1
|
Thomas WJW, Amas JC, Dolatabadian A, Huang S, Zhang F, Zandberg JD, Neik TX, Edwards D, Batley J. Recent advances in the improvement of genetic resistance against disease in vegetable crops. PLANT PHYSIOLOGY 2024; 196:32-46. [PMID: 38796840 PMCID: PMC11376385 DOI: 10.1093/plphys/kiae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/10/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Affiliation(s)
- William J W Thomas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Junrey C Amas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Aria Dolatabadian
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Shuanglong Huang
- Department of Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Jaco D Zandberg
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Ting Xiang Neik
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore
- NUS Agritech Centre, National University of Singapore, Singapore, 118258, Republic of Singapore
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
- Centre for Applied Bioinformatics, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| |
Collapse
|
2
|
Derbyshire MC, Newman TE, Thomas WJW, Batley J, Edwards D. The complex relationship between disease resistance and yield in crops. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2612-2623. [PMID: 38743906 PMCID: PMC11331782 DOI: 10.1111/pbi.14373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/03/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]
Abstract
In plants, growth and defence are controlled by many molecular pathways that are antagonistic to one another. This results in a 'growth-defence trade-off', where plants temporarily reduce growth in response to pests or diseases. Due to this antagonism, genetic variants that improve resistance often reduce growth and vice versa. Therefore, in natural populations, the most disease resistant individuals are often the slowest growing. In crops, slow growth may translate into a yield penalty, but resistance is essential for protecting yield in the presence of disease. Therefore, plant breeders must balance these traits to ensure optimal yield potential and yield stability. In crops, both qualitative and quantitative disease resistance are often linked with genetic variants that cause yield penalties, but this is not always the case. Furthermore, both crop yield and disease resistance are complex traits influenced by many aspects of the plant's physiology, morphology and environment, and the relationship between the molecular growth-defence trade-off and disease resistance-yield antagonism is not well-understood. In this article, we highlight research from the last 2 years on the molecular mechanistic basis of the antagonism between defence and growth. We then discuss the interaction between disease resistance and crop yield from a breeding perspective, outlining the complexity and nuances of this relationship and where research can aid practical methods for simultaneous improvement of yield potential and disease resistance.
Collapse
Affiliation(s)
- Mark C. Derbyshire
- Centre for Crop and Disease ManagementCurtin UniversityPerthWestern AustraliaAustralia
| | - Toby E. Newman
- Centre for Crop and Disease ManagementCurtin UniversityPerthWestern AustraliaAustralia
| | - William J. W. Thomas
- Centre for Applied Bioinformatics and School of Biological ScienceUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Jacqueline Batley
- Centre for Applied Bioinformatics and School of Biological ScienceUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - David Edwards
- Centre for Applied Bioinformatics and School of Biological ScienceUniversity of Western AustraliaPerthWestern AustraliaAustralia
| |
Collapse
|
3
|
Schreiber M, Jayakodi M, Stein N, Mascher M. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet 2024; 25:563-577. [PMID: 38378816 DOI: 10.1038/s41576-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 02/22/2024]
Abstract
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
Collapse
Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, Marburg, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| |
Collapse
|
4
|
Vasquez-Teuber P, Rouxel T, Mason AS, Soyer JL. Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:192. [PMID: 39052130 PMCID: PMC11272824 DOI: 10.1007/s00122-024-04641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/29/2024] [Indexed: 07/27/2024]
Abstract
Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.
Collapse
Affiliation(s)
- Paula Vasquez-Teuber
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez 595, Chillán, Chile
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France.
| |
Collapse
|
5
|
Ji G, Long Y, Cai G, Wang A, Yan G, Li H, Gao G, Xu K, Huang Q, Chen B, Li L, Li F, Nishio T, Shen J, Wu X. A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2882-2899. [PMID: 38421062 DOI: 10.1093/jxb/erae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.
Collapse
Affiliation(s)
- Gaoxiang Ji
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ying Long
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guangqin Cai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan,China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-0845, Japan
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
6
|
Jiang M, Chen M, Zeng J, Du Z, Xiao J. A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence. FRONTIERS IN PLANT SCIENCE 2024; 15:1371222. [PMID: 38567138 PMCID: PMC10986365 DOI: 10.3389/fpls.2024.1371222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences' repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan's performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.
Collapse
Affiliation(s)
- Meiye Jiang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Meili Chen
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Zhenglin Du
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
7
|
Amas JC, Bayer PE, Hong Tan W, Tirnaz S, Thomas WJW, Edwards D, Batley J. Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2100-2112. [PMID: 37431308 PMCID: PMC10502758 DOI: 10.1111/pbi.14116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/11/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023]
Abstract
Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.
Collapse
Affiliation(s)
- Junrey C. Amas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Wei Hong Tan
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - William J. W. Thomas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Centre for Applied BioinformaticsThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| |
Collapse
|
8
|
Rogo U, Fambrini M, Pugliesi C. Embryo Rescue in Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:3106. [PMID: 37687352 PMCID: PMC10489947 DOI: 10.3390/plants12173106] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023]
Abstract
Embryo rescue (ER) techniques are among the oldest and most successful in vitro tissue culture protocols used with plant species. ER refers to a series of methods that promote the development of an immature or lethal embryo into a viable plant. Intraspecific, interspecific, or intergeneric crosses allow the introgression of important alleles of agricultural interest from wild species, such as resistance or tolerance to abiotic and biotic stresses or morphological traits in crops. However, pre-zygotic and post-zygotic reproductive barriers often present challenges in achieving successful hybridization. Pre-zygotic barriers manifest as incompatibility reactions that hinder pollen germination, pollen tube growth, or penetration into the ovule occurring in various tissues, such as the stigma, style, or ovary. To overcome these barriers, several strategies are employed, including cut-style or graft-on-style techniques, the utilization of mixed pollen from distinct species, placenta pollination, and in vitro ovule pollination. On the other hand, post-zygotic barriers act at different tissues and stages ranging from early embryo development to the subsequent growth and reproduction of the offspring. Many crosses among different genera result in embryo abortion due to the failure of endosperm development. In such cases, ER techniques are needed to rescue these hybrids. ER holds great promise for not only facilitating successful crosses but also for obtaining haploids, doubled haploids, and manipulating the ploidy levels for chromosome engineering by monosomic and disomic addition as well substitution lines. Furthermore, ER can be used to shorten the reproductive cycle and for the propagation of rare plants. Additionally, it has been repeatedly used to study the stages of embryonic development, especially in embryo-lethal mutants. The most widely used ER procedure is the culture of immature embryos taken and placed directly on culture media. In certain cases, the in vitro culture of ovule, ovaries or placentas enables the successful development of young embryos from the zygote stage to maturity.
Collapse
Affiliation(s)
| | | | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (U.R.); (M.F.)
| |
Collapse
|
9
|
Yuan K, Zhao X, Sun W, Yang L, Zhang Y, Wang Y, Ji J, Han F, Fang Z, Lv H. Map-based cloning and CRISPR/Cas9-based editing uncover BoNA1 as the causal gene for the no-anthocyanin-accumulation phenotype in curly kale ( Brassica oleracea var. sabellica). HORTICULTURE RESEARCH 2023; 10:uhad133. [PMID: 37564271 PMCID: PMC10410298 DOI: 10.1093/hr/uhad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/19/2023] [Indexed: 08/12/2023]
Abstract
Brassica oleracea comprises several important vegetable and ornamental crops, including curly kale, ornamental kale, cabbage, broccoli, and others. The accumulation of anthocyanins, important secondary metabolites valuable to human health, in these plants varies widely and is responsible for their pink to dark purple colors. Some curly kale varieties lack anthocyanins, making these plants completely green. The genetic basis of this trait is still unknown. We crossed the curly kale inbred line BK2019 (without anthocyanins) with the cabbage inbred line YL1 (with anthocyanins) and the Chinese kale inbred line TO1000 (with anthocyanins) to generate segregating populations. The no-anthocyanin trait was genetically controlled by a recessive gene, bona1. We generated a linkage map and mapped bona1 to a 256-kb interval on C09. We identified one candidate gene, Bo9g058630, in the target genomic region; this gene is homologous to AT5G42800, which encodes a dihydroflavonol-4-reductase-like (DFR-like) protein in Arabidopsis. In BK2019, a 1-bp insertion was observed in the second exon of Bo9g058630 and directly produced a stop codon. To verify the candidate gene function, CRISPR/Cas9 gene editing technology was applied to knock out Bo9g058630. We generated three bona1 mutants, two of which were completely green with no anthocyanins, confirming that Bo9g058630 corresponds to BoNA1. Different insertion/deletion mutations in BoNA1 exons were found in all six of the other no-anthocyanin kale varieties examined, supporting that independent disruption of BoNA1 resulted in no-anthocyanin varieties of B. oleracea. This study improves the understanding of the regulation mechanism of anthocyanin accumulation in B. oleracea subspecies.
Collapse
Affiliation(s)
- Kaiwen Yuan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinyu Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenru Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Fang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
10
|
Ma X, Zhu M, Liu W, Li J, Liao Y, Liu D, Jin M, Fu C, Wang F. Bulk segregant analysis coupled with transcriptomics and metabolomics revealed key regulators of bacterial leaf blight resistance in rice. BMC PLANT BIOLOGY 2023; 23:332. [PMID: 37349684 DOI: 10.1186/s12870-023-04347-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Bacterial leaf blight (BLB) is a highly destructive disease, causing significant yield losses in rice (Oryza sativa). Genetic variation is contemplated as the most effective measure for inducing resistance in plants. The mutant line T1247 derived from R3550 (BLB susceptible) was highly resistant to BLB. Therefore, by utilizing this valuable source, we employed bulk segregant analysis (BSA) and transcriptome profiling to identify the genetic basis of BLB resistance in T1247. RESULTS The differential subtraction method in BSA identified a quantitative trait locus (QTL) on chromosome 11 spanning a 27-27.45 Mb region with 33 genes and 4 differentially expressed genes (DEGs). Four DEGs (P < 0.01) with three putative candidate genes, OsR498G1120557200, OsR498G1120555700, and OsR498G1120563600,0.01 in the QTL region were identified with specific regulation as a response to BLB inoculation. Moreover, transcriptome profiling identified 37 resistance analogs genes displaying differential regulation. CONCLUSIONS Our study provides a substantial addition to the available information regarding QTLs associated with BLB, and further functional verification of identified candidate genes can broaden the scope of understanding the BLB resistance mechanism in rice.
Collapse
Affiliation(s)
- Xiaozhi Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Manshan Zhu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wuge Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jinhua Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Yilong Liao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Mengya Jin
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Chongyun Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China.
- Guangdong Rice Engineering Laboratory, Guangzhou, China.
| | - Feng Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China.
- Guangdong Rice Engineering Laboratory, Guangzhou, China.
| |
Collapse
|
11
|
Sun Y, Kou DR, Li Y, Ni JP, Wang J, Zhang YM, Wang QN, Jiang B, Wang X, Sun YX, Xu XT, Tan XJ, Zhang YJ, Kong XD. Pan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection. BMC Genomics 2023; 24:332. [PMID: 37322453 DOI: 10.1186/s12864-023-09443-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.
Collapse
Affiliation(s)
- Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
| | - Dou-Rong Kou
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yan Li
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | | | - Jing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yong-Mei Zhang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Qing-Nan Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Bin Jiang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xu Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yue-Xin Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xin-Tong Xu
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Xiao-Juan Tan
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Yong-Jun Zhang
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | | |
Collapse
|
12
|
Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. TRENDS IN PLANT SCIENCE 2023; 28:685-697. [PMID: 36764870 DOI: 10.1016/j.tplants.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 05/13/2023]
Abstract
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.
Collapse
Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Irwin Goldman
- Department of Horticulture, College of Agricultural and Life Sciences, University of Wisconsin Madison, WI 53706, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SE 23053, Sweden.
| |
Collapse
|
13
|
Huang B, Yan H, Sun M, Jin Y. Novel discovery in roles of structural variations and RWP-RK transcription factors in heat tolerance for pearl millet. STRESS BIOLOGY 2023; 3:12. [PMID: 37676357 PMCID: PMC10442032 DOI: 10.1007/s44154-023-00092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/03/2023] [Indexed: 09/08/2023]
Abstract
Global warming adversely affects crop production worldwide. Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants. However, the roles of structural variations (SVs) in heat stress tolerance remain unclear. In a recent article, Yan et al. (Nat Genet 1-12, 2023) constructed the first pan-genome of pearl millet (Pennisetum glaucum) and identified key SVs linked to genes involved in regulating plant tolerance to heat stress for an important crop with a superior ability to thrive in extremely hot and arid climates. Through multi-omics analyses integrating by pan-genomics, comparative genomics, transcriptomics, population genetics and and molecular biological technologies, they found RWP-RK transcription factors cooperating with endoplasmic reticulum-related genes play key roles in heat tolerance in pearl millet. The results in this paper provided novel insights to advance the understanding of the genetic and genomic basis of heat tolerance and an exceptional resource for molecular breeding to improve heat tolerance in pearl millet and other crops.
Collapse
Affiliation(s)
- Bingru Huang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
14
|
Resistance strategies for defense against Albugo candida causing white rust disease. Microbiol Res 2023; 270:127317. [PMID: 36805163 DOI: 10.1016/j.micres.2023.127317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/12/2022] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Albugo candida, the causal organism of white rust, is an oomycete obligate pathogen infecting crops of Brassicaceae family occurred on aerial part, including vegetable and oilseed crops at all growth stages. The disease expression is characterized by local infection appearing on the abaxial region developing white or creamy yellow blister (sori) on leaves and systemic infections cause hypertrophy and hyperplasia leading to stag-head of reproductive organ. To overcome this problem, several disease management strategies like fungicide treatments were used in the field and disease-resistant varieties have also been developed using conventional and molecular breeding. Due to high variability among A. candida isolates, there is no single approach available to understand the diverse spectrum of disease symptoms. In absence of resistance sources against pathogen, repetitive cultivation of genetically-similar varieties locally tends to attract oomycete pathogen causing heavy yield losses. In the present review, a deep insight into the underlying role of the non-host resistance (NHR) defence mechanism available in plants, and the strategies to exploit available gene pools from plant species that are non-host to A. candida could serve as novel sources of resistance. This work summaries the current knowledge pertaining to the resistance sources available in non-host germ plasm, the understanding of defence mechanisms and the advance strategies covers molecular, biochemical and nature-based solutions in protecting Brassica crops from white rust disease.
Collapse
|
15
|
Xu L, Wang Y, Dong J, Zhang W, Tang M, Zhang W, Wang K, Chen Y, Zhang X, He Q, Zhang X, Wang K, Wang L, Ma Y, Xia K, Liu L. A chromosome-level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:990-1004. [PMID: 36648398 PMCID: PMC10106849 DOI: 10.1111/pbi.14011] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 05/04/2023]
Abstract
High-quality radish (Raphanus sativus) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly hampered functional genomics research and genome-assisted breeding. Here, using a NAU-LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi-C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein-coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole-genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus. By comparing against the existing Xin-li-mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647-bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3, resulting into its low promoter activity and late-bolting phenotype of NAU-LB cultivar. Importantly, introgression of this 647-bp insertion allele, RsVRN1In-536 , into early-bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late-bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome-guided breeding and improvement in radish.
Collapse
Affiliation(s)
- Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Weilan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- School of Life SciencesNantong UniversityNantongChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Xiaoli Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Qing He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Xinyu Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lun Wang
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Yinbo Ma
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Kai Xia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| |
Collapse
|
16
|
Yamamoto M, Ishii T, Ogura M, Akanuma T, Zhu XY, Kitashiba H. S haplotype collection in Brassicaceae crops-an updated list of S haplotypes. BREEDING SCIENCE 2023; 73:132-145. [PMID: 37404351 PMCID: PMC10316313 DOI: 10.1270/jsbbs.22091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/07/2023] [Indexed: 07/06/2023]
Abstract
Self-incompatibility is the system that inhibits pollen germination and pollen tube growth by self-pollen. This trait is important for the breeding of Brassica and Raphanus species. In these species, self-incompatibility is governed by the S locus, which contains three linked genes (a set called the S haplotype), i.e., S-locus receptor kinase, S-locus cysteine-rich protein/S-locus protein 11, and S-locus glycoprotein. A large number of S haplotypes have been identified in Brassica oleracea, B. rapa, and Raphanus sativus to date, and the nucleotide sequences of their many alleles have also been registered. In this state, it is important to avoid confusion between S haplotypes, i.e., an identical S haplotype with different names and a different S haplotype with an identical S haplotype number. To mitigate this issue, we herein constructed a list of S haplotypes that are easily accessible to the latest nucleotide sequences of S-haplotype genes, together with revisions to and an update of S haplotype information. Furthermore, the histories of the S-haplotype collection in the three species are reviewed, the importance of the collection of S haplotypes as a genetic resource is discussed, and the management of information on S haplotypes is proposed.
Collapse
Affiliation(s)
- Masaya Yamamoto
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Tomoko Ishii
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Marina Ogura
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Takashi Akanuma
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Xing-Yu Zhu
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba Aobaku, Sendai, Miyagi 980-8572, Japan
| |
Collapse
|
17
|
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
|
18
|
Zhang X, Zhang S, Liu Z, Zhao W, Zhang X, Song J, Jia H, Yang W, Ma Y, Wang Y, Xie K, Budahn H, Wang H. Characterization and acceleration of genome shuffling and ploidy reduction in synthetic allopolyploids by genome sequencing and editing. Nucleic Acids Res 2022; 51:198-217. [PMID: 36583364 PMCID: PMC9841408 DOI: 10.1093/nar/gkac1209] [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: 10/22/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022] Open
Abstract
Polyploidy and the subsequent ploidy reduction and genome shuffling are the major driving forces of genome evolution. Here, we revealed short-term allopolyploid genome evolution by sequencing a synthetic intergeneric hybrid (Raphanobrassica, RRCC). In this allotetraploid, the genome deletion was quick, while rearrangement was slow. The core and high-frequency genes tended to be retained while the specific and low-frequency genes tended to be deleted in the hybrid. The large-fragment deletions were enriched in the heterochromatin region and probably derived from chromosome breaks. The intergeneric translocations were primarily of short fragments dependent on homoeology, indicating a gene conversion origin. To accelerate genome shuffling, we developed an efficient genome editing platform for Raphanobrassica. By editing Fanconi Anemia Complementation Group M (FANCM) genes, homoeologous recombination, chromosome deletion and secondary meiosis with additional ploidy reduction were accelerated. FANCM was shown to be a checkpoint of meiosis and controller of ploidy stability. By simultaneously editing FLIP genes, gene conversion was precisely introduced, and mosaic genes were produced around the target site. This intergeneric hybrid and genome editing platform not only provides models that facilitate experimental evolution research by speeding up genome shuffling and conversion but also accelerates plant breeding by enhancing intergeneric genetic exchange and creating new genes.
Collapse
Affiliation(s)
- Xiaohui Zhang
- To whom correspondence should be addressed. Tel: +86 10 82105947; Fax: +86 10 62174123;
| | | | | | - Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoxue Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huixia Jia
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenlong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan); College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Holger Budahn
- Institute for Breeding Research on Horticultural Crops, Julius-Kuehn-Institute, Federal Research Centre for Cultivated Plants, D-06484 Quedlinburg, Germany
| | - Haiping Wang
- Correspondence may also be addressed to Haiping Wang. Tel: +86 10 82105942; Fax: +86 10 62174123;
| |
Collapse
|
19
|
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
|
20
|
Zandberg JD, Fernandez CT, Danilevicz MF, Thomas WJW, Edwards D, Batley J. The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics. PLANTS (BASEL, SWITZERLAND) 2022; 11:2740. [PMID: 36297764 PMCID: PMC9610009 DOI: 10.3390/plants11202740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.
Collapse
Affiliation(s)
- Jaco D. Zandberg
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | - Monica F. Danilevicz
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - William J. W. Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- Center for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
21
|
Naqvi RZ, Siddiqui HA, Mahmood MA, Najeebullah S, Ehsan A, Azhar M, Farooq M, Amin I, Asad S, Mukhtar Z, Mansoor S, Asif M. Smart breeding approaches in post-genomics era for developing climate-resilient food crops. FRONTIERS IN PLANT SCIENCE 2022; 13:972164. [PMID: 36186056 PMCID: PMC9523482 DOI: 10.3389/fpls.2022.972164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
Collapse
|
22
|
Shaw RK, Shen Y, Yu H, Sheng X, Wang J, Gu H. Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L. Int J Mol Sci 2022; 23:9280. [PMID: 36012543 PMCID: PMC9409056 DOI: 10.3390/ijms23169280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/04/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.
Collapse
Affiliation(s)
| | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| |
Collapse
|
23
|
Li W, Lu J, Yang C, Xia S. Identification of receptor-like proteins induced by Sclerotinia sclerotiorum in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:944763. [PMID: 36061811 PMCID: PMC9429810 DOI: 10.3389/fpls.2022.944763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Heightening the resistance of plants to microbial infection is a widely concerned issue, especially for economical crops. Receptor-like proteins (RLPs), typically with tandem leucine-rich repeats (LRRs) domain, play a crucial role in mediating immune activation, being an indispensable constituent in the first layer of defense. Based on an analysis of orthologs among Brassica rapa, Brassica oleracea, and Brassica napus using Arabidopsis thaliana RLPs as a reference framework, we found that compared to A. thaliana, there were some obvious evolutionary diversities of RLPs among the three Brassicaceae species. BnRLP encoding genes were unevenly distributed on chromosomes, mainly on chrA01, chrA04, chrC03, chrC04, and chrC06. The orthologs of five AtRLPs (AtRLP3, AtRLP10, AtRLP17, AtRLP44, and AtRLP51) were highly conserved, but retrenchment and functional centralization occurred in Brassicaceae RLPs during evolution. The RLP proteins were clustered into 13 subgroups. Ten BnRLPs presented expression specificity between R and S when elicited by Sclerotinia sclerotiorum, which might be fabulous candidates for S. sclerotiorum resistance research.
Collapse
Affiliation(s)
- Wei Li
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- College of Life Science, Chongqing Normal University, Chongqing, China
| | - Junxing Lu
- College of Life Science, Chongqing Normal University, Chongqing, China
| | - Chenghuizi Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| |
Collapse
|
24
|
Vining KJ, Pandelova I, Lange I, Parrish AN, Lefors A, Kronmiller B, Liachko I, Kronenberg Z, Srividya N, Lange BM. Chromosome-level genome assembly of Mentha longifolia L. reveals gene organization underlying disease resistance and essential oil traits. G3 GENES|GENOMES|GENETICS 2022; 12:6584825. [PMID: 35551385 PMCID: PMC9339296 DOI: 10.1093/g3journal/jkac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Mentha longifolia (L.) Huds., a wild, diploid mint species, has been developed as a model for mint genetic and genomic research to aid breeding efforts that target Verticillium wilt disease resistance and essential oil monoterpene composition. Here, we present a near-complete, chromosome-scale mint genome assembly for M. longifolia USDA accession CMEN 585. This new assembly is an update of a previously published genome draft, with dramatic improvements. A total of 42,107 protein-coding genes were annotated and placed on 12 chromosomal scaffolds. One hundred fifty-three genes contained conserved sequence domains consistent with nucleotide binding site-leucine-rich-repeat plant disease resistance genes. Homologs of genes implicated in Verticillium wilt resistance in other plant species were also identified. Multiple paralogs of genes putatively involved in p-menthane monoterpenoid biosynthesis were identified and several cases of gene clustering documented. Heterologous expression of candidate genes, purification of recombinant target proteins, and subsequent enzyme assays allowed us to identify the genes underlying the pathway that leads to the most abundant monoterpenoid volatiles. The bioinformatic and functional analyses presented here are laying the groundwork for using marker-assisted selection in improving disease resistance and essential oil traits in mints.
Collapse
Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University , Corvallis, OR 97331, USA
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University , Corvallis, OR 97331, USA
| | - Iris Lange
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Andrew Lefors
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Brent Kronmiller
- Center for Quantitative Life Sciences, Oregon State University , Corvallis, OR 97331, USA
| | | | | | - Narayanan Srividya
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - B Markus Lange
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| |
Collapse
|
25
|
Inturrisi F, Bayer PE, Cantila AY, Tirnaz S, Edwards D, Batley J. In silico integration of disease resistance QTL, genes and markers with the Brassica juncea physical map. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:37. [PMID: 37309382 PMCID: PMC10248627 DOI: 10.1007/s11032-022-01309-5] [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: 12/30/2021] [Accepted: 06/09/2022] [Indexed: 06/14/2023]
Abstract
Brassica juncea (AABB), Indian mustard, is a source of disease resistance genes for a wide range of pathogens. The availability of reference genome sequences for B. juncea has made it possible to characterise the genomic structure and distribution of these disease resistance genes. Potentially functional disease resistance genes can be identified by co-localization with genetically mapped disease resistance quantitative trait loci (QTL). Here we identify and characterise disease resistance gene analogs (RGAs), including nucleotide-binding site-leucine-rich repeat (NLR), receptor-like kinase (RLK) and receptor-like protein (RLP) classes, and investigate their association with disease resistance QTL intervals. The molecular genetic marker sequences for four white rust (Albugo candida) disease resistance QTL, six blackleg (Leptosphaeria maculans) disease resistance QTL and BjCHI1, a gene cloned from B. juncea for hypocotyl rot disease, were extracted from previously published studies and used to compare with candidate RGAs. Our results highlight the complications for the identification of functional resistance genes, including the duplicated appearance of genetic markers for several resistance loci, including Ac2(t), AcB1-A4.1, AcB1-A5.1, Rlm6 and PhR2 in both the A and B genomes, due to the presence of homoeologous regions. Furthermore, the white rust loci, Ac2(t) and AcB1-A4.1, mapped to the same position on chromosome A04 and may be different alleles of the same gene. Despite these challenges, a total of nine candidate genomic regions hosting 14 RLPs, 28 NLRs and 115 RLKs were identified. This study facilitates the mapping and cloning of functional resistance genes for applications in crop improvement programs. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01309-5.
Collapse
Affiliation(s)
- Fabian Inturrisi
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Aldrin Y. Cantila
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA Australia
| |
Collapse
|
26
|
Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. BIOLOGY 2022; 11:biology11060821. [PMID: 35741342 PMCID: PMC9220128 DOI: 10.3390/biology11060821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Developing cultivars with resistance genes (R genes) is an effective strategy to support high yield and quality in Brassica crops. The availability of clone R gene and genomic sequences in Brassica species and Arabidopsis thaliana provide the opportunity to compare genomic regions and survey R genes across genomic databases. In this paper, we aim to identify genes related to cloned genes through sequence identity, providing a repertoire of species-wide related R genes in Brassica crops. The comprehensive list of candidate R genes can be used as a reference for functional analysis. Abstract Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
Collapse
|
27
|
Sun Y, Wang J, Li Y, Jiang B, Wang X, Xu WH, Wang YQ, Zhang PT, Zhang YJ, Kong XD. Pan-Genome Analysis Reveals the Abundant Gene Presence/Absence Variations Among Different Varieties of Melon and Their Influence on Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:835496. [PMID: 35401600 PMCID: PMC8990847 DOI: 10.3389/fpls.2022.835496] [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: 12/14/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Melon (Cucumismelo L.) is an important vegetable crop that has been subjected to domestication and improvement. Several varieties of melons with diverse phenotypes have been produced. In this study, we constructed a melon pan-genome based on 297 accessions comprising 168 Mb novel sequences and 4,325 novel genes. Based on the results, there were abundant genetic variations among different melon groups, including 364 unfavorable genes in the IMP_A vs. LDR_A group, 46 favorable genes, and 295 unfavorable genes in the IMP_M vs. LDR_M group. The distribution of 709 resistance gene analogs (RGAs) was also characterized across 297 melon lines, of which 603 were core genes. Further, 106 genes were found to be variable, 55 of which were absent in the reference melon genome. Using gene presence/absence variation (PAV)-based genome-wide association analysis (GWAS), 13 gene PAVs associated with fruit length, fruit shape, and fruit width were identified, four of which were located in pan-genome additional contigs.
Collapse
Affiliation(s)
- Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yan Li
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Jiang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Xu Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Wen-Hui Xu
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yu-Qing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Pei-Tao Zhang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yong-Jun Zhang
- Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | |
Collapse
|
28
|
Rijzaani H, Bayer PE, Rouard M, Doležel J, Batley J, Edwards D. The pangenome of banana highlights differences between genera and genomes. THE PLANT GENOME 2022; 15:e20100. [PMID: 34227250 DOI: 10.1002/tpg2.20100] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 05/19/2023]
Abstract
Banana (Musaceae family) has a complex genetic history and includes a genus Musa with a variety of cultivated clones with edible fruits, Ensete species that are grown for their edible corm, and monospecific Musella whose generic status has been questioned. The most commonly exported banana cultivars belong to Cavendish, a subgroup of Musa triploid cultivars, which is under threat by fungal pathogens, though there are also related species M. balbisiana Colla (B genome), M. textilis Née (T genome), and M. schizocarpa N. W. Simmonds (S genome), along with hybrids of these genomes, which potentially host genes of agronomic interest. Here we present the first cross-genus pangenome of banana, which contains representatives of the Musa and Ensete genera. Clusters based on gene presence-absence variation (PAV) clearly separate Musa and Ensete, while Musa is split further based on species. These results present the first pangenome study across genus boundaries and identifies genes that differentiate between Musaceae species, information that may support breeding programs in these crops.
Collapse
Affiliation(s)
- Habib Rijzaani
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- Indonesian Agency for Agricultural Research and Development, Jakarta, Indonesia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| |
Collapse
|
29
|
Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
| |
Collapse
|
30
|
Tay Fernandez CG, Nestor BJ, Danilevicz MF, Marsh JI, Petereit J, Bayer PE, Batley J, Edwards D. Expanding Gene-Editing Potential in Crop Improvement with Pangenomes. Int J Mol Sci 2022; 23:ijms23042276. [PMID: 35216392 PMCID: PMC8879065 DOI: 10.3390/ijms23042276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.
Collapse
|
31
|
Hu H, Scheben A, Verpaalen B, Tirnaz S, Bayer PE, Hodel RGJ, Batley J, Soltis DE, Soltis PS, Edwards D. Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. THE NEW PHYTOLOGIST 2022; 233:1548-1555. [PMID: 34328223 PMCID: PMC9292397 DOI: 10.1111/nph.17658] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/26/2021] [Indexed: 05/03/2023]
Affiliation(s)
- Haifei Hu
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Armin Scheben
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring Harbor,NY11724USA
| | - Brent Verpaalen
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Richard G. J. Hodel
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20013‐7012USA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Douglas E. Soltis
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- The Genetics InstituteUniversity of FloridaGainesvilleFL32610USA
- The Biodiversity InstituteUniversity of FloridaGainesvilleFL32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- The Genetics InstituteUniversity of FloridaGainesvilleFL32610USA
- The Biodiversity InstituteUniversity of FloridaGainesvilleFL32611USA
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| |
Collapse
|
32
|
Liang Y, Huang Y, Chen K, Kong X, Li M. Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation. BMC PLANT BIOLOGY 2022; 22:21. [PMID: 34996379 PMCID: PMC8740461 DOI: 10.1186/s12870-021-03408-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/15/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome. RESULTS In the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL). CONCLUSION The identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus.
Collapse
Affiliation(s)
- Yu Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China.
| | - Yang Huang
- School of Mechanical and Electrical Engineering, Guilin University of Electronic Technology, Guilin, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangdong Kong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, College of Life Science, Guangxi Normal University, Guilin, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
33
|
Tay Fernandez CG, Marsh JI, Nestor BJ, Gill M, Golicz AA, Bayer PE, Edwards D. An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth. Methods Mol Biol 2022; 2512:73-80. [PMID: 35818000 DOI: 10.1007/978-1-0716-2429-6_5] [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] [Indexed: 06/15/2023]
Abstract
Presence-absence variants (PAV) are genomic regions present in some individuals of a species, but not others. PAVs have been shown to contribute to genomic diversity, especially in bacteria and plants. These structural variations have been linked to traits and can be used to track a species' evolutionary history. PAVs are usually called by aligning short read sequence data from one or more individuals to a reference genome or pangenome assembly, and then comparing coverage. Regions where reads do not align define absence in that individual, and the regions are classified as PAVs. The method below details how to align sequence reads to a reference and how to use the sequencing-coverage calculator Mosdepth to identify PAVs and construct a PAV table for use in downstream comparative genome analysis.
Collapse
Affiliation(s)
- Cassandria G Tay Fernandez
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Jacob I Marsh
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Benjamin J Nestor
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mitchell Gill
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Agnieszka A Golicz
- Department of Plant Breeding, Justus Liebig University Gießen, Gießen, Germany
| | - Philipp E Bayer
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - David Edwards
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia.
| |
Collapse
|
34
|
Tay Fernandez C. Making a Pangenome Using the Iterative Mapping Approach. Methods Mol Biol 2022; 2443:259-271. [PMID: 35037211 DOI: 10.1007/978-1-0716-2067-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.
Collapse
|
35
|
Zhang X, Liu T, Wang J, Wang P, Qiu Y, Zhao W, Pang S, Li X, Wang H, Song J, Zhang W, Yang W, Sun Y, Li X. Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes. MOLECULAR PLANT 2021; 14:2032-2055. [PMID: 34384905 DOI: 10.1016/j.molp.2021.08.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/27/2021] [Accepted: 08/05/2021] [Indexed: 05/22/2023]
Abstract
Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.
Collapse
Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tongjin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China
| | - Jinglei Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Peng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Pang
- Berry Genomics Corporation, Beijing 100015, China
| | - Xiaoman Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenlin Zhang
- Berry Genomics Corporation, Beijing 100015, China
| | - Wenlong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuyan Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
36
|
Shaw RK, Shen Y, Wang J, Sheng X, Zhao Z, Yu H, Gu H. Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L. FRONTIERS IN PLANT SCIENCE 2021; 12:742553. [PMID: 34938304 PMCID: PMC8687090 DOI: 10.3389/fpls.2021.742553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Brassica oleracea is one of the most important species of the Brassicaceae family encompassing several economically important vegetables produced and consumed worldwide. But its sustainability is challenged by a range of pathogens, among which black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the most serious and destructive seed borne bacterial disease, causing huge yield losses. Host-plant resistance could act as the most effective and efficient solution to curb black rot disease for sustainable production of B. oleracea. Recently, 'omics' technologies have emerged as promising tools to understand the host-pathogen interactions, thereby gaining a deeper insight into the resistance mechanisms. In this review, we have summarized the recent achievements made in the emerging omics technologies to tackle the black rot challenge in B. oleracea. With an integrated approach of the omics technologies such as genomics, proteomics, transcriptomics, and metabolomics, it would allow better understanding of the complex molecular mechanisms underlying black rot resistance. Due to the availability of sequencing data, genomics and transcriptomics have progressed as expected for black rot resistance, however, other omics approaches like proteomics and metabolomics are lagging behind, necessitating a holistic and targeted approach to address the complex questions of Xcc-Brassica interactions. Genomic studies revealed that the black rot resistance is a complex trait and is mostly controlled by quantitative trait locus (QTL) with minor effects. Transcriptomic analysis divulged the genes related to photosynthesis, glucosinolate biosynthesis and catabolism, phenylpropanoid biosynthesis pathway, ROS scavenging, calcium signalling, hormonal synthesis and signalling pathway are being differentially expressed upon Xcc infection. Comparative proteomic analysis in relation to susceptible and/or resistance interactions with Xcc identified the involvement of proteins related to photosynthesis, protein biosynthesis, processing and degradation, energy metabolism, innate immunity, redox homeostasis, and defence response and signalling pathways in Xcc-Brassica interaction. Specifically, most of the studies focused on the regulation of the photosynthesis-related proteins as a resistance response in both early and later stages of infection. Metabolomic studies suggested that glucosinolates (GSLs), especially aliphatic and indolic GSLs, its subsequent hydrolysis products, and defensive metabolites synthesized by jasmonic acid (JA)-mediated phenylpropanoid biosynthesis pathway are involved in disease resistance mechanisms against Xcc in Brassica species. Multi-omics analysis showed that JA signalling pathway is regulating resistance against hemibiotrophic pathogen like Xcc. So, the bonhomie between omics technologies and plant breeding is going to trigger major breakthroughs in the field of crop improvement by developing superior cultivars with broad-spectrum resistance. If multi-omics tools are implemented at the right scale, we may be able to achieve the maximum benefits from the minimum. In this review, we have also discussed the challenges, future prospects, and the way forward in the application of omics technologies to accelerate the breeding of B. oleracea for disease resistance. A deeper insight about the current knowledge on omics can offer promising results in the breeding of high-quality disease-resistant crops.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
37
|
Hufnagel B, Soriano A, Taylor J, Divol F, Kroc M, Sanders H, Yeheyis L, Nelson M, Péret B. Pangenome of white lupin provides insights into the diversity of the species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2532-2543. [PMID: 34346542 PMCID: PMC8633493 DOI: 10.1111/pbi.13678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/07/2021] [Accepted: 07/22/2021] [Indexed: 05/21/2023]
Abstract
White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization of genomic diversity is still missing. Here, we report the genome sequencing of 39 accessions that were used to establish a white lupin pangenome. We defined 32 068 core genes that are present in all individuals and 14 822 that are absent in some and may represent a gene pool for breeding for improved productivity, grain quality, and stress adaptation. We used this new pangenome resource to identify candidate genes for alkaloid synthesis, a key grain quality trait. The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability within this crop. Thus, this pangenome resource is an important step towards the effective and efficient genetic improvement of white lupin to help meet the rapidly growing demand for plant protein sources for human and animal consumption.
Collapse
Affiliation(s)
- Bárbara Hufnagel
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
- Present address:
CIRADUMR AGAP InstitutSEAPAG TeamPetit‐BourgGuadeloupeF‐97170French West Indies
| | | | | | - Fanchon Divol
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
| | - Magdalena Kroc
- Institute of Plant Genetics Polish Academy of SciencesPoznanPoland
| | | | | | | | - Benjamin Péret
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
| |
Collapse
|
38
|
Degrave A, Wagner M, George P, Coudard L, Pinochet X, Ermel M, Gay EJ, Fudal I, Moreno‐Rico O, Rouxel T, Balesdent M. A new avirulence gene of Leptosphaeria maculans, AvrLm14, identifies a resistance source in American broccoli (Brassica oleracea) genotypes. MOLECULAR PLANT PATHOLOGY 2021; 22:1599-1612. [PMID: 34467616 PMCID: PMC8578820 DOI: 10.1111/mpp.13131] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 05/19/2023]
Abstract
In many cultivated crops, sources of resistance to diseases are sparse and rely on introgression from wild relatives. Agricultural crops often are allopolyploids resulting from interspecific crosses between related species, which are sources of diversity for resistance genes. This is the case for Brassica napus (oilseed rape, canola), an interspecific hybrid between Brassica rapa (turnip) and Brassica oleracea (cabbage). B. napus has a narrow genetic basis and few effective resistance genes against stem canker (blackleg) disease, caused by the fungus Leptosphaeria maculans, are currently available. B. rapa diversity has proven to be a valuable source of resistance (Rlm, LepR) genes, while B. oleracea genotypes were mostly considered susceptible. Here we identified a new resistance source in B. oleracea genotypes from America, potentially effective against French L. maculans isolates under both controlled and field conditions. Genetic analysis of fungal avirulence and subsequent cloning and validation identified a new avirulence gene termed AvrLm14 and suggested a typical gene-for-gene interaction between AvrLm14 and the postulated Rlm14 gene. AvrLm14 shares all the usual characteristics of L. maculans avirulence genes: it is hosted in a genomic region enriched in transposable elements and heterochromatin marks H3K9me3, its expression is repressed during vegetative growth but shows a strong overexpression 5-9 days following cotyledon infection, and it encodes a small secreted protein enriched in cysteine residues with few matches in databases. Similar to the previously cloned AvrLm10-A, AvrLm14 contributes to reduce lesion size on susceptible cotyledons, pointing to a complex interplay between effectors promoting or reducing lesion development.
Collapse
Affiliation(s)
| | - Marine Wagner
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | | | - Laurent Coudard
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | - Xavier Pinochet
- TERRES INOVIA, campus INRA Agro ParisTechThiverval‐GrignonFrance
| | - Magali Ermel
- INRAE, Institut Agro, Univ Rennes, IGEPPLe RheuFrance
| | - Elise J. Gay
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | - Isabelle Fudal
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | | | - Thierry Rouxel
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | | |
Collapse
|
39
|
Bayer PE, Scheben A, Golicz AA, Yuan Y, Faure S, Lee H, Chawla HS, Anderson R, Bancroft I, Raman H, Lim YP, Robbens S, Jiang L, Liu S, Barker MS, Schranz ME, Wang X, King GJ, Pires JC, Chalhoub B, Snowdon RJ, Batley J, Edwards D. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2488-2500. [PMID: 34310022 PMCID: PMC8633514 DOI: 10.1111/pbi.13674] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/11/2021] [Accepted: 07/20/2021] [Indexed: 05/26/2023]
Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
Collapse
Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Armin Scheben
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVICAustralia
| | - Yuxuan Yuan
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - HueyTyng Lee
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Harmeet Singh Chawla
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Robyn Anderson
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural Institute, PMBWagga WaggaNSWAustralia
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeonSouth Korea
| | | | - Lixi Jiang
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Shengyi Liu
- Chinese Academy of Agricultural SciencesOil Crops Research InstituteWuhanChina
| | - Michael S. Barker
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - M. Eric Schranz
- Biosystematics GroupWageningen University and Research CenterWageningenThe Netherlands
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences (IVF, CAAS)BeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - J. Chris Pires
- Division of Biological SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Boulos Chalhoub
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| |
Collapse
|
40
|
Yuan Y, Bayer PE, Batley J, Edwards D. Current status of structural variation studies in plants. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2153-2163. [PMID: 34101329 PMCID: PMC8541774 DOI: 10.1111/pbi.13646] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 05/23/2023]
Abstract
Structural variations (SVs) including gene presence/absence variations and copy number variations are a common feature of genomes in plants and, together with single nucleotide polymorphisms and epigenetic differences, are responsible for the heritable phenotypic diversity observed within and between species. Understanding the contribution of SVs to plant phenotypic variation is important for plant breeders to assist in producing improved varieties. The low resolution of early genetic technologies and inefficient methods have previously limited our understanding of SVs in plants. However, with the rapid expansion in genomic technologies, it is possible to assess SVs with an ever-greater resolution and accuracy. Here, we review the current status of SV studies in plants, examine the roles that SVs play in phenotypic traits, compare current technologies and assess future challenges for SV studies.
Collapse
Affiliation(s)
- Yuxuan Yuan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
- School of Life Sciences and State Key Laboratory for AgrobiotechnologyThe Chinese University of Hong KongHong Kong SARChina
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| |
Collapse
|
41
|
Amas J, Anderson R, Edwards D, Cowling W, Batley J. Status and advances in mining for blackleg (Leptosphaeria maculans) quantitative resistance (QR) in oilseed rape (Brassica napus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3123-3145. [PMID: 34104999 PMCID: PMC8440254 DOI: 10.1007/s00122-021-03877-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/29/2021] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Quantitative resistance (QR) loci discovered through genetic and genomic analyses are abundant in the Brassica napus genome, providing an opportunity for their utilization in enhancing blackleg resistance. Quantitative resistance (QR) has long been utilized to manage blackleg in Brassica napus (canola, oilseed rape), even before major resistance genes (R-genes) were extensively explored in breeding programmes. In contrast to R-gene-mediated qualitative resistance, QR reduces blackleg symptoms rather than completely eliminating the disease. As a polygenic trait, QR is controlled by numerous genes with modest effects, which exerts less pressure on the pathogen to evolve; hence, its effectiveness is more durable compared to R-gene-mediated resistance. Furthermore, combining QR with major R-genes has been shown to enhance resistance against diseases in important crops, including oilseed rape. For these reasons, there has been a renewed interest among breeders in utilizing QR in crop improvement. However, the mechanisms governing QR are largely unknown, limiting its deployment. Advances in genomics are facilitating the dissection of the genetic and molecular underpinnings of QR, resulting in the discovery of several loci and genes that can be potentially deployed to enhance blackleg resistance. Here, we summarize the efforts undertaken to identify blackleg QR loci in oilseed rape using linkage and association analysis. We update the knowledge on the possible mechanisms governing QR and the advances in searching for the underlying genes. Lastly, we lay out strategies to accelerate the genetic improvement of blackleg QR in oilseed rape using improved phenotyping approaches and genomic prediction tools.
Collapse
Affiliation(s)
- Junrey Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - Robyn Anderson
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| | - Wallace Cowling
- School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001 Australia
| |
Collapse
|
42
|
Skidmore ZL, Campbell KM, Cotto KC, Griffith M, Griffith OL. Exploring the Genomic Landscape of Cancer Patient Cohorts with GenVisR. Curr Protoc 2021; 1:e252. [PMID: 34506690 PMCID: PMC8439545 DOI: 10.1002/cpz1.252] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The creation of visualizations to interpret genomics data remains an important aspect of data science within computational biology. The GenVisR Bioconductor package was created to lower the entry point for publication-quality graphics and has remained a popular suite of tools within this domain. GenVisR supports visualizations covering a breadth of topics including functions to produce visual summaries of copy-number alterations, somatic variants, sequence quality metrics, and more. Recently, the GenVisR package has undergone significant updates to increase performance and functionality. To demonstrate the utility of GenVisR, we present protocols for use of the updated Waterfall() function to create a customizable Oncoprint-style plot of the mutational landscape of a tumor cohort. We explain the basics of installation, data import, configuration, plotting, clinical annotation, and customization. A companion online workshop describing the GenVisR library, Waterfall() function, and other genomic visualization tools is available at genviz.org. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generating a Waterfall() plot from original mutation data Basic Protocol 2: Adding clinical data to a Waterfall() plot Basic Protocol 3: Customizing mutation burden in Waterfall() plots Basic Protocol 4: Brief exploration of customizable options Support Protocol 1: Installing GenVisR.
Collapse
Affiliation(s)
- Zachary L. Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Katie M. Campbell
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Kelsy C. Cotto
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
| | - Obi L. Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO, USA
| |
Collapse
|
43
|
Kahlon PS, Stam R. Polymorphisms in plants to restrict losses to pathogens: From gene family expansions to complex network evolution. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102040. [PMID: 33882435 DOI: 10.1016/j.pbi.2021.102040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Genetic polymorphisms are the basis of the natural diversity seen in all life on earth, also in plant-pathogen interactions. Initially, studies on plant-pathogen interaction focused on reporting phenotypic variation in resistance properties and on the identification of underlying major genes. Nowadays, the field of plant-pathogen interactions is moving from focusing on families of single dominant genes involved in gene-for-gene interactions to an understanding of the plant immune system in the context of a much more complex signaling network and quantitative resistance. Simultaneously, studies on pathosystems from the wild and genome analyses advanced, revealing tremendous variation in natural plant populations. It is now imperative to place studies on genetic diversity and evolution of plant-pathogen interactions in the appropriate molecular biological, as well as evolutionary, context.
Collapse
Affiliation(s)
- Parvinderdeep S Kahlon
- TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Remco Stam
- TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany.
| |
Collapse
|
44
|
Razzaq A, Kaur P, Akhter N, Wani SH, Saleem F. Next-Generation Breeding Strategies for Climate-Ready Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:620420. [PMID: 34367194 PMCID: PMC8336580 DOI: 10.3389/fpls.2021.620420] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Climate change is a threat to global food security due to the reduction of crop productivity around the globe. Food security is a matter of concern for stakeholders and policymakers as the global population is predicted to bypass 10 billion in the coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations in microbiome applications, and exploiting the natural variations in underutilized crops is an excellent way forward to fulfill future food requirements. In this review, we describe the next-generation breeding tools that can be used to increase crop production by developing climate-resilient superior genotypes to cope with the future challenges of global food security. Recent innovations in genomic-assisted breeding (GAB) strategies allow the construction of highly annotated crop pan-genomes to give a snapshot of the full landscape of genetic diversity (GD) and recapture the lost gene repertoire of a species. Pan-genomes provide new platforms to exploit these unique genes or genetic variation for optimizing breeding programs. The advent of next-generation clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such as prime editing, base editing, and de nova domestication, has institutionalized the idea that genome editing is revamped for crop improvement. Also, the availability of versatile Cas orthologs, including Cas9, Cas12, Cas13, and Cas14, improved the editing efficiency. Now, the CRISPR/Cas systems have numerous applications in crop research and successfully edit the major crop to develop resistance against abiotic and biotic stress. By adopting high-throughput phenotyping approaches and big data analytics tools like artificial intelligence (AI) and machine learning (ML), agriculture is heading toward automation or digitalization. The integration of speed breeding with genomic and phenomic tools can allow rapid gene identifications and ultimately accelerate crop improvement programs. In addition, the integration of next-generation multidisciplinary breeding platforms can open exciting avenues to develop climate-ready crops toward global food security.
Collapse
Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Naheed Akhter
- College of Allied Health Professional, Faculty of Medical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| |
Collapse
|
45
|
Mehta S, Chakraborty A, Roy A, Singh IK, Singh A. Fight Hard or Die Trying: Current Status of Lipid Signaling during Plant-Pathogen Interaction. PLANTS (BASEL, SWITZERLAND) 2021; 10:1098. [PMID: 34070722 PMCID: PMC8228701 DOI: 10.3390/plants10061098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/15/2021] [Accepted: 05/24/2021] [Indexed: 12/29/2022]
Abstract
Plant diseases pose a substantial threat to food availability, accessibility, and security as they account for economic losses of nearly $300 billion on a global scale. Although various strategies exist to reduce the impact of diseases, they can introduce harmful chemicals to the food chain and have an impact on the environment. Therefore, it is necessary to understand and exploit the plants' immune systems to control the spread of pathogens and enable sustainable agriculture. Recently, growing pieces of evidence suggest a functional myriad of lipids to be involved in providing structural integrity, intracellular and extracellular signal transduction mediators to substantial cross-kingdom cell signaling at the host-pathogen interface. Furthermore, some pathogens recognize or exchange plant lipid-derived signals to identify an appropriate host or development, whereas others activate defense-related gene expression. Typically, the membrane serves as a reservoir of lipids. The set of lipids involved in plant-pathogen interaction includes fatty acids, oxylipins, phospholipids, glycolipids, glycerolipids, sphingolipids, and sterols. Overall, lipid signals influence plant-pathogen interactions at various levels ranging from the communication of virulence factors to the activation and implementation of host plant immune defenses. The current review aims to summarize the progress made in recent years regarding the involvement of lipids in plant-pathogen interaction and their crucial role in signal transduction.
Collapse
Affiliation(s)
- Sahil Mehta
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India;
| | - Amrita Chakraborty
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Kamýcká 129, Suchdol, 165 21 Prague 6, Czech Republic; (A.C.); (A.R.)
| | - Amit Roy
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Kamýcká 129, Suchdol, 165 21 Prague 6, Czech Republic; (A.C.); (A.R.)
- Excelentní Tým pro Mitigaci (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Kamýcká 129, Suchdol, 165 21 Prague 6, Czech Republic
| | - Indrakant K. Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi 110007, India
| |
Collapse
|
46
|
Li P, Su T, Zhao X, Wang W, Zhang D, Yu Y, Bayer PE, Edwards D, Yu S, Zhang F. Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:966-976. [PMID: 33283404 PMCID: PMC8131043 DOI: 10.1111/pbi.13522] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/11/2020] [Accepted: 12/01/2020] [Indexed: 05/10/2023]
Abstract
Brassica rapa displays a wide range of morphological diversity which is exploited for a variety of food crops. Here we present a high-quality genome assembly for pak choi (Brassica rapa L. subsp. chinensis), an important non-heading leafy vegetable, and comparison with the genomes of heading type Chinese cabbage and the oilseed form, yellow sarson. Gene presence-absence variation (PAV) and genomic structural variations (SV) were identified, together with single nucleotide polymorphisms (SNPs). The structure and expression of genes for leaf morphology and flowering were compared between the three morphotypes revealing candidate genes for these traits in B. rapa. The pak choi genome assembly and its comparison with other B. rapa genome assemblies provides a valuable resource for the genetic improvement of this important vegetable crop and as a model to understand the diversity of morphological variation across Brassica species.
Collapse
Affiliation(s)
- Peirong Li
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agriculture and Forestry Sciences (BAAFS)BeijingChina
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
- Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina
| |
Collapse
|
47
|
Zhang Y, Edwards D, Batley J. Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding. THE PLANT GENOME 2021; 14:e20060. [PMID: 33179454 DOI: 10.1002/tpg2.20060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub-genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.
Collapse
Affiliation(s)
- Yueqi Zhang
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| |
Collapse
|
48
|
Scossa F, Alseekh S, Fernie AR. Integrating multi-omics data for crop improvement. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153352. [PMID: 33360148 DOI: 10.1016/j.jplph.2020.153352] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/26/2023]
Abstract
Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.
Collapse
Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178, Rome, Italy.
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
| |
Collapse
|
49
|
Cantila AY, Saad NSM, Amas JC, Edwards D, Batley J. Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives. Int J Mol Sci 2020; 22:E313. [PMID: 33396785 PMCID: PMC7795555 DOI: 10.3390/ijms22010313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/20/2022] Open
Abstract
Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.
Collapse
Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia; (A.Y.C.); (N.S.M.S.); (J.C.A.); (D.E.)
| |
Collapse
|
50
|
Frontiers in Dissecting and Managing Brassica Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes. Int J Mol Sci 2020; 21:ijms21238964. [PMID: 33255840 PMCID: PMC7728316 DOI: 10.3390/ijms21238964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
The Brassica genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of Brassica genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for B. rapa, B. oleracea and B. napus. Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important Brassica genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible individuals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA diversity characterised in the limited number of Brassica assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA diversity, greatly expanding breeding resources that can be utilised for crop improvement.
Collapse
|