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Wu Q, Su Y, Pan YB, Xu F, Zou W, Que B, Lin P, Sun T, Grisham MP, Xu L, Que Y. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:1035266. [PMID: 36311133 PMCID: PMC9608552 DOI: 10.3389/fpls.2022.1035266] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/27/2022] [Indexed: 06/01/2023]
Abstract
Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases worldwide. In this study, a cross was made between a smut-resistant variety YT93-159 and a smut-susceptible variety ROC22, and 312 progenies were obtained. Two bulks of progenies were then constructed, one consisted of 27 highly smut resistant progenies and the other 24 smut susceptible progenies. Total RNAs of the progenies of each bulk, were pooled and subject to bulked segregant RNA-sequence analysis (BSR-Seq). A total of 164.44 Gb clean data containing 2,341,449 SNPs and 64,999 genes were obtained, 7,295 of which were differentially expressed genes (DEGs). These DEGs were mainly enriched in stress-related metabolic pathways, including carbon metabolism, phenylalanine metabolism, plant hormone signal transduction, glutathione metabolism, and plant-pathogen interactions. Besides, 45,946 high-quality, credible SNPs, a 1.27 Mb region at Saccharum spontaneum chromosome Chr5B (68,904,827 to 70,172,982), and 129 candidate genes were identified to be associated with smut resistance. Among them, twenty-four genes, either encoding key enzymes involved in signaling pathways or being transcription factors, were found to be very closely associated with stress resistance. RT-qPCR analysis demonstrated that they played a positive role in smut resistance. Finally, a potential molecular mechanism of sugarcane and S. scitamineum interaction is depicted that activations of MAPK cascade signaling, ROS signaling, Ca2+ signaling, and PAL metabolic pathway and initiation of the glyoxalase system jointly promote the resistance to S. scitamineum in sugarcane. This study provides potential SNP markers and candidate gene resources for smut resistance breeding in sugarcane.
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Affiliation(s)
- Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong-Bao Pan
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Beibei Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- International College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peixia Lin
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Michael P. Grisham
- USDA-ARS, Southeast Area, Sugarcane Research Unit, Houma, LA, United States
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Shaibu AS, Zhang S, Ma J, Feng Y, Huai Y, Qi J, Li J, Abdelghany AM, Azam M, Htway HTP, Sun J, Li B. The GmSNAP11 Contributes to Resistance to Soybean Cyst Nematode Race 4 in Glycine max. FRONTIERS IN PLANT SCIENCE 2022; 13:939763. [PMID: 35860531 PMCID: PMC9289622 DOI: 10.3389/fpls.2022.939763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Soybean cyst nematode (SCN) has devastating effects on soybean production, making it crucial to identify genes conferring SCN resistance. Here we employed next-generation sequencing-based bulked segregant analysis (BSA) to discover genomic regions, candidate genes, and diagnostic markers for resistance to SCN race 4 (SCN4) in soybean. Phenotypic analysis revealed highly significant differences among the reactions of 145 recombinant inbred lines (RILs) to SCN4. In combination with euclidean distance (ED) and Δsingle-nucleotide polymorphism (SNP)-index analyses, we identified a genomic region on Gm11 (designated as rhg1-paralog) associated with SCN4 resistance. Overexpression and RNA interference analyzes of the two candidate genes identified in this region (GmPLAC8 and GmSNAP11) revealed that only GmSNAP11 significantly contributes to SCN4 resistance. We developed a diagnostic marker for GmSNAP11. Using this marker, together with previously developed markers for SCN-resistant loci, rhg1 and Rhg4, we evaluated the relationship between genotypes and SCN4 resistance in 145 RILs and 30 soybean accessions. The results showed that all the SCN4-resistant lines harbored all the three loci, however, some lines harboring the three loci were still susceptible to SCN4. This suggests that these three loci are necessary for the resistance to SCN4, but they alone cannot confer full resistance. The GmSNAP11 and the diagnostic markers developed could be used in genomic-assisted breeding to develop soybean varieties with increased resistance to SCN4.
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Affiliation(s)
- Abdulwahab S. Shaibu
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Agronomy, Bayero University Kano, Kano, Nigeria
| | - Shengrui Zhang
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junkui Ma
- Institute of Industrial Crop Research, Shanxi Academy of Agricultural Sciences, Fenyang, China
| | - Yue Feng
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanyuan Huai
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Qi
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Li
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahmed M. Abdelghany
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Azam
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honey Thet Paing Htway
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junming Sun
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Li
- The National Engineering Research Center for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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3
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Li P, Li G, Zhang YW, Zuo JF, Liu JY, Zhang YM. A combinatorial strategy to identify various types of QTLs for quantitative traits using extreme phenotype individuals in an F 2 population. PLANT COMMUNICATIONS 2022; 3:100319. [PMID: 35576159 PMCID: PMC9251438 DOI: 10.1016/j.xplc.2022.100319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/07/2022] [Accepted: 03/22/2022] [Indexed: 06/09/2023]
Abstract
Theoretical and applied studies demonstrate the difficulty of detecting extremely over-dominant and small-effect genes for quantitative traits via bulked segregant analysis (BSA) in an F2 population. To address this issue, we proposed an integrated strategy for mapping various types of quantitative trait loci (QTLs) for quantitative traits via a combination of BSA and whole-genome sequencing. In this strategy, the numbers of read counts of marker alleles in two extreme pools were used to predict the numbers of read counts of marker genotypes. These observed and predicted numbers were used to construct a new statistic, Gw, for detecting quantitative trait genes (QTGs), and the method was named dQTG-seq1. This method was significantly better than existing BSA methods. If the goal was to identify extremely over-dominant and small-effect genes, another reserved DNA/RNA sample from each extreme phenotype F2 plant was sequenced, and the observed numbers of marker alleles and genotypes were used to calculate Gw to detect QTGs; this method was named dQTG-seq2. In simulated and real rice dataset analyses, dQTG-seq2 could identify many more extremely over-dominant and small-effect genes than BSA and QTL mapping methods. dQTG-seq2 may be extended to other heterogeneous mapping populations. The significance threshold of Gw in this study was determined by permutation experiments. In addition, a handbook for the R software dQTG.seq, which is available at https://cran.r-project.org/web/packages/dQTG.seq/index.html, has been provided in the supplemental materials for the users' convenience. This study provides a new strategy for identifying all types of QTLs for quantitative traits in an F2 population.
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Affiliation(s)
- Pei Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guo Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ya-Wen Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin-Yang Liu
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Lin Z, Xie F, Triviño M, Zhao T, Coppens F, Sterck L, Bosch M, Franklin-Tong VE, Nowack MK. Self-incompatibility requires GPI anchor remodeling by the poppy PGAP1 ortholog HLD1. Curr Biol 2022; 32:1909-1923.e5. [PMID: 35316654 DOI: 10.1016/j.cub.2022.02.072] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/25/2022] [Accepted: 02/24/2022] [Indexed: 11/25/2022]
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are tethered to the outer leaflet of the plasma membrane where they function as key regulators of a plethora of biological processes in eukaryotes. Self-incompatibility (SI) plays a pivotal role regulating fertilization in higher plants through recognition and rejection of "self" pollen. Here, we used Arabidopsis thaliana lines that were engineered to be self-incompatible by expression of Papaver rhoeas SI determinants for an SI suppressor screen. We identify HLD1/AtPGAP1, an ortholog of the human GPI-inositol deacylase PGAP1, as a critical component required for the SI response. Besides a delay in flowering time, no developmental defects were observed in HLD1/AtPGAP1 knockout plants, but SI was completely abolished. We demonstrate that HLD1/AtPGAP1 functions as a GPI-inositol deacylase and that this GPI-remodeling activity is essential for SI. Using GFP-SKU5 as a representative GPI-AP, we show that the HLD1/AtPGAP1 mutation does not affect GPI-AP production and targeting but affects their cleavage and release from membranes in vivo. Our data not only implicate GPI-APs in SI, providing new directions to investigate SI mechanisms, but also identify a key functional role for GPI-AP remodeling by inositol deacylation in planta.
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Affiliation(s)
- Zongcheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB, Ghent 9052, Belgium; Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.
| | - Fei Xie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Marina Triviño
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB, Ghent 9052, Belgium; Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, UK
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth SY23 3EB, UK.
| | | | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB, Ghent 9052, Belgium.
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5
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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6
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Chen DG, Zhou XQ, Chen K, Chen PL, Guo J, Liu CG, Chen YD. Fine-mapping and candidate gene analysis of a major locus controlling leaf thickness in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:6. [PMID: 35103045 PMCID: PMC8792131 DOI: 10.1007/s11032-022-01275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/13/2022] [Indexed: 05/16/2023]
Abstract
UNLABELLED Leaf thickness is an important trait in rice (Oryza sativa L.). It affects both photosynthesis and sink-resource efficiency. However, compared to leaf length and length width, reports seldom focused on leaf thickness due to the complicated measurement and minor difference. To identify the quantitative trait loci (QTL) and explore the genetic mechanism regulating the natural variation of leaf thickness, we crossed a high leaf thickness variety Aixiuzhan (AXZ) to a thin leaf thickness variety Yangdao No.6 (YD 6) and evaluated 585 F2 individuals. We further use bulked sergeant analysis with whole-genome resequencing (BSA-seq) to identify five genomic regions, including chromosomes 1, 6, 9, 10, and 12. These regions represented significant allele frequency differentiation between thick and thin leaf thickness among the mixed pool offspring. Moreover, we conducted a linkage mapping using 276 individuals derived from the F2 population. We fine-mapped and confirmed that chromosome 9 contributed the primary explanation of phenotypic variance. We fine-mapped the candidate regions and confirmed that the chromosome 9 region contributed to flag leaf thickness in rice. We observed the virtual cellular slices and found that the bundle sheath cells in YD 6 flag leaf veins are fewer than AXZ. We analyzed the potential regions on chromosome 9 and narrowed the QTL candidate intervals in the 928-kb region. Candidate genes of this major QTL were listed as potentially controlled leaf thickness. These results provide promising evidence that cloning leaf thickness is associated with yield production in rice. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11032-022-01275-y.
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Affiliation(s)
- Da-gang Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Xin-qiao Zhou
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ke Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Ping-li Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Jie Guo
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Chuan-guang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - You-ding Chen
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
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7
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Bommisetty R, Chakravartty N, Bodanapu R, Naik JB, Panda SK, Lekkala SP, Lalam K, Thomas G, Mallikarjuna SJ, Eswar GR, Kadambari GM, Bollineni SN, Issa K, Akkareddy S, Srilakshmi C, Hariprasadreddy K, Rameshbabu P, Sudhakar P, Gupta S, Lachagari VBR, Vemireddy LR. Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.). Mol Biol Rep 2020; 47:8615-8627. [PMID: 33098552 DOI: 10.1007/s11033-020-05904-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/07/2020] [Indexed: 01/05/2023]
Abstract
Rice (Oryza sativa L.) yield enhancement is one of the prime objectives of plant breeders. Elucidation of the inheritance of grain weight, a key yield component trait, is of paramount importance for raising the yield thresholds in rice. In the present investigation, we employed Next-Generation Sequencing based QTL-seq approach to identify major genomic regions associated with grain weight using mapping populations derived from a cross between BPT5204 and MTU3626. QTL-seq analysis identified three grain weight quantitative trait loci (QTL) viz., qGW1 (35-40 Mb), qGW7 (10-18 Mb), and qGW8 (2-5 Mb) on chromosomes 1, 7 and 8, respectively and all are found to be novel. Further, qGW8 was confirmed through conventional QTL mapping in F2, F3 and BC1F2 populations and found to explain the phenotypic variance of 17.88%, 16.70% and 15.00%, respectively, indicating a major QTL for grain weight. Based on previous reports, two candidate genes in the qGW8 QTL were predicted i.e., LOC_Os08g01490 (Cytochrome P450), and LOC_Os08g01680 (WD domain, G-beta repeat domain containing protein) and through in silico analysis they were found to be highly expressed in reproductive organs during different stages of grain development. Here, we have demonstrated that QTL-seq is one of the rapid approaches to uncover novel QTLs controlling complex traits. The candidate genes identified in the present study undoubtedly enhance our understanding of the mechanism and inheritance of the grain weight. These candidate genes can be exploited for yield enhancement after confirmation through complementary studies.
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Affiliation(s)
- Reddyyamini Bommisetty
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | | | - Reddaiah Bodanapu
- AgriGenome Labs Pvt Ltd., SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India
| | - Jeevula B Naik
- Regional Agricultural Research Station, ANGRAU, Tirupati, 517502, India
| | - Sanjib K Panda
- Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Sivarama P Lekkala
- AgriGenome Labs Pvt Ltd., SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India
| | - Krishna Lalam
- AgriGenome Labs Pvt Ltd., SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India
| | - George Thomas
- AgriGenome Labs Pvt Ltd., SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India
| | - S J Mallikarjuna
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - G R Eswar
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - Gopalakrishna M Kadambari
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | | | - Keerthi Issa
- Regional Agricultural Research Station, ANGRAU, Tirupati, 517502, India
| | | | - C Srilakshmi
- Agricultural Research Station, ANGRAU, Nellore, India
| | - K Hariprasadreddy
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - P Rameshbabu
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - P Sudhakar
- Department of Crop Physiology, S.V Agricultural College, ANGRAU, Tirupati, 517502, India
| | - Saurabh Gupta
- AgriGenome Labs Pvt Ltd., SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India
| | - V B R Lachagari
- AgriGenome Labs Pvt Ltd., SINC, IKP Knowledge Park, Genome Valley, Hyderabad, India.
| | - Lakshminarayana R Vemireddy
- Department of Genetics and Plant Breeding, S.V Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India.
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8
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Heuermann MC, Rosso MG, Mascher M, Brandt R, Tschiersch H, Altschmied L, Altmann T. Combining next-generation sequencing and progeny testing for rapid identification of induced recessive and dominant mutations in maize M 2 individuals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:851-862. [PMID: 31169333 PMCID: PMC6899793 DOI: 10.1111/tpj.14431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 05/31/2023]
Abstract
Molecular identification of mutant alleles responsible for certain phenotypic alterations is a central goal of genetic analyses. In this study we describe a rapid procedure suitable for the identification of induced recessive and dominant mutations applied to two Zea mays mutants expressing a dwarf and a pale green phenotype, respectively, which were obtained through pollen ethyl methanesulfonate (EMS) mutagenesis. First, without prior backcrossing, induced mutations (single nucleotide polymorphisms, SNPs) segregating in a (M2 ) family derived from a heterozygous (M1 ) parent were identified using whole-genome shotgun (WGS) sequencing of a small number of (M2 ) individuals with mutant and wild-type phenotypes. Second, the state of zygosity of the mutation causing the phenotype was determined for each sequenced individual by phenotypic segregation analysis of the self-pollinated (M3 ) offspring. Finally, we filtered for segregating EMS-induced SNPs whose state of zygosity matched the determined state of zygosity of the mutant locus in each sequenced (M2 ) individuals. Through this procedure, combining sequencing of individuals and Mendelian inheritance, three and four SNPs in linkage passed our zygosity filter for the homozygous dwarf and heterozygous pale green mutation, respectively. The dwarf mutation was found to be allelic to the an1 locus and caused by an insertion in the largest exon of the AN1 gene. The pale green mutation affected the nuclear W2 gene and was caused by a non-synonymous amino acid exchange in encoded chloroplast DNA polymerase with a predicted deleterious effect. This coincided with lower cpDNA levels in pale green plants.
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Affiliation(s)
- Marc C. Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Mario G. Rosso
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Ronny Brandt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
- Max Planck‐Genome‐Centre CologneMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829KölnGermany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
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9
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A high-quality cucumber genome assembly enhances computational comparative genomics. Mol Genet Genomics 2019; 295:177-193. [PMID: 31620884 DOI: 10.1007/s00438-019-01614-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/30/2019] [Indexed: 01/12/2023]
Abstract
Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data from three individuals to analyse the polymorphisms. Using this approach, we uncovered differentiation aspects in the genomes of the inbred B10 line. The newly assembled genome sequence (B10v3) has the highest contiguity and quality characteristics among the currently available cucumber genome draft sequences. Standard and newly designed approaches were used to predict single nucleotide and structural variants that were unique among the three individual genomes. Some of the variant predictions spanned protein-coding genes and their promoters, and some were in the neighbourhood of annotated interspersed repetitive elements, indicating that the highly inbred homozygous plants remained genetically dynamic. This is the first bioinformatic comparative genomics study of a single highly inbred plant line. For this project, we developed a polymorphism prediction method with optimized precision parameters, which allowed the effective detection of small nucleotide variants (SNVs). This methodology could significantly improve bioinformatic pipelines for comparative genomics and thus has great practical potential in genomic metadata handling.
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10
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Javorka P, Raxwal VK, Najvarek J, Riha K. artMAP: A user-friendly tool for mapping ethyl methanesulfonate-induced mutations in Arabidopsis. PLANT DIRECT 2019; 3:e00146. [PMID: 31245783 PMCID: PMC6560221 DOI: 10.1002/pld3.146] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 05/27/2023]
Abstract
Mapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP makes the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).
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Affiliation(s)
| | | | | | - Karel Riha
- CEITECMasaryk UniversityBrnoCzech Republic
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11
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Whole Genome Resequencing from Bulked Populations as a Rapid QTL and Gene Identification Method in Rice. Int J Mol Sci 2018; 19:ijms19124000. [PMID: 30545055 PMCID: PMC6321147 DOI: 10.3390/ijms19124000] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 11/16/2022] Open
Abstract
Most Quantitative Trait Loci (QTL) and gene isolation approaches, such as positional- or map-based cloning, are time-consuming and low-throughput methods. Understanding and detecting the genetic material that controls a phenotype is a key means to functionally analyzing genes as well as to enhance crop agronomic traits. In this regard, high-throughput technologies have great prospects for changing the paradigms of DNA marker revealing, genotyping, and for discovering crop genetics and genomic study. Bulk segregant analysis, based on whole genome resequencing approaches, permits the rapid isolation of the genes or QTL responsible for the causative mutation of the phenotypes. MutMap, MutMap Gap, MutMap+, modified MutMap, and QTL-seq methods are among those approaches that have been confirmed to be fruitful gene mapping approaches for crop plants, such as rice, irrespective of whether the characters are determined by polygenes. As a result, in the present study we reviewed the progress made by all these methods to identify QTL or genes in rice.
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12
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Franck CM, Westermann J, Bürssner S, Lentz R, Lituiev DS, Boisson-Dernier A. The Protein Phosphatases ATUNIS1 and ATUNIS2 Regulate Cell Wall Integrity in Tip-Growing Cells. THE PLANT CELL 2018; 30:1906-1923. [PMID: 29991535 PMCID: PMC6139677 DOI: 10.1105/tpc.18.00284] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/08/2018] [Accepted: 06/29/2018] [Indexed: 05/10/2023]
Abstract
Fast tip-growing plant cells such as pollen tubes (PTs) and root hairs (RHs) require a robust coordination between their internal growth machinery and modifications of their extracellular rigid, yet extensible, cell wall (CW). Part of this essential coordination is governed by members of the Catharanthus roseus receptor-like kinase1-like (CrRLK1L) subfamily of RLKs with FERONIA (FER) and its closest homologs, ANXUR1 (ANX1) and ANX2, controlling CW integrity during RH and PT growth, respectively. Recently, Leucine-Rich Repeat Extensin 8 (LRX8) to LRX11 were also shown to be important for CW integrity in PTs. We previously reported an anx1 anx2 suppressor screen in Arabidopsis thaliana that revealed MARIS (MRI) as a positive regulator of both FER- and ANX1/2-dependent CW integrity pathways. Here, we characterize a suppressor that exhibits a weak rescue of the anx1 anx2 PT bursting phenotype and a short RH phenotype. The corresponding suppressor mutation causes a D94N substitution in a Type One Protein Phosphatase we named ATUNIS1 (AUN1). We show that AUN1 and its closest homolog, AUN2, are nucleocytoplasmic negative regulators of tip growth. Moreover, we demonstrate that AUN1D94N and AUN1H127A harboring mutations in key amino acids of the conserved catalytic site of phosphoprotein phosphatases function as dominant amorphic variants that repress PT growth. Finally, genetic interaction studies using the hypermorph MRIR240C and amorph AUN1D94N dominant variants indicate that LRX8-11 and ANX1/2 function in distinct but converging pathways to fine-tune CW integrity during tip growth.
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Affiliation(s)
| | | | - Simon Bürssner
- University of Cologne, Biocenter, 50674 Cologne, Germany
| | - Roswitha Lentz
- University of Cologne, Biocenter, 50674 Cologne, Germany
| | - Dmytro Sergiiovych Lituiev
- Institute for Computational Health Sciences, University of California, San Francisco, California 94158
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Centre, University of Zurich, 8008 Zurich, Switzerland
| | - Aurélien Boisson-Dernier
- University of Cologne, Biocenter, 50674 Cologne, Germany
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Centre, University of Zurich, 8008 Zurich, Switzerland
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13
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Dougherty L, Singh R, Brown S, Dardick C, Xu K. Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1499-1516. [PMID: 29361034 PMCID: PMC5888915 DOI: 10.1093/jxb/erx490] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/19/2017] [Indexed: 05/19/2023]
Abstract
To unlock the power of next generation sequencing-based bulked segregant analysis in allele discovery in out-crossing woody species, and to understand the genetic control of the weeping trait, an F1 population from the cross 'Cheal's Weeping' × 'Evereste' was used to create two genomic DNA pools 'weeping' (17 progeny) and 'standard' (16 progeny). Illumina pair-end (2 × 151 bp) sequencing of the pools to a 27.1× (weeping) and a 30.4× (standard) genome (742.3 Mb) coverage allowed detection of 84562 DNA variants specific to 'weeping', 92148 specific to 'standard', and 173169 common to both pools. A detailed analysis of the DNA variant genotypes in the pools predicted three informative segregation types of variants: (type I) in weeping pool-specific variants, and (type II) and (type III) in variants common to both pools, where the first allele is assumed to be weeping linked and the allele shown in bold is a variant in relation to the reference genome. Conducting variant allele frequency and density-based mappings revealed four genomic regions with a significant association with weeping: a major locus, Weeping (W), on chromosome 13 and others on chromosomes 10 (W2), 16 (W3), and 5 (W4). The results from type I variants were noisier and less certain than those from type II and type III variants, demonstrating that although type I variants are often the first choice, type II and type III variants represent an important source of DNA variants that can be exploited for genetic mapping in out-crossing woody species. Confirmation of the mapping of W and W2, investigation into their genetic interactions, and identification of expressed genes in the W and W2 regions provided insight into the genetic control of weeping and its expressivity in Malus.
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Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | - Raksha Singh
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | - Susan Brown
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | | | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
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14
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Singh VK, Khan AW, Saxena RK, Sinha P, Kale SM, Parupalli S, Kumar V, Chitikineni A, Vechalapu S, Sameer Kumar CV, Sharma M, Ghanta A, Yamini KN, Muniswamy S, Varshney RK. Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:906-914. [PMID: 28027425 PMCID: PMC5466435 DOI: 10.1111/pbi.12685] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 05/05/2023]
Abstract
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species.
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Affiliation(s)
- Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Swathi Parupalli
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Vinay Kumar
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | | | - Mamta Sharma
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Anuradha Ghanta
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Kalinati Narasimhan Yamini
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)‐GulbargaUniversity of Agricultural Sciences (UAS)RaichurKarnatakaIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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15
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Abstract
In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of ethyl methanesulfonate (EMS)-mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error-prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequences in wild-type siblings and heterozygous in segregating families. This region contained a single nonsynonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the Sorghum ortholog encoding the gibberellic acid (GA) biosynthetic enzyme ent-kaurene oxidase. Application of exogenous GA rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks cosegregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.
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16
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Song J, Li Z, Liu Z, Guo Y, Qiu LJ. Next-Generation Sequencing from Bulked-Segregant Analysis Accelerates the Simultaneous Identification of Two Qualitative Genes in Soybean. FRONTIERS IN PLANT SCIENCE 2017; 8:919. [PMID: 28620406 PMCID: PMC5449466 DOI: 10.3389/fpls.2017.00919] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/16/2017] [Indexed: 05/03/2023]
Abstract
Next-generation sequencing (NGS)-based bulked-segregant analysis (BSA) approaches have been proven successful for rapidly mapping genes in plant species. However, most such methods are based on mutants and usually only one gene controlling the mutant phenotype is identified. In this study, NGS-based BSA was employed to map simultaneously two qualitative genes controlling cotyledon color of seed in soybean. Yellow-cotyledon (YC) and green-cotyledon (GC) bulks from progenies of a biparental population (Zhonghuang 30 × Jiyu 102) were sequenced. The SNP-index of each SNP locus in YC and GC bulks was calculated and two genomic regions on chromosomes 1 and 11 harboring, respectively, loci qCC1 and qCC2 were identified by Δ(SNP-index) analysis. These two BSA-seq-derived loci were further validated with SSR markers and fine-mapped. qCC1 was mapped to a 30.7-kb region containing four annotated genes and qCC2 was mapped to a 67.7-kb region with nine genes. These two regions contained, respectively, genes D1 and D2, which had previously been identified by homology-based cloning as being associated with cotyledon color. Sequence analysis of the NGS data also identified a frameshift deletion in the coding region of D1. These results suggested that BSA-seq could accelerate the mapping of loci controlling qualitative traits, even if a trait is controlled by more than one locus.
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Affiliation(s)
| | | | | | - Yong Guo
- *Correspondence: Li-Juan Qiu, Yong Guo,
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17
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Pereira AM, Lopes AL, Coimbra S. Arabinogalactan Proteins as Interactors along the Crosstalk between the Pollen Tube and the Female Tissues. FRONTIERS IN PLANT SCIENCE 2016; 7:1895. [PMID: 28018417 PMCID: PMC5159419 DOI: 10.3389/fpls.2016.01895] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/30/2016] [Indexed: 05/19/2023]
Abstract
Arabinogalactan proteins (AGPs) have long been considered to be implicated in several steps of the reproductive process of flowering plants. Pollen tube growth along the pistil tissues requires a multiplicity of signaling pathways to be activated and turned off precisely, at crucial timepoints, to guarantee successful fertilization and seed production. In the recent years, an outstanding effort has been made by the plant reproduction scientific community in order to better understand this process. This resulted in the discovery of a fairly substantial number of new players essential for reproduction, as well as their modes of action and interactions. Besides all the indications of AGPs involvement in reproduction, there were no convincing evidences about it. Recently, several studies came out to prove what had long been suggested about this complex family of glycoproteins. AGPs consist of a large family of hydroxyproline-rich proteins, predicted to be anchored to the plasma membrane and extremely rich in sugars. These two last characteristics always made them perfect candidates to be involved in signaling mechanisms, in several plant developmental processes. New findings finally relate AGPs to concrete functions in plant reproduction. In this review, it is intended not only to describe how different molecules and signaling pathways are functioning to achieve fertilization, but also to integrate the recent discoveries about AGPs along this process.
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Affiliation(s)
- Ana M. Pereira
- Departamento de Biologia, Faculdade de Ciências da Universidade do PortoPorto, Portugal
- Biosystems and Integrative Sciences InstitutePorto, Portugal
| | - Ana L. Lopes
- Departamento de Biologia, Faculdade de Ciências da Universidade do PortoPorto, Portugal
- Biosystems and Integrative Sciences InstitutePorto, Portugal
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do PortoPorto, Portugal
- Biosystems and Integrative Sciences InstitutePorto, Portugal
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18
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Smýkal P, K Varshney R, K Singh V, Coyne CJ, Domoney C, Kejnovský E, Warkentin T. From Mendel's discovery on pea to today's plant genetics and breeding : Commemorating the 150th anniversary of the reading of Mendel's discovery. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2267-2280. [PMID: 27717955 DOI: 10.1007/s00122-016-2803-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
KEY MESSAGE This work discusses several selected topics of plant genetics and breeding in relation to the 150th anniversary of the seminal work of Gregor Johann Mendel. In 2015, we celebrated the 150th anniversary of the presentation of the seminal work of Gregor Johann Mendel. While Darwin's theory of evolution was based on differential survival and differential reproductive success, Mendel's theory of heredity relies on equality and stability throughout all stages of the life cycle. Darwin's concepts were continuous variation and "soft" heredity; Mendel espoused discontinuous variation and "hard" heredity. Thus, the combination of Mendelian genetics with Darwin's theory of natural selection was the process that resulted in the modern synthesis of evolutionary biology. Although biology, genetics, and genomics have been revolutionized in recent years, modern genetics will forever rely on simple principles founded on pea breeding using seven single gene characters. Purposeful use of mutants to study gene function is one of the essential tools of modern genetics. Today, over 100 plant species genomes have been sequenced. Mapping populations and their use in segregation of molecular markers and marker-trait association to map and isolate genes, were developed on the basis of Mendel's work. Genome-wide or genomic selection is a recent approach for the development of improved breeding lines. The analysis of complex traits has been enhanced by high-throughput phenotyping and developments in statistical and modeling methods for the analysis of phenotypic data. Introgression of novel alleles from landraces and wild relatives widens genetic diversity and improves traits; transgenic methodologies allow for the introduction of novel genes from diverse sources, and gene editing approaches offer possibilities to manipulate gene in a precise manner.
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Affiliation(s)
- Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University in Olomouc, Slechtitelu 27, Olomouc, Czech Republic.
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | | | | | - Eduard Kejnovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Thomas Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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19
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Doitsidou M, Jarriault S, Poole RJ. Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans. Genetics 2016; 204:451-474. [PMID: 27729495 PMCID: PMC5068839 DOI: 10.1534/genetics.115.186197] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023] Open
Abstract
The use of next-generation sequencing (NGS) has revolutionized the way phenotypic traits are assigned to genes. In this review, we describe NGS-based methods for mapping a mutation and identifying its molecular identity, with an emphasis on applications in Caenorhabditis elegans In addition to an overview of the general principles and concepts, we discuss the main methods, provide practical and conceptual pointers, and guide the reader in the types of bioinformatics analyses that are required. Owing to the speed and the plummeting costs of NGS-based methods, mapping and cloning a mutation of interest has become straightforward, quick, and relatively easy. Removing this bottleneck previously associated with forward genetic screens has significantly advanced the use of genetics to probe fundamental biological processes in an unbiased manner.
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Affiliation(s)
- Maria Doitsidou
- Centre for Integrative Physiology, University of Edinburgh, EH8 9XD, Scotland
| | - Sophie Jarriault
- L'Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104/Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404, France
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, WC1E 6BT, United Kingdom
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20
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Onda Y, Mochida K. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques. Curr Genomics 2016; 17:358-67. [PMID: 27499684 PMCID: PMC4955029 DOI: 10.2174/1389202917666160331202742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/31/2022] Open
Abstract
Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
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21
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Dugard CK, Mertz RA, Rayon C, Mercadante D, Hart C, Benatti MR, Olek AT, SanMiguel PJ, Cooper BR, Reiter WD, McCann MC, Carpita NC. The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2. PLANT PHYSIOLOGY 2016; 171:1905-20. [PMID: 27217494 PMCID: PMC4936543 DOI: 10.1104/pp.15.01922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 05/19/2016] [Indexed: 05/23/2023]
Abstract
Traditional marker-based mapping and next-generation sequencing was used to determine that the Arabidopsis (Arabidopsis thaliana) low cell wall arabinose mutant murus5 (mur5) encodes a defective allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2 (RGP2). Marker analysis of 13 F2 confirmed mutant progeny from a recombinant mapping population gave a rough map position on the upper arm of chromosome 5, and deep sequencing of DNA from these 13 lines gave five candidate genes with G→A (C→T) transitions predicted to result in amino acid changes. Of these five, only insertional mutant alleles of RGP2, a gene that encodes a UDP-arabinose mutase that interconverts UDP-arabinopyranose and UDP-arabinofuranose, exhibited the low cell wall arabinose phenotype. The identities of mur5 and two SALK insertional alleles were confirmed by allelism tests and overexpression of wild-type RGP2 complementary DNA placed under the control of the 35S promoter in the three alleles. The mur5 mutation results in the conversion of cysteine-257 to tyrosine-257 within a conserved hydrophobic cluster predicted to be distal to the active site and essential for protein stability and possible heterodimerization with other isoforms of RGP.
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Affiliation(s)
- Christopher K Dugard
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Rachel A Mertz
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Catherine Rayon
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Davide Mercadante
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Christopher Hart
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Matheus R Benatti
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Anna T Olek
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Phillip J SanMiguel
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Bruce R Cooper
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Wolf-Dieter Reiter
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Maureen C McCann
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
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22
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Singh VK, Khan AW, Saxena RK, Kumar V, Kale SM, Sinha P, Chitikineni A, Pazhamala LT, Garg V, Sharma M, Sameer Kumar CV, Parupalli S, Vechalapu S, Patil S, Muniswamy S, Ghanta A, Yamini KN, Dharmaraj PS, Varshney RK. Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1183-94. [PMID: 26397045 PMCID: PMC5054876 DOI: 10.1111/pbi.12470] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 05/20/2023]
Abstract
To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing-based bulked segregant analysis (Seq-BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R- and S-bulks with the help of draft genome sequence and reference-guided assembly of ICPL 20096 (resistant parent). Seq-BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re-sequenced and their combined analysis with R- and S-bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2-Mb flanking regions of seven candidate SNPs identified through Seq-BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re-sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan_01839 for SMD resistance and C.cajan_03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics-assisted breeding in pigeonpea.
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Affiliation(s)
- Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Swathi Parupalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Suyash Patil
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India
| | - Anuradha Ghanta
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India
| | - Kalinati Narasimhan Yamini
- Institute of Biotechnology, Professor Jayshankar Telangana State Agricultural University (PJTSAU), Telangana, India
| | - Pallavi Subbanna Dharmaraj
- Agricultural Research Station (ARS)-Gulbarga, University of Agricultural Sciences (UAS), Raichur, Karnataka, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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23
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A subunit of the oligosaccharyltransferase complex is required for interspecific gametophyte recognition in Arabidopsis. Nat Commun 2016; 7:10826. [PMID: 26964640 PMCID: PMC4792959 DOI: 10.1038/ncomms10826] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/21/2016] [Indexed: 12/11/2022] Open
Abstract
Species-specific gamete recognition is a key premise to ensure reproductive success and the maintenance of species boundaries. During plant pollen tube (PT) reception, gametophyte interactions likely allow the species-specific recognition of signals from the PT (male gametophyte) by the embryo sac (female gametophyte), resulting in PT rupture, sperm release, and double fertilization. This process is impaired in interspecific crosses between Arabidopsis thaliana and related species, leading to PT overgrowth and a failure to deliver the sperm cells. Here we show that ARTUMES (ARU) specifically regulates the recognition of interspecific PTs in A. thaliana. ARU, identified in a genome-wide association study (GWAS), exclusively influences interspecific--but not intraspecific--gametophyte interactions. ARU encodes the OST3/6 subunit of the oligosaccharyltransferase complex conferring protein N-glycosylation. Our results suggest that glycosylation patterns of cell surface proteins may represent an important mechanism of gametophyte recognition and thus speciation.
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24
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Receptor-like cytoplasmic kinase MARIS functions downstream of CrRLK1L-dependent signaling during tip growth. Proc Natl Acad Sci U S A 2015; 112:12211-6. [PMID: 26378127 DOI: 10.1073/pnas.1512375112] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Growing plant cells need to rigorously coordinate external signals with internal processes. For instance, the maintenance of cell wall (CW) integrity requires the coordination of CW sensing with CW remodeling and biosynthesis to avoid growth arrest or integrity loss. Despite the involvement of receptor-like kinases (RLKs) of the Catharanthus roseus RLK1-like (CrRLK1L) subfamily and the reactive oxygen species-producing NADPH oxidases, it remains largely unknown how this coordination is achieved. ANXUR1 (ANX1) and ANX2, two redundant members of the CrRLK1L subfamily, are required for tip growth of the pollen tube (PT), and their closest homolog, FERONIA, controls root-hair tip growth. Previously, we showed that ANX1 overexpression mildly inhibits PT growth by oversecretion of CW material, whereas pollen tubes of anx1 anx2 double mutants burst spontaneously after germination. Here, we report the identification of suppressor mutants with improved fertility caused by the rescue of anx1 anx2 pollen tube bursting. Mapping of one these mutants revealed an R240C nonsynonymous substitution in the activation loop of a receptor-like cytoplasmic kinase (RLCK), which we named MARIS (MRI). We show that MRI is a plasma membrane-localized member of the RLCK-VIII subfamily and is preferentially expressed in both PTs and root hairs. Interestingly, mri-knockout mutants display spontaneous PT and root-hair bursting. Moreover, expression of the MRI(R240C) mutant, but not its wild-type form, partially rescues the bursting phenotypes of anx1 anx2 PTs and fer root hairs but strongly inhibits wild-type tip growth. Thus, our findings identify a novel positive component of the CrRLK1L-dependent signaling cascade that coordinates CW integrity and tip growth.
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25
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Lindner H, Kessler SA, Müller LM, Shimosato-Asano H, Boisson-Dernier A, Grossniklaus U. TURAN and EVAN mediate pollen tube reception in Arabidopsis Synergids through protein glycosylation. PLoS Biol 2015; 13:e1002139. [PMID: 25919390 PMCID: PMC4412406 DOI: 10.1371/journal.pbio.1002139] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/19/2015] [Indexed: 11/18/2022] Open
Abstract
Pollen tube (PT) reception in flowering plants describes the crosstalk between the male and female gametophytes upon PT arrival at the synergid cells of the ovule. It leads to PT growth arrest, rupture, and sperm cell release, and is thus essential to ensure double fertilization. Here, we describe TURAN (TUN) and EVAN (EVN), two novel members of the PT reception pathway that is mediated by the FERONIA (FER) receptor-like kinase (RLK). Like fer, mutations in these two genes lead to PT overgrowth inside the female gametophyte (FG) without PT rupture. Mapping by next-generation sequencing, cytological analysis of reporter genes, and biochemical assays of glycoproteins in RNAi knockdown mutants revealed both genes to be involved in protein N-glycosylation in the endoplasmic reticulum (ER). TUN encodes a uridine diphosphate (UDP)-glycosyltransferase superfamily protein and EVN a dolichol kinase. In addition to their common role during PT reception in the synergids, both genes have distinct functions in the pollen: whereas EVN is essential for pollen development, TUN is required for PT growth and integrity by affecting the stability of the pollen-specific FER homologs ANXUR1 (ANX1) and ANX2. ANX1- and ANX2-YFP reporters are not expressed in tun pollen grains, but ANX1-YFP is degraded via the ER-associated degradation (ERAD) pathway, likely underlying the anx1/2-like premature PT rupture phenotype of tun mutants. Thus, as in animal sperm–egg interactions, protein glycosylation is essential for the interaction between the female and male gametophytes during PT reception to ensure fertilization and successful reproduction. Protein glycosylation is essential for gametophyte interactions between the male pollen tube and the female ovule in plants, reminiscent of gamete interactions during fertilization in mammals. In flowering plants, gametes are produced by the haploid, multicellular male (pollen), and female (embryo sac) gametophytes, which develop within the reproductive organs of the flower. Successful fertilization depends on delivery of the sperm cells to the embryo sac, which is embedded in the ovule, by the pollen tube. Upon arrival of the pollen tube at the opening of the ovule, crosstalk between male and female gametophytes, known as pollen tube reception, ensues; the pollen tube slows or stops its growth, then resumes rapid growth, and finally bursts to release the sperm cells and effect double fertilization. Although several members of the pollen tube reception pathway, including the receptor-like kinase FERONIA, have been identified, the molecular mechanisms underlying this communication process remain unclear. Here, we show that protein N-glycosylation is required for normal pollen tube reception. A mutant screen identified two genes, TURAN and EVAN, which are involved in protein N-glycosylation in the endoplasmic reticulum. Both genes act in the FERONIA-mediated pollen tube reception pathway, which is impaired in these mutants. Thus, in plants, a “dual recognition system,” involving interactions between both protein and glycosyl residues on the surface of male and female gametophytes, appears to be required for successful pollen tube reception, conceptually similar to sperm–egg interactions in mammals, for which N-glycosylation of cell surface proteins also plays an important role.
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Affiliation(s)
- Heike Lindner
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zürich, Switzerland
| | - Sharon A. Kessler
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zürich, Switzerland
| | - Lena M. Müller
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zürich, Switzerland
| | - Hiroko Shimosato-Asano
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zürich, Switzerland
| | - Aurélien Boisson-Dernier
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zürich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology & Zurich-Basel Plant Science Center, University of Zurich, CH-8008 Zürich, Switzerland
- * E-mail:
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26
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Bohra A, Singh NP. Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement. Biotechnol Lett 2015; 37:1529-39. [PMID: 25851953 DOI: 10.1007/s10529-015-1836-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/02/2015] [Indexed: 01/28/2023]
Abstract
Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India,
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27
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Thole JM, Strader LC. Next-generation sequencing as a tool to quickly identify causative EMS-generated mutations. PLANT SIGNALING & BEHAVIOR 2015; 10:e1000167. [PMID: 26039464 PMCID: PMC4622007 DOI: 10.1080/15592324.2014.1000167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The advent of next generation sequencing has influenced every aspect of biological research. Many labs are now using whole genome sequencing in Arabidopsis thaliana as a means to quickly identify EMS-generated mutations present in isolated mutants. Following identification of these mutations, examination of T-DNA insertional alleles defective in candidate genes or complementation of the mutant phenotype with a wild type copy of candidate genes can be used to verify which mutation is causative for the phenotype of interest. Here, we discuss the benefits and pitfalls of using this method to identify mutations underlying phenotypes.
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Affiliation(s)
- J. M. Thole
- Department of Biology; St. Louis University, St. Louis, MO, USA
| | - L. C. Strader
- Department of Biology; Washington University in St. Louis, St. Louis, MO, USA
- Correspondence to: Lucia Strader;
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28
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Sun H, Schneeberger K. SHOREmap v3.0: fast and accurate identification of causal mutations from forward genetic screens. Methods Mol Biol 2015; 1284:381-95. [PMID: 25757783 DOI: 10.1007/978-1-4939-2444-8_19] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Whole-genome resequencing of pools of recombinant mutant genomes allows direct linking of phenotypic traits to causal mutations. Such analysis, called mapping-by-sequencing, combines classical genetic mapping and next-generation sequencing by relying on selection-induced patterns within genome-wide allele frequency (AF) in pooled genomes. Mapping-by-sequencing can be performed with computational tools such as SHOREmap. Previous versions of SHOREmap, however, did not implement standardized analyses, but were specifically designed for particular experimental settings. Here, we introduce the usage of a novel and advanced implementation of SHOREmap (version 3.0), including several new features like file readers for commonly used file formats, SNP marker selection, and a stable calculation of mapping intervals. SHOREmap can be downloaded at shoremap.org.
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Affiliation(s)
- Hequan Sun
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
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29
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Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
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Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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30
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Chang FM, Ou TY, Cheng WN, Chou ML, Lee KC, Chin YP, Lin CP, Chang KD, Lin CT, Su CH. Short-term exposure to fluconazole induces chromosome loss in Candida albicans: an approach to produce haploid cells. Fungal Genet Biol 2014; 70:68-76. [PMID: 25038494 DOI: 10.1016/j.fgb.2014.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/16/2014] [Accepted: 06/19/2014] [Indexed: 02/07/2023]
Abstract
Candida albicans is considered to be an obligate diploid fungus. Here, we describe an approach to isolate aneuploids or haploids induced by the short-term (12-16 h) exposure of diploid reference strains SC5314 and CAI4 to the most commonly used antifungal drug, fluconazole, followed by repeated single-cell separation among small morphologically distinct colonies in the inhibition zone. The isolated strains had altered cell morphology and LOH events in the MTL and other marker alleles of the analyzed loci at 8 chromosomes of C. albicans with decreased DNA content. The present study employed next-generation sequencing (NGS) combined flow cytometry analysis of the DNA content to analyze the haploid, autodiploid, and aneuploid strains that arose from the fluconazole treatment instead of using the conventional single nucleotide polymorphism/comparative genome hybridization (SNP/CGH) method. A multiple-alignment tool was also developed based on sequenced data from NGS to establish haplotype mapping for each chromosome of the selected strains. These findings revealed that C. albicans experiences 'concerted chromosome loss' to form strains with homozygous alleles and that it even has a haploid status after short-term exposure to fluconazole. Additionally, we developed a new platform to analyze chromosome copy number using NGS.
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Affiliation(s)
- Fang-Mo Chang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsong-Yih Ou
- Division of Infectious Disease, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wei-Ning Cheng
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Li Chou
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan
| | - Kai-Cheng Lee
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Ping Chin
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan
| | | | | | - Che-Tong Lin
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ching-Hua Su
- Department of Microbiology and Immunology, Taipei Medical University, Taipei, Taiwan.
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31
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Pacurar DI, Pacurar ML, Pacurar AM, Gutierrez L, Bellini C. A novel viable allele of Arabidopsis CULLIN1 identified in a screen for superroot2 suppressors by next generation sequencing-assisted mapping. PLoS One 2014; 9:e100846. [PMID: 24955772 PMCID: PMC4067405 DOI: 10.1371/journal.pone.0100846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/30/2014] [Indexed: 11/19/2022] Open
Abstract
Map-based cloning (MBC) is the conventional approach for linking phenotypes to genotypes, and has been successfully used to identify causal mutations in diverse organisms. Next-generation sequencing (NGS) technologies offer unprecedented possibilities to sequence the entire genomes of organisms, thereby in principle enabling direct identification of causal mutations without mapping. However, although mapping-by-sequencing has proven to be a cost effective alternative to classical MBC in particular situations, methods based solely on NGS still have limitations and need to be refined. Aiming to identify the causal mutations in suppressors of Arabidopsis thaliana superroot2 phenotype, generated by ethyl methane sulfonate (EMS) treatment, we combined NGS and classical mapping, to rapidly identify the point mutations and restrict the number of testable candidates by defining the chromosomal intervals containing the causal mutations, respectively. The NGS-assisted mapping approach we describe here facilitates unbiased identification of virtually any causal EMS-generated mutation by overlapping the identification (deep sequencing) and validation (mapping) steps. To exemplify the useful marriage of the two approaches we discuss the strategy used to identify a new viable recessive allele of the Arabidopsis CULLIN1 gene in the non-reference Wassilewskija (Ws-4) accession.
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Affiliation(s)
- Daniel I. Pacurar
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- * E-mail:
| | - Monica L. Pacurar
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
- Present address: SweTree Technologies AB, Umeå, Sweden
| | - Andrea M. Pacurar
- Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
| | - Laurent Gutierrez
- Molecular biology platform (CRRBM), Université de Picardie Jules Verne, Amiens, France
| | - Catherine Bellini
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Institut Jean-Pierre Bourgin, French National Institute for Agricultural Research (UMR1318 INRA-AgroParisTech), Versailles, France
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32
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014; 15:R78. [PMID: 24917130 PMCID: PMC4073093 DOI: 10.1186/gb-2014-15-6-r78] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/10/2014] [Indexed: 01/02/2023] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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33
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014. [PMID: 24917130 DOI: 10.1186/gb‐2014‐15‐6‐r78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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34
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Wolf S, Höfte H. Growth Control: A Saga of Cell Walls, ROS, and Peptide Receptors. THE PLANT CELL 2014; 26:1848-1856. [PMID: 24808052 PMCID: PMC4079354 DOI: 10.1105/tpc.114.125518] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 03/19/2014] [Accepted: 04/22/2014] [Indexed: 05/18/2023]
Abstract
Despite an increasingly detailed understanding of endogenous and environmental growth-controlling signals and their signaling networks, little is known on how these networks are integrated with the cell expansion machinery. Members of the CrRLK1L family control cell wall properties and cell expansion in a variety of developmental and environmental contexts. Two recent reports provide exciting new insights into the mode of action of these RLKs. One study shows that one family member, FERONIA (FER), is required for the production of hydroxyl radicals in the female gametophyte, which causes pollen tube rupture and sperm cell release during fertilization. Another study shows that FER is a receptor for a signaling peptide (Rapid Alkalinization Factor 1 [RALF1]) that triggers cell wall alkalinization and growth arrest, possibly through the inhibition of plasma membrane H+-ATPase activity. RALF1 belongs to a large gene family, with a wide range of expression patterns. Other CrRLK1L family members therefore may also be receptors for RALF-like peptides. These findings have important implications for our understanding of the control of cell wall integrity during growth and raise new intriguing questions.
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Affiliation(s)
- Sebastian Wolf
- Centre for Organismal Studies Heidelberg, 69120 Heidelberg, Germany
| | - Herman Höfte
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, INRA-AgroParisTech, Saclay Plant Science, INRA, 78000 Versailles, France
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35
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Wijnen CL, Keurentjes JJB. Genetic resources for quantitative trait analysis: novelty and efficiency in design from an Arabidopsis perspective. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:103-9. [PMID: 24657834 DOI: 10.1016/j.pbi.2014.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 05/11/2023]
Abstract
The use of genetic resources for the analysis of quantitative traits finds its roots in crop breeding but has seen a rejuvenation in Arabidopsis thaliana thanks to specific tools and genomic approaches. Although widely used in numerous crop and natural species, many approaches were first developed in this reference plant. We will discuss the scientific background and historical use of mapping populations in Arabidopsis and highlight the technological innovations that drove the development of novel strategies. We will especially lay emphasis on the methodologies used to generate the diverse population types and designate possible applications. Finally we highlight some of the most recent developments in generating genetic mapping resources and suggest specific usage for these novel tools and concepts.
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Affiliation(s)
- Cris L Wijnen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, Amsterdam 1098 XH, The Netherlands.
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36
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Krothapalli K, Buescher EM, Li X, Brown E, Chapple C, Dilkes BP, Tuinstra MR. Forward genetics by genome sequencing reveals that rapid cyanide release deters insect herbivory of Sorghum bicolor. Genetics 2013; 195:309-18. [PMID: 23893483 PMCID: PMC3781961 DOI: 10.1534/genetics.113.149567] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole genome sequencing has allowed rapid progress in the application of forward genetics in model species. In this study, we demonstrated an application of next-generation sequencing for forward genetics in a complex crop genome. We sequenced an ethyl methanesulfonate-induced mutant of Sorghum bicolor defective in hydrogen cyanide release and identified the causal mutation. A workflow identified the causal polymorphism relative to the reference BTx623 genome by integrating data from single nucleotide polymorphism identification, prior information about candidate gene(s) implicated in cyanogenesis, mutation spectra, and polymorphisms likely to affect phenotypic changes. A point mutation resulting in a premature stop codon in the coding sequence of dhurrinase2, which encodes a protein involved in the dhurrin catabolic pathway, was responsible for the acyanogenic phenotype. Cyanogenic glucosides are not cyanogenic compounds but their cyanohydrins derivatives do release cyanide. The mutant accumulated the glucoside, dhurrin, but failed to efficiently release cyanide upon tissue disruption. Thus, we tested the effects of cyanide release on insect herbivory in a genetic background in which accumulation of cyanogenic glucoside is unchanged. Insect preference choice experiments and herbivory measurements demonstrate a deterrent effect of cyanide release capacity, even in the presence of wild-type levels of cyanogenic glucoside accumulation. Our gene cloning method substantiates the value of (1) a sequenced genome, (2) a strongly penetrant and easily measurable phenotype, and (3) a workflow to pinpoint a causal mutation in crop genomes and accelerate in the discovery of gene function in the postgenomic era.
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Affiliation(s)
| | - Elizabeth M. Buescher
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Xu Li
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Elliot Brown
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Brian P. Dilkes
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
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Fekih R, Takagi H, Tamiru M, Abe A, Natsume S, Yaegashi H, Sharma S, Sharma S, Kanzaki H, Matsumura H, Saitoh H, Mitsuoka C, Utsushi H, Uemura A, Kanzaki E, Kosugi S, Yoshida K, Cano L, Kamoun S, Terauchi R. MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS One 2013; 8:e68529. [PMID: 23874658 PMCID: PMC3707850 DOI: 10.1371/journal.pone.0068529] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/29/2013] [Indexed: 11/19/2022] Open
Abstract
Advances in genome sequencing technologies have enabled researchers and breeders to rapidly associate phenotypic variation to genome sequence differences. We recently took advantage of next-generation sequencing technology to develop MutMap, a method that allows rapid identification of causal nucleotide changes of rice mutants by whole genome resequencing of pooled DNA of mutant F2 progeny derived from crosses made between candidate mutants and the parental line. Here we describe MutMap+, a versatile extension of MutMap, that identifies causal mutations by comparing SNP frequencies of bulked DNA of mutant and wild-type progeny of M3 generation derived from selfing of an M2 heterozygous individual. Notably, MutMap+ does not necessitate artificial crossing between mutants and the wild-type parental line. This method is therefore suitable for identifying mutations that cause early development lethality, sterility, or generally hamper crossing. Furthermore, MutMap+ is potentially useful for gene isolation in crops that are recalcitrant to artificial crosses.
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Affiliation(s)
- Rym Fekih
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- United Graduate School of Iwate University, Morioka, Iwate, Japan
| | - Muluneh Tamiru
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Satoshi Natsume
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- United Graduate School of Iwate University, Morioka, Iwate, Japan
| | | | | | - Shiveta Sharma
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | | | | | | | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Aiko Uemura
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Eiko Kanzaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | | | - Liliana Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- * E-mail:
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38
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James GV, Patel V, Nordström KJV, Klasen JR, Salomé PA, Weigel D, Schneeberger K. User guide for mapping-by-sequencing in Arabidopsis. Genome Biol 2013; 14:R61. [PMID: 23773572 PMCID: PMC3706810 DOI: 10.1186/gb-2013-14-6-r61] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/17/2013] [Indexed: 12/27/2022] Open
Abstract
Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.
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40
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Lindner H, Müller LM, Boisson-Dernier A, Grossniklaus U. CrRLK1L receptor-like kinases: not just another brick in the wall. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:659-69. [PMID: 22884521 DOI: 10.1016/j.pbi.2012.07.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/13/2012] [Accepted: 07/20/2012] [Indexed: 05/18/2023]
Abstract
In plants, receptor-like kinases regulate many processes during reproductive and vegetative development. The Arabidopsis subfamily of Catharanthus roseus RLK1-like kinases (CrRLK1Ls) comprises 17 members with a putative extracellular carbohydrate-binding malectin-like domain. Only little is known about the functions of these proteins, although mutant analyses revealed a role during cell elongation, polarized growth, and fertilization. However, the molecular nature of the underlying signal transduction cascades remains largely unknown. CrRLK1L proteins are also involved in biotic and abiotic stress responses. It is likely that carbohydrate-rich ligands transmit a signal, which could originate from cell wall components, an arriving pollen tube, or a pathogen attack. Thus, post-translational modifications could be crucial for CrRLK1L signal transduction and ligand binding.
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Affiliation(s)
- Heike Lindner
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
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