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Pan L, Liu M, Kang Y, Mei X, Hu G, Bao C, Zheng Y, Zhao H, Chen C, Wang N. Comprehensive genomic analyses of Vigna unguiculata provide insights into population differentiation and the genetic basis of key agricultural traits. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 36965079 DOI: 10.1111/pbi.14047] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/09/2023] [Accepted: 03/22/2023] [Indexed: 06/18/2023]
Abstract
Vigna unguiculata is an important legume crop worldwide. The subsp. sesquipedalis and unguiculata are the two major types grown; the former is mainly grown in Asia to produce fresh pods, while the latter is mainly grown in Africa to produce seeds. Here, a chromosome-scale genome for subsp. sesquipedalis was generated by combining high-fidelity (HiFi) long-read sequencing with high-throughput chromosome conformation capture (Hi-C) technology. The genome size for all contigs and N50 were 594 and 18.5 Mb, respectively. The Hi-C interaction map helped cluster 91% of the contigs into 11 chromosomes. Genome comparisons between subsp. sesquipedalis and unguiculata revealed extensive genomic variations, and some variations resulted in gene loss. A germplasm panel with 315 accessions of V. unguiculata was resequenced, and a genomic variation map was constructed. Population structure and phylogenetic analyses suggested that subsp. sesquipedalis originated from subsp. unguiculata. Highly differentiated genomic regions were also identified, and a number of genes functionally enriched in adaptations were located in these regions. Two traits, pod length (PL) and pod width (PW), were observed for this germplasm, and genome-wide association analysis of these traits was performed. The quantitative trait loci (QTLs) for these two traits were identified, and their candidate genes were uncovered. Interestingly, genomic regions of PL QTLs also showed strong signals of artificial selection. Taken together, the results of this study provide novel insights into the population differentiation and genetic basis of key agricultural traits in V. unguiculata.
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Affiliation(s)
- Lei Pan
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Minghui Liu
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Yan Kang
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Xiang Mei
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Gege Hu
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Chun Bao
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Yu Zheng
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Huixia Zhao
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Chanyou Chen
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
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Rapeseed Domestication Affects the Diversity of Rhizosphere Microbiota. Microorganisms 2023; 11:microorganisms11030724. [PMID: 36985297 PMCID: PMC10056747 DOI: 10.3390/microorganisms11030724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Rhizosphere microbiota is important for plant growth and health. Domestication is a process to select suitable plants to satisfy the needs of humans, which may have great impacts on the interaction between the host and its rhizosphere microbiota. Rapeseed (Brassica napus) is an important oilseed crop derived from the hybridization between Brassica rapa and Brassica oleracea ~7500 years ago. However, variations in rhizosphere microbiota along with rapeseed domestication remain poorly understood. Here, we characterized the composition and structure of the rhizosphere microbiota among diverse rapeseed accessions, including ten B. napus, two B. rapa, and three B. oleracea accessions through bacterial 16S rRNA gene sequencing. B. napus exhibited a higher Shannon index and different bacterial relative abundance compared with its wild relatives in rhizosphere microbiota. Moreover, artificial synthetic B. napus lines G3D001 and No.2127 showed significantly different rhizosphere microbiota diversity and composition from other B. napus accessions and their ancestors. The core rhizosphere microbiota of B. napus and its wild relatives was also described. FAPROTAX annotation predicted that the synthetic B. napus lines had more abundant pathways related to nitrogen metabolism, and the co-occurrence network results demonstrated that Rhodoplanes acted as hub nodes to promote nitrogen metabolism in the synthetic B. napus lines. This study provides new insights into the impacts of rapeseed domestication on the diversity and community structure of rhizosphere microbiota, which may highlight the contribution of rhizosphere microbiota to plant health.
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Single trait versus principal component based association analysis for flowering related traits in pigeonpea. Sci Rep 2022; 12:10453. [PMID: 35729192 PMCID: PMC9211048 DOI: 10.1038/s41598-022-14568-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 03/18/2022] [Indexed: 11/08/2022] Open
Abstract
Pigeonpea, a tropical photosensitive crop, harbors significant diversity for days to flowering, but little is known about the genes that govern these differences. Our goal in the current study was to use genome wide association strategy to discover the loci that regulate days to flowering in pigeonpea. A single trait as well as a principal component based association study was conducted on a diverse collection of 142 pigeonpea lines for days to first and fifty percent of flowering over 3 years, besides plant height and number of seeds per pod. The analysis used seven association mapping models (GLM, MLM, MLMM, CMLM, EMLM, FarmCPU and SUPER) and further comparison revealed that FarmCPU is more robust in controlling both false positives and negatives as it incorporates multiple markers as covariates to eliminate confounding between testing marker and kinship. Cumulatively, a set of 22 SNPs were found to be associated with either days to first flowering (DOF), days to fifty percent flowering (DFF) or both, of which 15 were unique to trait based, 4 to PC based GWAS while 3 were shared by both. Because PC1 represents DOF, DFF and plant height (PH), four SNPs found associated to PC1 can be inferred as pleiotropic. A window of ± 2 kb of associated SNPs was aligned with available transcriptome data generated for transition from vegetative to reproductive phase in pigeonpea. Annotation analysis of these regions revealed presence of genes which might be involved in floral induction like Cytochrome p450 like Tata box binding protein, Auxin response factors, Pin like genes, F box protein, U box domain protein, chromatin remodelling complex protein, RNA methyltransferase. In summary, it appears that auxin responsive genes could be involved in regulating DOF and DFF as majority of the associated loci contained genes which are component of auxin signaling pathways in their vicinity. Overall, our findings indicates that the use of principal component analysis in GWAS is statistically more robust in terms of identifying genes and FarmCPU is a better choice compared to the other aforementioned models in dealing with both false positive and negative associations and thus can be used for traits with complex inheritance.
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Raboanatahiry N, Chao H, He J, Li H, Yin Y, Li M. Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:862363. [PMID: 35360294 PMCID: PMC8963808 DOI: 10.3389/fpls.2022.862363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Rahman M, Hoque A, Roy J. Linkage disequilibrium and population structure in a core collection of Brassica napus (L.). PLoS One 2022; 17:e0250310. [PMID: 35231054 PMCID: PMC8887726 DOI: 10.1371/journal.pone.0250310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 02/14/2022] [Indexed: 11/19/2022] Open
Abstract
Estimation of genetic diversity in rapeseed is important for sustainable breeding program to provide an option for the development of new breeding lines. The objective of this study was to elucidate the patterns of genetic diversity within and among different structural groups, and measure the extent of linkage disequilibrium (LD) of 383 globally distributed rapeseed germplasm using 8,502 single nucleotide polymorphism (SNP) markers. We divided the germplasm collection into five subpopulations (P1 to P5) according to geographic and growth habit-related patterns. All subpopulations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.24) between most of the combinations. The rutabaga type showed highest divergence with spring and winter types. Higher divergence was also found between winter and spring types. Admixture model based structure analysis, principal component and neighbor-joining tree analysis placed all subpopulations into three distinct clusters. Admixed genotype constituted 29.24% of total genotypes, while remaining 70.76% belongs to identified clusters. Overall, mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 45 kb distance for whole genome. The LD decay was slower in C genome (< 93 kb); relative to the A genome (< 21 kb) which was confirmed by availability of larger haplotype blocks in C genome than A genome. The findings regarding LD pattern and population structure will help to utilize the collection as an important resource for association mapping efforts to identify genes useful in crop improvement as well as for selection of parents for hybrid breeding.
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Affiliation(s)
- Mukhlesur Rahman
- Department of Pant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Ahasanul Hoque
- Department of Pant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Jayanta Roy
- Department of Pant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
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Song X, Wei Y, Xiao D, Gong K, Sun P, Ren Y, Yuan J, Wu T, Yang Q, Li X, Nie F, Li N, Feng S, Pei Q, Yu T, Zhang C, Liu T, Wang X, Yang J. Brassica carinata genome characterization clarifies U's triangle model of evolution and polyploidy in Brassica. PLANT PHYSIOLOGY 2021; 186:388-406. [PMID: 33599732 PMCID: PMC8154070 DOI: 10.1093/plphys/kiab048] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/12/2021] [Indexed: 05/03/2023]
Abstract
Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent agronomic traits. Here, the high-quality genome sequence of B. carinata is reported. Characterization revealed a genome anchored to 17 chromosomes with a total length of 1.087 Gb and an N50 scaffold length of 60 Mb. Repetitive sequences account for approximately 634 Mb or 58.34% of the B. carinata genome. Notably, 51.91% of 97,149 genes are confined to the terminal 20% of chromosomes as a result of the expansion of repeats in pericentromeric regions. Brassica carinata shares one whole-genome triplication event with the five other species in U's triangle, a classic model of evolution and polyploidy in Brassica. Brassica carinata was deduced to have formed ∼0.047 Mya, which is slightly earlier than B. napus but later than B. juncea. Our analysis indicated that the relationship between the two subgenomes (BcaB and BcaC) is greater than that between other two tetraploid subgenomes (BjuB and BnaC) and their respective diploid parents. RNA-seq datasets and comparative genomic analysis were used to identify several key genes in pathways regulating disease resistance and glucosinolate metabolism. Further analyses revealed that genome triplication and tandem duplication played important roles in the expansion of those genes in Brassica species. With the genome sequencing of B. carinata completed, the genomes of all six Brassica species in U's triangle are now resolved. The data obtained from genome sequencing, transcriptome analysis, and comparative genomic efforts in this study provide valuable insights into the genome evolution of the six Brassica species in U's triangle.
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Affiliation(s)
- Xiaoming Song
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68526, USA
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yanping Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ke Gong
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Pengchuan Sun
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yiming Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaqing Yuan
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Wu
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Qihang Yang
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Xinyu Li
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Nan Li
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Shuyan Feng
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Qiaoying Pei
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Yu
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Author for communication:
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiyin Wang
- Center for Genomics and Bio-computing/School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
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Dakouri A, Lamara M, Karim MM, Wang J, Chen Q, Gossen BD, Strelkov SE, Hwang SF, Peng G, Yu F. Identification of resistance loci against new pathotypes of Plasmodiophora brassicae in Brassica napus based on genome-wide association mapping. Sci Rep 2021; 11:6599. [PMID: 33758222 PMCID: PMC7987998 DOI: 10.1038/s41598-021-85836-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/05/2021] [Indexed: 11/11/2022] Open
Abstract
Genetic resistance is a successful strategy for management of clubroot (Plasmodiophora brassicae) of brassica crops, but resistance can break down quickly. Identification of novel sources of resistance is especially important when new pathotypes arise. In the current study, the reaction of 177 accessions of Brassica napus to four new, virulent pathotypes of P. brassicae was assessed. Each accession was genotyped using genotyping by sequencing to identify and map novel sources of clubroot resistance using mixed linear model (MLM) analysis. The majority of accessions were highly susceptible (70–100 DSI), but a few accessions exhibited strong resistance (0–20 DSI) to pathotypes 5X (21 accessions), 3A (8), 2B (7), and 3D (15), based on the Canadian Clubroot Differential system. In total, 301,753 SNPs were mapped to 19 chromosomes. Population structure analysis indicated that the 177 accessions belong to seven major populations. SNPs were associated with resistance to each pathotype using MLM. In total, 13 important SNP loci were identified, with 9 SNPs mapped to the A-genome and 4 to the C-genome. The SNPs were associated with resistance to pathotypes 5X (2 SNPs), 3A (4), 2B (5) and 3D (6). A Blast search of 1.6 Mb upstream and downstream from each SNP identified 13 disease-resistance genes or domains. The distance between a SNP locus and the nearest resistance gene ranged from 0.04 to 0.74 Mb. The resistant lines and SNP markers identified in this study can be used to breed for resistance to the most prevalent new pathotypes of P. brassicae in Canada.
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Affiliation(s)
- Abdulsalam Dakouri
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Mebarek Lamara
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada.,Institut de Recherche Sur Les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue, 445 boul. de l'Université, Rouyn-Noranda, QC, J9X 5E4, Canada
| | - Md Masud Karim
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Jinghe Wang
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Qilin Chen
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Bruce D Gossen
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Alberta, Canada
| | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Alberta, Canada
| | - Gary Peng
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Fengqun Yu
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Canada.
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Yang S, Gill RA, Zaman QU, Ulhassan Z, Zhou W. Insights on SNP types, detection methods and their utilization in Brassica species: Recent progress and future perspectives. J Biotechnol 2020; 324:11-20. [PMID: 32979432 DOI: 10.1016/j.jbiotec.2020.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/15/2020] [Accepted: 09/20/2020] [Indexed: 01/09/2023]
Abstract
The genus Brassica, family Brassicaceae (Cruciferae), comprises many important species of oil crops, vegetables and medicinal plants including B. rapa, B. oleracea, B. nigra, B. napus, B. juncea, B. carinata. Genomic researches in Brassica species is constrained by polyploidization, mainly due to its complicated genomic structure. However, rapid development of methods for detecting single nucleotide polymorphisms (SNP), such as next generation sequencing and SNP microarray, has accelerated release of reference Brassica species genomes as well as discovery of large numbers and genome-wide SNPs, thus intensifying forward genetics in this genus. In this review, we summarize biological characteristics, classification and various methods for detecting SNPs, focusing on high-throughput techniques. Moreover, we describe the pivotal roles of SNPs in genetic diversity, linkage map construction and QTL mapping, comparative genomics, linkage disequilibrium and genome-wide association studies. These insights are expected to deepen our understanding and guide further advancements in Brassica species research.
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Affiliation(s)
- Su Yang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China.
| | - Qamar U Zaman
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China
| | - Zaid Ulhassan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
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Hu D, Zhang W, Zhang Y, Chang S, Chen L, Chen Y, Shi Y, Shen J, Meng J, Zou J. Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1106-1118. [PMID: 30467941 PMCID: PMC6523605 DOI: 10.1111/pbi.13041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Brassica napus (An An Cn Cn ) is an important worldwide oilseed crop, but it is a young allotetraploid with a short evolutionary history and limited genetic diversity. To significantly broaden its genetic diversity and create a novel heterotic population for sustainable rapeseed breeding, this study reconstituted the genome of B. napus by replacing it with the subgenomes from 122 accessions of Brassica rapa (Ar Ar ) and 74 accessions of Brassica carinata (Bc Bc Cc Cc ) and developing a novel gene pool of B. napus through five rounds of extensive recurrent selection. When compared with traditional B. napus using SSR markers and high-throughput SNP/Indel markers through genotyping by sequencing, the newly developed gene pool and its homozygous progenies exhibited a large genetic distance, rich allelic diversity, new alleles and exotic allelic introgression across all 19 AC chromosomes. In addition to the abundant genomic variation detected in the AC genome, we also detected considerable introgression from the eight chromosomes of the B genome. Extensive trait variation and some genetic improvements were present from the early recurrent selection to later generations. This novel gene pool produced equally rich phenotypic variation and should be valuable for rapeseed genetic improvement. By reconstituting the genome of B. napus by introducing subgenomic variation within and between the related species using intense selection and recombination, the whole genome could be substantially reorganized. These results serve as an example of the manipulation of the genome of a young allopolyploid and provide insights into its rapid genome evolution affected by interspecific and intraspecific crosses.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenshan Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yikai Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Lunlin Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yingying Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yongdi Shi
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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Wei D, Cui Y, Mei J, Qian L, Lu K, Wang ZM, Li J, Tang Q, Qian W. Genome-wide identification of loci affecting seed glucosinolate contents in Brassica napus L. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:611-623. [PMID: 30183130 DOI: 10.1111/jipb.12717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests. However, the presence of high levels of glucosinolates severely diminishes the nutritional value of seed meals made from rapeseed (Brassica napus L.). To identify the loci affecting seed glucosinolate content (SGC), we conducted genome-wide resequencing in a population of 307 diverse B. napus accessions from the three B. napus ecotype groups, namely, spring, winter, and semi-winter. These resequencing data were used for a genome-wide association study (GWAS) to identify the loci affecting SGC. In the three ecotype groups, four common and four ecotype-specific haplotype blocks (HBs) were significantly associated with SGC. To identify candidate genes controlling SGC, transcriptome analysis was carried out in 36 accessions showing extreme SGC values. Analyses of haplotypes, genomic variation, and candidate gene expression pointed to five and three candidate genes in the common and spring group-specific HBs, respectively. Our expression analyses demonstrated that additive effects of the three candidate genes in the spring group-specific HB play important roles in the SGC of B. napus.
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Affiliation(s)
- Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha 410128, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Zhi-Min Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Qinglin Tang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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11
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Malmberg MM, Barbulescu DM, Drayton MC, Shinozuka M, Thakur P, Ogaji YO, Spangenberg GC, Daetwyler HD, Cogan NOI. Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola. FRONTIERS IN PLANT SCIENCE 2018; 9:1809. [PMID: 30581450 PMCID: PMC6292936 DOI: 10.3389/fpls.2018.01809] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/21/2018] [Indexed: 05/25/2023]
Abstract
Whole genome sequencing offers genome wide, unbiased markers, and inexpensive library preparation. With the cost of sequencing decreasing rapidly, many plant genomes of modest size are amenable to skim whole genome resequencing (skim WGR). The use of skim WGR in diverse sample sets without the use of imputation was evaluated in silico in 149 canola samples representative of global diversity. Fastq files with an average of 10x coverage of the reference genome were used to generate skim samples representing 0.25x, 0.5x, 1x, 2x, 3x, 4x, and 5x sequencing coverage. Applying a pre-defined list of SNPs versus de novo SNP discovery was evaluated. As skim WGR is expected to result in some degree of insufficient allele sampling, all skim coverage levels were filtered at a range of minimum read depths from a relaxed minimum read depth of 2 to a stringent read depth of 5, resulting in 28 list-based SNP sets. As a broad recommendation, genotyping pre-defined SNPs between 1x and 2x coverage with relatively stringent depth filtering is appropriate for a diverse sample set of canola due to a balance between marker number, sufficient accuracy, and sequencing cost, but depends on the intended application. This was experimentally examined in two sample sets with different genetic backgrounds: 1x coverage of 1,590 individuals from 84 Australian spring type four-parent crosses aimed at maximizing diversity as well as one commercial F1 hybrid, and 2x coverage of 379 doubled haploids (DHs) derived from a subset of the four-parent crosses. To determine optimal coverage in a simpler genetic background, the DH sample sequence coverage was further down sampled in silico. The flexible and cost-effective nature of the protocol makes it highly applicable across a range of species and purposes.
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Affiliation(s)
- M. Michelle Malmberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Michelle C. Drayton
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Maiko Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Preeti Thakur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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12
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Hegelund JN, Liang C, Lauridsen UB, Kemp O, Lütken H, Müller R. Increasing genetic variability in oilseed rape (Brassica napus) - Genotypes and phenotypes of oilseed rape transformed by wild type Agrobacterium rhizogenes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:20-26. [PMID: 29650153 DOI: 10.1016/j.plantsci.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/26/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
Brassica napus (oilseed rape) is a major oil crop worldwide. Due to the short domestication period of oilseed rape the genetic variability is limited compared to other crops. Transfer of rol and aux genes from Agrobacterium rhizogenes is used in horticulture to increase genetic variability. In the current study, we explore transformation by A. rhizogenes as a biotechnological approach in breeding for more branched and shorter oilseed rape. In the 2nd generation of transformed oilseed rape, branch numbers increased significantly by 49% from 7.7 ± 0.4 to 11.5 ± 1.9 when comparing rol+/aux+ plants with WT. Simultaneously, the apical height of plants was reduced by 25% from 81.3 ± 1.9 cm to 62.4 ± 6.7 cm in rol+/aux+ plants at the onset of flowering. Reproductive parameters affecting yield as seed size and number were negatively affected in rol+/aux+ plants. Interestingly, oil composition was changed in rol+/aux+ seeds. Oleic acid (ω9) contents were reduced by more than 3% whereas α-linolenic acid (ω6) increased by more than 25% in mature seeds. To obtain shorter and more branched breeding material of oilseed rape we suggest crossing plants with the rol+/aux+ genotype back into the parental breeding line. This could reduce the negative impact of rol+/aux+ on yield.
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Affiliation(s)
- Josefine Nymark Hegelund
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 9-13, 2630 Taastrup, Denmark.
| | - Chang Liang
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 9-13, 2630 Taastrup, Denmark
| | - Uffe Bjerre Lauridsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 9-13, 2630 Taastrup, Denmark
| | - Oliver Kemp
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 9-13, 2630 Taastrup, Denmark
| | - Henrik Lütken
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 9-13, 2630 Taastrup, Denmark
| | - Renate Müller
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 9-13, 2630 Taastrup, Denmark
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13
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Zou J, Hu D, Mason AS, Shen X, Wang X, Wang N, Grandke F, Wang M, Chang S, Snowdon RJ, Meng J. Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:507-519. [PMID: 28703467 PMCID: PMC5811809 DOI: 10.1111/pbi.12791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 05/20/2023]
Abstract
Introgression of genomic variation between and within related crop species is a significant evolutionary approach for population differentiation, genome reorganization and trait improvement. Using the Illumina Infinium Brassica 60K SNP array, we investigated genomic changes in a panel of advanced generation new-type Brassica napus breeding lines developed from hundreds of interspecific crosses between 122 Brassica rapa and 74 Brassica carinata accessions, and compared them with representative accessions of their three parental species. The new-type B. napus population presented rich genetic diversity and abundant novel genomic alterations, consisting of introgressions from B. rapa and B. carinata, novel allelic combinations, reconstructed linkage disequilibrium patterns and haplotype blocks, and frequent deletions and duplications (nonrandomly distributed), particularly in the C subgenome. After a much shorter, but very intensive, selection history compared to traditional B. napus, a total of 15 genomic regions with strong selective sweeps and 112 genomic regions with putative signals of selective sweeps were identified. Some of these regions were associated with important agronomic traits that were selected for during the breeding process, while others were potentially associated with restoration of genome stability and fertility after interspecific hybridization. Our results demonstrate how a novel method for population-based crop genetic improvement can lead to rapid adaptation, restoration of genome stability and positive responses to artificial selection.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Xueqi Shen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaohua Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Nian Wang
- College of Horticulture & Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Fabian Grandke
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Meng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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14
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Malmberg MM, Shi F, Spangenberg GC, Daetwyler HD, Cogan NOI. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:508. [PMID: 29725344 PMCID: PMC5917405 DOI: 10.3389/fpls.2018.00508] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.
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Affiliation(s)
- M. Michelle Malmberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Fan Shi
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
| | - German C. Spangenberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- *Correspondence: Noel O. I. Cogan,
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15
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Wang X, Chen Y, Thomas CL, Ding G, Xu P, Shi D, Grandke F, Jin K, Cai H, Xu F, Yi B, Broadley MR, Shi L. Genetic variants associated with the root system architecture of oilseed rape (Brassica napus L.) under contrasting phosphate supply. DNA Res 2017; 24:407-417. [PMID: 28430897 PMCID: PMC5737433 DOI: 10.1093/dnares/dsx013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/29/2017] [Indexed: 12/29/2022] Open
Abstract
Breeding crops with ideal root system architecture for efficient absorption of phosphorus is an important strategy to reduce the use of phosphate fertilizers. To investigate genetic variants leading to changes in root system architecture, 405 oilseed rape cultivars were genotyped with a 60K Brassica Infinium SNP array in low and high P environments. A total of 285 single-nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels. Nine single-nucleotide polymorphisms corroborate a previous linkage analysis of root system architecture quantitative trait loci in the BnaTNDH population. One peak single-nucleotide polymorphism region on A3 was associated with all root system architecture traits and co-localized with a quantitative trait locus for primary root length at low phosphorus. Two more single-nucleotide polymorphism peaks on A5 for root dry weight at low phosphorus were detected in both growth systems and co-localized with a quantitative trait locus for the same trait. The candidate genes identified on A3 form a haplotype ‘BnA3Hap’, that will be important for understanding the phosphorus/root system interaction and for the incorporation into Brassica napus breeding programs.
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Affiliation(s)
- Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanling Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Catherine L Thomas
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12?5RD, UK
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Dexu Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Fabian Grandke
- Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen 35392, Germany
| | - Kemo Jin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12?5RD, UK
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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16
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Wei D, Cui Y, He Y, Xiong Q, Qian L, Tong C, Lu G, Ding Y, Li J, Jung C, Qian W. A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4791-4801. [PMID: 28992309 PMCID: PMC5853444 DOI: 10.1093/jxb/erx311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop. Despite a short period of domestication and breeding, rapeseed has formed three diverse ecotype groups, namely spring, winter, and semi-winter. However, the genetic changes among the three ecotype groups have remained largely unknown. To detect selective signals, a set of 327 accessions from a worldwide collection were genotyped using a Brassica array, producing 33 186 high-quality single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) was unevenly distributed across the genome. A total of 705 (78.2%) weak LD regions were found in the A subgenome, whereas 445 (72.6%) strong LD regions were in the C subgenome. By calculating the nucleotide diversity and population differentiation indices, a total of 198 selective sweeps were identified across ecotype groups, spanning 5.91% (37.9 Mb) of the genome. Within these genome regions, a few known functional genes or loci were found to be in association with environmental adaptability and yield-related traits. In particular, all 12 SNPs detected in significant association with flowering time among accessions were in the selection regions between ecotype groups. These findings provide new insights into the structure of the B. napus genome and uncover the footprints of domestication and breeding.
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Affiliation(s)
- Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Chaobo Tong
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guangyuan Lu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Christian Jung
- Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Correspondence:
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17
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Raboanatahiry N, Chao H, Guo L, Gan J, Xiang J, Yan M, Zhang L, Yu L, Li M. Synteny analysis of genes and distribution of loci controlling oil content and fatty acid profile based on QTL alignment map in Brassica napus. BMC Genomics 2017; 18:776. [PMID: 29025408 PMCID: PMC5639739 DOI: 10.1186/s12864-017-4176-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022] Open
Abstract
Background Deciphering the genetic architecture of a species is a good way to understand its evolutionary history, but also to tailor its profile for breeding elite cultivars with desirable traits. Aligning QTLs from diverse population in one map and utilizing it for comparison, but also as a basis for multiple analyses assure a stronger evidence to understand the genetic system related to a given phenotype. Results In this study, 439 genes involved in fatty acid (FA) and triacylglycerol (TAG) biosyntheses were identified in Brassica napus. B. napus genome showed mixed gene loss and insertion compared to B. rapa and B. oleracea, and C genome had more inserted genes. Identified QTLs for oil (OC-QTLs) and fatty acids (FA-QTLs) from nine reported populations were projected on the physical map of the reference genome “Darmor-bzh” to generate a map. Thus, 335 FA-QTLs and OC-QTLs could be highlighted and 82 QTLs were overlapping. Chromosome C3 contained 22 overlapping QTLs with all trait studied except for C18:3. In total, 218 candidate genes which were potentially involved in FA and TAG were identified in 162 QTLs confidence intervals and some of them might affect many traits. Also, 76 among these candidate genes were found inside 57 overlapping QTLs, and candidate genes for oil content were in majority (61/76 genes). Then, sixteen genes were found in overlapping QTLs involving three populations, and the remaining 60 genes were found in overlapping QTLs of two populations. Interaction network and pathway analysis of these candidate genes indicated ten genes that might have strong influence over the other genes that control fatty acids and oil formation. Conclusion The present results provided new information for genetic basis of FA and TAG formation in B. napus. A map including QTLs from numerous populations was built, which could serve as reference to study the genome profile of B. napus, and new potential genes emerged which might affect seed oil. New useful tracks were showed for the selection of population or/and selection of interesting genes for breeding improvement purpose. Electronic supplementary material The online version of this article (10.1186/s12864-017-4176-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Key Laboratory of Molecular Biology, Huazhong University of Science and Technology, Wuhan, 430074, China.,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 435599, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Key Laboratory of Molecular Biology, Huazhong University of Science and Technology, Wuhan, 430074, China.,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 435599, China
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Key Laboratory of Molecular Biology, Huazhong University of Science and Technology, Wuhan, 430074, China.,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 435599, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 435599, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 435599, China
| | - Mingli Yan
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China.
| | - Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Key Laboratory of Molecular Biology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Key Laboratory of Molecular Biology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Key Laboratory of Molecular Biology, Huazhong University of Science and Technology, Wuhan, 430074, China. .,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 435599, China.
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18
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Wang X, Long Y, Wang N, Zou J, Ding G, Broadley MR, White PJ, Yuan P, Zhang Q, Luo Z, Liu P, Zhao H, Zhang Y, Cai H, King GJ, Xu F, Meng J, Shi L. Breeding histories and selection criteria for oilseed rape in Europe and China identified by genome wide pedigree dissection. Sci Rep 2017; 7:1916. [PMID: 28507329 PMCID: PMC5432491 DOI: 10.1038/s41598-017-02188-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/13/2017] [Indexed: 12/17/2022] Open
Abstract
Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape (Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor-bzh. Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees. IBD number and length were greater in the Ningyou7 pedigree than in the Tapidor pedigree. Seventy nine QTLs for flowering time, seed quality and root morphology traits were identified in the IBDs of Tapidor and Ningyou7. Many more candidate genes had been selected within the Ningyou7 pedigree than within the Tapidor pedigree. These results highlight differences in the transfer of favorable gene clusters controlling key traits during selection breeding in Europe and China.
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Affiliation(s)
- Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Biotechnology Research Institute, Chinese Academy of agricultural Science, Beijing, 100081, China
| | - Nian Wang
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom
- King Saud University, Riyadh, 11451, Saudi Arabia
| | - Pan Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Zhao
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Cai
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China.
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Balsalobre TWA, da Silva Pereira G, Margarido GRA, Gazaffi R, Barreto FZ, Anoni CO, Cardoso-Silva CB, Costa EA, Mancini MC, Hoffmann HP, de Souza AP, Garcia AAF, Carneiro MS. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 2017; 18:72. [PMID: 28077090 PMCID: PMC5225503 DOI: 10.1186/s12864-016-3383-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes. RESULTS We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes. CONCLUSIONS This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.
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Affiliation(s)
- Thiago Willian Almeida Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Guilherme da Silva Pereira
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Rodrigo Gazaffi
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Fernanda Zatti Barreto
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Carina Oliveira Anoni
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Cláudio Benício Cardoso-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Estela Araújo Costa
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Melina Cristina Mancini
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Hermann Paulo Hoffmann
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Antonio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
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Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection. Sci Rep 2016; 6:38496. [PMID: 27924947 PMCID: PMC5141495 DOI: 10.1038/srep38496] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/11/2016] [Indexed: 01/28/2023] Open
Abstract
Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome Dt7 and four potential candidate genes for FL were identified. Analyzing the geographical distribution of favorable haplotypes (FHs) among these lines revealed that two favorable haplotype frequencies (FHFs) were higher in accessions from low-latitude regions than in accessions from high-latitude regions. However, the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China. Furthermore, the FHFs differed among cultivars developed during different breeding periods. These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China and provide a foundation for the further improvement of fiber quality traits.
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Li L, Luo Y, Chen B, Xu K, Zhang F, Li H, Huang Q, Xiao X, Zhang T, Hu J, Li F, Wu X. A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1483. [PMID: 27746804 PMCID: PMC5044777 DOI: 10.3389/fpls.2016.01483] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/20/2016] [Indexed: 05/19/2023]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute – Chinese Academy of Agricultural SciencesWuhan, China
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22
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Li L, Luo Y, Chen B, Xu K, Zhang F, Li H, Huang Q, Xiao X, Zhang T, Hu J, Li F, Wu X. A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1483. [PMID: 27746804 DOI: 10.3389/fpls.2015.01483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/20/2016] [Indexed: 05/26/2023]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR.
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Affiliation(s)
- Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Yujie Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Fugui Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Tianyao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Jihong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
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Breeding signature of combining ability improvement revealed by a genomic variation map from recurrent selection population in Brassica napus. Sci Rep 2016; 6:29553. [PMID: 27412721 PMCID: PMC4944167 DOI: 10.1038/srep29553] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/17/2016] [Indexed: 11/30/2022] Open
Abstract
Combining ability is crucial for parent selection in crop hybrid breeding. The present investigation and results had revealed the underlying genetic factors which might contribute in adequate combining ability, further assisting in enhancing heterosis and stability. Here, we conducted a large-scale analysis of genomic variation in order to define genomic regions affecting the combining ability in recurrent selection population of rapeseed. A population of 175 individuals was genotyped with the Brassica60K SNP chip. 525 hybrids were assembled with three different testers and used to evaluate the general combining ability (GCA) in three environments. By detecting the changes of the genomic variation, we identified 376 potential genome regions, spanning 3.03% of rapeseed genome which provided QTL-level resolution on potentially selected variants. More than 96% of these regions were located in the C subgenome, indicating that C subgenome had sustained stronger selection pressure in the breeding program than the A subgenome. In addition, a high level of linkage disequilibrium in rapeseed genome was detected, suggesting that marker-assisted selection for the population improvement might be easily implemented. This study outlines the evidence for high GCA on a genomic level and provided underlying molecular mechanism for recurrent selection improvement in B. napus.
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Liu S, Fan C, Li J, Cai G, Yang Q, Wu J, Yi X, Zhang C, Zhou Y. A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1203-15. [PMID: 26912143 DOI: 10.1007/s00122-016-2697-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/02/2016] [Indexed: 05/04/2023]
Abstract
A set of additive loci for seed oil content were identified using association mapping and one of the novel loci on the chromosome A5 was validated by linkage mapping. Increasing seed oil content is one of the most important goals in the breeding of oilseed crops including Brassica napus, yet the genetic basis for variations in this important trait remains unclear. By genome-wide association study of seed oil content using 521 B. napus accessions genotyped with the Brassica 60K SNP array, we identified 50 loci significantly associated with seed oil content using three statistical models, the general linear model, the mixed linear model and the Anderson-Darling test. Together, the identified loci could explain approximately 80 % of the total phenotypic variance, and 29 of these loci have not been reported previously. Furthermore, a novel locus on the chromosome A5 that could increase 1.5-1.7 % of seed oil content was validated in an independent bi-parental linkage population. Haplotype analysis showed that the favorable alleles for seed oil content exhibit cumulative effects. Our results thus provide valuable information for understanding the genetic control of seed oil content in B. napus and may facilitate marker-based breeding for a higher seed oil content in this important oil crop.
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Affiliation(s)
- Sheng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Guangqin Cai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinqi Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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25
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Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing. PLoS One 2016; 11:e0146383. [PMID: 26730738 PMCID: PMC4701484 DOI: 10.1371/journal.pone.0146383] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/16/2015] [Indexed: 01/15/2023] Open
Abstract
High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome “Darmor-bzh.” The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.
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26
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Liu J, Wang W, Mei D, Wang H, Fu L, Liu D, Li Y, Hu Q. Characterizing Variation of Branch Angle and Genome-Wide Association Mapping in Rapeseed (Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:21. [PMID: 26870051 PMCID: PMC4740498 DOI: 10.3389/fpls.2016.00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/08/2016] [Indexed: 05/20/2023]
Abstract
Changes in the rapeseed branch angle alter plant architecture, allowing more efficient light capture as planting density increases. In this study, a natural population of rapeseed was grown in three environments and evaluated for branch angle trait to characterize their phenotypic patterns and genotype with a 60K Brassica Infinium SNP array. Significant phenotypic variation was observed from 20 to 70°. As a result, 25 significant quantitative trait loci (QTL) associated with branch angle were identified on chromosomes A2, A3, A7, C3, C5, and C7 by the MLM model in TASSEL 4.0. Orthologs of the functional candidate genes involved in branch angle were identified. Among the key QTL, the peak SNPs were close to the key orthologous genes BnaA.Lazy1 and BnaC.Lazy1 on A3 and C3 homologous genome blocks. With the exception of Lazy (LA) orthologous genes, SQUMOSA PROMOTER BINDING PROTEIN LIKE 14 (SPL14) and an auxin-responsive GRETCHEN HAGEN 3 (GH3) genes from Arabidopsis thaliana were identified close to two clusters of SNPs on the A7 and C7 chromosomes. These findings on multiple novel loci and candidate genes of branch angle will be useful for further understanding and genetic improvement of plant architecture in rapeseed.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Wenxiang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Desheng Mei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Li Fu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Daoming Liu
- Agricultural Sciences Institute of Lu'an MunicipalLu'an, China
| | - Yunchang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Qiong Hu
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Wang N, Chen B, Xu K, Gao G, Li F, Qiao J, Yan G, Li J, Li H, Wu X. Association Mapping of Flowering Time QTLs and Insight into Their Contributions to Rapeseed Growth Habits. FRONTIERS IN PLANT SCIENCE 2016; 7:338. [PMID: 27047517 PMCID: PMC4805649 DOI: 10.3389/fpls.2016.00338] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/04/2016] [Indexed: 05/02/2023]
Abstract
Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p-value of 4.06 × 10(-4); the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth habits. These results will be applied to rapeseed breeding programs, and they will aid in our understanding of the relation between flowering time variations and growth habits in plants.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Xiaoming Wu
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Wang N, Chen B, Xu K, Gao G, Li F, Qiao J, Yan G, Li J, Li H, Wu X. Association Mapping of Flowering Time QTLs and Insight into Their Contributions to Rapeseed Growth Habits. FRONTIERS IN PLANT SCIENCE 2016; 7:338. [PMID: 27047517 DOI: 10.3359/fpls.2016.00338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 03/04/2016] [Indexed: 05/18/2023]
Abstract
Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p-value of 4.06 × 10(-4); the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth habits. These results will be applied to rapeseed breeding programs, and they will aid in our understanding of the relation between flowering time variations and growth habits in plants.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China; College of Horticulture and Forestry Sciences, Huazhong Agricultural UniversityWuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop 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, Oil Crop 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, Oil Crop 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, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop 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, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences Wuhan, China
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Qiao J, Cai M, Yan G, Wang N, Li F, Chen B, Gao G, Xu K, Li J, Wu X. High-throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:409-18. [PMID: 26031705 DOI: 10.1111/pbi.12395] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/26/2015] [Accepted: 04/09/2015] [Indexed: 05/14/2023]
Abstract
Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts.
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Affiliation(s)
- Jiangwei Qiao
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Mengxian Cai
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guixin Yan
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Nian Wang
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, 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, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Binyun Chen
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, 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, 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, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jun Li
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoming Wu
- Key laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Millar JL, Khan D, Becker MG, Chan A, Dufresne A, Sumner M, Belmonte MF. Chalazal seed coat development in Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:45-54. [PMID: 26706057 DOI: 10.1016/j.plantsci.2015.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 05/03/2023]
Abstract
The chalazal seed coat (CZSC) is a maternal subregion adjacent to the funiculus which serves as the first point of entry into the developing seed. This subregion is of particular interest in Brassica napus (canola) because of its location within the seed and its putative contribution to seed filling processes. In this study, the CZSC of canola was characterized at an anatomical and molecular level to (i) describe the cellular and subcellular features of the CZSC throughout seed development, (ii) reveal cellular features of the CZSC that relate to transport processes, (iii) study gene activity of transporters and transcriptional regulators in the CZSC subregion over developmental time, and (iv) briefly investigate the contribution of the A and C constituent genomes to B. napus CZSC gene activity. We found that the CZSC contains terminating ends of xylem and phloem as well as a mosaic of endomembrane and plasmodesmatal connections, suggesting that this subregion is likely involved in the transport of material and information from the maternal tissues of the plant to other regions of the seed. Laser microdissection coupled with quantitative RT-PCR identified the relative abundance of sugar, water, auxin and amino acid transporter homologs inherited from the constituent genomes of this complex polyploid. We also studied the expression of three transcription factors that were shown to co-express with these biological processes providing a preliminary framework for the regulatory networks responsible for seed filling in canola and discuss the relationship of the CZSC to other regions and subregions of the seed and its role in seed development.
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Affiliation(s)
- Jenna L Millar
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Deirdre Khan
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Michael G Becker
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Ainsley Chan
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - André Dufresne
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Michael Sumner
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Mark F Belmonte
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada.
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Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement. Int J Genomics 2015; 2015:230985. [PMID: 26448924 PMCID: PMC4581553 DOI: 10.1155/2015/230985] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 08/03/2015] [Accepted: 08/05/2015] [Indexed: 12/02/2022] Open
Abstract
The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus (AnAnCC genome), B. rapa (ArAr genome), and its hybrid F1 (AnArC genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement.
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Fu Y, Lu K, Qian L, Mei J, Wei D, Peng X, Xu X, Li J, Frauen M, Dreyer F, Snowdon RJ, Qian W. Development of genic cleavage markers in association with seed glucosinolate content in canola. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1029-37. [PMID: 25748114 DOI: 10.1007/s00122-015-2487-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 02/24/2015] [Indexed: 05/21/2023]
Abstract
The orthologues of Arabidopsis involved in seed glucosinolates metabolism within QTL confidence intervals were identified, and functional markers were developed to facilitate breeding for ultra-low glucosinolates in canola. Further reducing the content of seed glucosinolates will have a positive impact on the seed quality of canola (Brassica napus). In this study 43 quantitative trait loci (QTL) for seed glucosinolate (GSL) content in a low-GSL genetic background were mapped over seven environments in Germany and China in a doubled haploid population from a cross between two low-GSL oilseed rape parents with transgressive segregation. By anchoring these QTL to the reference genomes of B. rapa and B. oleracea, we identified 23 orthologues of Arabidopsis involved in GSL metabolism within the QTL confidence intervals. Sequence polymorphisms between the corresponding coding regions of the parental lines were used to develop cleaved amplified polymorphic site markers for two QTL-linked genes, ISOPROPYLMALATE DEHYDROGENASE1 and ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE 3. The genic cleavage markers were mapped in the DH population into the corresponding intervals of QTL explaining 3.36-6.88 and 4.55-8.67 % of the phenotypic variation for seed GSL, respectively. The markers will facilitate breeding for ultra-low seed GSL content in canola.
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Affiliation(s)
- Ying Fu
- College of Agronomy and Biotechnology, Southwest University, 400716, Chongqing, China
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Qian L, Qian W, Snowdon RJ. Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome. BMC Genomics 2014; 15:1170. [PMID: 25539568 PMCID: PMC4367848 DOI: 10.1186/1471-2164-15-1170] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/18/2014] [Indexed: 02/07/2023] Open
Abstract
Background High-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns of population structure and linkage disequilibrium (LD). In this study we used the Brassica 60kSNP Illumina consortium genotyping array to assess the influence of selection and breeding for important agronomic traits on LD and haplotype structure in a diverse panel of 203 Chinese semi-winter rapeseed (Brassica napus) breeding lines. Results Population structure and principal coordinate analysis, using a subset of the SNPs, revealed diversification into three subpopulations and one mixed population, reflecting targeted introgressions from external gene pools during breeding. Pairwise LD analysis within the A- and C-subgenomes of allopolyploid B. napus revealed that mean LD, at a threshold of r2 = 0.1, decayed on average around ten times more rapidly in the A-subgenome (0.25-0.30 Mb) than in the C-subgenome (2.00-2.50 Mb). A total of 3,097 conserved haplotype blocks were detected over a total length of 182.49 Mb (15.17% of the genome). The mean size of haplotype blocks was considerably longer in the C-subgenome (102.85 Kb) than in the A-subgenome (33.51 Kb), and extremely large conserved haplotype blocks were found on a number of C-genome chromosomes. Comparative sequence analysis revealed conserved blocks containing homoloeogous quantitative trait loci (QTL) for seed erucic acid and glucosinolate content, two key seed quality traits under strong agronomic selection. Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues. Conclusions The data we present in this paper provide evidence for strong selection of large chromosome regions associated with important rapeseed seed quality traits conferred by C-subgenome QTL. This implies that an increase in genetic diversity and recombination within the C-genome is particularly important for breeding. The resolution of genome-wide association studies is also expected to vary greatly across different genome regions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1170) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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