1
|
Zhang Z, Zhang J, Kang L, Qiu X, Xu S, Xu J, Guo Y, Niu Z, Niu B, Bi A, Zhao X, Xu D, Wang J, Yin C, Lu F. Structural variation discovery in wheat using PacBio high-fidelity sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39239888 DOI: 10.1111/tpj.17011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 08/09/2024] [Accepted: 08/22/2024] [Indexed: 09/07/2024]
Abstract
Structural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed due to their complex nature and the limitations of early genomic technologies. By applying the PacBio high-fidelity (HiFi) sequencing for wheat genomes, we performed a comprehensive evaluation of mainstream long-read aligners and SV callers in SV detection. The results indicated that the accuracy of deletion discovery is markedly influenced by callers, accounting for 87.73% of the variance, whereas both aligners (38.25%) and callers (49.32%) contributed substantially to the accuracy variance for insertions. Among the aligners, Winnowmap2 and NGMLR excelled in detecting deletions and insertions, respectively. For SV callers, SVIM achieved the best performance. We demonstrated that combining the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the effect of sequencing depth on the accuracy of SV detection, revealing that low-coverage HiFi sequencing is sufficiently robust for high-quality SV discovery. This study thoroughly evaluated SV discovery approaches and established optimal workflows for investigating structural variations using low-coverage HiFi sequencing in the wheat genome, which will advance SV discovery and decipher the biological functions of SVs in wheat and many other plants.
Collapse
Affiliation(s)
- Zhiliang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jijin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lipeng Kang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuebing Qiu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Song Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yafei Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zelin Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beirui Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Aoyue Bi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daxing Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
2
|
Hu H, Li R, Zhao J, Batley J, Edwards D. Technological Development and Advances for Constructing and Analyzing Plant Pangenomes. Genome Biol Evol 2024; 16:evae081. [PMID: 38669452 PMCID: PMC11058698 DOI: 10.1093/gbe/evae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.
Collapse
Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Risheng Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
3
|
Pace BA, Perales HR, Gonzalez-Maldonado N, Mercer KL. Physiological traits contribute to growth and adaptation of Mexican maize landraces. PLoS One 2024; 19:e0290815. [PMID: 38300909 PMCID: PMC10833551 DOI: 10.1371/journal.pone.0290815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/06/2023] [Indexed: 02/03/2024] Open
Abstract
Local adaptation of populations results from an interplay between their environment and genetics. If functional trait variation influences plant performance, populations can adapt to their local environment. However, populations may also respond plastically to environmental challenges, altering phenotype without shifting allele frequencies. The level of local adaptation in crop landraces and their capacity for plasticity in response to environmental change may predict their continued utility to farmers facing climate change. Yet we understand little about how physiological traits potentially underlying local adaptation of cultivars influence fitness. Farmers in Mexico-the crop center of origin for maize-manage and rely upon a high diversity of landraces. We studied maize grown in Chiapas, Mexico, where strong elevational gradients cover a relatively small geographic area. We reciprocally transplanted 12 populations sourced from three elevational zones (600, 1550 and 2150 m) back into those elevations for two years using a modified split-split plot design to model effects of environment, genetics, and their interaction. We studied physiological and growth traits, including photosynthetic rate, stomatal conductance, stomatal density, relative growth rate (RGR), and seed production. Maize fitness showed indications of local adaptation with highland and midland types performing poorly at warmer lowland locations, though patterns depended on the year. Several physiological traits, including stomatal conductance, were affected by G x E interactions, some of which indicated non-adaptive plastic responses with potential fitness implications. We discerned a significant positive relationship between fitness and relative growth rate. Growth rates in highland landraces were outperformed by midland and lowland landraces grown in high temperature, lowland garden. Lowland landrace stomatal conductance was diminished compared to that of highland landraces in the cooler highland garden. Thus, both adaptive and non-adaptive physiological responses of maize landraces in southern Mexico may have implications for fitness, as well as responses to climate change.
Collapse
Affiliation(s)
- Brian A. Pace
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, United States of America
| | - Hugo R. Perales
- Department of Agroecology, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, Mexico
| | - Noelymar Gonzalez-Maldonado
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
- Department of Land, Air and Water Resources, University of California, Davis, California, United States of America
| | - Kristin L. Mercer
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
| |
Collapse
|
4
|
Munasinghe M, Read A, Stitzer MC, Song B, Menard CC, Ma KY, Brandvain Y, Hirsch CN, Springer N. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS Genet 2023; 19:e1011086. [PMID: 38134220 PMCID: PMC10773942 DOI: 10.1371/journal.pgen.1011086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 01/08/2024] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.
Collapse
Affiliation(s)
- Manisha Munasinghe
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Andrew Read
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michelle C. Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Claire C. Menard
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Kristy Yubo Ma
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, Minnesota, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nathan Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| |
Collapse
|
5
|
Liu J, Dawe RK. Large haplotypes highlight a complex age structure within the maize pan-genome. Genome Res 2023; 33:359-370. [PMID: 36854668 PMCID: PMC10078284 DOI: 10.1101/gr.276705.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.
Collapse
Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
6
|
Shi J, Tian Z, Lai J, Huang X. Plant pan-genomics and its applications. MOLECULAR PLANT 2023; 16:168-186. [PMID: 36523157 DOI: 10.1016/j.molp.2022.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species. With rapid progress in genome sequencing technologies, pan-genome research in plants is now accelerating. Here we review recent advances in plant pan-genomics, including major driving forces of structural variations that constitute the variable sequences, methodological innovations for representing the pan-genome, and major successes in constructing plant pan-genomes. We also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources, which have remarkable advantages over numerous previously assembled less-than-perfect genomes, are expected to become new references for genetic studies and plant breeding.
Collapse
Affiliation(s)
- Junpeng Shi
- State Key Laboratory of Biocontrol, School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| |
Collapse
|
7
|
Hill MJ, Penning BW, McCann MC, Carpita NC. COMPILE: a GWAS computational pipeline for gene discovery in complex genomes. BMC PLANT BIOLOGY 2022; 22:315. [PMID: 35778686 PMCID: PMC9250234 DOI: 10.1186/s12870-022-03668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. RESULTS COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. CONCLUSIONS The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
Collapse
Affiliation(s)
- Matthew J Hill
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan W Penning
- USDA-ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| |
Collapse
|
8
|
Song JM, Zhang Y, Zhou ZW, Lu S, Ma W, Lu C, Chen LL, Guo L. Oil plant genomes: current state of the science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2859-2874. [PMID: 35560205 DOI: 10.1093/jxb/erab472] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/22/2021] [Indexed: 05/25/2023]
Abstract
Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.
Collapse
Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhi-Wei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
9
|
Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives. Genes (Basel) 2022; 13:genes13040598. [PMID: 35456404 PMCID: PMC9031676 DOI: 10.3390/genes13040598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 01/25/2023] Open
Abstract
Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host–pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.
Collapse
|
10
|
Murithi A, Olsen MS, Kwemoi DB, Veronica O, Ertiro BT, L. M. S, Beyene Y, Das B, Prasanna BM, Gowda M. Discovery and Validation of a Recessively Inherited Major-Effect QTL Conferring Resistance to Maize Lethal Necrosis (MLN) Disease. Front Genet 2021; 12:767883. [PMID: 34868253 PMCID: PMC8640137 DOI: 10.3389/fgene.2021.767883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Maize lethal necrosis (MLN) is a viral disease with a devastating effect on maize production. Developing and deploying improved varieties with resistance to the disease is important to effectively control MLN; however, little is known about the causal genes and molecular mechanism(s) underlying MLN resistance. Screening thousands of maize inbred lines revealed KS23-5 and KS23-6 as two of the most promising donors of MLN resistance alleles. KS23-5 and KS23-6 lines were earlier developed at the University of Hawaii, United States, on the basis of a source population constituted using germplasm from Kasetsart University, Thailand. Both linkage mapping and association mapping approaches were used to discover and validate genomic regions associated with MLN resistance. Selective genotyping of resistant and susceptible individuals within large F2 populations coupled with genome-wide association study identified a major-effect QTL (qMLN06_157) on chromosome 6 for MLN disease severity score and area under the disease progress curve values in all three F2 populations involving one of the KS23 lines as a parent. The major-effect QTL (qMLN06_157) is recessively inherited and explained 55%-70% of the phenotypic variation with an approximately 6 Mb confidence interval. Linkage mapping in three F3 populations and three F2 populations involving KS23-5 or KS23-6 as one of the parents confirmed the presence of this major-effect QTL on chromosome 6, demonstrating the efficacy of the KS23 allele at qMLN06.157 in varying populations. This QTL could not be identified in population that was not derived using KS23 lines. Validation of this QTL in six F2 populations with 20 SNPs closely linked with qMLN06.157 was further confirmed its consistent expression across populations and its recessive nature of inheritance. On the basis of the consistent and effective resistance afforded by the KS23 allele at qMLN06.157, the QTL can be used in both marker-assisted forward breeding and marker-assisted backcrossing schemes to improve MLN resistance of breeding populations and key lines for eastern Africa.
Collapse
Affiliation(s)
- Ann Murithi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Michael S. Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Daniel B. Kwemoi
- National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda
| | - Ogugo Veronica
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Suresh L. M.
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| |
Collapse
|
11
|
Qiu Y, O’Connor CH, Della Coletta R, Renk JS, Monnahan PJ, Noshay JM, Liang Z, Gilbert A, Anderson SN, McGaugh SE, Springer NM, Hirsch CN. Whole-genome variation of transposable element insertions in a maize diversity panel. G3 (BETHESDA, MD.) 2021; 11:jkab238. [PMID: 34568911 PMCID: PMC8473971 DOI: 10.1093/g3journal/jkab238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome-wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short-read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 nonredundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e., LTRs, Helitrons, and TIRs) had different frequency distributions within the population. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high-frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 < 0.5) that potentially represent information that has not been well captured in previous SNP-based marker-trait association studies. This study provides a population scale genome-wide assessment of TE variation in maize and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.
Collapse
Affiliation(s)
- Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Christine H O’Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Jonathan S Renk
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Patrick J Monnahan
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Amanda Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah N Anderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
12
|
Noshay JM, Liang Z, Zhou P, Crisp PA, Marand AP, Hirsch CN, Schmitz RJ, Springer NM. Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 (BETHESDA, MD.) 2021; 11:6288454. [PMID: 34849810 PMCID: PMC8496265 DOI: 10.1093/g3journal/jkab190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Accessible chromatin and unmethylated DNA are associated with many genes and cis-regulatory elements. Attempts to understand natural variation for accessible chromatin regions (ACRs) and unmethylated regions (UMRs) often rely upon alignments to a single reference genome. This limits the ability to assess regions that are absent in the reference genome assembly and monitor how nearby structural variants influence variation in chromatin state. In this study, de novo genome assemblies for four maize inbreds (B73, Mo17, Oh43, and W22) are utilized to assess chromatin accessibility and DNA methylation patterns in a pan-genome context. A more complete set of UMRs and ACRs can be identified when chromatin data are aligned to the matched genome rather than a single reference genome. While there are UMRs and ACRs present within genomic regions that are not shared between genotypes, these features are 6- to 12-fold enriched within regions between genomes. Characterization of UMRs present within shared genomic regions reveals that most UMRs maintain the unmethylated state in other genotypes with only ∼5% being polymorphic between genotypes. However, the majority (71%) of UMRs that are shared between genotypes only exhibit partial overlaps suggesting that the boundaries between methylated and unmethylated DNA are dynamic. This instability is not solely due to sequence variation as these partially overlapping UMRs are frequently found within genomic regions that lack sequence variation. The ability to compare chromatin properties among individuals with structural variation enables pan-epigenome analyses to study the sources of variation for accessible chromatin and unmethylated DNA.
Collapse
Affiliation(s)
- Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Peter A Crisp
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | | | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| |
Collapse
|
13
|
Ranawat B, Mishra S, Singh A. Enterobacter hormaechei (MF957335) enhanced yield, disease and salinity tolerance in tomato. Arch Microbiol 2021; 203:2659-2667. [PMID: 33712862 DOI: 10.1007/s00203-021-02226-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/05/2021] [Accepted: 02/11/2021] [Indexed: 10/21/2022]
Abstract
Soil salinity is one of the major limiting factors for poor crop yield in the world. Increasing salinity in the soil is a challenge for agriculture. In the recent past, plant growth-promoting rhizobacteria (PGPR) are being used to enhance plant growth in various conditions. However, the saline-tolerant PGPR are of great use for plant growth under saline condition. In the present study, saline-tolerant E. hormaechei (MF957335) was isolated from saline water. E. hormaechei (MF957335) was tested for its potassium and calcium solubilizing efficiency using Scanning Electron Microscopy-Energy Dispersive X-Ray (SEM-EDX). E. hormaechei (MF957335) and K-Feldspar treatments significantly increased plant growth as compared to untreated plants (negative control). E. hormaechei (MF957335) significantly increased fresh biomass, shoot and root length of tomato plants. Among all the NaCl treatments, maximum fruits (9.66) were achieved in 250 mM NaCl + E. hormaechei treatment. Similar results with increased fruit numbers were obtained in K-Feldspar-treated plants. Apart from the plant growth, fresh biomass and fruit numbers, tomatoes from K-Feldspar-treated plants were large, fleshy and deep red colored. The study could demonstrate bioavailability of potassium from K-feldspar for tomato cultivation. Control plants tomato were small, non-fleshy, yellowish red, and infected with calcium deficiency disease blossom-end rot. The present study demonstrates the role of E. hormaechei (MF957335) in plant growth, yield promotion and disease tolerance by potassium and calcium solubilization, respectively. The study showed that E. hormaechei (MF957335) could be applied to saline and non-saline soils to enhance tomato yield.
Collapse
Affiliation(s)
- Bablesh Ranawat
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sandhya Mishra
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aneesha Singh
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
14
|
Song Y, Bu C, Chen P, Liu P, Zhang D. Miniature inverted repeat transposable elements cis-regulate circular RNA expression and promote ethylene biosynthesis, reducing heat tolerance in Populus tomentosa. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1978-1994. [PMID: 33258949 DOI: 10.1093/jxb/eraa570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Transposable elements (TEs) and their reverse complementary sequence pairs (RCPs) are enriched around loci that produce circular RNAs (circRNAs) in plants. However, the function of these TE-RCP pairs in modulating circRNA expression remains elusive. Here, we identified 4609 circRNAs in poplar (Populus tomentosa) and showed that miniature inverted repeat transposable elements (MITEs)-RCPs were enriched in circRNA flanking regions. Moreover, we used expression quantitative trait nucleotide (eQTN) mapping to decipher the cis-regulatory role of MITEs. eQTN results showed that 14 single-nucleotide polymorphisms (SNPs) were significantly associated with Circ_0000408 and Circ_0003418 levels and the lead associated SNPs were located in MITE-RCP regions, indicating that MITE-RCP sequence variations affect exon circularization. Overexpression and knockdown analysis showed that Circ_0003418 positively modulated its parental gene, which encodes the RING-type E3 ligase XBAT32, and specifically increased the expression of the PtoXBAT32.5 transcript variant, which lacks the E3 ubiquitin ligase domain. Under heat stress, PtoXBAT32.5 expression was induced with up-regulation of Circ_0003418, resulting in increased production of ethylene and peroxidation of membrane lipids. Our findings thus reveal the cis-regulatory mechanism by which a MITE-RCP pair affects circRNA abundance in poplar and indicate that Circ_0003418 is a negative regulator of poplar heat tolerance via the ubiquitin-mediated protein modification pathway.
Collapse
Affiliation(s)
- Yuepeng Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Chenhao Bu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Panfei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Peng Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, P. R. China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P. R. China
| |
Collapse
|
15
|
Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
Collapse
Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| |
Collapse
|
16
|
Li Z, Zhou P, Della Coletta R, Zhang T, Brohammer AB, H O'Connor C, Vaillancourt B, Lipzen A, Daum C, Barry K, de Leon N, Hirsch CD, Buell CR, Kaeppler SM, Springer NM, Hirsch CN. Single-parent expression drives dynamic gene expression complementation in maize hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:93-107. [PMID: 33098691 DOI: 10.1111/tpj.15042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Single-parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non-presence/absence (non-PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non-PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non-PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non-PAV SPE genes. The expression of parentally silent alleles in hybrids of non-PAV SPE genes was relatively rare but occurred in most hybrids. Non-PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non-additive expression. This study provides a comprehensive understanding of the nature of non-PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.
Collapse
Affiliation(s)
- Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Tifu Zhang
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| |
Collapse
|
17
|
Lu Y, Moran Lauter AN, Makkena S, Scott MP, Evans MMS. Insights into the molecular control of cross-incompatibility in Zea mays. PLANT REPRODUCTION 2020; 33:117-128. [PMID: 32865620 DOI: 10.1007/s00497-020-00394-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Gametophytic cross-incompatibility systems in corn have been the subject of genetic studies for more than a century. They have tremendous economic potential as a genetic mechanism for controlling fertilization without controlling pollination. Three major genetically distinct and functionally equivalent cross-incompatibility systems exist in Zea mays: Ga1, Tcb1, and Ga2. All three confer reproductive isolation between maize or teosinte varieties with different haplotypes at any one locus. These loci confer genetically separable functions to the silk and pollen: a female function that allows the silk to block fertilization by non-self-type pollen and a male function that overcomes the block of the female function from the same locus. Identification of some of these genes has shed light on the reproductive isolation they confer. The identification of both male and female factors as pectin methylesterases reveals the importance of pectin methylesterase activity in controlling the decision between pollen acceptance versus rejection, possibly by regulating the degree of methylesterification of the pollen tube cell wall. The appropriate level and spatial distribution of pectin methylesterification is critical for pollen tube growth and is affected by both pectin methylesterases and pectin methylesterase inhibitors. We present a molecular model that explains how cross-incompatibility systems may function that can be tested in Zea and uncharacterized cross-incompatibility systems. Molecular characterization of these loci in conjunction with further refinement of the underlying molecular and cellular mechanisms will allow researchers to bring new and powerful tools to bear on understanding reproductive isolation in Zea mays and related species.
Collapse
Affiliation(s)
- Yongxian Lu
- Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, 94305, USA
| | | | | | - M Paul Scott
- Corn Insects and Crop Genetics Research Unit, USDA ARS, Ames, IA, 50011, USA
| | - Matthew M S Evans
- Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, 94305, USA.
| |
Collapse
|
18
|
Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding. Mol Biol Rep 2020; 47:3155-3167. [PMID: 32162128 DOI: 10.1007/s11033-020-05365-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Plant molecular breeding is expected to give significant gains in cultivar development through development and utilization of suitable molecular marker systems for genetic diversity analysis, rapid DNA fingerprinting, identification of true hybrids, trait mapping and marker-assisted selection. Transposable elements (TEs) are the most abundant component in a genome and being used as genetic markers in the plant molecular breeding. Here, we review on the high copious transposable element belonging to class-II DNA TEs called "miniature inverted-repeat transposable elements" (MITEs). MITEs are ubiquitous, short and non-autonomous DNA transposable elements which have a tendency to insert into genes and genic regions have paved a way for the development of functional DNA marker systems in plant genomes. This review summarises the characteristics of MITEs, principles and methodologies for development of MITEs based DNA markers, bioinformatics tools and resources for plant MITE discovery and their utilization in crop improvement.
Collapse
|
19
|
Renny-Byfield S, Baumgarten A. Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci. BMC Genomics 2020; 21:98. [PMID: 32000670 PMCID: PMC6993463 DOI: 10.1186/s12864-020-6517-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 01/20/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Repetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes has limited large-scale intraspecific comparisons to a handful of model organisms where multiple reference genomes are available. RESULTS We examine repeat content variation in the genomes of 94 elite inbred maize lines using graph-based repeat clustering, a reference-free and rapid assay of repeat content. We examine population structure using genome-wide repeat profiles, and demonstrate the stiff-stalk and non-stiff-stalk heterotic populations are homogenous with regard to global repeat content. In contrast, and similar to previously reported results, the same individuals show clear differentiation, and aggregate into two populations when examining population structure using genome-wide SNPs. Additionally, we develop a novel kmer based technique to examine the chromosomal distribution of repeat clusters in silico and show a cluster dependent association with gene density. CONCLUSION Our results indicate global repeat content variation in the heterotic populations of maize has not diverged, and is uncoupled from population stratification at SNP loci. We show that repeat families exhibit divergent patterns with regard to chromosomal distribution, some repeat clusters accumulate in regions of high gene density, whereas others aggregate in regions of low gene density.
Collapse
|
20
|
Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM. Transposable elements contribute to dynamic genome content in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1052-1065. [PMID: 31381222 DOI: 10.1111/tpj.14489] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 05/05/2023]
Abstract
Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400 000 TEs that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://github.com/SNAnderson/maizeTE_variation; https://mcstitzer.github.io/maize_TEs.
Collapse
Affiliation(s)
- Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Michelle C Stitzer
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, CA, 95616, USA
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| |
Collapse
|
21
|
Mabire C, Duarte J, Darracq A, Pirani A, Rimbert H, Madur D, Combes V, Vitte C, Praud S, Rivière N, Joets J, Pichon JP, Nicolas SD. High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics 2019; 20:848. [PMID: 31722668 PMCID: PMC6854671 DOI: 10.1186/s12864-019-6136-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Insertions/deletions (InDels) and more specifically presence/absence variations (PAVs) are pervasive in several species and have strong functional and phenotypic effect by removing or drastically modifying genes. Genotyping of such variants on large panels remains poorly addressed, while necessary for approaches such as association mapping or genomic selection. Results We have developed, as a proof of concept, a new high-throughput and affordable approach to genotype InDels. We first identified 141,000 InDels by aligning reads from the B73 line against the genome of three temperate maize inbred lines (F2, PH207, and C103) and reciprocally. Next, we designed an Affymetrix® Axiom® array to target these InDels, with a combination of probes selected at breakpoint sites (13%) or within the InDel sequence, either at polymorphic (25%) or non-polymorphic sites (63%) sites. The final array design is composed of 662,772 probes and targets 105,927 InDels, including PAVs ranging from 35 bp to 129kbp. After Affymetrix® quality control, we successfully genotyped 86,648 polymorphic InDels (82% of all InDels interrogated by the array) on 445 maize DNA samples with 422,369 probes. Genotyping InDels using this approach produced a highly reliable dataset, with low genotyping error (~ 3%), high call rate (~ 98%), and high reproducibility (> 95%). This reliability can be further increased by combining genotyping of several probes calling the same InDels (< 0.1% error rate and > 99.9% of call rate for 5 probes). This “proof of concept” tool was used to estimate the kinship matrix between 362 maize lines with 57,824 polymorphic InDels. This InDels kinship matrix was highly correlated with kinship estimated using SNPs from Illumina 50 K SNP arrays. Conclusions We efficiently genotyped thousands of small to large InDels on a sizeable number of individuals using a new Affymetrix® Axiom® array. This powerful approach opens the way to studying the contribution of InDels to trait variation and heterosis in maize. The approach is easily extendable to other species and should contribute to decipher the biological impact of InDels at a larger scale.
Collapse
Affiliation(s)
- Clément Mabire
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Jorge Duarte
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Aude Darracq
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Ali Pirani
- Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA, 95051, USA
| | - Hélène Rimbert
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France.,Present address: GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Delphine Madur
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Valérie Combes
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Clémentine Vitte
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Sébastien Praud
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Nathalie Rivière
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Johann Joets
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | | | - Stéphane D Nicolas
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France.
| |
Collapse
|
22
|
Luo Z, Han L, Qian J, Li L. Circular RNAs exhibit extensive intraspecific variation in maize. PLANTA 2019; 250:69-78. [PMID: 30904942 DOI: 10.1007/s00425-019-03145-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Comprehensive transcriptome profiling uncovers extensive intraspecific variation of circular RNAs in maize, shedding light on genomic and phenotypic variation among maize inbred lines. Circular RNAs (circRNAs) are single-strand, covalently closed transcripts. A substantial number of circRNAs have been identified and shown to be associated with phenotypic variation in various species. However, little is known about the intraspecific variation of circRNAs in maize (Zea mays L.). Here, we collected a large transcriptomic dataset (by circRNA-seq and mRNA-seq) from seedling leaves of the reference maize inbred lines B73 and Mo17. We identified over 1500 circRNAs in these lines using two circRNA detection methods, CIRCexplorer2 and CIRI. Notably, a substantial proportion of circRNAs varied in terms of sequence or expression level between lines, pointing to extensive intraspecific variation of circRNAs in maize. GO and KEGG analyses showed that genes producing circRNAs with intraspecific variation were more likely to be enriched in multiple functional groups, compared with those that did not produce circRNAs. These findings suggest that circRNAs could be utilized as an indicator of genomic and phenotypic variation among maize inbred lines. Ribosomal profiling revealed that several circRNAs might have translational capacity in maize. These results uncover the extensive intraspecific variation of circRNAs and pave the way for further understanding the molecular mechanisms underlying phenotypic variation at the circRNA level in maize.
Collapse
Affiliation(s)
- Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jia Qian
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
23
|
Imran M, Barboza AL, Asad S, Khalid ZM, Mukhtar Z. Expression patterns of cp4- epsps gene in diverse transgenic Saccharum officinarum L. genotypes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:779-786. [PMID: 31168239 PMCID: PMC6522613 DOI: 10.1007/s12298-019-00650-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/25/2019] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
Glyphosate, a functional analogue of phosphoenolpyruvate (PEP), blocks the shikimate pathway by inhibiting the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19) through interference with the conversion of (shikimate-3-phosphate) S3P and PEP to 5-enolpyruvylshikimate-3-phosphate (EPSP) and subsequently leads to plant death. This metabolic pathway possesses great potential to be used for development of herbicide resistant transgenic crops and here in this study, we wanted to check the expression potential of CP4-EPSPS gene in various sugarcane genotypes. A synthetic version of CP4-EPSPS gene synthesized commercially, cloned in pGreen0029 vector, was transformed into regenerable embryogenic calli of three different sugarcane cultivars HSF-240, S2003US-778 and S2003US-114 using biolistic gene transfer approach for comparative transcriptional studies. Transgenic lines screened by PCR analysis were subjected to Southern hybridization for checking transgene integration patterns. All the tested lines were found to contain multiple (3-6) insert copies. Putative transgenic plants produced the CP4-EPSPS protein which was detected using immunoblot analysis. The CP4-EPSPS transcript expression detected by qRT-PCR was found to vary from genotype to genotype and is being reported first time. In vitro glyphosate assay showed that transformed plants were conferring herbicide tolerance. It is concluded that different cultivars of sugarcane give variable expression of the same transgene and reasons for this phenomenon needs to be investigated.
Collapse
Affiliation(s)
- Muhammad Imran
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Andre Luiz Barboza
- Laboratory of Genomics and Molecular Biology, Department of Biological Sciences, Escola Superior Agricultura Luiz De Quiroz, University of Sao Paulo, Piracicaba, SP Brazil
| | - Shaheen Asad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Zafar M. Khalid
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| |
Collapse
|
24
|
Lu X, Fu X, Wang D, Wang J, Chen X, Hao M, Wang J, Gervers KA, Guo L, Wang S, Yin Z, Fan W, Shi C, Wang X, Peng J, Chen C, Cui R, Shu N, Zhang B, Han M, Zhao X, Mu M, Yu JZ, Ye W. Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:945-955. [PMID: 30407717 PMCID: PMC6587942 DOI: 10.1111/pbi.13030] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 05/21/2023]
Abstract
Although efforts have been taken to exploit diversity for yield and quality improvements, limited progress on using beneficial alleles in domesticated and undomesticated cotton varieties is limited. Given the complexity and limited amount of genomic information since the completion of four cotton genomes, characterizing significant variations and haplotype block inheritance under artificial selection has been challenging. Here we sequenced Gossypium hirsutum L. cv CRI-12 (the cotton variety with the largest acreage in China), its parental cultivars, and progeny cultivars, which were bred by the different institutes in China. In total, 3.3 million SNPs were identified and 118, 126 and 176 genes were remarkably correlated with Verticillium wilt, salinity and drought tolerance in CRI-12, respectively. Transcriptome-wide analyses of gene expression, and functional annotations, have provided support for the identification of genes tied to these tolerances. We totally discovered 58 116 haplotype blocks, among which 23 752 may be inherited and 1029 may be recombined under artificial selection. This survey of genetic diversity identified loci that may have been subject to artificial selection and documented the haplotype block inheritance and recombination, shedding light on the genetic mechanism of artificial selection and guiding breeding efforts for the genetic improvement of cotton.
Collapse
Affiliation(s)
- Xuke Lu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Xiaoqiong Fu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Delong Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Junyi Wang
- Hangzhou 1 Gene Technology CO., LTDHangzhouZhejiangChina
| | - Xiugui Chen
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Meirong Hao
- Hangzhou 1 Gene Technology CO., LTDHangzhouZhejiangChina
| | - Junjuan Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Kyle A. Gervers
- Crop Germplasm Research UnitSouthern Plains Agricultural Research CenterUS Department of Agriculture—Agricultural Research Service (USDA‐ARS)College StationTXUSA
| | - Lixue Guo
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Shuai Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Zujun Yin
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Weili Fan
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Chunwei Shi
- Hangzhou 1 Gene Technology CO., LTDHangzhouZhejiangChina
| | - Xiaoge Wang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Jun Peng
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Chao Chen
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Ruifeng Cui
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Na Shu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Binglei Zhang
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Mingge Han
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Xiaojie Zhao
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - Min Mu
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| | - John Z. Yu
- Crop Germplasm Research UnitSouthern Plains Agricultural Research CenterUS Department of Agriculture—Agricultural Research Service (USDA‐ARS)College StationTXUSA
| | - Wuwei Ye
- State Key Laboratory of Cotton BiologyKey Laboratory for Cotton Genetic ImprovementInstitute of Cotton Research of Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangHenanChina
| |
Collapse
|
25
|
Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions. Proc Natl Acad Sci U S A 2019; 116:10734-10743. [PMID: 30992374 DOI: 10.1073/pnas.1903809116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While studying spontaneous mutations at the maize bronze (bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new bz mutations from several Bz stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable bz mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous wx mutations [Wessler S (1997) The Mutants of Maize, pp 385-386]. Similar mutations were recovered at the closely linked sh locus. These events occurred with a frequency of 2-4 × 10-5 in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, like Hopscotch, Magellan, and Bs2, a Bs1 variant, were described previously; others, like Foto and Focou in 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition of Hopscotch, Magellan, and Bs2 occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.
Collapse
|
26
|
Andorf C, Beavis WD, Hufford M, Smith S, Suza WP, Wang K, Woodhouse M, Yu J, Lübberstedt T. Technological advances in maize breeding: past, present and future. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:817-849. [PMID: 30798332 DOI: 10.1007/s00122-019-03306-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/05/2019] [Indexed: 05/18/2023]
Abstract
Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.
Collapse
Affiliation(s)
| | - William D Beavis
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Matthew Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011-1010, USA
| | - Stephen Smith
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Walter P Suza
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA.
| |
Collapse
|
27
|
Dissecting Heterosis During the Ear Inflorescence Development Stage in Maize via a Metabolomics-based Analysis. Sci Rep 2019; 9:212. [PMID: 30659214 PMCID: PMC6338801 DOI: 10.1038/s41598-018-36446-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/13/2018] [Indexed: 11/08/2022] Open
Abstract
Heterosis can increase the yield of many crops and has been extensively applied in agriculture. In maize, female inflorescence architecture directly determines grain yield. Thus, exploring the relationship between early maize ear inflorescence development and heterosis regarding yield-related traits may be helpful for characterizing the molecular mechanisms underlying heterotic performance. In this study, we fine mapped the overdominant heterotic locus (hlEW2b), associated with ear width, in an approximately 1.98-Mb region based on analyses of chromosome segment substitution lines and the corresponding testcross population. Maize ear inflorescences at the floral meristem stage were collected from two inbred lines, one chromosome segment substitution line that carried hlEW2b (sub-CSSL16), the receptor parent lx9801, and the Zheng58 × sub-CSSL16 and Zheng58 × lx9801 hybrid lines. A total of 256 metabolites were identified, including 31 and 24 metabolites that were differentially accumulated between the two hybrid lines and between the two inbred lines, respectively. Most of these metabolites are involved in complex regulatory mechanisms important for maize ear development. For example, nucleotides are basic metabolites affecting cell composition and carbohydrate synthesis. Additionally, nicotinate and nicotinamide metabolism is important for photosynthesis, plant stress responses, and cell expansion. Moreover, flavonoid and phenolic metabolites regulate auxin transport and cell apoptosis. Meanwhile, phytohormone biosynthesis and distribution influence the cell cycle and cell proliferation. Our results revealed that changes in metabolite contents may affect the heterotic performance related to ear width and yield in maize hybrid lines. This study provides new clues in heterosis at the metabolomics level and implies that differentially accumulated metabolites made distinct contributions to the heterosis at an early stage of ear inflorescences development.
Collapse
|
28
|
Dluzewska J, Szymanska M, Ziolkowski PA. Where to Cross Over? Defining Crossover Sites in Plants. Front Genet 2018; 9:609. [PMID: 30619450 PMCID: PMC6299014 DOI: 10.3389/fgene.2018.00609] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
It is believed that recombination in meiosis serves to reshuffle genetic material from both parents to increase genetic variation in the progeny. At the same time, the number of crossovers is usually kept at a very low level. As a consequence, many organisms need to make the best possible use from the one or two crossovers that occur per chromosome in meiosis. From this perspective, the decision of where to allocate rare crossover events becomes an important issue, especially in self-pollinating plant species, which experience limited variation due to inbreeding. However, the freedom in crossover allocation is significantly limited by other, genetic and non-genetic factors, including chromatin structure. Here we summarize recent progress in our understanding of those processes with a special emphasis on plant genomes. First, we focus on factors which influence the distribution of recombination initiation sites and discuss their effects at both, the single hotspot level and at the chromosome scale. We also briefly explain the aspects of hotspot evolution and their regulation. Next, we analyze how recombination initiation sites translate into the development of crossovers and their location. Moreover, we provide an overview of the sequence polymorphism impact on crossover formation and chromosomal distribution.
Collapse
Affiliation(s)
- Julia Dluzewska
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Piotr A Ziolkowski
- Department of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| |
Collapse
|
29
|
Xiaodong X, Olukolu B, Yang Q, Balint-Kurti P. Identification of a locus in maize controlling response to a host-selective toxin derived from Cochliobolus heterostrophus, causal agent of southern leaf blight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2601-2612. [PMID: 30191251 DOI: 10.1007/s00122-018-3175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/25/2018] [Indexed: 06/08/2023]
Abstract
A host-selective, proteinaceous maize toxin was identified from the culture filtrate of the maize pathogen Cochliobolus heterostrophus. A dominant gene for toxin susceptibility was identified on maize chromosome 4. A toxic activity was identified from the culture filtrate (CF) of the fungus Cochliobolus heterostrophus, causal agent of the maize disease southern leaf blight (SLB) with differential toxicity on maize lines. Two independent mapping populations; a 113-line recombinant inbred line population and a 258-line association population, were used to map loci associated with sensitivity to the CF at the seedling stage. A major QTL on chromosome 4 was identified at the same locus using both populations. Mapping in the association population defined a 400 kb region that contained the sensitivity locus. By comparing CF-sensitivity of the parents of the RIL population with that of the F1 progeny, we determined that the sensitivity allele was dominant. No relationship was observed between CF-sensitivity in seedlings and SLB susceptibility in mature plants; however, a significant correlation (- 0.58) was observed between SLB susceptibility and CF-sensitivity in seedlings. The activity of the CF was light-dependent and was sensitive to pronase, indicating that the toxin was proteinaceous.
Collapse
Affiliation(s)
- Xie Xiaodong
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA
| | - Bode Olukolu
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Qin Yang
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA
- College of Agronomy and State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, 27695-7616, USA.
- USDA-ARS Plant Science Research Unit, Raleigh, NC, 27695, USA.
| |
Collapse
|
30
|
Cossu RM, Casola C, Giacomello S, Vidalis A, Scofield DG, Zuccolo A. LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes. Genome Biol Evol 2018; 9:3449-3462. [PMID: 29228262 PMCID: PMC5751070 DOI: 10.1093/gbe/evx260] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 12/29/2022] Open
Abstract
The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.
Collapse
Affiliation(s)
- Rosa Maria Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Amaryllis Vidalis
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Section of Population Epigenetics and Epigenomics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Douglas G Scofield
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Sweden
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Istituto di Genomica Applicata, Udine, Italy
| |
Collapse
|
31
|
Wallace JG, Rodgers-Melnick E, Buckler ES. On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics. Annu Rev Genet 2018; 52:421-444. [DOI: 10.1146/annurev-genet-120116-024846] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.
Collapse
Affiliation(s)
- Jason G. Wallace
- Department of Crop and Soil Sciences, The University of Georgia, Athens, Georgia 30602, USA
| | | | - Edward S. Buckler
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
32
|
Uliano-Silva M, Dondero F, Dan Otto T, Costa I, Lima NCB, Americo JA, Mazzoni CJ, Prosdocimi F, Rebelo MDF. A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei. Gigascience 2018; 7:4750781. [PMID: 29267857 PMCID: PMC5836269 DOI: 10.1093/gigascience/gix128] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/11/2017] [Indexed: 11/13/2022] Open
Abstract
Background For more than 25 years, the golden mussel, Limnoperna fortunei, has aggressively invaded South American freshwaters, having travelled more than 5000 km upstream across 5 countries. Along the way, the golden mussel has outcompeted native species and economically harmed aquaculture, hydroelectric powers, and ship transit. We have sequenced the complete genome of the golden mussel to understand the molecular basis of its invasiveness and search for ways to control it. Findings We assembled the 1.6-Gb genome into 20 548 scaffolds with an N50 length of 312 Kb using a hybrid and hierarchical assembly strategy from short and long DNA reads and transcriptomes. A total of 60 717 coding genes were inferred from a customized transcriptome-trained AUGUSTUS run. We also compared predicted protein sets with those of complete molluscan genomes, revealing an exacerbation of protein-binding domains in L. fortunei. Conclusions We built one of the best bivalve genome assemblies available using a cost-effective approach using Illumina paired-end, mate-paired, and PacBio long reads. We expect that the continuous and careful annotation of L. fortunei's genome will contribute to the investigation of bivalve genetics, evolution, and invasiveness, as well as to the development of biotechnological tools for aquatic pest control.
Collapse
Affiliation(s)
- Marcela Uliano-Silva
- Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Francesco Dondero
- Department of Science and Technological Innovation (DiSIT), Università del Piemonte Orientale Amedeo Avogadro, Vercelli-Novara-Alessandria, Italy
| | - Thomas Dan Otto
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Centre of Immunobiology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Igor Costa
- Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nicholas Costa Barroso Lima
- Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Bioinformatics Laboratory (LabInfo) of the National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil
| | - Juliana Alves Americo
- Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Camila Junqueira Mazzoni
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Francisco Prosdocimi
- Leopoldo de Meis Biomedical Biochemistry Institute (IBqM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauro de Freitas Rebelo
- Carlos Chagas Filho Biophysics Institute (IBCCF), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
33
|
A Megabase-Scale Deletion is Associated with Phenotypic Variation of Multiple Traits in Maize. Genetics 2018; 211:305-316. [PMID: 30389804 PMCID: PMC6325712 DOI: 10.1534/genetics.118.301567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/26/2018] [Indexed: 11/18/2022] Open
Abstract
Genomic deletions are pervasive in the maize (Zea mays L.) genome, and play important roles in phenotypic variation and adaptive evolution. However, little is known about the biological functions of these genomic deletions. Here, we report the biological function of a megabase-scale deletion, which we identified by position-based cloning of the multi-trait weakened (muw) mutant, which is inherited as a single recessive locus. MUW was mapped to a 5.16-Mb region on chromosome 2. The 5.16-Mb deletion in the muw mutant led to the loss of 48 genes and was responsible for a set of phenotypic abnormities, including wilting leaves, poor yield performance, reduced plant height, increased stomatal density, and rapid water loss. While muw appears to have resulted from double-stranded break repair that was not dependent on intragenomic DNA homology, extensive duplication of maize genes may have mitigated its effects and facilitated its survival.
Collapse
|
34
|
Wicker T, Gundlach H, Spannagl M, Uauy C, Borrill P, Ramírez-González RH, De Oliveira R, Mayer KFX, Paux E, Choulet F. Impact of transposable elements on genome structure and evolution in bread wheat. Genome Biol 2018; 19:103. [PMID: 30115100 PMCID: PMC6097303 DOI: 10.1186/s13059-018-1479-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/11/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. RESULTS The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid. CONCLUSIONS Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.
Collapse
Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Heidrun Gundlach
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Philippa Borrill
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | | | - Romain De Oliveira
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Klaus F X Mayer
- PGSB Plant Genome and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Munich, Germany
| | - Etienne Paux
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France
| | - Frédéric Choulet
- GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France.
| |
Collapse
|
35
|
Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 2018; 50:1289-1295. [PMID: 30061735 DOI: 10.1038/s41588-018-0182-0] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 06/05/2018] [Indexed: 12/24/2022]
Abstract
Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.
Collapse
|
36
|
The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet 2018; 50:1282-1288. [PMID: 30061736 DOI: 10.1038/s41588-018-0158-0] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/17/2018] [Indexed: 11/08/2022]
Abstract
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.
Collapse
|
37
|
Jones MW, Penning BW, Jamann TM, Glaubitz JC, Romay C, Buckler ES, Redinbaugh MG. Diverse Chromosomal Locations of Quantitative Trait Loci for Tolerance to Maize chlorotic mottle virus in Five Maize Populations. PHYTOPATHOLOGY 2018; 108:748-758. [PMID: 29287150 DOI: 10.1094/phyto-09-17-0321-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The recent rapid emergence of maize lethal necrosis (MLN), caused by coinfection of maize with Maize chlorotic mottle virus (MCMV) and a second virus usually from the family Potyviridae, is causing extensive losses for farmers in East Africa, Southeast Asia, and South America. Although the genetic basis of resistance to potyviruses is well understood in maize, little was known about resistance to MCMV. The responses of five maize inbred lines (KS23-5, KS23-6, N211, DR, and Oh1VI) to inoculation with MCMV, Sugarcane mosaic virus, and MLN were characterized. All five lines developed fewer symptoms than susceptible controls after inoculation with MCMV; however, the virus was detected in systemic leaf tissue from each of the lines similarly to susceptible controls, indicating that the lines were tolerant of MCMV rather than resistant to it. Except for KS23-5, the inbred lines also developed fewer symptoms after inoculation with MLN than susceptible controls. To identify genetic loci associated with MCMV tolerance, large F2 or recombinant inbred populations were evaluated for their phenotypic responses to MCMV, and the most resistant and susceptible plants were genotyped by sequencing. One to four quantitative trait loci (QTL) were identified in each tolerant population using recombination frequency and positional mapping strategies. In contrast to previous studies of virus resistance in maize, the chromosomal positions and genetic character of the QTL were unique to each population. The results suggest that different, genotype-specific mechanisms are associated with MCMV tolerance in maize. These results will allow for the development of markers for marker-assisted selection of MCMV- and MLN-tolerant maize hybrids for disease control.
Collapse
Affiliation(s)
- Mark W Jones
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn, Soybean and Wheat Quality Research Unit, Wooster, OH 44691; third author: Department of Crop Sciences, University of Illinois, Urbana 61801; fourth and fifth authors: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; sixth author: USDA-ARS Plant, Soil and Nutrition Research and Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; and seventh author: Department of Plant Pathology, Ohio State University, Wooster 44691
| | - Bryan W Penning
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn, Soybean and Wheat Quality Research Unit, Wooster, OH 44691; third author: Department of Crop Sciences, University of Illinois, Urbana 61801; fourth and fifth authors: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; sixth author: USDA-ARS Plant, Soil and Nutrition Research and Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; and seventh author: Department of Plant Pathology, Ohio State University, Wooster 44691
| | - Tiffany M Jamann
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn, Soybean and Wheat Quality Research Unit, Wooster, OH 44691; third author: Department of Crop Sciences, University of Illinois, Urbana 61801; fourth and fifth authors: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; sixth author: USDA-ARS Plant, Soil and Nutrition Research and Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; and seventh author: Department of Plant Pathology, Ohio State University, Wooster 44691
| | - Jeff C Glaubitz
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn, Soybean and Wheat Quality Research Unit, Wooster, OH 44691; third author: Department of Crop Sciences, University of Illinois, Urbana 61801; fourth and fifth authors: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; sixth author: USDA-ARS Plant, Soil and Nutrition Research and Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; and seventh author: Department of Plant Pathology, Ohio State University, Wooster 44691
| | - Cinta Romay
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn, Soybean and Wheat Quality Research Unit, Wooster, OH 44691; third author: Department of Crop Sciences, University of Illinois, Urbana 61801; fourth and fifth authors: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; sixth author: USDA-ARS Plant, Soil and Nutrition Research and Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; and seventh author: Department of Plant Pathology, Ohio State University, Wooster 44691
| | - Edward S Buckler
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn, Soybean and Wheat Quality Research Unit, Wooster, OH 44691; third author: Department of Crop Sciences, University of Illinois, Urbana 61801; fourth and fifth authors: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; sixth author: USDA-ARS Plant, Soil and Nutrition Research and Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; and seventh author: Department of Plant Pathology, Ohio State University, Wooster 44691
| | - Margaret G Redinbaugh
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn, Soybean and Wheat Quality Research Unit, Wooster, OH 44691; third author: Department of Crop Sciences, University of Illinois, Urbana 61801; fourth and fifth authors: Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; sixth author: USDA-ARS Plant, Soil and Nutrition Research and Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; and seventh author: Department of Plant Pathology, Ohio State University, Wooster 44691
| |
Collapse
|
38
|
The Functional Impact of Transposable Elements on the Diversity of Plant Genomes. DIVERSITY 2018. [DOI: 10.3390/d10020018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
39
|
Darracq A, Vitte C, Nicolas S, Duarte J, Pichon JP, Mary-Huard T, Chevalier C, Bérard A, Le Paslier MC, Rogowsky P, Charcosset A, Joets J. Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics 2018; 19:119. [PMID: 29402214 PMCID: PMC5800051 DOI: 10.1186/s12864-018-4490-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, they have been only scarcely characterized at the sequence level and the extent of presence/absence variation and relative chromosomal landscape of inbred-specific regions remain to be elucidated. RESULTS De novo genome sequencing of the French F2 maize inbred line revealed 10,044 novel genomic regions larger than 1 kb, making up 88 Mb of DNA, that are present in F2 but not in B73 (PAV). This set of maize PAV sequences allowed us to annotate PAV content and to analyze sequence breakpoints. Using PAV genotyping on a collection of 25 temperate lines, we also analyzed Linkage Disequilibrium in PAVs and flanking regions, and PAV frequencies within maize genetic groups. CONCLUSIONS We highlight the possible role of MMEJ-type double strand break repair in maize PAV formation and discover 395 new genes with transcriptional support. Pattern of linkage disequilibrium within PAVs strikingly differs from this of flanking regions and is in accordance with the intuition that PAVs may recombine less than other genomic regions. We show that most PAVs are ancient, while some are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Characterization of such PAVs will provide useful material for further association genetic studies in European and temperate maize.
Collapse
Affiliation(s)
- Aude Darracq
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Clémentine Vitte
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane Nicolas
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | - Tristan Mary-Huard
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- MIA, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Céline Chevalier
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Bérard
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, Evry, France
| | | | - Peter Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Alain Charcosset
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- Genetique Quantitative et Evolution – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| |
Collapse
|
40
|
Chen L, Zhang P, Fan Y, Lu Q, Li Q, Yan J, Muehlbauer GJ, Schnable PS, Dai M, Li L. Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize. THE NEW PHYTOLOGIST 2018; 217:1292-1306. [PMID: 29155438 DOI: 10.1111/nph.14901] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/18/2017] [Indexed: 05/21/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules. Recent studies have shown that circRNAs can arise from the transcripts of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. We performed circRNA-Seq on B73 seedling leaves and uncovered 2804 high-confidence maize circRNAs, which show distinct genomic features. Comprehensive analyses demonstrated that sequences related to LINE1-like elements (LLEs) and their Reverse Complementary Pairs (LLERCPs) are significantly enriched in the flanking regions of circRNAs. Interestingly, as the number of LLERCPs increase, the accumulation of circRNAs varies, whereas that of linear transcripts decreases. Furthermore, genes with LLERCP-mediated circRNAs are enriched among loci that are associated with phenotypic variation. These results suggest that circRNAs are likely to be involved in the modulation of phenotypic variation by LLERCPs. Further, we showed that the presence/absence variation of LLERCPs was associated with expression variation of circRNA-circ1690 and was related to ear height, potentially through the interplay between circRNAs and functional linear transcripts. Our first study of maize circRNAs uncovers a potential new way for transposons to modulate transcriptomic and phenotypic variations.
Collapse
Affiliation(s)
- Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiong Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | | | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
41
|
|
42
|
Borgognone A, Castanera R, Muguerza E, Pisabarro AG, Ramírez L. Somatic transposition and meiotically driven elimination of an active helitron family in Pleurotus ostreatus. DNA Res 2017; 24:103-115. [PMID: 28431016 PMCID: PMC5397611 DOI: 10.1093/dnares/dsw060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/14/2016] [Indexed: 01/31/2023] Open
Abstract
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny. Further investigation of HELPO2 flanking sites showed that gene conversion may contribute to the elimination of such repetitive elements in meiosis, favouring the presence of HELPO2 vacant loci. In addition, the analysis of HELPO2 content in a reconstructed pedigree of subclones maintained under different culture conditions revealed an event of helitron somatic transposition. Additional analyses of genome and transcriptome data indicated that P. ostreatus carries active RNAi machinery that could be involved in the control of transposable element proliferation. Our results provide the first evidence of helitron mobilization in the fungal kingdom and highlight the interaction between genome defence mechanisms and invasive DNA.
Collapse
Affiliation(s)
| | | | | | | | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| |
Collapse
|
43
|
Structure and Origin of the White Cap Locus and Its Role in Evolution of Grain Color in Maize. Genetics 2017; 206:135-150. [PMID: 28159756 PMCID: PMC5419465 DOI: 10.1534/genetics.116.198911] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/22/2017] [Indexed: 11/18/2022] Open
Abstract
Selection for yellow- and white-grain types has been central to postdomestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that Wc is exclusive to maize, where it is prevalent in white-grain (y1) varieties. Moreover, Ccd1 copy number varies extensively among Wc alleles (from 1 to 23 copies), and confers a proportional range of Ccd1 expression in diverse organs. We propose that this dynamic source of quantitative variation in Ccd1 expression was created in maize shortly after domestication by a two-step, Tam3L transposon-mediated process. First, a chromosome segment containing Ccd1 and several nearby genes duplicated at a position 1.9 Mb proximal to the progenitor Ccd1r locus on chromosome 9. Second, a subsequent interaction of Tam3L transposons at the new locus created a 28-kb tandem duplication, setting up expansion of Ccd1 copy number by unequal crossing over. In this way, transposon-mediated variation in copy number at the Wc locus generated phenotypic variation that provided a foundation for breeding and selection of white-grain color in maize.
Collapse
|
44
|
Wang H, Zhang X, Yang H, Liu X, Li H, Yuan L, Li W, Fu Z, Tang J, Kang D. Identification of heterotic loci associated with grain yield and its components using two CSSL test populations in maize. Sci Rep 2016; 6:38205. [PMID: 27917917 PMCID: PMC5137037 DOI: 10.1038/srep38205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 11/07/2016] [Indexed: 11/17/2022] Open
Abstract
Heterosis has widely been used to increase grain yield and quality. In this study, the genetic basis of heterosis on grain yield and its main components in maize were examined over 2 years in two locations in two test populations constructed from a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058). Of the 169 heterotic loci (HL) associated with grain yield and its five components identified in CSSL × Zheng58 and CSSL × Xun9058 test populations, only 25 HL were detected in both populations. The comparison of quantitative trait loci (QTLs) detected in the CSSL population with HL detected in the two test populations revealed that only 15.46% and 17.35% of the HL in the given populations respectively, shared the same chromosomal regions as that of the corresponding QTLs and showed dominant effects as well as pleiotropism with additive and dominant effects. In addition, most of the HL (74.23% and 74.49%) had overdominant effects. These results suggest that overdominance is the main contributor to the effects of heterosis on grain yield and its components in maize, and different HL are associated with heterosis for different traits in different hybrids.
Collapse
Affiliation(s)
- Hongqiu Wang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangge Zhang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huili Yang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoyang Liu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huimin Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liang Yuan
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiyuan Fu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, China
| | - Dingming Kang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
45
|
Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. THE PLANT CELL 2016; 28:2700-2714. [PMID: 27803309 PMCID: PMC5155341 DOI: 10.1105/tpc.16.00353] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 05/18/2023]
Abstract
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.
Collapse
Affiliation(s)
- Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Megan J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ilya Soifer
- Calico Labs, San Francisco, California 94080
| | | | | | | | - Fei Lu
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Christopher J Fields
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Chris L Wright
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Edward Buckler
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
- U.S. Department of Agriculture/Agricultural Research Services, Ithaca, New York 14850
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- DOE Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics-Enabled Plant Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Mark A Mikel
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| |
Collapse
|
46
|
Sun XQ, Li DH, Xue JY, Yang SH, Zhang YM, Li MM, Hang YY. Insertion DNA Accelerates Meiotic Interchromosomal Recombination in Arabidopsis thaliana. Mol Biol Evol 2016; 33:2044-53. [PMID: 27189569 DOI: 10.1093/molbev/msw087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nucleotide insertions/deletions are ubiquitous in eukaryotic genomes, and the resulting hemizygous (unpaired) DNA has significant, heritable effects on adjacent DNA. However, little is known about the genetic behavior of insertion DNA. Here, we describe a binary transgenic system to study the behavior of insertion DNA during meiosis. Transgenic Arabidopsis lines were generated to carry two different defective reporter genes on nonhomologous chromosomes, designated as "recipient" and "donor" lines. Double hemizygous plants (harboring unpaired DNA) were produced by crossing between the recipient and the donor, and double homozygous lines (harboring paired DNA) via self-pollination. The transfer of the donor's unmutated sequence to the recipient generated a functional β-glucuronidase gene, which could be visualized by histochemical staining and corroborated by polymerase chain reaction amplification and sequencing. More than 673 million seedlings were screened, and the results showed that meiotic ectopic recombination in the hemizygous lines occurred at a frequency >6.49-fold higher than that in the homozygous lines. Gene conversion might have been exclusively or predominantly responsible for the gene correction events. The direct measurement of ectopic recombination events provided evidence that an insertion, in the absence of an allelic counterpart, could scan the entire genome for homologous counterparts with which to pair. Furthermore, the unpaired (hemizygous) architectures could accelerate ectopic recombination between itself and interchromosomal counterparts. We suggest that the ectopic recombination accelerated by hemizygous architectures may be a general mechanism for interchromosomal recombination through ubiquitously dispersed repeat sequences in plants, ultimately contributing to genetic renovation and eukaryotic evolution.
Collapse
Affiliation(s)
- Xiao-Qin Sun
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ding-Hong Li
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jia-Yu Xue
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Si-Hai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yan-Mei Zhang
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Mi-Mi Li
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yue-Yu Hang
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
47
|
Li D, Zeng R, Li Y, Zhao M, Chao J, Li Y, Wang K, Zhu L, Tian WM, Liang C. Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids. Sci Rep 2016; 6:24984. [PMID: 27108962 PMCID: PMC4842955 DOI: 10.1038/srep24984] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
As an important industrial material, natural rubber is mainly harvested from the rubber tree. Rubber tree breeding is inefficient, expensive and time-consuming, whereas marker-assisted selection is a feasible method for early selection of high-yield hybrids. We thus sequenced and analyzed the transcriptomes of two parent rubber trees (RRIM 600 and PR 107) and their most productive hybrids (RY 7-33-97 and RY 7-20-59) to understand their gene expression patterns and genetic variations including single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels). We discovered >31,000 genetic variations in 112,702 assembled unigenes. Our results showed that the higher yield in F1 hybrids was positively associated with their higher genome heterozygosity, which was further confirmed by genotyping 10 SNPs in 20 other varieties. We also showed that RY 7-33-97 and RY 7-20-59 were genetically closer to RRIM 600 and PR 107, respectively, in agreement with both their phenotypic similarities and gene expression profiles. After identifying ethylene- and jasmonic acid–responsive genes at the transcription level, we compared and analyzed the genetic variations underlying rubber biosynthesis and the jasmonic acid and ethylene pathways in detail. Our results suggest that genome-wide genetic variations play a substantive role in maintaining rubber tree heterosis.
Collapse
Affiliation(s)
- Dejun Li
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Rizhong Zeng
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Yan Li
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
| | - Manman Zhao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.,College of Horticulture &Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinquan Chao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Yu Li
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Kai Wang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
| | - Wei-Min Tian
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
| |
Collapse
|
48
|
Hardigan MA, Crisovan E, Hamilton JP, Kim J, Laimbeer P, Leisner CP, Manrique-Carpintero NC, Newton L, Pham GM, Vaillancourt B, Yang X, Zeng Z, Douches DS, Jiang J, Veilleux RE, Buell CR. Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum. THE PLANT CELL 2016; 28:388-405. [PMID: 26772996 PMCID: PMC4790865 DOI: 10.1105/tpc.15.00538] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 12/29/2015] [Accepted: 01/14/2016] [Indexed: 05/02/2023]
Abstract
Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways.
Collapse
Affiliation(s)
- Michael A Hardigan
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Emily Crisovan
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jeongwoon Kim
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Parker Laimbeer
- Department of Horticulture, Virginia Tech, Blacksburg, Virginia 24061
| | - Courtney P Leisner
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | | | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gina M Pham
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Xueming Yang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | | | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| |
Collapse
|
49
|
Yeo FKS, Wang Y, Vozabova T, Huneau C, Leroy P, Chalhoub B, Qi XQ, Niks RE, Marcel TC. Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:289-304. [PMID: 26542283 PMCID: PMC4733143 DOI: 10.1007/s00122-015-2627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 10/17/2015] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars. ABSTRACT Partial and non-host resistances to rust fungi in barley (Hordeum vulgare) may be based on pathogen-associated molecular pattern (PAMP)-triggered immunity. Understanding partial resistance may help to understand non-host resistance, and vice versa. We constructed two non-gridded BAC libraries from cultivar Vada and line SusPtrit. Vada is immune to non-adapted Puccinia rust fungi, and partially resistant to P. hordei. SusPtrit is susceptible to several non-adapted rust fungi, and has been used for mapping QTLs for non-host and partial resistance. The BAC libraries help to identify genes determining the natural variation for partial and non-host resistances of barley to rust fungi. A major-effect QTL, Rphq2, for partial resistance to P. hordei was mapped in a complete Vada and an incomplete SusPtrit contig. The physical distance between the markers flanking Rphq2 was 195 Kbp in Vada and at least 226 Kbp in SusPtrit. This marker interval was predicted to contain 12 genes in either accession, of which only five genes were in common. The haplotypes represented by Vada and SusPtrit were found in 57 and 43%, respectively, of a 194 barley accessions panel. The lack of homology between the two haplotypes probably explains the suppression of recombination in the Rphq2 area and limit further genetic resolution in fine mapping. The possible candidate genes for Rphq2 encode peroxidases, kinases and a member of seven-in-absentia protein family. This result suggests that Rphq2 does not belong to the NB-LRR gene family and does not resemble any of the partial resistance genes cloned previously.
Collapse
Affiliation(s)
- F K S Yeo
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- Department of Plant Science and Environmental Ecology, Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Y Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - T Vozabova
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- The Institute of Botany of the Academy of Science of the Czech Republic, Zámek 1, 252 43, Průhonice, Czech Republic
| | - C Huneau
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - P Leroy
- INRA, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
- Université Blaise Pascal, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
| | - B Chalhoub
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - X Q Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - R E Niks
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands.
| | - T C Marcel
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- INRA, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
- AgroParisTech, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
| |
Collapse
|
50
|
Springer NM, Lisch D, Li Q. Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. THE PLANT CELL 2016; 28:314-25. [PMID: 26869701 PMCID: PMC4790878 DOI: 10.1105/tpc.15.00911] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/10/2016] [Indexed: 05/02/2023]
Abstract
Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.
Collapse
Affiliation(s)
- Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108
| |
Collapse
|