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Margasyuk SD, Vlasenok MA, Li G, Cao C, Pervouchine DD. RNAcontacts: A Pipeline for Predicting Contacts from RNA Proximity Ligation Assays. Acta Naturae 2023; 15:51-57. [PMID: 37153509 PMCID: PMC10154773 DOI: 10.32607/actanaturae.11893] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/20/2023] [Indexed: 05/09/2023] Open
Abstract
High-throughput RNA proximity ligation assays are molecular methods that are used to simultaneously analyze the spatial proximity of many RNAs in living cells. Their principle is based on cross-linking, fragmentation, and subsequent religation of RNAs, followed by high-throughput sequencing. The generated fragments have two different types of splits, one resulting from pre-mRNA splicing and the other formed by the ligation of spatially close RNA strands. Here, we present RNAcontacts, a universal pipeline for detecting RNA-RNA contacts in high-throughput RNA proximity ligation assays. RNAcontacts circumvents the inherent problem of mapping sequences with two distinct types of splits using a two-pass alignment, in which splice junctions are inferred from a control RNA-seq experiment on the first pass and then provided to the aligner as bona fide introns on the second pass. Compared to previously developed methods, our approach allows for a more sensitive detection of RNA contacts and has a higher specificity with respect to splice junctions that are present in the biological sample. RNAcontacts automatically extracts contacts, clusters their ligation points, computes the read support, and generates tracks for visualizing through the UCSC Genome Browser. The pipeline is implemented in Snakemake, a reproducible and scalable workflow management system for rapid and uniform processing of multiple datasets. RNAcontacts is a generic pipeline for the detection of RNA contacts that can be used with any proximity ligation method as long as one of the interacting partners is RNA. RNAcontacts is available via the GitHub repository https://github.com/smargasyuk/ RNAcontacts/.
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Affiliation(s)
- S. D. Margasyuk
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
| | - M. A. Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
| | - G. Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058 China
| | - Ch. Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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Barbosa PAM, Fritsche-Neto R, Andrade MC, Petroli CD, Burgueño J, Galli G, Willcox MC, Sonder K, Vidal-Martínez VA, Sifuentes-Ibarra E, Molnar TL. Introgression of Maize Diversity for Drought Tolerance: Subtropical Maize Landraces as Source of New Positive Variants. FRONTIERS IN PLANT SCIENCE 2021; 12:691211. [PMID: 34630452 PMCID: PMC8495256 DOI: 10.3389/fpls.2021.691211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Current climate change models predict an increased frequency and intensity of drought for much of the developing world within the next 30 years. These events will negatively affect maize yields, potentially leading to economic and social instability in many smallholder farming communities. Knowledge about the genetic resources available for traits related to drought tolerance has great importance in developing breeding program strategies. The aim of this research was to study a maize landrace introgression panel to identify chromosomal regions associated with a drought tolerance index. For that, we performed Genome-Wide Association Study (GWAS) on 1326 landrace progenies developed by the CIMMYT Genetic Resources Program, originating from 20 landraces populations collected in arid regions. Phenotypic data were obtained from early testcross trials conducted in three sites and two contrasting irrigation environments, full irrigation (well-watered) and reduced irrigation (drought). The populations were genotyped using the DArTSeq® platform, and a final set of 5,695 SNPs markers was used. The genotypic values were estimated using spatial adjustment in a two-stage analysis. First, we performed the individual analysis for each site/irrigation treatment combination. The best linear unbiased estimates (BLUEs) were used to calculate the Harmonic Mean of Relative Performance (HMRP) as a drought tolerance index for each testcross. The second stage was a joint analysis, which was performed using the HMRP to obtain the best linear unbiased predictions (BLUPs) of the index for each genotype. Then, GWAS was performed to determine the marker-index associations and the marker-Grain Yield (GY) associations for the two irrigation treatments. We detected two significant markers associated with the drought-tolerance index, four associated with GY in drought condition, and other four associated with GY in irrigated conditions each. Although each of these markers explained less than 0.1% of the phenotypic variation for the index and GY, we found two genes likely related to the plant response to drought stress. For these markers, alleles from landraces provide a slightly higher yield under drought conditions. Our results indicate that the positive diversity delivered by landraces are still present on the backcrosses and this is a potential breeding strategy for improving maize for drought tolerance and for trait introgression bringing new superior allelic diversity from landraces to breeding populations.
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Affiliation(s)
- Pedro Augusto Medeiros Barbosa
- Allogamous Plant Breeding Laboratory, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Roberto Fritsche-Neto
- Allogamous Plant Breeding Laboratory, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | | | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Giovanni Galli
- Allogamous Plant Breeding Laboratory, Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Martha C. Willcox
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Kai Sonder
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Víctor A. Vidal-Martínez
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Mexico City, Mexico
| | - Ernesto Sifuentes-Ibarra
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Mexico City, Mexico
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3
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Zou X, Du Y, Wang X, Wang Q, Zhang B, Chen J, Chen M, Doyle JJ, Ge S. Genome evolution in Oryza allopolyploids of various ages: Insights into the process of diploidization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:721-735. [PMID: 33145857 DOI: 10.1111/tpj.15066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/18/2020] [Accepted: 10/28/2020] [Indexed: 05/20/2023]
Abstract
The prevalence and recurrence of whole-genome duplication in plants and its major role in evolution have been well recognized. Despite great efforts, many aspects of genome evolution, particularly the temporal progression of genomic responses to allopolyploidy and the underlying mechanisms, remain poorly understood. The rice genus Oryza consists of both recently formed and older allopolyploid species, representing an attractive system for studying the genome evolution after allopolyploidy. In this study, through screening BAC libraries and sequencing and annotating the targeted BAC clones, we generated orthologous genomic sequences surrounding the DEP1 locus, a major grain yield QTL in cultivated rice, from four Oryza polyploids of various ages and their likely diploid genome donors or close relatives. Based on sequenced DEP1 region and published data from three other genomic regions, we investigated the temporal evolutionary dynamics of four polyploid genomes at both genetic and expression levels. In the recently formed BBCC polyploid, Oryza minuta, genome dominance was not observed and its short-term responses to allopolyploidy are mainly manifested as a high proportion of homoeologous gene pairs showing unequal expression. This could partly be explained by parental legacy, rewiring of divergent regulatory networks and epigenetic modulation. Moreover, we detected an ongoing diploidization process in this genus, and suggest that the expression divergence driven by changes of selective constraint probably plays a big role in the long-term diploidization. These findings add novel insights into our understanding of genome evolution after allopolyploidy, and could facilitate crop improvements through hybridization and polyploidization.
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Affiliation(s)
- Xinhui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yusu Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bing Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinfeng Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingsheng Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jeff J Doyle
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Wang J, Orlov YL, Li X, Zhou Y, Liu Y, Yuan C, Chen M. In situ dissecting the evolution of gene duplication with different histone modification patterns based on high-throughput data analysis in Arabidopsis thaliana. PeerJ 2021; 9:e10426. [PMID: 33505781 PMCID: PMC7792519 DOI: 10.7717/peerj.10426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/03/2020] [Indexed: 02/04/2023] Open
Abstract
Background Genetic regulation is known to contribute to the divergent expression of duplicate genes; however, little is known about how epigenetic modifications regulate the expression of duplicate genes in plants. Methods The histone modification (HM) profile patterns of different modes of gene duplication, including the whole genome duplication, proximal duplication, tandem duplication and transposed duplication were characterized based on ChIP-chip or ChIP-seq datasets. In this study, 10 distinct HM marks including H2Bub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me2, H3K27me1, H3K27me3, H3K36me3 and H3K14ac were analyzed. Moreover, the features of gene duplication with different HM patterns were characterized based on 88 RNA-seq datasets of Arabidopsis thaliana. Results This study showed that duplicate genes in Arabidopsis have a more similar HM pattern than single-copy genes in both their promoters and protein-coding regions. The evolution of HM marks is found to be coupled with coding sequence divergence and expression divergence after gene duplication. We found that functionally selective constraints may impose on epigenetic evolution after gene duplication. Furthermore, duplicate genes with distinct functions have more divergence in histone modification compared with the ones with the same function, while higher expression divergence is found with mutations of chromatin modifiers. This study shows the role of epigenetic marks in regulating gene expression and functional divergence after gene duplication in plants based on sequencing data.
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Affiliation(s)
- Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P. R. China.,Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, P. R. China.,Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Yuriy L Orlov
- The Digital Health Institute, I.M Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Novosibirsk State University, Novosibirsk, Russia.,Agrarian and Technological Institute, Peoples' Friendship University of Russia (RUDN), Moscow, Russia
| | - Xue Li
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, P. R. China.,Institute of Hematology, Zhejiang University, Hangzhou, P. R. China
| | - Yincong Zhou
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Yongjing Liu
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Chunhui Yuan
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, P. R. China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, P. R. China
| | - Ming Chen
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P. R. China.,Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, P. R. China
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5
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Wang T, Huang D, Chen B, Mao N, Qiao Y, Ji M. Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp. Genes Genomics 2018; 40:321-331. [DOI: 10.1007/s13258-018-0647-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/04/2018] [Indexed: 12/26/2022]
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Zhang H, Cao Y, Shang C, Li J, Wang J, Wu Z, Ma L, Qi T, Fu C, Bai Z, Hu B. Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification. PLoS One 2017; 12:e0185439. [PMID: 28945786 PMCID: PMC5612761 DOI: 10.1371/journal.pone.0185439] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/12/2017] [Indexed: 12/20/2022] Open
Abstract
The GRAS gene family is a large plant-specific family of transcription factors that are involved in diverse processes during plant development. Medicago truncatula is an ideal model plant for genetic research in legumes, and specifically for studying nodulation, which is crucial for nitrogen fixation. In this study, 59 MtGRAS genes were identified and classified into eight distinct subgroups based on phylogenetic relationships. Motifs located in the C-termini were conserved across the subgroups, while motifs in the N-termini were subfamily specific. Gene duplication was the main evolutionary force for MtGRAS expansion, especially proliferation of the LISCL subgroup. Seventeen duplicated genes showed strong effects of purifying selection and diverse expression patterns, highlighting their functional importance and diversification after duplication. Thirty MtGRAS genes, including NSP1 and NSP2, were preferentially expressed in nodules, indicating possible roles in the process of nodulation. A transcriptome study, combined with gene expression analysis under different stress conditions, suggested potential functions of MtGRAS genes in various biological pathways and stress responses. Taken together, these comprehensive analyses provide basic information for understanding the potential functions of GRAS genes, and will facilitate further discovery of MtGRAS gene functions.
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Affiliation(s)
- Hailing Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingping Cao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chen Shang
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jikai Li
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jianli Wang
- Pratacultural Sciences Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Zhenying Wu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Lichao Ma
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Tianxiong Qi
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Zetao Bai
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- * E-mail: (ZB); (BH)
| | - Baozhong Hu
- College of Life Science, Northeast Agricultural University, Harbin, China
- Harbin University, Harbin, China
- * E-mail: (ZB); (BH)
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7
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Vicient CM, Casacuberta JM. Impact of transposable elements on polyploid plant genomes. ANNALS OF BOTANY 2017; 120:195-207. [PMID: 28854566 PMCID: PMC5737689 DOI: 10.1093/aob/mcx078] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants. SCOPE This review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa. These include direct effects on genes, by providing them with new coding or regulatory sequences, an effect on the epigenetic status of the chromatin close to genes, and more subtle effects by imposing diverse evolutionary constraints to different chromosomal regions. These effects are particularly relevant after polyploidization events. Polyploidization often induces bursts of transposition probably due to a relaxation in their epigenetic control, and, in the short term, this can increase the rate of gene mutations and changes in gene regulation due to the insertion of TEs next to or into genes. Over longer times, TE bursts may induce global changes in genome structure due to inter-element recombination including losses of large genome regions and chromosomal rearrangements that reduce the genome size and the chromosome number as part of a process called diploidization. CONCLUSIONS TEs play an essential role in genome and gene evolution, in particular after polyploidization events. Polyploidization can induce TE activity that may explain part of the new phenotypes observed. TEs may also play a role in the diploidization that follows polyploidization events. However, the extent to which TEs contribute to diploidization and fractionation bias remains unclear. Investigating the multiple factors controlling TE dynamics and the nature of ancient and recent polyploid genomes may shed light on these processes.
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Affiliation(s)
- Carlos M. Vicient
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
- For correspondence. E-mail
| | - Josep M. Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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Cao Y, Li S, Wang Z, Chang F, Kong J, Gai J, Zhao T. Identification of Major Quantitative Trait Loci for Seed Oil Content in Soybeans by Combining Linkage and Genome-Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2017; 8:1222. [PMID: 28747922 PMCID: PMC5506190 DOI: 10.3389/fpls.2017.01222] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/28/2017] [Indexed: 05/20/2023]
Abstract
Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley. One recombinant inbred line (RIL) population (NJMN-RIL), with 104 lines developed from a cross between M8108 and NN1138-2, was planted in five environments to investigate phenotypic data, and a new genetic map with 2,062 specific-locus amplified fragment markers was constructed to map oil content QTLs. A derived F2 population between MN-5 (a line of NJMN-RIL) and NN1138-2 was also developed to confirm one major QTL. A soybean breeding germplasm population (279 lines) was established to perform a genome-wide association study (GWAS) using 59,845 high-quality single nucleotide polymorphism markers. In the NJMN-RIL population, 8 QTLs were found that explained a range of phenotypic variance from 6.3 to 26.3% in certain planting environments. Among them, qOil-5-1, qOil-10-1, and qOil-14-1 were detected in different environments, and qOil-5-1 was further confirmed using the secondary F2 population. Three loci located on chromosomes 5 and 20 were detected in a 2-year long GWAS, and one locus that overlapped with qOil-5-1 was found repeatedly and treated as the same locus. qOil-5-1 was further localized to a linkage disequilibrium block region of approximately 440 kb. These results will not only increase our understanding of the genetic control of seed oil content in soybean, but will also be helpful in marker-assisted selection for breeding high seed oil content soybean and gene cloning to elucidate the mechanisms of seed oil content.
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Affiliation(s)
| | | | | | | | | | - Junyi Gai
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
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9
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Li F, Fan K, Ma F, Yue E, Bibi N, Wang M, Shen H, Hasan MMU, Wang X. Genomic Identification and Comparative Expansion Analysis of the Non-Specific Lipid Transfer Protein Gene Family in Gossypium. Sci Rep 2016; 6:38948. [PMID: 27976679 PMCID: PMC5157027 DOI: 10.1038/srep38948] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/16/2016] [Indexed: 11/16/2022] Open
Abstract
Plant non-specific lipid transfer proteins (nsLTPs) are involved in many biological processes. In this study, 51, 47 and 91 nsLTPs were identified in Gossypium arboreum, G. raimondii and their descendant allotetraploid G. hirsutum, respectively. All the nsLTPs were phylogenetically divided into 8 distinct subfamilies. Besides, the recent duplication, which is considered cotton-specific whole genome duplication, may have led to nsLTP expansion in Gossypium. Both tandem and segmental duplication contributed to nsLTP expansion in G. arboreum and G. hirsutum, while tandem duplication was the dominant pattern in G. raimondii. Additionally, the interspecific orthologous gene pairs in Gossypium were identified. Some GaLTPs and GrLTPs lost their orthologs in the At and Dt subgenomes, respectively, of G. hirsutum. The distribution of these GrLTPs and GaLTPs within each subfamily was complementary, suggesting that the loss and retention of nsLTPs in G. hirsutum might not be random. Moreover, the nsLTPs in the At and Dt subgenomes might have evolved symmetrically. Furthermore, both intraspecific and interspecific orthologous genes showed considerable expression variation, suggesting that their functions were strongly differentiated. Our results lay an important foundation for expansion and evolutionary analysis of the nsLTP family in Gossypium, and advance nsLTP studies in other plants, especially polyploid plants.
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Affiliation(s)
- Feng Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Kai Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Fanglu Ma
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Erkui Yue
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Noreen Bibi
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Ming Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Hao Shen
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Md Mosfeq-Ul Hasan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
| | - Xuede Wang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China
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10
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Multiple origins of BBCC allopolyploid species in the rice genus (Oryza). Sci Rep 2015; 5:14876. [PMID: 26460928 PMCID: PMC4602239 DOI: 10.1038/srep14876] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/10/2015] [Indexed: 11/16/2022] Open
Abstract
In the rice genus (Oryza), about one half of the species are allopolyploids. These species are not only important resources for rice breeding but also provide a unique opportunity for studying evolution of polyploid species. In the present study, we sequenced four biparentally inherited nuclear loci and three maternally inherited chloroplast fragments from all diploid and tetraploid species with the B- and C-genome types in this genus. We detected at least three independent origins of three BC-genome tetraploid species. Specifically, the diploid O. punctata (B-genome) and O. officinalis (C-genome) were the parental progenitors of O. minuta and O. malampuzhaensis with O. punctata being the maternal donors, whereas the diploid O. punctata and O. eichingeri (C-genome) were the progenitors of tetraploid O. punctata with O. punctata being the paternal donor. Our relaxed clock analyses suggest that all the BBCC species originated within the last one million years, which is coincident with the severe climate oscillations occurred during the last ice age, implying the potential impact of climate change on their formations and dispersals. In addition, our results support previous taxonomic arguments that the tetraploid O. punctata might be better treated as a separate species (O. schweinfurthiana).
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Jenkins AM, Muskavitch MAT. Evolution of an epigenetic gene ensemble within the genus Anopheles. Genome Biol Evol 2015; 7:901-15. [PMID: 25724208 PMCID: PMC5322554 DOI: 10.1093/gbe/evv041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Epigenetic control of gene expression has important implications for the regulation of developmental processes, for mediating homeostasis and responses to the external environment, and for transgenerational inheritance of gene expression patterns. Genes that mediate epigenetic control have been well-characterized in Drosophila melanogaster, and we have identified and analyzed an orthologous gene ensemble in Anopheles gambiae that comprises 169 orthologs related to a 215-member epigenetic gene ensemble in D. melanogaster. We find that this ensemble is highly conserved among anopheline mosquitoes, as we identify only seven gene family expansion/contraction events within the ensemble among 12 mosquito species we have studied within the genus Anopheles. Comparative analyses of the epigenetic gene expression across the genera Drosophila and Anopheles reveal distinct tissue-associated expression patterns in the two genera, but similar temporal expression patterns. The A. gambiae complex and D. melanogaster subgroup epigenetic gene ensembles exhibit similar evolutionary rates, as assessed by their respective dN/dS values. These differences in tissue-associated expression patterns, in contrast to similarities in evolutionary rates and temporal expression patterns, may imply that some members of the epigenetic gene ensemble have been redeployed within one or both genera, in comparison to the most recent common ancestor of these two clades. Members of this epigenetic gene ensemble may constitute another set of potential targets for vector control and enable further reductions in the burden of human malaria, by analogy to recent success in development of small molecule antagonists for mammalian epigenetic machinery.
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Affiliation(s)
| | - Marc A T Muskavitch
- Department of Biology, Boston College Discovery Research, Biogen Idec, Cambridge, Massachusetts
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