1
|
Yu J, Lei S, Fang S, Tai N, Yu W, Yang Z, Gu L, Wang H, Du X, Zhu B, Cai M. Identification, Characterization, and Cytological Analysis of Several Unexpected Hybrids Derived from Reciprocal Crosses between Raphanobrassica and Its Diploid Parents. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091875. [PMID: 37176933 PMCID: PMC10181067 DOI: 10.3390/plants12091875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
Interspecific hybridization and accompanying backcross between crops and relatives have been recognized as a powerful method to broaden genetic diversity and transfer desirable adaptive traits. Crosses between radish (Raphanus sativus, RR, 2n = 18) and Brassica oleracea (CC, 2n = 18), which formed allotetraploid Raphanobrassica (RRCC, 2n = 36), initiated the construction of resynthetic allopolyploids. However, these progenies from the backcrosses between Raphanobrassica and the two diploid parents have not been well deciphered. Herein, thousands of backcrosses using both Raphanobrassica and the two diploid parents as pollen donors were employed. Several hybrids with expected (2n = 27) and unexpected chromosome numbers (2n = 26 and 2n = 36) were obtained. Fluorescence in situ hybridization (FISH) analysis with R-genome-specific sequences as probes demonstrated that the genome structures of the two expected hybrids were RRC and CCR, and the genome structures of the three unexpected hybrids were RRRC, CCCR, and RRC' (harbouring an incomplete C genome). The unexpected hybrids with extra R or C genomes showed similar phenotypic characteristics to their expected hybrids. FISH analysis with C-genome-specific sequences as probes demonstrated that the unexpected allotetraploid hybrids exhibited significantly more intergenomic chromosome pairings than the expected hybrids. The expected and unexpected hybrids provide not only novel germplasm resources for the breeding of radish and B. oleracea but also very important genetic material for genome dosage analysis.
Collapse
Affiliation(s)
- Jie Yu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Shaolin Lei
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China
| | - Shiting Fang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Niufang Tai
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Wei Yu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Ziwei Yang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| |
Collapse
|
2
|
Amas JC, Thomas WJW, Zhang Y, Edwards D, Batley J. Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species. PHYTOPATHOLOGY 2023:PHYTO08220289FI. [PMID: 36324059 DOI: 10.1094/phyto-08-22-0289-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.
Collapse
Affiliation(s)
- Junrey C Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - William J W Thomas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Yueqi Zhang
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| |
Collapse
|
3
|
Cantila AY, Thomas WJW, Bayer PE, Edwards D, Batley J. Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:3010. [PMID: 36432742 PMCID: PMC9693284 DOI: 10.3390/plants11223010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
Collapse
|
4
|
Germplasm Enhancement and Identification of Loci Conferring Resistance against Plasmodiophora brassicae in Broccoli. Genes (Basel) 2022; 13:genes13091600. [PMID: 36140766 PMCID: PMC9498593 DOI: 10.3390/genes13091600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
In order to breed broccoli and other Brassica materials to be highly resistant to clubroot disease, 41 Brassicaceae varieties were developed and identified between 2020 and 2021. Seven known clubroot genes were used for screening these materials. In addition, the resistant and susceptible broccoli cultivars were designed for observing their differences in the infection process with Plasmodiophora brassicae. The results showed that 90% of total materials had carried more than two clubroot resistance genes: one material carried two disease resistance genes, four materials carried seven genes for clubroot resistance, two materials carried six genes for clubroot resistance, and in total 32% of these materials carried five genes for clubroot resistance. As a result, several new genotypes of Brassicaceae germplasm were firstly created and obtained based on distant hybridization and identification of loci conferring resistance against Plasmodiophora brassicae in this study. We found and revealed that similar infection models of Plasmodiophora brassicae occurred in susceptible and resistant cultivars of broccoli, but differences in infection efficiency of Plasmodiophora brassicae also existed in both materials. For resistant broccoli plants, a small number of conidia formed in the root hair, and only a few spores could enter the cortex without forming sporangia while sporangia could form in susceptible plants. Our study could provide critical Brassica materials for breeding resistant varieties and new insight into understanding the mechanism of plant resistance.
Collapse
|
5
|
Guo Y, Li B, Li M, Zhu H, Yang Q, Liu X, Qu L, Fan L, Wang T. Efficient marker-assisted breeding for clubroot resistance in elite Pol-CMS rapeseed varieties by updating the PbBa8.1 locus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:41. [PMID: 37313506 PMCID: PMC10248692 DOI: 10.1007/s11032-022-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Clubroot disease poses a severe threat to rapeseed (Brassica napus) production worldwide and has recently been spreading across China at an unprecedented pace. Breeding and cultivation of resistant varieties constitute a promising and environment-friendly approach to mitigating this threat. In this study, the clubroot resistance locus PbBa8.1 was successfully transferred into SC4, a shared paternal line of three elite varieties in five generations by marker-assisted backcross breeding. Kompetitive allele specific PCR (KASP) markers of clubroot resistance gene PbBa8.1 and its linked high erucic acid gene (FAE1) were designed and applied for foreground selection, and 1,000 single-nucleotide polymorphisms (SNPs) were selected and used for the background selection. This breeding strategy produced recombinants with the highest recovery ratio of the recurrent parent genome (> 95%) at BC2F2 while breaking the linkage with FAE1 during the selection. An updated version of the paternal line (SC4R) was generated at BC2F3, showing significantly improved clubroot resistance at the seedling stage via artificial inoculation, and was comparable to that of the donor parent. Field trials of the three elite varieties and their updated versions in five environments indicated similar agronomic appearance and final yield. The introduced breeding strategy precisely pyramids the PbBa8.1 and FAE1 loci with the assistance of technical markers in a shorter period and could be applied to other desirable traits for directional improvement in the future. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01305-9.
Collapse
Affiliation(s)
- Yiming Guo
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Bao Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Mei Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Hongjian Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128 China
| | - Qian Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Xinhong Liu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Liang Qu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Lianyi Fan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Tonghua Wang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| |
Collapse
|
6
|
Zhan Z, Shah N, Jia R, Li X, Zhang C, Piao Z. Transferring of clubroot-resistant locus CRd from Chinese cabbage ( Brassica rapa) to canola ( Brassica napus) through interspecific hybridization. BREEDING SCIENCE 2022; 72:189-197. [PMID: 36408323 PMCID: PMC9653189 DOI: 10.1270/jsbbs.21052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/24/2022] [Indexed: 06/16/2023]
Abstract
Clubroot, caused by Plasmodiophora brassicae is one of the most severe threats to brassica species in China and worldwide. Breeding for clubroot resistant varieties is one of the best ways to overcome this disease. In this study, we introduced clubroot resistance (CR) gene CRd from Chinese cabbage (85-74) into elite Brassica napus inbred line Zhongshuang 11 through interspecific hybridization and subsequent backcrossing with whole-genome molecular marker-assisted selection (MAS). The resistant test of CRd to P. brassicae isolates was evaluated in the greenhouse as well as in field conditions. Close linkage markers and the whole-chromosome background marker selection approach improved the recovery rate from 78.3% in BC1 to 100% in BC3F1. The improved clubroot-resistant variety, Zhongshuang11R, was successfully selected in the BC3F2 generation. The greenhouse and field resistant tests revealed that Zhongshuang11R was resistant to P. brassicae pathotypes. The agronomic characteristics of Zhongshuang11R were similar to those of its recurrent parental line, including oil content, composition of fatty acid, plant height, primary effective branches, grain yield per plant and thousand-seed weight. In addition, the oil quality could satisfy the quality requirements for commercial rapeseed oil. Our results will enrich the resistant resources of canola and will certainly accelerate clubroot resistance breeding programs in B. napus.
Collapse
Affiliation(s)
- Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Nadil Shah
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ru Jia
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| |
Collapse
|
7
|
Gan C, Yan C, Pang W, Cui L, Fu P, Yu X, Qiu Z, Zhu M, Piao Z, Deng X. Identification of Novel Locus RsCr6 Related to Clubroot Resistance in Radish ( Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:866211. [PMID: 35665145 PMCID: PMC9161170 DOI: 10.3389/fpls.2022.866211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Clubroot is a devastating disease that causes substantial yield loss worldwide. However, the inheritance and molecular mechanisms of clubroot resistance during pathogen infection in radish remain largely unclear. In this study, we investigated the inheritance of clubroot resistance in the F2 population derived from crossing clubroot-resistant (CR) and clubroot-susceptible inbred lines "GLX" and "XNQ," respectively. Genetic analysis revealed that a single dominant gene controlled the clubroot resistance of "GLX" with a Mendelian ratio of resistance and susceptibility of nearly 3:1. Bulked segregant analysis combined with whole-genome resequencing (BSA-seq) was performed to detect the target region of RsCr6 on chromosome Rs8. Linkage analysis revealed that the RsCr6 locus was located between two markers, HB321 and HB331, with an interval of approximately 92 kb. Based on the outcomes of transcriptome analysis, in the RsCr6 locus, the R120263140 and R120263070 genes with a possible relation to clubroot resistance were considered candidate genes. In addition, three core breeding materials containing the two reported quantitative trait loci (QTLs) and our novel locus RsCr6 targeting clubroot resistance were obtained using marker-assisted selection (MAS) technology. This study reveals a novel locus responsible for clubroot resistance in radishes. Further analysis of new genes may reveal the molecular mechanisms underlying the clubroot resistance of plants and provide a theoretical basis for radish resistance breeding.
Collapse
Affiliation(s)
- Caixia Gan
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Chenghuan Yan
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenxing Pang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Lei Cui
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Pengyu Fu
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Xiaoqing Yu
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhengming Qiu
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Meiyu Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiaohui Deng
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
8
|
Quan C, Chen G, Li S, Jia Z, Yu P, Tu J, Shen J, Yi B, Fu T, Dai C, Ma C. Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2336-2353. [PMID: 35139197 DOI: 10.1093/jxb/erac047] [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: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.
Collapse
Affiliation(s)
- Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Guoting Chen
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Sijia Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Pugang Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| |
Collapse
|
9
|
Wang J, Hu T, Wang W, Hu H, Wei Q, Yan Y, He J, Hu J, Bao C. Comparative transcriptome analysis reveals distinct responsive biological processes in radish genotypes contrasting for Plasmodiophora brassicae interaction. Gene 2022; 817:146170. [PMID: 35031420 DOI: 10.1016/j.gene.2021.146170] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/16/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022]
Abstract
Plasmodiophora brassicae is a protozoan pathogen that causes clubroot disease, which is one of the most destructive diseases for Brassica crops, including radish. However, little is known about the molecular mechanism of clubroot resistance in radish. In this study, we performed a comparative transcriptome analysis between resistant and susceptible radish inoculated with P. brassicae. More differentially expressed genes (DEGs) were identified at 28 days after inoculation (DAI) compared to 7 DAI in both genotypes. Gene ontology (GO) and KEGG enrichment indicated that stress/defense response, secondary metabolic biosynthesis, hormone metabolic process, and cell periphery are directly involved in the defense response process. Further analysis of the transcriptome revealed that effector-triggered immunity (ETI) plays key roles in the defense response. The plant hormones jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) related genes are activated in clubroot defense in the resistant line. Auxin (AUX) hormone related genes are activated in the developing galls of susceptible radish. Our study provides a global transcriptional overview for clubroot development for insights into the P. brassicae defense mechanisms in radish.
Collapse
Affiliation(s)
- Jinglei Wang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Tianhua Hu
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wuhong Wang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haijiao Hu
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qingzhen Wei
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yaqin Yan
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiangming He
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jingfeng Hu
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Chonglai Bao
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| |
Collapse
|
10
|
Zhang L, He J, He H, Wu J, Li M. Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica. HORTICULTURE RESEARCH 2021; 8:246. [PMID: 34848691 PMCID: PMC8633066 DOI: 10.1038/s41438-021-00672-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 05/04/2023]
Abstract
Raphanobrassica (RrRrCrCr, 2n = 4x = 36), which is generated by distant hybridization between the maternal parent Raphanus sativus (RsRs, 2n = 2x = 18) and the paternal parent Brassica oleracea (C°C°, 2n = 2x = 18), displays intermediate silique phenotypes compared to diploid progenitors. However, the hybrid shares much more similarities in silique phenotypes with those of B. oleracea than those of R. sativus. Strikingly, the silique of Raphanobrassica is obviously split into two parts. To investigate the gene expression patterns behind these phenomena, transcriptome analysis was performed on the upper, middle, and lower sections of pods (RCsiu, RCsim, and RCsil), seeds in the upper and lower sections of siliques (RCseu and RCsel) from Raphanobrassica, whole pods (Rsi and Csi) and all seeds in the siliques (Rse and Cse) from R. sativus and B. oleracea. Transcriptome shock was observed in all five aforementioned tissues of Raphanobrassica. Genome-wide unbalanced biased expression and expression level dominance were also discovered, and both of them were toward B. oleracea in Raphanobrassica, which is consistent with the observed phenotypes. The present results reveal the global gene expression patterns of different sections of siliques of Raphanobrassica, pods, and seeds of B. oleracea and R. sativus, unraveling the tight correlation between global gene expression patterns and phenotypes of the hybrid and its parents.
Collapse
Affiliation(s)
- Libin Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianjie He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongsheng He
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiangsheng Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maoteng Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| |
Collapse
|
11
|
Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites. Cells 2021; 10:cells10092358. [PMID: 34572008 PMCID: PMC8466703 DOI: 10.3390/cells10092358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 01/11/2023] Open
Abstract
Intergeneric crosses between Brassica species and Raphanus sativus have produced crops with prominent shoot and root systems of Brassica and R. sativus, respectively. It is necessary to discriminate donor genomes when studying cytogenetic stability in distant crosses to identify homologous chromosome pairing, and microsatellite repeats have been used to discriminate subgenomes in allopolyploids. To identify genome-specific microsatellites, we explored the microsatellite content in three Brassica species (B. rapa, AA, B. oleracea, CC, and B. nigra, BB) and R. sativus (RR) genomes, and validated their genome specificity by fluorescence in situ hybridization. We identified three microsatellites showing A, C, and B/R genome specificity. ACBR_msat14 and ACBR_msat20 were detected in the A and C chromosomes, respectively, and ACBR_msat01 was detected in B and R genomes. However, we did not find a microsatellite that discriminated the B and R genomes. The localization of ACBR_msat20 in the 45S rDNA array in ×Brassicoraphanus 977 corroborated the association of the 45S rDNA array with genome rearrangement. Along with the rDNA and telomeric repeat probes, these microsatellites enabled the easy identification of homologous chromosomes. These data demonstrate the utility of microsatellites as probes in identifying subgenomes within closely related Brassica and Raphanus species for the analysis of genetic stability of new synthetic polyploids of these genomes.
Collapse
|
12
|
Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
Collapse
Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
13
|
Li Q, Xu B, Du Y, Peng A, Ren X, Si J, Song H. Development of Ogura CMS restorers in Brassica oleracea subspecies via direct Rfo B gene transformation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1123-1132. [PMID: 33404672 DOI: 10.1007/s00122-020-03757-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
The Ogura CMS RfoB restorer developing via RfoB gene transformation was utilized to produce specific morphological Ogura CMS restorers and clubroot resistance lines in Brassica oleracea subspecies. Brassica oleracea vegetables including cabbage, cauliflower, kohlrabi, Brussels sprouts and Chinese kale are morphologically very different despite being members of the same species. The Ogura cytoplasmic male sterility (CMS) system is the most stable strategy for the hybrid breeding of these species. However, this limits the utilization of some excellent genes due to the lack of fertile restorer genes in the system. Herein, to efficaciously use Ogura CMS, the Ogura CMS RfoB restorer was produced by transforming the modified RfoB restorer gene into the Ogura CMS line 'CMS2016' of B. oleracea var. capitata. This gene was shown to recover fertility of natural Ogura CMS lines in B. oleracea subspecies and create transient Ogura CMS RfoB restorers such as the clubroot resistance Ogura CMS RfoB restorer. Interestingly, clubroot resistant individuals without transgenic elements were screened in the progenies of hybrids between B. oleracea inbred lines and the clubroot resistance Ogura CMS RfoB restorer. In addition, 18 different morphological Ogura CMS restorers were developed to specifically recover fertile of Ogura CMS cultivars in B. oleracea subspecies.
Collapse
Affiliation(s)
- Qinfei Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bingbing Xu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yangmei Du
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ao Peng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xuesong Ren
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jun Si
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hongyuan Song
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China.
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China.
- Chongqing Key Laboratory of Olericulture, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| |
Collapse
|
14
|
Zhan Z, Jiang Y, Shah N, Hou Z, Zhou Y, Dun B, Li S, Zhu L, Li Z, Piao Z, Zhang C. Association of Clubroot Resistance Locus PbBa8.1 With a Linkage Drag of High Erucic Acid Content in the Seed of the European Turnip. FRONTIERS IN PLANT SCIENCE 2020; 11:810. [PMID: 32595684 PMCID: PMC7301908 DOI: 10.3389/fpls.2020.00810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/19/2020] [Indexed: 05/12/2023]
Abstract
Clubroot caused by Plasmodiophora brassicae is a severe threat to the production of Brassica napus, worldwide. The cultivation of resistant varieties is the most efficient and environmentally friendly way to limit disease spread. We developed a highly resistant B. napus line, ZHE226, containing the resistance locus PbBa8.1. However, ZHE226 seeds contain high erucic acid content, which limits its cultivation owing to its low edible oil quality. A segregation population of BC3F2 was developed by crossing ECD04, a resistant European turnip donor, with Huangshuang5, an elite variety with no erucic acid in its seeds, as a recurrent plant. Fine mapping using the bulk segregation analysis sequencing (BSA-Seq) approach detected PbBa8.1 within a 2.9 MB region on chromosome A08. Interestingly, the previously reported resistance gene Crr1a was found in the same region. Genetic analysis revealed that the CAP-134 marker for Crr1a was closely linked with clubroot resistance (CR). Thus, PbBa8.1 and Crr1a might be allelic for CR. Moreover, comparative and genetic analysis showed that high erucic acid in the seeds of ZHE226 was due to linkage drag of fatty acid elongase 1 (FAE1) in the ECD04 line, which was located in the interval of PbBa8.1 with a physical and genetic distance of 729 Kb and 1.86 cm, respectively. Finally, a clubroot-resistant line with a low erucic acid content was successfully developed through gene-specific molecular marker assistant selection from BC4F4. These results will accelerate CR breeding programs in B. napus.
Collapse
Affiliation(s)
- Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yingfen Jiang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Crop Science, Anhui Academy of Agricultural Science, Hefei, China
| | - Nadil Shah
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhaoke Hou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuanwei Zhou
- Yichang Academy of Agricultural Science, Yichang, China
| | - Bicheng Dun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shisheng Li
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, College of Biology and Agriculture Resource, Huanggang Normal University, Huanggang, China
| | - Li Zhu
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, College of Biology and Agriculture Resource, Huanggang Normal University, Huanggang, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
15
|
Prieto P, Naranjo T. Analytical Methodology of Meiosis in Autopolyploid and Allopolyploid Plants. Methods Mol Biol 2020; 2061:141-168. [PMID: 31583658 DOI: 10.1007/978-1-4939-9818-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Meiosis is the cellular process responsible for producing gametes with half the genetic content of the parent cells. Integral parts of the process in most diploid organisms include the recognition, pairing, synapsis, and recombination of homologous chromosomes, which are prerequisites for balanced segregation of half-bivalents during meiosis I. In polyploids, the presence of more than two sets of chromosomes adds to the basic meiotic program of their diploid progenitors the possibility of interactions between more than two chromosomes and the formation of multivalents, which has implications on chromosome segregations and fertility. The mode of how chromosomes behave in meiosis in competitive situations has been the aim of many studies in polyploid species, some of which are considered here. But polyploids are also of interest in the study of meiosis because some of them tolerate the loss of chromosome segments or complete chromosomes as well as the addition of chromosomes from related species. Deletions allow to assess the effect of specific chromosome segments on meiotic behavior. Introgression lines are excellent materials to monitor the behavior of a given chromosome in the genetic background of the recipient species. We focus on this approach here as based on studies carried out in bread wheat, which is commonly used as a model species for meiosis studies. In addition to highlighting the relevance of the use of materials derived from polyploids in the study of meiosis, cytogenetics tools such as fluorescence in situ hybridization and the immunolabeling of proteins interacting with DNA are also emphasized.
Collapse
Affiliation(s)
- Pilar Prieto
- Departamento de Mejora Genética, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Tomás Naranjo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain.
| |
Collapse
|
16
|
Hu D, Zhang W, Zhang Y, Chang S, Chen L, Chen Y, Shi Y, Shen J, Meng J, Zou J. Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1106-1118. [PMID: 30467941 PMCID: PMC6523605 DOI: 10.1111/pbi.13041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Brassica napus (An An Cn Cn ) is an important worldwide oilseed crop, but it is a young allotetraploid with a short evolutionary history and limited genetic diversity. To significantly broaden its genetic diversity and create a novel heterotic population for sustainable rapeseed breeding, this study reconstituted the genome of B. napus by replacing it with the subgenomes from 122 accessions of Brassica rapa (Ar Ar ) and 74 accessions of Brassica carinata (Bc Bc Cc Cc ) and developing a novel gene pool of B. napus through five rounds of extensive recurrent selection. When compared with traditional B. napus using SSR markers and high-throughput SNP/Indel markers through genotyping by sequencing, the newly developed gene pool and its homozygous progenies exhibited a large genetic distance, rich allelic diversity, new alleles and exotic allelic introgression across all 19 AC chromosomes. In addition to the abundant genomic variation detected in the AC genome, we also detected considerable introgression from the eight chromosomes of the B genome. Extensive trait variation and some genetic improvements were present from the early recurrent selection to later generations. This novel gene pool produced equally rich phenotypic variation and should be valuable for rapeseed genetic improvement. By reconstituting the genome of B. napus by introducing subgenomic variation within and between the related species using intense selection and recombination, the whole genome could be substantially reorganized. These results serve as an example of the manipulation of the genome of a young allopolyploid and provide insights into its rapid genome evolution affected by interspecific and intraspecific crosses.
Collapse
Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenshan Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yikai Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Lunlin Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yingying Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yongdi Shi
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|