto, 619-0244, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
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17
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Sun X, Gao Y, Lu Y, Zhang X, Luo S, Li X, Liu M, Feng D, Gu A, Chen X, Xuan S, Wang Y, Shen S, Bonnema G, Zhao J. Genetic analysis of the "head top shape" quality trait of Chinese cabbage and its association with rosette leaf variation. HORTICULTURE RESEARCH 2021; 8:106. [PMID: 33931629 PMCID: PMC8087666 DOI: 10.1038/s41438-021-00541-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/10/2021] [Accepted: 03/05/2021] [Indexed: 05/08/2023]
Abstract
The agricultural and consumer quality of Chinese cabbage is determined by its shape. The shape is defined by the folding of the heading leaves, which defines the head top shape (HTS). The overlapping HTS, in which the heading leaves curve inward and overlap at the top, is the shape preferred by consumers. To understand the genetic regulation of HTS, we generated a large segregating F2 population from a cross between pak choi and Chinese cabbage, with phenotypes ranging from nonheading to heading with either outward curving or inward curving overlapping heading leaves. HTS was correlated with plant height, outer/rosette leaf length, and petiole length. A high-density genetic map was constructed. Quantitative trait locus (QTL) analysis resulted in the identification of 22 QTLs for leafy head-related traits, which included five HTS QTLs. Bulked segregant analysis (BSA) was used to confirm HTS QTLs and identify candidate genes based on informative single-nucleotide polymorphisms. Interestingly, the HTS QTLs colocalized with QTLs for plant height, outer/rosette leaf, and petiole length, consistent with the observed phenotypic correlations. Combined QTL analysis and BSA laid a foundation for molecular marker-assisted breeding of Chinese cabbage HTS and directions for further research on the genetic regulation of this trait.
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Affiliation(s)
- Xiaoxue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Ying Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yin Lu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xiaomeng Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuangxia Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xing Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Daling Feng
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Aixia Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| | - Guusje Bonnema
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
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18
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Yu C, Yan C, Liu Y, Liu Y, Jia Y, Lavelle D, An G, Zhang W, Zhang L, Han R, Larkin RM, Chen J, Michelmore RW, Kuang H. Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce. Proc Natl Acad Sci U S A 2020; 117:33668-33678. [PMID: 33288708 PMCID: PMC7776633 DOI: 10.1073/pnas.2019698117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Leafy head is a unique type of plant architecture found in some vegetable crops, with leaves bending inward to form a compact head. The genetic and molecular mechanisms underlying leafy head in vegetables remain poorly understood. We genetically fine-mapped and cloned a major quantitative trait locus controlling heading in lettuce. The candidate gene (LsKN1) is a homolog of knotted 1 (KN1) from Zea mays Complementation and CRISPR/Cas9 knockout experiments confirmed the role of LsKN1 in heading. In heading lettuce, there is a CACTA-like transposon inserted into the first exon of LsKN1 (LsKN1▽). The transposon sequences act as a promoter rather than an enhancer and drive high expression of LsKN1▽. The enhanced expression of LsKN1▽ is necessary but not sufficient for heading in lettuce. Data from ChIP-sequencing, electrophoretic mobility shift assays, and dual luciferase assays indicate that the LsKN1▽ protein binds the promoter of LsAS1 and down-regulates its expression to alter leaf dorsoventrality. This study provides insight into plant leaf development and will be useful for studies on heading in other vegetable crops.
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Affiliation(s)
- Changchun Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Chenghuan Yan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Yuling Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Yali Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Yue Jia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Dean Lavelle
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Guanghui An
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Lei Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Rongkui Han
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), Ministry of Agriculture (MOA), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070 Wuhan, People's Republic of China;
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19
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Li Y, Liu GF, Ma LM, Liu TK, Zhang CW, Xiao D, Zheng HK, Chen F, Hou XL. A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. HORTICULTURE RESEARCH 2020; 7:212. [PMID: 33372175 PMCID: PMC7769993 DOI: 10.1038/s41438-020-00449-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/28/2020] [Accepted: 12/09/2020] [Indexed: 05/12/2023]
Abstract
Non-heading Chinese cabbage (NHCC) is an important leafy vegetable cultivated worldwide. Here, we report the first high-quality, chromosome-level genome of NHCC001 based on PacBio, Hi-C, and Illumina sequencing data. The assembled NHCC001 genome is 405.33 Mb in size with a contig N50 of 2.83 Mb and a scaffold N50 of 38.13 Mb. Approximately 53% of the assembled genome is composed of repetitive sequences, among which long terminal repeats (LTRs, 20.42% of the genome) are the most abundant. Using Hi-C data, 97.9% (396.83 Mb) of the sequences were assigned to 10 pseudochromosomes. Genome assessment showed that this B. rapa NHCC001 genome assembly is of better quality than other currently available B. rapa assemblies and that it contains 48,158 protein-coding genes, 99.56% of which are annotated in at least one functional database. Comparative genomic analysis confirmed that B. rapa NHCC001 underwent a whole-genome triplication (WGT) event shared with other Brassica species that occurred after the WGD events shared with Arabidopsis. Genes related to ascorbic acid metabolism showed little variation among the three B. rapa subspecies. The numbers of genes involved in glucosinolate biosynthesis and catabolism were higher in NHCC001 than in Chiifu and Z1, due primarily to tandem duplication. The newly assembled genome will provide an important resource for research on B. rapa, especially B. rapa ssp. chinensis.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gao-Feng Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li-Ming Ma
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Tong-Kun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chang-Wei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Fei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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20
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Neik TX, Amas J, Barbetti M, Edwards D, Batley J. Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1336. [PMID: 33050509 PMCID: PMC7599536 DOI: 10.3390/plants9101336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.
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Affiliation(s)
- Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway 47500, Selangor, Malaysia;
| | - Junrey Amas
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Martin Barbetti
- School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
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21
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Gao Y, Lu Y, Li X, Li N, Zhang X, Su X, Feng D, Liu M, Xuan S, Gu A, Wang Y, Chen X, Zhao J, Shen S. Development and Application of SSR Markers Related to Genes Involved in Leaf Adaxial-Abaxial Polarity Establishment in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). Front Genet 2020; 11:773. [PMID: 32793286 PMCID: PMC7391075 DOI: 10.3389/fgene.2020.00773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
In Chinese cabbage (Brassica rapa L. ssp. pekinensis), leaf adaxial-abaxial (ad-ab) polarity is tightly related to leaf incurvature, an essential factor for the formation of leafy heads. Therefore, identification of the genes responsible for leaf ad-ab polarity and studying their genetic variation may clarify the mechanism of leafy head formation. By comparing the sequences of the genes regulating leaf ad-ab polarity development in Arabidopsis thaliana (A. thaliana), 41 candidate genes distributed on 10 chromosomes were found to be responsible for the establishment of ad-ab polarity in Chinese cabbage. Orthologous genes, including 10 single copies, 14 double copies, and one triple copies, were detected in the Chinese cabbage. The gene structure and conserved domain analyses showed that the number of exons of the 41 candidate genes range from one to 25, and that most genes share the conserved motifs 1, 6, and 10. Based on the 41 candidate genes, 341 simple sequence repeats (SSRs) were detected, including five replicated types: single, double, triple, quintuple, and sextuple nucleotide replications. Among these sequence repeat (SSR) loci, 323 loci were used to design 969 specific primers, and 362 primer pairs were selected randomly and evaluated using 12 Chinese cabbage accessions with different heading types. 23 primer pairs resulting with clear, polymorphic bands, combined with other 127 markers, was used to construct a linkage map by using an F2 population containing 214 lines derived from the hybrid of the overlapping heading Chinese cabbage “14Q-141” and the outward curling heading Chinese cabbage “14Q-279.” The result showed that the sequences of markers in the genetic linkage map and the physical map was consistent in general. Our study could help to accelerate the breeding process of leafy head quality in Chinese cabbage.
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Affiliation(s)
- Ying Gao
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China.,Agriculture and Rural Affairs Bureau of Xindu District, Xingtai, China
| | - Yin Lu
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Xiaoguang Li
- Institute of Forestry and Fruits, Xingtai Academy of Agricultural Sciences, Xingtai, China
| | - Na Li
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Xiaomeng Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Xiangjie Su
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Daling Feng
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Aixia Gu
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, 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, China
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22
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Nvsvrot T, Xia W, Xiao Z, Zhan C, Liu M, Yang X, Zhang Y, Wang N. Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar. PHYTOPATHOLOGY 2020; 110:900-906. [PMID: 31958037 DOI: 10.1094/phyto-10-19-0402-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Poplar trees (Populus spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by Melampsora spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (R) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an R gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the R gene could be used as a diagnostic marker for future poplar molecular breeding.
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Affiliation(s)
- Tashbek Nvsvrot
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenxiu Xia
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Logistics Service Group, Wuhan University, Wuhan, 430070, China
| | - Zheng'ang Xiao
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang Zhan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqing Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
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23
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Ren W, Wu F, Bai J, Li X, Yang X, Xue W, Liu H, He Y. BcpLH organizes a specific subset of microRNAs to form a leafy head in Chinese cabbage ( Brassica rapa ssp. pekinensis). HORTICULTURE RESEARCH 2020; 7:1. [PMID: 31908804 PMCID: PMC6938484 DOI: 10.1038/s41438-019-0222-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/07/2019] [Accepted: 10/24/2019] [Indexed: 05/18/2023]
Abstract
HYL1 (HYPONASTIC LEAVES 1) in Arabidopsis thaliana encodes a double-stranded RNA-binding protein needed for proper miRNA maturation, and its null mutant hyl1 shows a typical leaf-incurvature phenotype. In Chinese cabbage, BcpLH (Brassica rapa ssp. pekinensis LEAFY HEADS), a close homolog of HYL1, is differentially expressed in juvenile leaves, which are flat, and in adult leaves, which display extreme incurvature. BcpLH lacks protein-protein interaction domains and is much shorter than HYL1. To test whether BcpLH is associated with defects in microRNA (miRNA) biogenesis and leaf flatness, we enhanced and repressed the activity of BcpLH by transgenics and investigated BcpLH-dependent miRNAs and plant morphology. BcpLH promoted miRNA biogenesis by the proper processing of primary miRNAs. BcpLH downregulation via antisense decreased a specific subset of miRNAs and increased the activities of their target genes, causing upward curvature of rosette leaves and early leaf incurvature, concurrent with the enlargement, earliness, and round-to-oval shape transition of leafy heads. Moreover, BcpLH-dependent miRNAs in Chinese cabbage are not the same as HYL1-dependent miRNAs in Arabidopsis. We suggest that BcpLH controls a specific subset of miRNAs in Chinese cabbage and coordinates the direction, extent, and timing of leaf curvature during head formation in Brassica rapa.
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Affiliation(s)
- Wenqing Ren
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
- Graduate School of the Chinese Academy of Sciences, Shanghai, 200032 China
| | - Feijie Wu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Jinjuan Bai
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Xiaorong Li
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Xi Yang
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Wanxin Xue
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
| | - Heng Liu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture, Zhanjiang, Guangdong, China
| | - Yuke He
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Fenglin Road 300, Shanghai, 200032 China
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24
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Luo X, Xu L, Wang Y, Dong J, Chen Y, Tang M, Fan L, Zhu Y, Liu L. An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:274-286. [PMID: 31218798 PMCID: PMC6920339 DOI: 10.1111/pbi.13195] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/19/2023]
Abstract
High-density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high-resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra-high-density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole-genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish.
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Affiliation(s)
- Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Guizhou Institute of BiotechnologyGuizhou Academy of Agricultural SciencesGuiyangChina
| | | | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yuelin Zhu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
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25
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Yu J, Gao L, Liu W, Song L, Xiao D, Liu T, Hou X, Zhang C. Transcription Coactivator ANGUSTIFOLIA3 (AN3) Regulates Leafy Head Formation in Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2019; 10:520. [PMID: 31114598 PMCID: PMC6502973 DOI: 10.3389/fpls.2019.00520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 04/04/2019] [Indexed: 05/24/2023]
Abstract
Leafy head formation in Chinese cabbage (B. rapa ssp. pekinensis cv. Bre) results from leaf curvature, which is under the tight control of genes involved in the adaxial-abaxial patterning during leaf development. The transcriptional coactivator ANGUSTIFOLIA3 (AN3) binds to the SWI/SNF chromatin remodeling complexes formed around ATPases such as BRAHMA (BRM) in order to regulate transcription in various aspects of leaf development such as cell proliferation, leaf primordia expansion, and leaf adaxial/abaxial patterning in Arabidopsis. However, its regulatory function in Chinese cabbage remains poorly understood. Here, we analyzed the expression patterns of the Chinese cabbage AN3 gene (BrAN3) before and after leafy head formation, and produced BrAN3 gene silencing plants by using the turnip yellow mosaic virus (TYMV)-derived vector in order to explore its potential function in leafy head formation in Chinese cabbage. We found that BrAN3 had distinct expression patterns in the leaves of Chinese cabbage at the rosette and heading stages. We also found silencing of BrAN3 stimulated leafy head formation at the early stage. Transcriptome analysis indicated that silencing of BrAN3 modulated the hormone signaling pathways of auxin, ethylene, GA, JA, ABA, BR, CK, and SA in Chinese cabbage. Our study offers unique insights into the function of BrAN3 in leafy head formation in Chinese cabbage.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liwei Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Lixiao Song
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Sun X, Basnet RK, Yan Z, Bucher J, Cai C, Zhao J, Bonnema G. Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage ( Brassica rapa). HORTICULTURE RESEARCH 2019; 6:130. [PMID: 31814983 PMCID: PMC6885048 DOI: 10.1038/s41438-019-0212-9] [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: 05/16/2019] [Revised: 09/21/2019] [Accepted: 10/19/2019] [Indexed: 05/10/2023]
Abstract
Chinese cabbage plants go through seedling and rosette stages before forming their leafy head. Chinese cabbage plants resemble pak-choi plants at their seedling stage, but in their rosette stage the leaves of Chinese cabbage differentiate, as they increase in size with shorter petioles. In order to understand the molecular pathways that play a role in leafy head formation, transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype. The two Chinese cabbages differed in many aspects, among others earliness, leaf size and shape, leaf numbers, and leafy head shape. Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi, from the later developmental stages of both Chinese cabbages (rosette, folding, and heading). Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi. Three clusters included genes with transcript abundance affected by both genotype and developmental stage, whereas two clusters showed only genotype effects. This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis, with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light. The other clusters contained many genes in the MapMan categories Cell, showing again differences between pak-choi and both Chinese cabbages. We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi, especially at the rosette stage. Overall, comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.
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Affiliation(s)
- XiaoXue Sun
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Ram Kumar Basnet
- Quantitative genetics department, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, Fijnaart, 4793 RS The Netherlands
| | - Zhichun Yan
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Chengcheng Cai
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Guusje Bonnema
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
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Sun X, Luo S, Luo L, Wang X, Chen X, Lu Y, Shen S, Zhao J, Bonnema G. Genetic Analysis of Chinese Cabbage Reveals Correlation Between Rosette Leaf and Leafy Head Variation. FRONTIERS IN PLANT SCIENCE 2018; 9:1455. [PMID: 30337935 PMCID: PMC6180146 DOI: 10.3389/fpls.2018.01455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/12/2018] [Indexed: 05/24/2023]
Abstract
To understand the genetic regulation of the domestication trait leafy-head formation of Chinese cabbages, we exploit the diversity within Brassica rapa. To improve our understanding of the relationship between variation in rosette-leaves and leafy heads, we phenotyped a diversity set of 152 Chinese cabbages. This showed correlation between rosette-leaf traits and both head traits and heading capacity. Interestingly, the leaf number of the mature head is not correlated to heading degree nor head shape. We then chose a non-heading pak choi genotype to cross to a Chinese cabbage to generate populations segregating for the leafy head traits. Both a large F2 (485 plants) and a smaller Doubled Haploid (88 lines) mapping population were generated. A high density DH-88 genetic map using the Brassica SNP array and an F2 map with a subset of these SNPs and InDel markers was used for quantitative trait locus (QTL) analysis. Thirty-one quantitative trait loci (QTLs) were identified for phenotypes of rosette-leaves in time and both heading degree and several heading traits. On chromosome A06 in both DH-88 and F2-485 QTLs for rosette leaf length and petiole length at different developmental days and an F2 QTL for head height co-located. Variation in head height, width and weight all correlate with variation in heading degree with co-locating QTLs, respectively, on chromosome A03, A05, and A08 in F2-485. The correlation between rosette-leaf and heading traits provides not only insight in the leaf requirements to form a head, but also can be used for selection by Chinese cabbage breeders.
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Affiliation(s)
- XiaoXue Sun
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Shuangxia Luo
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
| | - Lei Luo
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xing Wang
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yin Lu
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
| | - Guusje Bonnema
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, China
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Zhang W, Mirlohi S, Li X, He Y. Identification of Functional Single-Nucleotide Polymorphisms Affecting Leaf Hair Number in Brassica rapa. PLANT PHYSIOLOGY 2018; 177:490-503. [PMID: 29686057 PMCID: PMC6001316 DOI: 10.1104/pp.18.00025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/09/2018] [Indexed: 05/29/2023]
Abstract
Leaf traits affect plant agronomic performance; for example, leaf hair number provides a morphological indicator of drought and insect resistance. Brassica rapa crops have diverse phenotypes, and many B. rapa single-nucleotide polymorphisms (SNPs) have been identified and used as molecular markers for plant breeding. However, which SNPs are functional for leaf hair traits and, therefore, effective for breeding purposes remains unknown. Here, we identify a set of SNPs in the B. rapa ssp. pekinenesis candidate gene BrpHAIRY LEAVES1 (BrpHL1) and a number of SNPs of BrpHL1 in a natural population of 210 B. rapa accessions that have hairy, margin-only hairy, and hairless leaves. BrpHL1 genes and their orthologs and paralogs have many SNPs. By intensive mutagenesis and genetic transformation, we selected the functional SNPs for leaf hairs by the exclusion of nonfunctional SNPs and the orthologous and paralogous genes. The residue tryptophan-92 of BrpHL1a was essential for direct interaction with GLABROUS3 and, thus, necessary for the formation of leaf hairs. The accessions with the functional SNP leading to substitution of the tryptophan-92 residue had hairless leaves. The orthologous BrcHL1b from B. rapa ssp. chinensis regulates hair formation on leaf margins rather than leaf surfaces. The selected SNP for the hairy phenotype could be adopted as a molecular marker for insect resistance in Brassica spp. crops. Moreover, the procedures optimized here can be used to explain the molecular mechanisms of natural variation and to facilitate the molecular breeding of many crops.
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Affiliation(s)
- Wenting Zhang
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shirin Mirlohi
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaorong Li
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuke He
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and 40 Ecology, Chinese Academy of Sciences, Shanghai, China
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Gu A, Meng C, Chen Y, Wei L, Dong H, Lu Y, Wang Y, Chen X, Zhao J, Shen S. Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage. Front Genet 2017; 8:176. [PMID: 29312432 PMCID: PMC5733010 DOI: 10.3389/fgene.2017.00176] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/24/2017] [Indexed: 02/04/2023] Open
Abstract
In Chinese cabbage, heading type is a key agricultural trait of significant economic importance. Using a natural microspore-derived doubled haploid plant, we generated self-crossed progeny with overlapping or outward curling head morphotypes. Sequencing-based bulked segregant analysis (Seq-BSA) revealed a candidate region of 0.52 Mb (A06: 1,824,886~2,347,097 bp) containing genes enriched for plant hormone signal transduction. RNA Sequencing (RNA-Seq) analysis supported the hormone pathway enrichment leading to the identification of two key candidate genes, BrGH3.12 and BrABF1. The regulated homologous genes and the relationship between genes in this pathway were also revealed. Expression of BrGH3.12 varied significantly in the apical portion of the leaf, consistent with the morphological differences between overlapping and outward curling leaves. Transcript levels of BrABF1 in the top, middle and basal segments of the leaf were significantly different between the two types. The two morphotypes contained different concentrations of IAA in the apical portion of their leaves while levels of ABA differed significantly between plant types in the top, middle, and basal leaf segments. Results from Seq-BSA, RNA-Seq and metabolite analyses all support a role for IAA and ABA in heading type formation. These findings increase our understanding of the molecular basis for pattern formation of the leafy head in Chinese cabbage and will contribute to future work developing more desirable leafy head patterns.
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Affiliation(s)
- AiXia Gu
- 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, China
| | - Chuan Meng
- Economic Crop Research Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - YueQi Chen
- 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, China
| | - Lai Wei
- 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, China
| | - Hui Dong
- Shijiazhuang Pomology Institute, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yin Lu
- 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, China
| | - YanHua Wang
- 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, China
| | - XuePing Chen
- 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, China
| | - JianJun Zhao
- 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, China
| | - ShuXing Shen
- 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, China
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30
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Choi SR, Yu X, Dhandapani V, Li X, Wang Z, Lee SY, Oh SH, Pang W, Ramchiary N, Hong CP, Park S, Piao Z, Kim H, Lim YP. Integrated analysis of leaf morphological and color traits in different populations of Chinese cabbage (Brassica rapa ssp. pekinensis). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1617-1634. [PMID: 28577084 DOI: 10.1007/s00122-017-2914-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/27/2017] [Indexed: 05/22/2023]
Abstract
QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding. Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding. To enhance genetic control, quantitative trait loci (QTLs) for leaf color and plant architecture were identified using two immortalized populations with replications of 2 and 4 years. Overall, 158 and 80 QTLs associated with 23 and 14 traits were detected in the DH and RIL populations, respectively. Among them, 23 common robust-QTLs belonging to 12 traits were detected in common loci over the replications. Through comparative analysis, five crucifer genetic blocks corresponding to morphology trait (R, J&U, F and E) and color trait (F, E) were identified in three major linkage groups (A2, A3 and A7). These might be key conserved genomic regions involved with the respective traits. Through synteny analysis with Arabidopsis, 64 candidate genes involved in chlorophyll biosynthesis, cell proliferation and elongation were co-localized within QTL intervals. Among them, SCO3, ABI3, FLU, HCF153, HEMB1, CAB3 were mapped within QTLs for leaf color; and CYCD3;1, CYCB2;4, AN3, ULT1 and ANT were co-localized in QTL regions for leaf size. These robust QTLs and their candidate genes provide useful information for further research into leaf architecture with crop breeding.
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Affiliation(s)
- Su Ryun Choi
- Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Xiaona Yu
- Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Vignesh Dhandapani
- Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Xiaonan Li
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhi Wang
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, China
| | - Seo Yeon Lee
- Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Sang Heon Oh
- Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Wenxing Pang
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Suhyoung Park
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Wanju-gun, Jeollabuk-do, Korea
| | - Zhongyun Piao
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - HyeRan Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, Korea.
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Kawakatsu Y, Nakayama H, Kaminoyama K, Igarashi K, Yasugi M, Kudoh H, Nagano AJ, Yano K, Kubo N, Kimura S. A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey): evidence from QTL analysis. JOURNAL OF PLANT RESEARCH 2017; 130:539-550. [PMID: 28258381 DOI: 10.1007/s10265-017-0917-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/14/2016] [Indexed: 05/19/2023]
Abstract
Brassica rapa show a wide range of morphological variations. In particular, the leaf morphologies of the Japanese traditional leafy vegetables Mizuna and Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey) are distinctly different, even though they are closely related cultivars that are easy to cross. In addition to the differences in the gross morphology of leaves, some cultivars of Mibuna (Kyo-nishiki) have many trichomes on its leaves, whereas Mizuna (Kyo-mizore) does not. To identify the genes responsible for the different number of trichomes, we performed a quantitative trait loci (QTL) analysis of Mizuna and Mibuna. To construct linkage maps for these cultivars, we used RNA-seq data to develop cleaved amplified polymorphic sequence (CAPS) markers. We also performed a restriction site-associated DNA sequencing (RAD-seq) analysis to detect single-nucleotide polymorphisms (SNPs). Two QTL analyses were performed in different years, and both analyses indicated that the largest effect was found on LG A9. Expression analyses showed that a gene homologous to GLABRA1 (GL1), a transcription factor implicated in trichome development in Arabidopsis thaliana, and the sequences 3'-flanking (downstream) of BrGL1, differed considerably between Mizuna (Kyo-mizore) and Mibuna (Kyo-nishiki). These results indicate that BrGL1 on LG A9 is one of the candidate genes responsible for the difference in trichome number between Mizuna and Mibuna. Detecting genes that are responsible for morphological variations allows us to better understand the breeding history of Mizuna and Mibuna.
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Affiliation(s)
- Yaichi Kawakatsu
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Hokuto Nakayama
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Kaori Kaminoyama
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Kaori Igarashi
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Masaki Yasugi
- National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, 509-3, 2-chome, Hirano, Otsu, Shiga, 520-2113, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, 509-3, 2-chome, Hirano, Otsu, Shiga, 520-2113, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- JST PRESTO, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Oji, Kitainayazuma, Seika, Soraku, Kyoto, 619-0244, Japan
| | - Seisuke Kimura
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, 603-8555, Japan.
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32
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Cai C, Wang X, Liu B, Wu J, Liang J, Cui Y, Cheng F, Wang X. Brassica rapa Genome 2.0: A Reference Upgrade through Sequence Re-assembly and Gene Re-annotation. MOLECULAR PLANT 2017; 10:649-651. [PMID: 27890636 DOI: 10.1016/j.molp.2016.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 10/08/2016] [Accepted: 11/09/2016] [Indexed: 05/12/2023]
Affiliation(s)
- Chengcheng Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China
| | - Xiaobo Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China
| | - Bo Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China
| | - Yinan Cui
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China.
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, P.R. China.
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Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa. Sci Rep 2017; 7:40690. [PMID: 28094809 PMCID: PMC5240574 DOI: 10.1038/srep40690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/08/2016] [Indexed: 12/31/2022] Open
Abstract
More and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains. 700 RING finger protein genes were mapped to the 10 chromosomes of B. rapa with a range of 47 to 111 genes for each chromosome. 667 RING finger protein genes were expressed in at least one of the six tissues examined, indicating their involvement in various physiological and developmental processes in B. rapa. Hierarchical clustering analysis of RNA-seq data divided them into seven major groups, one of which includes 231 members preferentially expressed in leaf, and constitutes then a panel of gene candidates for studying the genetic and molecular mechanisms of leafy head traits in Brassica crops. Our results lay the foundation for further studies on the classification, evolution and putative functions of RING finger protein genes in Brassica species.
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Jian H, Yang B, Zhang A, Zhang L, Xu X, Li J, Liu L. Screening of Candidate Leaf Morphology Genes by Integration of QTL Mapping and RNA Sequencing Technologies in Oilseed Rape (Brassica napus L.). PLoS One 2017; 12:e0169641. [PMID: 28068426 PMCID: PMC5222374 DOI: 10.1371/journal.pone.0169641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/20/2016] [Indexed: 11/30/2022] Open
Abstract
Leaf size and shape play important roles in agronomic traits, such as yield, quality and stress responses. Wide variations in leaf morphological traits exist in cultivated varieties of many plant species. By now, the genetics of leaf shape and size have not been characterized in Brassica napus. In this study, a population of 172 recombinant inbred lines (RILs) was used for quantitative trait locus (QTL) analysis of leaf morphology traits. Furthermore, fresh young leaves of extreme lines with more leaf lobes (referred to as ‘A’) and extreme lines with fewer lobes (referred to as ‘B’) selected from the RIL population and leaves of dissected lines (referred to as ‘P’) were used for transcriptional analysis. A total of 31 QTLs for the leaf morphological traits tested in this study were identified on 12 chromosomes, explaining 5.32–39.34% of the phenotypic variation. There were 8, 6, 2, 5, 8, and 2 QTLs for PL (petiole length), PN (lobe number), LW (lamina width), LL (Lamina length), LL/LTL (the lamina size ratio) and LTL (leaf total length), respectively. In addition, 74, 1,166 and 1,272 differentially expressed genes (DEGs) were identified in ‘A vs B’, ‘A vs P’ and ‘B vs P’ comparisons, respectively. The Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict the functions of these DEGs. Gene regulators of leaf shape and size, such as ASYMMETRIC LEAVES 2, gibberellin 20-oxidase 3, genes encoding gibberellin-regulated family protein, genes encoding growth-regulating factor and KNOTTED1-like homeobox were also detected in DEGs. After integrating the QTL mapping and RNA sequencing data, 33 genes, including a gene encoding auxin-responsive GH3 family protein and a gene encoding sphere organelles protein-related gene, were selected as candidates that may control leaf shape. Our findings should be valuable for studies of the genetic control of leaf morphological trait regulation in B. napus.
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Affiliation(s)
- Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Bo Yang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Aoxiang Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Li Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, P. R. China
- * E-mail:
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Shah N, Hirakawa H, Kusakabe S, Sandal N, Stougaard J, Schierup MH, Sato S, Andersen SU. High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. DNA Res 2016; 23:487-494. [PMID: 27374610 PMCID: PMC5066174 DOI: 10.1093/dnares/dsw033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/01/2016] [Indexed: 11/13/2022] Open
Abstract
Recombinant inbred lines (RILs) derived from bi-parental populations are stable genetic resources, which are widely used for constructing genetic linkage maps. These genetic maps are essential for QTL mapping and can aid contig and scaffold anchoring in the final stages of genome assembly. In this study, two Lotus sp. RIL populations, Lotus japonicus MG-20 × Gifu and Gifu × L. burttii, were characterized by Illumina re-sequencing. Genotyping of 187 MG-20 × Gifu RILs at 87,140 marker positions and 96 Gifu × L. burttii RILs at 357,973 marker positions allowed us to accurately identify 1,929 recombination breakpoints in the MG-20 × Gifu RILs and 1,044 breakpoints in the Gifu × L. burttii population. The resulting high-density genetic maps now facilitate high-accuracy QTL mapping, identification of reference genome mis-assemblies, and characterization of structural variants.
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Affiliation(s)
- Niraj Shah
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Shohei Kusakabe
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Niels Sandal
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Jens Stougaard
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Shusei Sato
- Kazusa DNA Research Institute, Chiba 292-0818, Japan.,Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Stig Uggerhøj Andersen
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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Cheng F, Sun R, Hou X, Zheng H, Zhang F, Zhang Y, Liu B, Liang J, Zhuang M, Liu Y, Liu D, Wang X, Li P, Liu Y, Lin K, Bucher J, Zhang N, Wang Y, Wang H, Deng J, Liao Y, Wei K, Zhang X, Fu L, Hu Y, Liu J, Cai C, Zhang S, Zhang S, Li F, Zhang H, Zhang J, Guo N, Liu Z, Liu J, Sun C, Ma Y, Zhang H, Cui Y, Freeling MR, Borm T, Bonnema G, Wu J, Wang X. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet 2016; 48:1218-24. [PMID: 27526322 DOI: 10.1038/ng.3634] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/01/2016] [Indexed: 12/21/2022]
Abstract
Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.
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Affiliation(s)
- Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang, Nanjing, China
| | | | - Fenglan Zhang
- Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing Vegetable Research Center (BVRC), Beijing, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Bo Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yunxia Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Dongyuan Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Xiaobo Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Pingxia Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Ke Lin
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Johan Bucher
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Ningwen Zhang
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Yan Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Hui Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jie Deng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yongcui Liao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Keyun Wei
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xueming Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Lixia Fu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yunyan Hu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jisheng Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Chengcheng Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jifang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Ning Guo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Zhiyuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jin Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Chao Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yuan Ma
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Haijiao Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Yang Cui
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Micheal R Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkley, California, USA
| | - Theo Borm
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Guusje Bonnema
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.,Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
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Liang J, Liu B, Wu J, Cheng F, Wang X. Genetic Variation and Divergence of Genes Involved in Leaf Adaxial-Abaxial Polarity Establishment in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2016; 7:94. [PMID: 26904064 PMCID: PMC4746309 DOI: 10.3389/fpls.2016.00094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/18/2016] [Indexed: 05/26/2023]
Abstract
Alterations in leaf adaxial-abaxial (ad-ab) polarity are one of the main factors that influence leaf curvature. In Chinese cabbage, leaf incurvature is an essential prerequisite to the formation of a leafy head. Identifying ad-ab patterning genes and investigating their genetic variation may facilitate elucidation of the mechanisms underlying leaf incurvature during head formation. Comparative genomic analysis of 45 leaf ad-ab patterning genes in Brassica rapa based on 26 homologs of Arabidopsis thaliana indicated that these genes underwent expansion and were retained after whole genome triplication (WGT). We also assessed the nucleotide diversity and selection footprints of these 45 genes in a collection of 94 Brassica rapa accessions that were composed of heading and non-heading morphotypes. Six of the 45 genes showed significant negative Tajima's D indices and nucleotide diversity reduction in heading accessions compared to those in non-heading accessions, indicating that they underwent purifying selection. Further testing of the BrARF3.1 gene, which was one of the selection signals from a larger collection, confirmed that purifying selection did occur. Our results provide genetic evidence that ad-ab patterning genes are involved in leaf incurvature, which is associated with formation of a leafy head, as well as promote an understanding of the genetic mechanism underlying leafy head formation in Chinese cabbage.
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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-015-0037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Deokar AA, Ramsay L, Sharpe AG, Diapari M, Sindhu A, Bett K, Warkentin TD, Tar'an B. Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly. BMC Genomics 2014; 15:708. [PMID: 25150411 PMCID: PMC4158123 DOI: 10.1186/1471-2164-15-708] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/31/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly. RESULTS Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome. CONCLUSIONS A high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.
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Affiliation(s)
| | | | | | | | | | | | | | - Bunyamin Tar'an
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
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Abstract
The shoot apical meristem contains a pool of undifferentiated stem cells and generates all above-ground organs of the plant. During vegetative growth, cells differentiate from the meristem to initiate leaves while the pool of meristematic cells is preserved; this balance is determined in part by genetic regulatory mechanisms. To assess vegetative meristem growth and genetic control in Zea mays, we investigated its morphology at multiple time points and identified three stages of growth. We measured meristem height, width, plastochron internode length, and associated traits from 86 individuals of the intermated B73 × Mo17 recombinant inbred line population. For meristem height-related traits, the parents exhibited markedly different phenotypes, with B73 being very tall, Mo17 short, and the population distributed between. In the outer cell layer, differences appeared to be related to number of cells rather than cell size. In contrast, B73 and Mo17 were similar in meristem width traits and plastochron internode length, with transgressive segregation in the population. Multiple loci (6−9 for each trait) were mapped, indicating meristem architecture is controlled by many regions; none of these coincided with previously described mutants impacting meristem development. Major loci for height and width explaining 16% and 19% of the variation were identified on chromosomes 5 and 8, respectively. Significant loci for related traits frequently coincided, whereas those for unrelated traits did not overlap. With the use of three near-isogenic lines, a locus explaining 16% of the parental variation in meristem height was validated. Published expression data were leveraged to identify candidate genes in significant regions.
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Wang Y, Wu F, Bai J, He Y. BrpSPL9 (Brassica rapa ssp. pekinensis SPL9) controls the earliness of heading time in Chinese cabbage. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:312-21. [PMID: 24237584 DOI: 10.1111/pbi.12138] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/10/2013] [Accepted: 10/15/2013] [Indexed: 05/21/2023]
Abstract
The leafy heads of cabbage (Brassica oleracea), Chinese cabbage (Brassica rapa ssp. pekinensis), Brussels sprouts (B. oleracea ssp. gemmifera) and lettuce (Lactuca sativa) comprise extremely incurved leaves that are edible vegetable products. The heading time is important for high quality and yield of these crops. Here, we report that BrpSPL9-2 (B. rapa ssp. pekinensis SQUAMOSA PROMOTER BINDING-LIKE 9-2), a target gene of microRNA brp-miR156, controls the heading time of Chinese cabbage. Quantitative measurements of leaf shapes, sizes, colour and curvature indicated that heading is a late adult phase of vegetative growth. During the vegetative period, miR156 levels gradually decreased from the seedling stage to the heading one, whereas BrpSPL9-2 and BrpSPL15-1 mRNAs increased progressively and reached the highest levels at the heading stage. Overexpression of a mutated miR156-resistant form of BrpSPL9-2 caused the significant earliness of heading, concurrent with shortening of the seedling and rosette stages. By contrast, overexpression of miR156 delayed the folding time, concomitant with prolongation of the seedling and rosette stages. Morphological analysis reveals that the significant earliness of heading in the transgenic plants overexpressing BrpSPL9-2 gene was produced because the juvenile phase was absent and the early adult phase shortened, whereas the significant delay of folding in the transgenic plants overexpressing Brp-MIR156a was due to prolongation of the juvenile and early adult phases. Thus, miR156 and BrpSPL9 genes are potentially important for genetic improvement of earliness of Chinese cabbage and other crops.
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Affiliation(s)
- Yali Wang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Xiao D, Wang H, Basnet RK, Zhao J, Lin K, Hou X, Bonnema G. Genetic dissection of leaf development in Brassica rapa using a genetical genomics approach. PLANT PHYSIOLOGY 2014; 164:1309-25. [PMID: 24394778 PMCID: PMC3938622 DOI: 10.1104/pp.113.227348] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 01/01/2014] [Indexed: 05/20/2023]
Abstract
The paleohexaploid crop Brassica rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene Brassica rapa KIP-related protein2_A03 colocalized with QTLs for leaf shape and plant height; Brassica rapa Erecta_A09 colocalized with QTLs for leaf color and leaf shape; Brassica rapa Longifolia1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, Brassica rapa flowering locus C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. rapa.
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Mao Y, Wu F, Yu X, Bai J, Zhong W, He Y. MicroRNA319a-targeted Brassica rapa ssp. pekinensis TCP genes modulate head shape in chinese cabbage by differential cell division arrest in leaf regions. PLANT PHYSIOLOGY 2014; 164:710-20. [PMID: 24351684 PMCID: PMC3912100 DOI: 10.1104/pp.113.228007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/17/2013] [Indexed: 05/18/2023]
Abstract
Leafy heads of cabbage (Brassica oleracea), Chinese cabbage (Brassica rapa), and lettuce (Lactuca sativa) are composed of extremely incurved leaves. The shape of these heads often dictates the quality, and thus the commercial value, of these crops. Using quantitative trait locus mapping of head traits within a population of 150 recombinant inbred lines of Chinese cabbage, we investigated the relationship between expression levels of microRNA-targeted Brassica rapa ssp. pekinensis TEOSINTE BRANCHED1, cycloidea, and PCF transcription factor4 (BrpTCP4) genes and head shape. Here, we demonstrate that a cylindrical head shape is associated with relatively low BrpTCP4-1 expression, whereas a round head shape is associated with high BrpTCP4-1 expression. In the round-type Chinese cabbage, microRNA319 (miR319) accumulation and BrpTCP4-1 expression decrease from the apical to central regions of leaves. Overexpression of BrpMIR319a2 reduced the expression levels of BrpTCP4 and resulted in an even distribution of BrpTCP4 transcripts within all leaf regions. Changes in temporal and spatial patterns of BrpTCP4 expression appear to be associated with excess growth of both apical and interveinal regions, straightened leaf tips, and a transition from the round to the cylindrical head shape. These results suggest that the miR319a-targeted BrpTCP gene regulates the round shape of leafy heads via differential cell division arrest in leaf regions. Therefore, the manipulation of miR319a and BrpTCP4 genes is a potentially important tool for use in the genetic improvement of head shape in these crops.
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