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Yang S, Yu W, Wei X, Wang Z, Zhao Y, Zhao X, Tian B, Yuan Y, Zhang X. An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis). PLoS One 2020; 15:e0240042. [PMID: 33007009 PMCID: PMC7531813 DOI: 10.1371/journal.pone.0240042] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
Kompetitive allele-specific PCR (KASP) is a cost-effective single-step SNP genotyping technology, With an objective to enhance the marker repertoire and develop high efficient KASP-SNP markers in Chinese cabbage, we re-sequenced four Chinese cabbage doubled haploid (DH) lines, Y177-47, Y635-10, Y510-1 and Y510-9, and generated a total of more than 38.5 billion clean base pairs. A total of 827,720 SNP loci were identified with an estimated density of 3,217 SNPs/Mb. Further, a total of 387,354 SNPs with at least 30 bp to the next most adjacent SNPs on either side were selected as resource for KASP markers. From this resource, 258 (96.27%) of 268 SNP loci were successfully transformed into KASP-SNP markers using a Roche LightCycler 480-II instrument. Among these markers, 221 (85.66%) were co-dominant markers, 220 (85.27%) were non-synonymous SNPs, and 257 (99.6%) were newly developed markers. In addition, 53 markers were applied for genotyping of 34 Brassica rapa accessions. Cluster analysis separated these 34 accessions into three clusters based on heading types. The millions of SNP loci, a large set of resource for KASP markers, as well as the newly developed KASP markers in this study may facilitate further genetic and molecular breeding studies in Brassica rapa.
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Affiliation(s)
- Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wentao Yu
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
- College of Life Science, Zhengzhou University, Zhengzhou, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaobin Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Baoming Tian
- College of Life Science, Zhengzhou University, Zhengzhou, China
- * E-mail: (XW-Z); (BT); (YY)
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (XW-Z); (BT); (YY)
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (XW-Z); (BT); (YY)
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2
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Jiang J, Xiao Y, Chen H, Hu W, Zeng L, Ke H, Ditengou FA, Devisetty U, Palme K, Maloof J, Dehesh K. Retrograde Induction of phyB Orchestrates Ethylene-Auxin Hierarchy to Regulate Growth. PLANT PHYSIOLOGY 2020; 183:1268-1280. [PMID: 32430463 PMCID: PMC7333703 DOI: 10.1104/pp.20.00090] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/11/2020] [Indexed: 05/19/2023]
Abstract
Exquisitely regulated plastid-to-nucleus communication by retrograde signaling pathways is essential for fine-tuning of responses to the prevailing environmental conditions. The plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) has emerged as a stress signal transduced into a diverse ensemble of response outputs. Here, we demonstrate enhanced phytochrome B protein abundance in red light-grown MEcPP-accumulating ceh1 mutant Arabidopsis (Arabidopsis thaliana) plants relative to wild-type seedlings. We further establish MEcPP-mediated coordination of phytochrome B with auxin and ethylene signaling pathways and uncover differential hypocotyl growth of red light-grown seedlings in response to these phytohormones. Genetic and pharmacological interference with ethylene and auxin pathways outlines the hierarchy of responses, placing ethylene epistatic to the auxin signaling pathway. Collectively, our findings establish a key role of a plastidial retrograde metabolite in orchestrating the transduction of a repertoire of signaling cascades. This work positions plastids at the zenith of relaying information coordinating external signals and internal regulatory circuitry to secure organismal integrity.
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Affiliation(s)
- Jishan Jiang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Yanmei Xiao
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
- University of Freiburg, Faculty of Biology, BIOSS Centre for Biological Signaling Studies and ZBSA Centre for Biosystems Studies, 79104 Freiburg, Germany
| | - Hao Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Wei Hu
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Liping Zeng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Haiyan Ke
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Franck A Ditengou
- Department of Plant Biology, University of California, Davis, California 95616
| | - Upendra Devisetty
- University of Freiburg, Faculty of Biology, BIOSS Centre for Biological Signaling Studies and ZBSA Centre for Biosystems Studies, 79104 Freiburg, Germany
| | - Klaus Palme
- Department of Plant Biology, University of California, Davis, California 95616
| | - Julin Maloof
- University of Freiburg, Faculty of Biology, BIOSS Centre for Biological Signaling Studies and ZBSA Centre for Biosystems Studies, 79104 Freiburg, Germany
| | - Katayoon Dehesh
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
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3
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Iquebal MA, Sharma P, Jasrotia RS, Jaiswal S, Kaur A, Saroha M, Angadi UB, Sheoran S, Singh R, Singh GP, Rai A, Tiwari R, Kumar D. RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat. Sci Rep 2019; 9:13917. [PMID: 31558740 PMCID: PMC6763491 DOI: 10.1038/s41598-019-49915-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 01/08/2023] Open
Abstract
Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Amandeep Kaur
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Monika Saroha
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India.
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4
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Wei Y, Xiao D, Zhang C, Hou X. The Expanded SWEET Gene Family Following Whole Genome Triplication in Brassica rapa. Genes (Basel) 2019; 10:E722. [PMID: 31540414 PMCID: PMC6771021 DOI: 10.3390/genes10090722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 01/15/2023] Open
Abstract
The SWEET family, which includes transcripts of a cohort of plant hexose and sucrose transporters, is considered key to improving crop stress tolerance and yield through its role in manipulating the carbohydrate partitioning process. The functions and regulatory roles of this gene family are variable among different species; thus, to determine these roles, more species-specific information is needed. Brassica rapa displays complicated regulation after a whole-genome triplication (WGT) event, which provides enormous advantages for use in genetic studies, thus it is an ideal model for exploring the functional and regulatory roles of SWEETs from a genetic perspective. In this study, the results of a homology search and phylogenetic relationship analysis revealed the evolutionary footprint of SWEETs among different plant taxa, which showed that plant SWEETs may have originated from Clade II and then expanded from vascular plants. The amino acid sequence characteristics and an analysis of the exon-intron structure of BrSWEETs duplicates clarified that SWEETs retention occurred after a WGT event in B. rapa. An analysis of the transcriptional levels of BrSWEETs in different tissues identified the expression differences among duplicated co-orthologs. In addition, qRT-PCR indicated that the BrSWEETs' co-orthologs were varied in their stress responses. This study greatly enriches our knowledge of SWEETs in the B. rapa species, which will contribute to future studies on the Brassica-specific regulatory pathways and to creating genetic innovations.
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Affiliation(s)
- Yanping Wei
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
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5
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Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development. PLoS Genet 2019; 15:e1008367. [PMID: 31513571 PMCID: PMC6759183 DOI: 10.1371/journal.pgen.1008367] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/24/2019] [Accepted: 08/13/2019] [Indexed: 12/01/2022] Open
Abstract
Plant developmental dynamics can be heritable, genetically correlated with fitness and yield, and undergo selection. Therefore, characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically important for agricultural production and evolutionary ecology. We use hierarchical Bayesian Function-Valued Trait (FVT) models to estimate Brassica rapa growth curves throughout ontogeny, across two treatments, and in two growing seasons. We find genetic variation for plasticity of growth rates and final sizes, but not the inflection point (transition from accelerating to decelerating growth) of growth curves. There are trade-offs between growth rate and duration, indicating that selection for maximum yields at early harvest dates may come at the expense of late harvest yields and vice versa. We generate eigengene modules and determine which are co-expressed with FVT traits using a Weighted Gene Co-expression Analysis. Independently, we seed a Mutual Rank co-expression network model with FVT traits to identify specific genes and gene networks related to FVT. GO-analyses of eigengene modules indicate roles for actin/cytoskeletal genes, herbivore resistance/wounding responses, and cell division, while MR networks demonstrate a close association between metabolic regulation and plant growth. We determine that combining FVT Quantitative Trait Loci (QTL) and MR genes/WGCNA eigengene expression profiles better characterizes phenotypic variation than any single data type (i.e. QTL, gene, or eigengene alone). Our network analysis allows us to employ a targeted eQTL analysis, which we use to identify regulatory hotspots for FVT. We examine cis vs. trans eQTL that mechanistically link FVT QTL with structural trait variation. Colocalization of FVT, gene, and eigengene eQTL provide strong evidence for candidate genes influencing plant height. The study is the first to explore eQTL for FVT, and specifically do so in agroecologically relevant field settings. We estimate the developmental dynamics of plant growth using mathematical functions to fit continuous functions to discrete plant height data collected throughout growth, and we use the parameters defining these mathematical functions as data. We identify genomic regions controlling plant growth and filter a novel transcriptomic data set using network reconstruction models to identify the genes and eigengenes associated with plant height. We combine these genomic and transcriptomic data to predict variation in plant height, and we use quantitative genetics to mechanistically connect plant genetics, transcriptomics, and development. Our approach demonstrates two powerful methods for the type of data reduction (FVT modeling and gene expression network reconstruction for targeted eQTL analyses) and data integration that will be necessary for driving forward the field of genetics in the post-genomic era. To the best of our knowledge, we are the first to apply these techniques to continuous models of plant development, and the first to do so in agroecologically relevant field settings.
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6
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Schrager-Lavelle A, Gath NN, Devisetty UK, Carrera E, López-Díaz I, Blázquez MA, Maloof JN. The role of a class III gibberellin 2-oxidase in tomato internode elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:603-615. [PMID: 30394600 DOI: 10.1111/tpj.14145] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/20/2018] [Accepted: 10/25/2018] [Indexed: 05/27/2023]
Abstract
A network of environmental inputs and internal signaling controls plant growth, development and organ elongation. In particular, the growth-promoting hormone gibberellin (GA) has been shown to play a significant role in organ elongation. The use of tomato as a model organism to study elongation presents an opportunity to study the genetic control of internode-specific elongation in a eudicot species with a sympodial growth habit and substantial internodes that can and do respond to external stimuli. To investigate internode elongation, a mutant with an elongated hypocotyl and internodes but wild-type petioles was identified through a forward genetic screen. In addition to stem-specific elongation, this mutant, named tomato internode elongated -1 (tie-1) is more sensitive to the GA biosynthetic inhibitor paclobutrazol and has altered levels of intermediate and bioactive GAs compared with wild-type plants. The mutation responsible for the internode elongation phenotype was mapped to GA2oxidase 7, a class III GA 2-oxidase in the GA biosynthetic pathway, through a bulked segregant analysis and bioinformatic pipeline, and confirmed by transgenic complementation. Furthermore, bacterially expressed recombinant TIE protein was shown to have bona fide GA 2-oxidase activity. These results define a critical role for this gene in internode elongation and are significant because they further the understanding of the role of GA biosynthetic genes in organ-specific elongation.
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Affiliation(s)
- Amanda Schrager-Lavelle
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Natalie N Gath
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Upendra K Devisetty
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022, Valencia, Spain
| | - Isabel López-Díaz
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022, Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022, Valencia, Spain
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
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7
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Nozue K, Devisetty UK, Lekkala S, Mueller-Moulé P, Bak A, Casteel CL, Maloof JN. Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance. PLANT PHYSIOLOGY 2018; 178:1720-1732. [PMID: 30348816 PMCID: PMC6288734 DOI: 10.1104/pp.18.00920] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/08/2018] [Indexed: 05/21/2023]
Abstract
Plants have sophisticated mechanisms for sensing neighbor shade. To maximize their ability to compete for light, plants respond to shade through enhanced elongation and physiological changes. The shade avoidance response affects many different organs and growth stages, yet the signaling pathways underlying this response have mostly been studied in seedlings. We assayed transcriptome changes in response to shade across a 2-d time course in the wild type and 12 Arabidopsis (Arabidopsis thaliana) mutants. The resulting temporal map of transcriptional responses to shade defines early and late responses in adult plants, enabling us to determine connections between key signaling genes and downstream responses. We found a pervasive and unexpectedly strong connection between shade avoidance and genes related to salicylic acid, suggesting salicylic acid signaling to be an important shade avoidance growth regulator. We tested this connection and found that several mutants disrupting salicylic acid levels or signaling were defective in shade avoidance. The effect of these mutations on shade avoidance was specific to petiole elongation; neither hypocotyl nor flowering time responses were altered, thereby defining important stage-specific differences in the downstream shade avoidance signaling pathway. Shade treatment did not change salicylic acid levels, indicating that the mediation of shade avoidance by salicylic acid is not dependent on the modulation of salicylic acid levels. These results demonstrate that salicylic acid pathway genes also are key components of petiole shade avoidance.
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Affiliation(s)
- Kazunari Nozue
- Department of Plant Biology, University of California, Davis, California 95616
| | | | - Saradadevi Lekkala
- Department of Plant Biology, University of California, Davis, California 95616
| | | | - Aurélie Bak
- Department of Plant Pathology, University of California, Davis, California 95616
| | - Clare L Casteel
- Department of Plant Pathology, University of California, Davis, California 95616
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, California 95616
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8
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Jaiswal S, Antala TJ, Mandavia MK, Chopra M, Jasrotia RS, Tomar RS, Kheni J, Angadi UB, Iquebal MA, Golakia BA, Rai A, Kumar D. Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources. Sci Rep 2018; 8:3382. [PMID: 29467369 PMCID: PMC5821703 DOI: 10.1038/s41598-018-21560-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/04/2018] [Indexed: 01/12/2023] Open
Abstract
Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( http://webtom.cabgrid.res.in/pmdtdb/ ) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tushar J Antala
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - M K Mandavia
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Meenu Chopra
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rukam S Tomar
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Jashminkumar Kheni
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - B A Golakia
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
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9
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Hawkins AK, Garza ER, Dietz VA, Hernandez OJ, Hawkins WD, Burrell AM, Pepper AE. Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biol Evol 2017; 9:3478-3494. [PMID: 29220486 PMCID: PMC5751042 DOI: 10.1093/gbe/evx259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 12/26/2022] Open
Abstract
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.
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10
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Guadagno CR, Ewers BE, Speckman HN, Aston TL, Huhn BJ, DeVore SB, Ladwig JT, Strawn RN, Weinig C. Dead or Alive? Using Membrane Failure and Chlorophyll a Fluorescence to Predict Plant Mortality from Drought. PLANT PHYSIOLOGY 2017; 175:223-234. [PMID: 28710130 PMCID: PMC5580738 DOI: 10.1104/pp.16.00581] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 07/11/2017] [Indexed: 05/02/2023]
Abstract
Climate models predict widespread increases in both drought intensity and duration in the next decades. Although water deficiency is a significant determinant of plant survival, limited understanding of plant responses to extreme drought impedes forecasts of both forest and crop productivity under increasing aridity. Drought induces a suite of physiological responses; however, we lack an accurate mechanistic description of plant response to lethal drought that would improve predictive understanding of mortality under altered climate conditions. Here, proxies for leaf cellular damage, chlorophyll a fluorescence, and electrolyte leakage were directly associated with failure to recover from drought upon rewatering in Brassicarapa (genotype R500) and thus define the exact timing of drought-induced death. We validated our results using a second genotype (imb211) that differs substantially in life history traits. Our study demonstrates that whereas changes in carbon dynamics and water transport are critical indicators of drought stress, they can be unrelated to visible metrics of mortality, i.e. lack of meristematic activity and regrowth. In contrast, membrane failure at the cellular scale is the most proximate cause of death. This hypothesis was corroborated in two gymnosperms (Picea engelmannii and Pinus contorta) that experienced lethal water stress in the field and in laboratory conditions. We suggest that measurement of chlorophyll a fluorescence can be used to operationally define plant death arising from drought, and improved plant characterization can enhance surface model predictions of drought mortality and its consequences to ecosystem services at a global scale.
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Affiliation(s)
| | - Brent E Ewers
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
| | - Heather N Speckman
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
| | - Timothy Llewellyn Aston
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
| | - Bridger J Huhn
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Stanley B DeVore
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Joshua T Ladwig
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Rachel N Strawn
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
| | - Cynthia Weinig
- Botany Department, University of Wyoming, Laramie, Wyoming 82071
- Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
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11
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Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population. G3-GENES GENOMES GENETICS 2017; 7:2259-2270. [PMID: 28546385 PMCID: PMC5499133 DOI: 10.1534/g3.117.043000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.
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12
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Iquebal MA, Soren KR, Gangwar P, Shanmugavadivel PS, Aravind K, Singla D, Jaiswal S, Jasrotia RS, Chaturvedi SK, Singh NP, Varshney RK, Rai A, Kumar D. Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:958. [PMID: 28638398 PMCID: PMC5461349 DOI: 10.3389/fpls.2017.00958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/22/2017] [Indexed: 05/06/2023]
Abstract
Background: Chickpea (Cicer arietinum L.) contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harboring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable. Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea. Results: This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr). Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30,803 contigs using reference based assembly. We report 6,310 differentially expressed genes (DEGs), of which 3,037 were regulated by 980 miRNAs, 1,528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3,540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13,778 genic Single Nucleotide Polymorphism (SNP) putative markers and 1,174 Indels. Randomly selected 20 DEGs were validated using qPCR. Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in presence of herbicide. Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance. Conclusion: Reported DEGs can be used as genomic resource for future discovery of candidate genes associated with herbicide tolerance. Reported markers can be used for future association studies in order to develop marker assisted selection (MAS) for refinement. In endeavor of chickpea variety development programme, these findings can be of immense use in improving productivity of chickpea germplasm.
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Affiliation(s)
- Mir A. Iquebal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Khela R. Soren
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Priyanka Gangwar
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - P. S. Shanmugavadivel
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - K. Aravind
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Deepak Singla
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Rahul S. Jasrotia
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Sushil K. Chaturvedi
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Narendra P. Singh
- Division of Plant Biotechnology, Indian Institute of Pulses Research (ICAR)Kanpur, India
| | - Rajeev K. Varshney
- Genetic Gains, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
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13
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Byeon B, Bilichak A, Kovalchuk I. Computational Characterization of ncRNA Fragments in Various Tissues of the Brassica rapa Plant. Noncoding RNA 2017; 3:E17. [PMID: 29657288 PMCID: PMC5831936 DOI: 10.3390/ncrna3020017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 12/15/2022] Open
Abstract
Recently, a novel type of non-coding RNA (ncRNA), known as ncRNA fragments or ncRFs, has been characterised in various organisms, including plants. The biogenesis mechanism, function and abundance of ncRFs stemming from various ncRNAs are poorly understood, especially in plants. In this work, we have computationally analysed the composition of ncRNAs and the fragments that derive from them in various tissues of Brassica rapa plants, including leaves, meristem tissue, pollen, unfertilized and fertilized ova, embryo and endosperm. Detailed analysis of transfer RNA (tRNA) fragments (tRFs), ribosomal RNA (rRNA) fragments (rRFs), small nucleolar RNA (snoRNA) fragments (snoRFs) and small nuclear RNA (snRNA) fragments (snRFs) showed a predominance of tRFs, with the 26 nucleotides (nt) fraction being the largest. Mapping ncRF reads to full-length mature ncRNAs showed a strong bias for one or both termini. tRFs mapped predominantly to the 5' end, whereas snRFs mapped to the 3' end, suggesting that there may be specific biogenesis and retention mechanisms. In the case of tRFs, specific isoacceptors were enriched, including tRNAGly(UCC) and tRFAsp(GUC). The analysis showed that the processing of 26-nt tRF5' occurred by cleavage at the last unpaired nucleotide of the loop between the D arm and the anticodon arm. Further support for the functionality of ncRFs comes from the analysis of binding between ncRFs and their potential targets. A higher average percentage of binding at the first half of fragments was observed, with the highest percentage being at 2-6 nt. To summarise, our analysis showed that ncRFs in B. rapa are abundantly produced in a tissue-specific manner, with bias toward a terminus, the bias toward the size of generated fragments and the bias toward the targeting of specific biological processes.
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Affiliation(s)
- Boseon Byeon
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.
| | - Andriy Bilichak
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.
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14
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Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, Sinha NR. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 (BETHESDA, MD.) 2016; 6:3169-3184. [PMID: 27510891 PMCID: PMC5068939 DOI: 10.1534/g3.116.030536] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/01/2016] [Indexed: 12/23/2022]
Abstract
Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.
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Affiliation(s)
- Daniel Fulop
- Department of Plant Biology, University of California at Davis, California 95616
| | - Aashish Ranjan
- Department of Plant Biology, University of California at Davis, California 95616
| | - Itai Ofner
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Michael F Covington
- Department of Plant Biology, University of California at Davis, California 95616
| | - Daniel H Chitwood
- Department of Plant Biology, University of California at Davis, California 95616
| | - Donelly West
- Department of Plant Biology, University of California at Davis, California 95616
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California at Davis, California 95616
| | - Lauren Headland
- Department of Plant Biology, University of California at Davis, California 95616
| | - Daniel Zamir
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Julin N Maloof
- Department of Plant Biology, University of California at Davis, California 95616
| | - Neelima R Sinha
- Department of Plant Biology, University of California at Davis, California 95616
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15
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Lebaron C, Rosado A, Sauvage C, Gauffier C, German-Retana S, Moury B, Gallois JL. A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to potato virus Y in tomato albeit with a low durability. J Gen Virol 2016; 97:3063-3072. [PMID: 27655175 DOI: 10.1099/jgv.0.000609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Allele mining on susceptibility factors offers opportunities to find new sources of resistance among crop wild relatives for breeding purposes. As a proof of concept, we used available RNAseq data to investigate polymorphisms among the four tomato genes encoding translation initiation factors [eIF4E1 and eIF4E2, eIFiso4E and the related gene new cap-binding protein(nCBP)] to look for new potential resistance alleles to potyviruses. By analysing polymorphism among RNAseq data obtained for 20 tomato accessions, 10 belonging to the cultivated type Solanum lycopersicum and 10 belonging to the closest related wild species Solanum pimpinellifolium, we isolated one new eIF4E1 allele, in the S. pimpinellifolium LA0411 accession, which encodes a potential new resistance allele, mainly due to a polymorphism associated with an amino acid change within eIF4E1 region II. We confirmed that this new allele, pot12, is indeed associated with resistance to potato virus Y, although with a restricted resistance spectrum and a very low durability potential. This suggests that mutations occurring in eIF4E region II only may not be sufficient to provide efficient and durable resistance in plants. However, our study emphasizes the opportunity brought by RNAseq data to mine for new resistance alleles. Moreover, this approach could be extended to seek for putative new resistance alleles by screening for variant forms of susceptibility genes encoding plant host proteins known to interact with viral proteins.
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Affiliation(s)
| | | | | | | | | | - Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
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16
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Terol J, Tadeo F, Ventimilla D, Talon M. An RNA-Seq-based reference transcriptome for Citrus. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:938-50. [PMID: 26261026 DOI: 10.1111/pbi.12447] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/04/2015] [Accepted: 07/01/2015] [Indexed: 05/20/2023]
Abstract
Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C. medica, C. aurantifolia, C. limon, C. bergamia, C. clementina, C. deliciosa, C. reshni, C. maxima, C. paradisi, C. aurantium, C. sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C. clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19,739, and a total of 73,797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail.
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Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Francisco Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Daniel Ventimilla
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
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17
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Brock MT, Lucas LK, Anderson NA, Rubin MJ, Markelz RJC, Covington MF, Devisetty UK, Chapple C, Maloof JN, Weinig C. Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning. Mol Ecol 2016; 25:1122-40. [PMID: 26800256 DOI: 10.1111/mec.13542] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/29/2022]
Abstract
Floral attraction traits can significantly affect pollinator visitation patterns, but adaptive evolution of these traits may be constrained by correlations with other traits. In some cases, molecular pathways contributing to floral attraction are well characterized, offering the opportunity to explore loci potentially underlying variation among individuals. Here, we quantify the range of variation in floral UV patterning (i.e. UV 'bulls-eye nectar guides) among crop and wild accessions of Brassica rapa. We then use experimental crosses to examine the genetic architecture, candidate loci and biochemical underpinnings of this patterning as well as phenotypic manipulations to test the ecological impact. We find qualitative variation in UV patterning between wild (commonly lacking UV patterns) and crop (commonly exhibiting UV patterns) accessions. Similar to the majority of crops, recombinant inbred lines (RILs) derived from an oilseed crop × WI fast-plant® cross exhibit UV patterns, the size of which varies extensively among genotypes. In RILs, we further observe strong statistical-genetic and QTL correlations within petal morphological traits and within measurements of petal UV patterning; however, correlations between morphology and UV patterning are weak or nonsignificant, suggesting that UV patterning is regulated and may evolve independently of overall petal size. HPLC analyses reveal a high concentration of sinapoyl glucose in UV-absorbing petal regions, which, in concert with physical locations of UV-trait QTLs, suggest a regulatory and structural gene as candidates underlying observed quantitative variation. Finally, insects prefer flowers with UV bulls-eye patterns over those that lack patterns, validating the importance of UV patterning in pollen-limited populations of B. rapa.
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Affiliation(s)
- Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Nickolas A Anderson
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Michael F Covington
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Upendra K Devisetty
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
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18
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Zhang W, Kwon ST, Chen F, Kliebenstein DJ. Isolate Dependency of Brassica rapa Resistance QTLs to Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2016; 7:161. [PMID: 26925079 PMCID: PMC4756292 DOI: 10.3389/fpls.2016.00161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/30/2016] [Indexed: 05/04/2023]
Abstract
Generalist necrotrophic pathogens including Botrytis cinerea cause significant yield and financial losses on Brassica crops. However, there is little knowledge about the mechanisms underlying the complex interactions encoded by both host and pathogen genomes in this interaction. This potentially includes multiple layers of plant defense and pathogen virulence mechanisms that could complicate in breeding broad spectrum resistance within Brassica species. Glucosinolates (GSLs) are a diverse group of defense metabolites that play a key role in interaction between Brassica and biotic attackers. In this study, we utilized a collection of diverse B. cinerea isolates to investigate resistance within the Brassica rapa R500 × IMB211 recombinant inbred line population. We tested variation on lesion development and glucosinolate accumulation in parental lines and all population lines. We then mapped quantitative trait loci (QTL) for both resistances to B. cinerea and defense metabolites in this population. Phenotypic analysis and QTL mapping demonstrate that the genetic basis of resistance to B. cinerea in B. rapa is isolate specific and polygenic with transgressive segregation that both parents contribute resistance alleles. QTLs controlling defensive GSLs are highly dependent on pathogen infection. An overlap of two QTLs identified between resistance to B. cinerea and defense metabolites also showed isolate specific effects. This work suggests that directly searching for resistance loci may not be the best approach at improving resistance in B. rapa to necrotrophic pathogen.
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Affiliation(s)
- Wei Zhang
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- National and Local Joint Engineering Laboratory for Energy Plant Bio-oil Production and Application, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Soon-Tae Kwon
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- Department of Horticulture and Breeding, Andong National UniversityAndong, South Korea
| | - Fang Chen
- National and Local Joint Engineering Laboratory for Energy Plant Bio-oil Production and Application, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Daniel J. Kliebenstein
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- DynaMo Center of Excellence, University of CopenhagenCopenhagen, Denmark
- *Correspondence: Daniel J. Kliebenstein,
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19
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Gao Y, Zhang X, Wei J, Sun X, Yuan J, Li F, Xiang J. Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei. PLoS One 2015; 10:e0144350. [PMID: 26650402 PMCID: PMC4674093 DOI: 10.1371/journal.pone.0144350] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/17/2015] [Indexed: 12/27/2022] Open
Abstract
Molting is one of the most important biological processes in shrimp growth and development. All shrimp undergo cyclic molting periodically to shed and replace their exoskeletons. This process is essential for growth, metamorphosis, and reproduction in shrimp. However, the molecular mechanisms underlying shrimp molting remain poorly understood. In this study, we investigated global expression changes in the transcriptomes of the Pacific white shrimp, Litopenaeus vannamei, the most commonly cultured shrimp species worldwide. The transcriptome of whole L. vannamei was investigated by RNA-sequencing (RNA-seq) throughout the molting cycle, including the inter-molt (C), pre-molt (D0, D1, D2, D3, D4), and post-molt (P1 and P2) stages, and 93,756 unigenes were identified. Among these genes, we identified 5,117 genes differentially expressed (log2ratio ≥1 and FDR ≤0.001) in adjacent molt stages. The results were compared against the National Center for Biotechnology Information (NCBI) non-redundant protein/nucleotide sequence database, Swiss-Prot, PFAM database, the Gene Ontology database, and the Kyoto Encyclopedia of Genes and Genomes database in order to annotate gene descriptions, associate them with gene ontology terms, and assign them to pathways. The expression patterns for genes involved in several molecular events critical for molting, such as hormone regulation, triggering events, implementation phases, skelemin, immune responses were characterized and considered as mechanisms underlying molting in L. vannamei. Comparisons with transcriptomic analyses in other arthropods were also performed. The characterization of major transcriptional changes in genes involved in the molting cycle provides candidates for future investigation of the molecular mechanisms. The data generated in this study will serve as an important transcriptomic resource for the shrimp research community to facilitate gene and genome annotation and to characterize key molecular processes underlying shrimp development.
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Affiliation(s)
- Yi Gao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jiankai Wei
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqing Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianbo Yuan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
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20
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Dong X, Yi H, Han CT, Nou IS, Hur Y. GDSL esterase/lipase genes in Brassica rapa L.: genome-wide identification and expression analysis. Mol Genet Genomics 2015; 291:531-42. [DOI: 10.1007/s00438-015-1123-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/18/2015] [Indexed: 11/29/2022]
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21
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Witzel K, Neugart S, Ruppel S, Schreiner M, Wiesner M, Baldermann S. Recent progress in the use of 'omics technologies in brassicaceous vegetables. FRONTIERS IN PLANT SCIENCE 2015; 6:244. [PMID: 25926843 PMCID: PMC4396356 DOI: 10.3389/fpls.2015.00244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/26/2015] [Indexed: 05/21/2023]
Abstract
Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub-optimal irradiation. This review covers recent applications of 'omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality.
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Affiliation(s)
- Katja Witzel
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Susanne Neugart
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Silke Ruppel
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Monika Schreiner
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Melanie Wiesner
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
| | - Susanne Baldermann
- Leibniz-Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V.Großbeeren, Germany
- Institute of Nutritional Science, University of PotsdamNuthetal, Germany
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Kujur A, Bajaj D, Upadhyaya HD, Das S, Ranjan R, Shree T, Saxena MS, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. FRONTIERS IN PLANT SCIENCE 2015; 6:162. [PMID: 25873920 PMCID: PMC4379880 DOI: 10.3389/fpls.2015.00162] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/01/2015] [Indexed: 05/19/2023]
Abstract
The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93-96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13-89%)/functional allelic diversity (18-77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54-0.68) and extended LD decay (400-500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating important complex quantitative agronomic traits in chickpea. The numerous informative genome-wide SNPs, natural allelic diversity-led domestication pattern, and LD-based information generated in our study have got multidimensional applicability with respect to chickpea genomics-assisted breeding.
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Affiliation(s)
- Alice Kujur
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Rajeev Ranjan
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Tanima Shree
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | | | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB)New Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI)New Delhi, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Telangana, India
| | | | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
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Salem M, Paneru B, Al-Tobasei R, Abdouni F, Thorgaard GH, Rexroad CE, Yao J. Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout. PLoS One 2015; 10:e0121778. [PMID: 25793877 PMCID: PMC4368115 DOI: 10.1371/journal.pone.0121778] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 02/04/2015] [Indexed: 11/25/2022] Open
Abstract
Efforts to obtain a comprehensive genome sequence for rainbow trout are ongoing and will be complemented by transcriptome information that will enhance genome assembly and annotation. Previously, transcriptome reference sequences were reported using data from different sources. Although the previous work added a great wealth of sequences, a complete and well-annotated transcriptome is still needed. In addition, gene expression in different tissues was not completely addressed in the previous studies. In this study, non-normalized cDNA libraries were sequenced from 13 different tissues of a single doubled haploid rainbow trout from the same source used for the rainbow trout genome sequence. A total of ~1.167 billion paired-end reads were de novo assembled using the Trinity RNA-Seq assembler yielding 474,524 contigs > 500 base-pairs. Of them, 287,593 had homologies to the NCBI non-redundant protein database. The longest contig of each cluster was selected as a reference, yielding 44,990 representative contigs. A total of 4,146 contigs (9.2%), including 710 full-length sequences, did not match any mRNA sequences in the current rainbow trout genome reference. Mapping reads to the reference genome identified an additional 11,843 transcripts not annotated in the genome. A digital gene expression atlas revealed 7,678 housekeeping and 4,021 tissue-specific genes. Expression of about 16,000–32,000 genes (35–71% of the identified genes) accounted for basic and specialized functions of each tissue. White muscle and stomach had the least complex transcriptomes, with high percentages of their total mRNA contributed by a small number of genes. Brain, testis and intestine, in contrast, had complex transcriptomes, with a large numbers of genes involved in their expression patterns. This study provides comprehensive de novo transcriptome information that is suitable for functional and comparative genomics studies in rainbow trout, including annotation of the genome.
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Affiliation(s)
- Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America
- * E-mail:
| | - Bam Paneru
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America
| | - Fatima Abdouni
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, 37132, United States of America
| | - Gary H. Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington 99164, United States of America
| | - Caird E. Rexroad
- The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Leetown, West Virginia 25430, United States of America
| | - Jianbo Yao
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, West Virginia, 26506, United States of America
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