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Chang L, Liang J, Cai X, Zhang L, Li Y, Wu J, Wang X. Development of self-compatible Chinese cabbage lines of Chiifu through marker-assisted selection. FRONTIERS IN PLANT SCIENCE 2024; 15:1397018. [PMID: 38872891 PMCID: PMC11169807 DOI: 10.3389/fpls.2024.1397018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
The continuously refined genome assembly of the Chinese cabbage accession Chiifu is widely recognized as the reference for Brassica rapa. However, the high self-incompatibility of Chiifu limits its broader utilization. In this study, we report the development of self-compatible Chiifu lines through a meticulous marker-assisted selection (MAS) strategy, involving the substitution of the Chiifu allele of MLPK (M-locus protein kinase) with that from the self-compatible Yellow Sarson (YS). A YS-based marker (SC-MLPK) was employed to screen 841 B. rapa accessions, confirming that all eight accessions with the mlpk/mlpk (mm) genotype exhibited self-compatibility. Additionally, we designed 131 High-Resolution Melting (HRM) markers evenly distributed across the B. rapa genome as genomic background selection (GBS) markers to facilitate the introgression of self-compatibility from YS into Chiifu along with SC-MLPK. Genome background screening revealed that the BC3S1 population had a proportion of the recurrent parent genome (PR) ranging from 93.9% to 98.5%. From this population, we identified self-compatible individuals exhibiting a high number of pollen tubes penetrating stigmas (NPT) (>25) and a maximum compatibility index (CI) value of 7.5. Furthermore, we selected two individuals demonstrating significant similarity to Chiifu in both genetic background and morphological appearance, alongside self-compatibility. These selected individuals were self-pollinated to generate two novel lines designated as SC-Chiifu Lines. The development of these self-compatible Chiifu lines, together with the SC-MLPK marker and the set of HRM markers, represents valuable tools for B. rapa genetics and breeding.
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Affiliation(s)
| | | | | | | | | | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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2
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Feng Q, Yu J, Yu J, Hu M, Gu L, Wang H, Du X, Zhu B, Cai M. Identification and Genome-Wide Gene Expression Perturbation of a Trisomy in Chinese Kale ( Brassica oleracea var. alboglabra). PLANTS (BASEL, SWITZERLAND) 2023; 12:3199. [PMID: 37765363 PMCID: PMC10536521 DOI: 10.3390/plants12183199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Trisomy harbouring an extra copy of the chromosome generally causes a variety of physical and intellectual disabilities in mammals but is an extremely rare and important genetic stock in plants. In this study, a spontaneous trisomy plant in a Chinese kale accession (Brassica oleracea var. alboglabra, CC, 2n = 18) that showed significantly smaller plant architecture when compared to other normal plants was found and subsequently confirmed by cytological analysis in which the chromosome set of 2n = 19 and abnormal chromosome behaviour were observed. Then, based on the gene expression deviation determined by RNA-seq, the extra chromosome copy in this trisomy was identified as chromosome C2 (TC2). Compared to normal plants, TC2 not only showed generally upregulated differentially expressed genes (DEGs) on chromosome C2 (97.21% of 573 DEGs in chromosome C2) but also exhibited a whole-genome expression perturbation, in which 1329 DEGs (69.87% of total DEGs) were observed along two-copy chromosomes (trans-effect). The genes in the high (gene expression value > 100) and medium (100 > gene expression value > 10) groups were more prone to decreased gene expression, but the genes in the low group (10 > gene expression value > 0.1) showed upregulated expression deviation. In addition, GO (Gene ontology) annotation analysis revealed that the upregulated DEGs in the trans-effect group were overrepresented by the genes involved in the response to stress category, while the downregulated DEGs in the trans-effect group were mostly enriched in pathways related to DNA synthesis. In conclusion, we think our results can provide important resources for genetic analysis in B. oleracea and show some novel insights for understanding trisomy plant biology.
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Affiliation(s)
| | | | | | | | | | | | | | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (Q.F.); (J.Y.); (J.Y.); (M.H.); (L.G.); (H.W.); (X.D.)
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (Q.F.); (J.Y.); (J.Y.); (M.H.); (L.G.); (H.W.); (X.D.)
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3
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Zhao Y, Huang S, Zhang Y, Tan C, Feng H. Role of Brassica orphan gene BrLFM on leafy head formation in Chinese cabbage (Brassica rapa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:170. [PMID: 37420138 DOI: 10.1007/s00122-023-04411-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
Brassica orphan gene BrFLM, identified by two allelic mutants, was involved in leafy head formation in Chinese cabbage. Leafy head formation is a unique agronomic trait of Chinese cabbage that determines its yield and quality. In our previous study, an EMS mutagenesis Chinese cabbage mutant library was constructed using the heading Chinese cabbage double haploid (DH) line FT as the wild-type. Here, we screened two extremely similar leafy head deficiency mutants lfm-1 and lfm-2 with geotropic growth leaves from the library to investigate the gene(s) related to leafy head formation. Reciprocal crossing results showed that these two mutants were allelic. We utilized lfm-1 to identify the mutant gene(s). Genetic analysis showed that the mutated trait was controlled by a single nuclear gene Brlfm. Mutmap analysis showed that Brlfm was located on chromosome A05, and BraA05g012440.3C or BraA05g021450.3C were the candidate gene. Kompetitive allele-specific PCR analysis eliminated BraA05g012440.3C from the candidates. Sanger sequencing identified an SNP from G to A at the 271st nucleotide on BraA05g021450.3C. The sequencing of lfm-2 detected another non-synonymous SNP (G to A) located at the 266st nucleotide on BraA05g021450.3C, which verified its function on leafy head formation. We blasted BraA05g021450.3C on database and found that it belongs to a Brassica orphan gene encoding an unknown 13.74 kDa protein, named BrLFM. Subcellular localization showed that BrLFM was located in the nucleus. These findings reveal that BrLFM is involved in leafy head formation in Chinese cabbage.
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Affiliation(s)
- Yonghui Zhao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shengnan Huang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Yun Zhang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chong Tan
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
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Mokhtar MM, Abd-Elhalim HM, El Allali A. A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index. AOB PLANTS 2023; 15:plad015. [PMID: 37197714 PMCID: PMC10184434 DOI: 10.1093/aobpla/plad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/01/2023] [Indexed: 05/19/2023]
Abstract
Recent advances in genome sequencing have led to an increase in the number of sequenced genomes. However, the presence of repetitive sequences complicates the assembly of plant genomes. The LTR assembly index (LAI) has recently been widely used to assess the quality of genome assembly, as a higher LAI is associated with a higher quality of assembly. Here, we assessed the quality of assembled genomes of 1664 plant and algal genomes using LAI and reported the results as data repository called PlantLAI (https://bioinformatics.um6p.ma/PlantLAI). A number of 55 117 586 pseudomolecules/scaffolds with a total length of 988.11 gigabase-pairs were examined using the LAI workflow. A total of 46 583 551 accurate LTR-RTs were discovered, including 2 263 188 Copia, 2 933 052 Gypsy, and 1 387 311 unknown superfamilies. Consequently, only 1136 plant genomes are suitable for LAI calculation, with values ranging from 0 to 31.59. Based on the quality classification system, 476 diploid genomes were classified as draft, 472 as reference, and 135 as gold genomes. We also provide a free webtool to calculate the LAI of newly assembled genomes and the ability to save the result in the repository. The data repository is designed to fill in the gaps in the reported LAI of existing genomes, while the webtool is designed to help researchers calculate the LAI of their newly sequenced genomes.
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Affiliation(s)
| | - Haytham M Abd-Elhalim
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza 12619, Egypt
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Amas JC, Thomas WJW, Zhang Y, Edwards D, Batley J. Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species. PHYTOPATHOLOGY 2023:PHYTO08220289FI. [PMID: 36324059 DOI: 10.1094/phyto-08-22-0289-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.
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Affiliation(s)
- Junrey C Amas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - William J W Thomas
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Yueqi Zhang
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - David Edwards
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
| | - Jacqueline Batley
- School of Biological Sciences and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia 6001
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Noskova E, Abramov N, Iliutkin S, Sidorin A, Dobrynin P, Ulyantsev VI. GADMA2: more efficient and flexible demographic inference from genetic data. Gigascience 2022; 12:giad059. [PMID: 37609916 PMCID: PMC10445054 DOI: 10.1093/gigascience/giad059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/31/2023] [Accepted: 07/05/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Inference of complex demographic histories is a source of information about events that happened in the past of studied populations. Existing methods for demographic inference typically require input from the researcher in the form of a parameterized model. With an increased variety of methods and tools, each with its own interface, the model specification becomes tedious and error-prone. Moreover, optimization algorithms used to find model parameters sometimes turn out to be inefficient, for instance, by being not properly tuned or highly dependent on a user-provided initialization. The open-source software GADMA addresses these problems, providing automatic demographic inference. It proposes a common interface for several likelihood engines and provides global parameters optimization based on a genetic algorithm. RESULTS Here, we introduce the new GADMA2 software and provide a detailed description of the added and expanded features. It has a renovated core code base, new likelihood engines, an updated optimization algorithm, and a flexible setup for automatic model construction. We provide a full overview of GADMA2 enhancements, compare the performance of supported likelihood engines on simulated data, and demonstrate an example of GADMA2 usage on 2 empirical datasets. CONCLUSIONS We demonstrate the better performance of a genetic algorithm in GADMA2 by comparing it to the initial version and other existing optimization approaches. Our experiments on simulated data indicate that GADMA2's likelihood engines are able to provide accurate estimations of demographic parameters even for misspecified models. We improve model parameters for 2 empirical datasets of inbred species.
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Affiliation(s)
- Ekaterina Noskova
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
| | | | - Stanislav Iliutkin
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
| | - Anton Sidorin
- Laboratory of Biochemical Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, Moscow 119991, Russia
| | - Vladimir I Ulyantsev
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
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Zheng S, Szymański J, Shahaf N, Malitsky S, Meir S, Wang X, Aharoni A, Rogachev I. Metabolic diversity in a collection of wild and cultivated Brassica rapa subspecies. Front Mol Biosci 2022; 9:953189. [DOI: 10.3389/fmolb.2022.953189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
Brassica rapa (B. rapa) and its subspecies contain many bioactive metabolites that are important for plant defense and human health. This study aimed at investigating the metabolite composition and variation among a large collection of B. rapa genotypes, including subspecies and their accessions. Metabolite profiling of leaves of 102 B. rapa genotypes was performed using ultra-performance liquid chromatography coupled with a photodiode array detector and quadrupole time-of-flight mass spectrometry (UPLC-PDA-QTOF-MS/MS). In total, 346 metabolites belonging to different chemical classes were tentatively identified; 36 out of them were assigned with high confidence using authentic standards and 184 were those reported in B. rapa leaves for the first time. The accumulation and variation of metabolites among genotypes were characterized and compared to their phylogenetic distance. We found 47 metabolites, mostly representing anthocyanins, flavonols, and hydroxycinnamic acid derivatives that displayed a significant correlation to the phylogenetic relatedness and determined four major phylometabolic branches; 1) Chinese cabbage, 2) yellow sarson and rapid cycling, 3) the mizuna-komatsuna-turnip-caitai; and 4) a mixed cluster. These metabolites denote the selective pressure on the metabolic network during B. rapa breeding. We present a unique study that combines metabolite profiling data with phylogenetic analysis in a large collection of B. rapa subspecies. We showed how selective breeding utilizes the biochemical potential of wild B. rapa leading to highly diverse metabolic phenotypes. Our work provides the basis for further studies on B. rapa metabolism and nutritional traits improvement.
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Zhang H, Wafula EK, Eilers J, Harkess A, Ralph PE, Timilsena PR, dePamphilis CW, Waite JM, Honaas LA. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes. FRONTIERS IN PLANT SCIENCE 2022; 13:975942. [PMID: 36452099 PMCID: PMC9702816 DOI: 10.3389/fpls.2022.975942] [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: 06/22/2022] [Accepted: 09/21/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of sequencing technologies has led to a deeper understanding of plant genomes. However, direct experimental evidence connecting genes to important agronomic traits is still lacking in most non-model plants. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). An efficient way to identify genetic factors for important traits in non-model organisms can be to transfer knowledge across genomes. However, major obstacles exist, including complex evolutionary histories and variable quality and content of publicly available plant genomes. As researchers aim to link genes to traits of interest, these challenges can impede the transfer of experimental evidence across plant species, namely in the curation of high-quality, high-confidence gene models in an evolutionary context. Here we present a workflow using a collection of bioinformatic tools for the curation of deeply conserved gene families of interest across plant genomes. To study gene families involved in tree architecture in European pear and other rosaceous species, we used our workflow, plus a draft genome assembly and high-quality annotation of a second P. communis cultivar, 'd'Anjou.' Our comparative gene family approach revealed significant issues with the most recent 'Bartlett' genome - primarily thousands of missing genes due to methodological bias. After correcting assembly errors on a global scale in the 'Bartlett' genome, we used our workflow for targeted improvement of our genes of interest in both P. communis genomes, thus laying the groundwork for future functional studies in pear tree architecture. Further, our global gene family classification of 15 genomes across 6 genera provides a valuable and previously unavailable resource for the Rosaceae research community. With it, orthologs and other gene family members can be easily identified across any of the classified genomes. Importantly, our workflow can be easily adopted for any other plant genomes and gene families of interest.
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Affiliation(s)
- Huiting Zhang
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Eric K. Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jon Eilers
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Alex E. Harkess
- College of Agriculture, Auburn University, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Paula E. Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Claude W. dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jessica M. Waite
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Loren A. Honaas
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
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Alemán-Báez J, Qin J, Cai C, Zou C, Bucher J, Paulo MJ, Voorrips RE, Bonnema G. Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3611-3628. [PMID: 36057748 PMCID: PMC9519658 DOI: 10.1007/s00122-022-04205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.
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Affiliation(s)
- Jorge Alemán-Báez
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Jian Qin
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Chengcheng Cai
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Chunmei Zou
- Centre for Crop Systems Analysis, Wageningen University and Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Roeland E. Voorrips
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
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Palos K, Nelson Dittrich AC, Yu L, Brock JR, Railey CE, Wu HYL, Sokolowska E, Skirycz A, Hsu PY, Gregory BD, Lyons E, Beilstein MA, Nelson ADL. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae. THE PLANT CELL 2022; 34:3233-3260. [PMID: 35666179 PMCID: PMC9421480 DOI: 10.1093/plcell/koac166] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/05/2022] [Indexed: 06/01/2023]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth of RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement a harmonized identification and annotation effort for lincRNAs that enables cross-species functional and genomic comparisons as well as prioritization of functional candidates. In this study, we processed >24 Tera base pairs of RNA-seq data from >16,000 experiments to identify ∼130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify conserved motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our data set with sequence or transcriptional conservation. Finally, we used guilt-by-association analyses to assign putative functions to lincRNAs within our data set. We tested this approach on a subset of lincRNAs associated with germination and seed development, observing germination defects for Arabidopsis lines harboring T-DNA insertions at these loci. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, small open reading frames, or abiotic-stress modulated expression are a few of the annotations that will guide functional analyses into this cryptic portion of the transcriptome.
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Affiliation(s)
- Kyle Palos
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | | | - Li’ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
| | - Caylyn E Railey
- The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | | | | | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eric Lyons
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Mark A Beilstein
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
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11
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Cai C, Bucher J, Bakker FT, Bonnema G. Evidence for two domestication lineages supporting a middle-eastern origin for Brassica oleracea crops from diversified kale populations. HORTICULTURE RESEARCH 2022; 9:uhac033. [PMID: 35184188 PMCID: PMC8976692 DOI: 10.1093/hr/uhac033] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/24/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as "species") using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the "leafy head" lineage (LHL) and the "arrested inflorescence" lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.
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Affiliation(s)
- Chengcheng Cai
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University and Research, Wageningen, The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Freek T Bakker
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
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12
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Zenda T, Liu S, Dong A, Li J, Wang Y, Liu X, Wang N, Duan H. Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value. FRONTIERS IN PLANT SCIENCE 2021; 12:774994. [PMID: 34925418 PMCID: PMC8672198 DOI: 10.3389/fpls.2021.774994] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Songtao Liu
- Academy of Agriculture and Forestry Sciences, Hebei North University, Zhangjiakou, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yafei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinyue Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
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13
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Komarnytsky S, Retchin S, Vong CI, Lila MA. Gains and Losses of Agricultural Food Production: Implications for the Twenty-First Century. Annu Rev Food Sci Technol 2021; 13:239-261. [PMID: 34813357 DOI: 10.1146/annurev-food-082421-114831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The world food supply depends on a diminishing list of plant crops and animal livestock to not only feed the ever-growing human population but also improve its nutritional state and lower the disease burden. Over the past century or so, technological advances in agricultural and food processing have helped reduce hunger and poverty but have not adequately addressed sustainability targets. This has led to an erosion of agricultural biodiversity and balanced diets and contributed to climate change and rising rates of chronic metabolic diseases. Modern food supply chains have progressively lost dietary fiber, complex carbohydrates, micronutrients, and several classes of phytochemicals with high bioactivity and nutritional relevance. This review introduces the concept of agricultural food systems losses and focuses on improved sources of agricultural diversity, proteins with enhanced resilience, and novel monitoring, processing, and distribution technologies that are poised to improve food security, reduce food loss and waste, and improve health profiles in the near future. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Slavko Komarnytsky
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Sophia Retchin
- Kenan-Flagler Business School, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chi In Vong
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
| | - Mary Ann Lila
- Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina; .,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina
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14
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Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis). BMC Genomics 2021; 22:819. [PMID: 34773977 PMCID: PMC8590779 DOI: 10.1186/s12864-021-08110-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenous RNA (ceRNA) network that provides valuable information to better understand the vernalization response. RESULTS In this study, seeds sampled from the Chinese cabbage doubled haploid (DH) line 'FT' with or without vernalization treatment were used for whole-transcriptome sequencing. A total of 2702 differentially expressed (DE) mRNAs, 151 DE lncRNAs, 16 DE circRNAs, and 233 DE miRNAs were identified in the vernalization-treated seeds. Various transcription factors, such as WRKY, MYB, NAC, bHLH, MADS-box, zinc finger protein CONSTANS-like gene, and B3 domain protein, and regulatory proteins that play important roles in the vernalization pathway were identified. Additionally, we constructed a vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA‒DEmRNA, 67 DEmiRNA‒DElncRNA, and 12 DEmiRNA‒DEcircRNA interactions, in Chinese cabbage. Furthermore, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs, which are involved in the regulation of flowering time, floral organ formation, bolting, and flowering, were identified. CONCLUSIONS Our results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernalization in Chinese cabbage.
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15
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Kates HR, Anido FL, Sánchez-de la Vega G, Eguiarte LE, Soltis PS, Soltis DE. Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.618380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.
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16
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Ferreira de Carvalho J, Stoeckel S, Eber F, Lodé-Taburel M, Gilet MM, Trotoux G, Morice J, Falentin C, Chèvre AM, Rousseau-Gueutin M. Untangling structural factors driving genome stabilization in nascent Brassica napus allopolyploids. THE NEW PHYTOLOGIST 2021; 230:2072-2084. [PMID: 33638877 DOI: 10.1111/nph.17308] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/22/2021] [Indexed: 05/28/2023]
Abstract
Allopolyploids have globally higher fitness than their diploid progenitors; however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success. Using the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid Brassica napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors, and polyploid formation type. We evaluated the evolution of meiotic behavior and fertility and identified rearrangements in S1 to S9 lineages to explore the positive consequences of euploid selection on B. napus genome stability. Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a decrease in number of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number depended strongly on the genetic background and cytoplasm donor. The combined use of both self-fertilization and recurrent euploid selection allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success.
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Affiliation(s)
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Frédérique Eber
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | | | | | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, 35650, France
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17
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Blischak PD, Barker MS, Gutenkunst RN. Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data. Mol Biol Evol 2021; 37:2124-2136. [PMID: 32068861 DOI: 10.1093/molbev/msaa042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/04/2023] Open
Abstract
Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model's ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.
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Affiliation(s)
- Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.,Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ
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18
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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19
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Stansell Z, Björkman T. From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection. HORTICULTURE RESEARCH 2020; 7:159. [PMID: 33082966 PMCID: PMC7528014 DOI: 10.1038/s41438-020-00375-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/12/2020] [Accepted: 08/01/2020] [Indexed: 05/03/2023]
Abstract
Worldwide, broccoli (Brassica oleracea var. italica) is among the most economically important, nutritionally rich, and widely-grown vegetable crops. To explore the genomic basis of the dramatic changes in broccoli morphology in the last century, we evaluated 109 broccoli or broccoli/cauliflower intermediates for 24 horticultural traits. Genotype-by-sequencing markers were used to determine four subpopulations within italica: Calabrese broccoli landraces and hybrids, sprouting broccoli, and violet cauliflower, and to evaluate between and within group relatedness and diversity. While overall horticultural quality and harvest index of improved hybrid broccoli germplasm has increased by year of cultivar release, this improvement has been accompanied by a considerable reduction in allelic diversity when compared to the larger pool of germplasm. Two landraces are the most likely founding source of modern broccoli hybrids, and within these modern hybrids, we identified 13 reduction-in-diversity genomic regions, 53 selective sweeps, and 30 (>1 Mbp) runs of homozygosity. Landrace accessions collected in southern Italy contained 4.8-fold greater unique alleles per accessions compared to modern hybrids and provide a valuable resource in subsequent improvement efforts. This work broadens the understanding of broccoli germplasm, informs conservation efforts, and enables breeding for complex quality traits and regionally adapted cultivars.
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Affiliation(s)
- Zachary Stansell
- Cornell University, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
- Cornell AgriTech, Cornell University, Geneva, NY 14456 USA
| | - Thomas Björkman
- Cornell University, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
- Cornell AgriTech, Cornell University, Geneva, NY 14456 USA
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20
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Liu Z, Fan M, Yue EK, Li Y, Tao RF, Xu HM, Duan MH, Xu JH. Natural variation and evolutionary dynamics of transposable elements in Brassica oleracea based on next-generation sequencing data. HORTICULTURE RESEARCH 2020; 7:145. [PMID: 32922817 PMCID: PMC7459127 DOI: 10.1038/s41438-020-00367-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/22/2020] [Accepted: 06/19/2020] [Indexed: 06/02/2023]
Abstract
Brassica oleracea comprises various economically important vegetables and presents extremely diverse morphological variations. They provide a rich source of nutrition for human health and have been used as a model system for studying polyploidization. Transposable elements (TEs) account for nearly 40% of the B. oleracea genome and contribute greatly to genetic diversity and genome evolution. Although the proliferation of TEs has led to a large expansion of the B. oleracea genome, little is known about the population dynamics and evolutionary activity of TEs. A comprehensive mobilome profile of 45,737 TE loci was obtained from resequencing data from 121 diverse accessions across nine B. oleracea morphotypes. Approximately 70% (32,195) of the loci showed insertion polymorphisms between or within morphotypes. In particular, up to 1221 loci were differentially fixed among morphotypes. Further analysis revealed that the distribution of the population frequency of TE loci was highly variable across different TE superfamilies and families, implying a diverse expansion history during host genome evolution. These findings provide better insight into the evolutionary dynamics and genetic diversity of B. oleracea genomes and will potentially serve as a valuable resource for molecular markers and association studies between TE-based genomic variations and morphotype-specific phenotypic differentiation.
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Affiliation(s)
- Zhen Liu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
| | - Miao Fan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
| | - Er-Kui Yue
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
| | - Yu Li
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
| | - Ruo-Fu Tao
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
| | - Hai-Ming Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
| | - Ming-Hua Duan
- Zhejiang Zhengjingyuan Pharmacy Chain Co., Ltd. & Hangzhou Zhengcaiyuan Pharmaceutical Co., Ltd., 310021 Hangzhou, People’s Republic of China
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, 310058 Hangzhou, People’s Republic of China
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21
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Manchanda N, Portwood JL, Woodhouse MR, Seetharam AS, Lawrence-Dill CJ, Andorf CM, Hufford MB. GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations. BMC Genomics 2020; 21:193. [PMID: 32122303 PMCID: PMC7053122 DOI: 10.1186/s12864-020-6568-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/07/2020] [Indexed: 11/28/2022] Open
Abstract
Background Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types. Results Our application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies. Conclusions The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.
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Affiliation(s)
- Nancy Manchanda
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | | | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Carolyn J Lawrence-Dill
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.,Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
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22
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Boutte J, Maillet L, Chaussepied T, Letort S, Aury JM, Belser C, Boideau F, Brunet A, Coriton O, Deniot G, Falentin C, Huteau V, Lodé-Taburel M, Morice J, Trotoux G, Chèvre AM, Rousseau-Gueutin M, Ferreira de Carvalho J. Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2020; 11:577536. [PMID: 33281844 PMCID: PMC7689015 DOI: 10.3389/fpls.2020.577536] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/24/2020] [Indexed: 05/07/2023]
Abstract
Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa 'Z1' genome vs. the B. rapa 'Chiifu' genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa 'Z1' and B. rapa 'Chiifu' at the origin of important length differences in some chromosomes. For instance, lengths of 'Z1' and 'Chiifu' A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of 'Z1' compared to 'Chiifu.' Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in 'Z1' genome compared to 'Chiifu' on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.
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Affiliation(s)
- Julien Boutte
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
- *Correspondence: Julien Boutte,
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | | | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut de biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut de biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Franz Boideau
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | - Anael Brunet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | | | | | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | | | | | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
| | - Gwenn Trotoux
- IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France
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23
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Long noncoding RNAs in Brassica rapa L. following vernalization. Sci Rep 2019; 9:9302. [PMID: 31243302 PMCID: PMC6594933 DOI: 10.1038/s41598-019-45650-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 06/07/2019] [Indexed: 01/04/2023] Open
Abstract
Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species.
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Ferreira de Carvalho J, Lucas J, Deniot G, Falentin C, Filangi O, Gilet M, Legeai F, Lode M, Morice J, Trotoux G, Aury JM, Barbe V, Keller J, Snowdon R, He Z, Denoeud F, Wincker P, Bancroft I, Chèvre AM, Rousseau-Gueutin M. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:434-447. [PMID: 30604905 DOI: 10.1111/tpj.14228] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/14/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other donor has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus, on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared with cytosolic protein complexes and with genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and are undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neopolyploids showed no biased subgenome expression or maternal homogenization via gene conversion, despite the presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes that could be tested and generalized in other allopolyploid species.
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Affiliation(s)
| | - Jérémy Lucas
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenaëlle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Olivier Filangi
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Marie Gilet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Fabrice Legeai
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Maryse Lode
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Gwenn Trotoux
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
| | - Jean Keller
- UMR CNRS 6553 ECOBIO, OSUR, Université de Rennes 1, Rennes, 35042, France
| | - Rod Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - France Denoeud
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique, Genoscope, Institut de biologie François-Jacob, Evry, 91057, France
- UMR CNRS 8030, Evry, CP5706, France
- Université d'Evry-Val-d'Essonne, Université Paris-Saclay, Evry, 91000, France
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, 35653, France
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Kubo N, Onnazaka K, Mizuno S, Tsuji G. Classification of "nabana" ( Brassica rapa) cultivars and landraces based on simple sequence repeat markers. BREEDING SCIENCE 2019; 69:179-185. [PMID: 31086496 PMCID: PMC6507715 DOI: 10.1270/jsbbs.18126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/15/2018] [Indexed: 06/09/2023]
Abstract
Brassica rapa or B. napus vegetables for eating as young inflorescences and stalks are called "nabana". Japanese nabana includes "flower-bud type" and "stem-and-leaf type". Chinese and European types are also known (cai-xin, zicaitai, and broccoletto). We classified nabana belonging to B. rapa and other B. rapa vegetables. In a simple sequence repeat-based phylogram, 49 ingroup samples were classified into four groups (I-IV). Flower-bud and stem-and-leaf types were separated into groups I and III, respectively, with a slight overlap in group II. Cai-xin and non-heading Chinese cabbages were included in group IV. Broccoletto was placed in group III, close to turnips. Zicaitai cultivars were included in group II. We tested for clubroot resistance (CR) and its marker genotypes in nabana because of their agronomical importance. Ten cultivars were resistant to group 4 pathogen but not to group 2. Most of the CR cultivars had heterozygous resistance alleles in the CRb and Crr1 loci, consistent with inoculation tests. Our results suggest that Japanese nabana lines and foreign types were differentiated according to their consumption parts and cultivar origins, respectively. This study elucidates the relationships and CR properties of nabana and provides valuable information for the breeding of nabana cultivars.
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Affiliation(s)
- Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University,
1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522,
Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center,
74 Oji, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto 619-0244,
Japan
| | - Kumiko Onnazaka
- Kyoto Prefectural Kyoto Otokuni Agriculture Improvement Extension Center,
15 Tokudaiji Dangoden-cho, Nishikyogoku, Ukyo-ku, Kyoto 615-0846,
Japan
- Present address: Kyoto Prefectural Nantan Agriculture Improvement Extension Center21 Fujinoki, Oyama Higashi-machi, Sonobecho, Nantan, Kyoto 622-0041,
Japan
| | - Shinji Mizuno
- Warm Region Horticulture Institute, Chiba Prefectural Agriculture and Forestry Research Center,
1762 Yamamoto, Tateyama, Chiba 294-0014,
Japan
- Present address: College of Bioresource Sciences, Nihon University1866 Kameino, Fujisawa, Kanagawa 252-0880,
Japan
| | - Gento Tsuji
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University,
1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522,
Japan
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26
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Gaut BS, Seymour DK, Liu Q, Zhou Y. Demography and its effects on genomic variation in crop domestication. NATURE PLANTS 2018; 4:512-520. [PMID: 30061748 DOI: 10.1038/s41477-018-0210-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 05/20/2023]
Abstract
Over two thousand plant species have been modified morphologically through cultivation and human use. Here, we review three aspects of crop domestication that are currently undergoing marked revisions, due to analytical advancements and their application to whole genome resequencing (WGS) data. We begin by discussing the duration and demographic history of domestication. There has been debate as to whether domestication occurred quickly or slowly. The latter is tentatively supported both by fossil data and application of WGS data to sequentially Markovian coalescent methods that infer the history of effective population size. This history suggests the possibility of extended human impacts on domesticated lineages prior to their purposeful cultivation. We also make the point that demographic history matters, because it shapes patterns and levels of extant genetic diversity. We illustrate this point by discussing the evolutionary processes that contribute to the empirical observation that most crops examined to date have more putatively deleterious alleles than their wild relatives. These deleterious alleles may contribute to genetic load within crops and may be fitting targets for crop improvement. Finally, the same demographic factors are likely to shape the spectrum of structural variants (SVs) within crops. SVs are known to underlie many of the phenotypic changes associated with domestication and crop improvement, but we currently lack sufficient knowledge about the mechanisms that create SVs, their rates of origin, their population frequencies and their phenotypic effects.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Qingpo Liu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, China
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
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27
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Shea DJ, Shimizu M, Itabashi E, Miyaji N, Miyazaki J, Osabe K, Kaji M, Okazaki K, Fujimoto R. Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F 1 hybrid cultivar of Chinese cabbage. BREEDING SCIENCE 2018; 68:375-380. [PMID: 30100805 PMCID: PMC6081294 DOI: 10.1270/jsbbs.17124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
The genome-wide characterization of single nucleotide polymorphism (SNP) between cultivars or between inbred lines contributes to the creation of genetic markers that are important for plant breeding. Functional markers derived from polymorphisms within genes that affect phenotypic variation are especially valuable in plant breeding. Here, we report on the genome re-sequencing and analysis of the two parental inbred lines of the commercial F1 hybrid Chinese cabbage cultivar "W77". Through the genome-wide identification and classification of the SNPs and indels present in each parental line, we identified about 1,500 putative non-functional genes in each parent. We designed cleaved amplified polymorphic sequence (CAPS) markers using specific mutations found at Eco RI restriction sites in the parental lines and confirmed their Mendelian segregation by constructing a linkage map using 96 F2 plants derived from the F1 hybrid cultivar, "W77". Our results and data will be a useful genomic resource for future studies of gene function and metagenomic studies in Chinese cabbage.
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Affiliation(s)
- Daniel J. Shea
- Graduate School of Science and Technology, Niigata University,
Ikarashi-ninocho, Niigata 950-2181,
Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center,
Narita, Kitakami, Iwate 024-0003,
Japan
| | - Etsuko Itabashi
- Institute of Vegetable and Floriculture Science, NARO,
Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Naomi Miyaji
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Junji Miyazaki
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, La Trobe University,
Melbourne VICAustralia
| | - Kenji Osabe
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University,
Onna-son, Okinawa 904-0495,
Japan
| | - Makoto Kaji
- Watanabe Seed Co., Ltd.,
Machiyashiki, Misato-cho, Miyagi 987-0003,
Japan
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University,
Ikarashi-ninocho, Niigata 950-2181,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
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28
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Hempel P, Hohe A, Tränkner C. Molecular Reconstruction of an Old Pedigree of Diploid and Triploid Hydrangea macrophylla Genotypes. FRONTIERS IN PLANT SCIENCE 2018; 9:429. [PMID: 29720985 PMCID: PMC5915539 DOI: 10.3389/fpls.2018.00429] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/20/2018] [Indexed: 06/06/2023]
Abstract
The ornamental crop species Hydrangea macrophylla exhibits diploid and triploid levels of ploidy and develops lacecap (wild type) or mophead inflorescences. In order to characterize a H. macrophylla germplasm collection, we determined the inflorescence type and the 2C DNA content of 120 plants representing 43 cultivars. We identified 78 putative diploid and 39 putative triploid plants by flow cytometry. In our collection 69 out of 98 flowering plants produced lacecap inflorescences, whereas 29 plants developed mophead inflorescences. Surprisingly, 12 cultivars included diploid as well as triploid plants, while 5 cultivars contained plants with different inflorescence types. We genotyped this germplasm collection using 12 SSR markers that detected 2-7 alleles per marker, and identified 51 different alleles in this collection. We detected 62 distinct fingerprints, revealing a higher genetic variation than the number of cultivars suggested. Only one genotype per cultivar is expected due to the vegetative propagation of Hydrangea cultivars; however we identified 25 cultivars containing 2-4 different genotypes. These different genotypes explained the variation in DNA content and inflorescence type. Diploid and triploid plants with the same cultivar name were exclusively mix-ups. We therefor assume, that 36% of the tested plants were mislabeled. Based on the "Wädenswil" pedigree, which includes 31 of the tested cultivars, we predicted cultivar-specific fingerprints and identified at least 21 out of 31 cultivars by SSR marker-based reconstruction of the "Wädenswil" pedigree. Furthermore, we detected 4 putative interploid crosses between diploid and triploid plants in this pedigree. These interploid crosses resulted in diploid or/and triploid offspring, suggesting that crosses with triploids were successfully applied in breeding of H. macrophylla.
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Affiliation(s)
- Peter Hempel
- Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
- Faculty of Landscape Architecture, Horticulture and Forestry, University of Applied Sciences Erfurt, Erfurt, Germany
| | - Annette Hohe
- Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
- Faculty of Landscape Architecture, Horticulture and Forestry, University of Applied Sciences Erfurt, Erfurt, Germany
| | - Conny Tränkner
- Leibniz Institute of Vegetable and Ornamental Crops, Erfurt, Germany
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Shea DJ, Shimizu M, Nishida N, Fukai E, Abe T, Fujimoto R, Okazaki K. IntroMap: a signal analysis based method for the detection of genomic introgressions. BMC Genet 2017; 18:101. [PMID: 29202713 PMCID: PMC5716257 DOI: 10.1186/s12863-017-0568-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling. RESULTS We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Additionally we show, through targeted marker-based assays, validation of the IntroMap predicted regions for the hybrid cultivar. CONCLUSIONS This approach can be used to automate the screening of large populations, reducing the time and labor required, and can improve the accuracy of the detection of introgressed regions in comparison to a marker-based approach. In contrast to other approaches that generally rely upon a variant calling step, our method achieves accurate identification of introgressed regions without variant calling, relying solely upon alignment.
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Affiliation(s)
- Daniel J Shea
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Narita, Kitakami, 024-0003, Japan
| | - Namiko Nishida
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Eigo Fukai
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan
| | - Takashi Abe
- Department of Computer Science, Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Keiichi Okazaki
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
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Neik TX, Barbetti MJ, Batley J. Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:1788. [PMID: 29163558 PMCID: PMC5681527 DOI: 10.3389/fpls.2017.01788] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Martin J. Barbetti
- School of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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31
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Bird KA, An H, Gazave E, Gore MA, Pires JC, Robertson LD, Labate JA. Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L. FRONTIERS IN PLANT SCIENCE 2017; 8:321. [PMID: 28348571 PMCID: PMC5346582 DOI: 10.3389/fpls.2017.00321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/22/2017] [Indexed: 05/12/2023]
Abstract
The crop species Brassica rapa L. has significant economic importance around the world. However, the global distribution and complex evolutionary history of the species has made investigating its genetic population structure difficult. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption, and fodder for livestock. These subspecies include the oilseed morphotypes. oleifera (turnip rape), ssp. dichotoma (brown sarson/toria), ssp. trilocularis (yellow sarson); ssp. rapa (turnip); and Asian leafy vegetables ssp. pekinensis (Chinese cabbage), ssp. chinensis (bok choy), ssp. nipposinica (mizuna/mibuna), ssp. rapifera (rapini/broccoli rabe), ssp. narinosa (tatsoi), ssp parachinensis (choy sum), and ssp. perviridis (komatsuna). To date, studies have had insufficient sampling to determine the relationship of all morphotypes, especially oilseed morphotypes, and questions remain over the contribution of morphotype and geographic origin to population structure. We used genotyping-by-sequencing to score 18,272 single nucleotide polymorphism markers in a globally diverse panel of 333 B. rapa National Plant Germplasm System accessions that included 10 recognized subspecies. Our population genetic and phylogenetic analyses were broadly congruent and revealed five subpopulations that were largely reflective of morphotype and geography. These subpopulations were 1. European turnips/oilseed, 2. Asian turnips/oilseed, 3. yellow/brown sarson (ssp. trilocularis and ssp. dichotoma), 4. Chinese cabbage (ssp. pekinensis), and 5. bok choy, choy sum, and tatsoi (ssp. chinensis, ssp. parachinensis, ssp. narinosa). Additionally, we found evidence of polyphyly and/or paraphyly, particularly for oilseed morphotypes (ssp. oleifera and ssp. dichotoma) and turnips. The results of this study have provided improved resolution to the genetic and phylogenetic relationships of subspecies within the species B. rapa. Understanding of these relationships is key to the future genetic study and improvement of this globally important crop species.
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Affiliation(s)
- Kevin A. Bird
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
- *Correspondence: Kevin A. Bird
| | - Hong An
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - J. Chris Pires
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Larry D. Robertson
- Plant Genetic Resources Unit, United States Department of Agriculture-Agricultural Research ServiceGeneva, NY, USA
| | - Joanne A. Labate
- Plant Genetic Resources Unit, United States Department of Agriculture-Agricultural Research ServiceGeneva, NY, USA
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