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Sancho R, Catalán P, Contreras‐Moreira B, Juenger TE, Des Marais DL. Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon. Mol Ecol 2022; 31:5285-5306. [PMID: 35976181 PMCID: PMC9804473 DOI: 10.1111/mec.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 01/05/2023]
Abstract
Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.
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Affiliation(s)
- Rubén Sancho
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Bruno Contreras‐Moreira
- Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain,Estación Experimental de Aula Dei‐Consejo Superior de Investigaciones CientíficasZaragozaSpain,Fundación ARAIDZaragozaSpain
| | - Thomas E. Juenger
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
| | - David L. Des Marais
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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2
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Das A, Prakash A, Dedon N, Doty A, Siddiqui M, Preston JC. Variation in climatic tolerance, but not stomatal traits, partially explains Pooideae grass species distributions. ANNALS OF BOTANY 2021; 128:83-95. [PMID: 33772589 PMCID: PMC8318108 DOI: 10.1093/aob/mcab046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Grasses in subfamily Pooideae live in some of the world's harshest terrestrial environments, from frigid boreal zones to the arid windswept steppe. It is hypothesized that the climate distribution of species within this group is driven by differences in climatic tolerance, and that tolerance can be partially explained by variation in stomatal traits. METHODS We determined the aridity index (AI) and minimum temperature of the coldest month (MTCM) for 22 diverse Pooideae accessions and one outgroup, and used comparative methods to assess predicted relationships for climate traits versus fitness traits, stomatal diffusive conductance to water (gw) and speed of stomatal closure following drought and/or cold. KEY RESULTS Results demonstrate that AI and MTCM predict variation in survival/regreening following drought/cold, and gw under drought/cold is positively correlated with δ 13C-measured water use efficiency (WUE). However, the relationship between climate traits and fitness under drought/cold was not explained by gw or speed of stomatal closure. CONCLUSIONS These findings suggest that Pooideae distributions are at least partly determined by tolerance to aridity and above-freezing cold, but that variation in tolerance is not uniformly explained by variation in stomatal traits.
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Affiliation(s)
- Aayudh Das
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Anoob Prakash
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Natalie Dedon
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Alex Doty
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Muniba Siddiqui
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
| | - Jill C Preston
- The University of Vermont, Department of Plant Biology, Burlington, VT 05405, USA
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3
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Ellsworth PZ, Feldman MJ, Baxter I, Cousins AB. A genetic link between leaf carbon isotope composition and whole-plant water use efficiency in the C 4 grass Setaria. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:1234-1248. [PMID: 31968138 DOI: 10.1111/tpj.14696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/18/2019] [Accepted: 01/02/2020] [Indexed: 05/13/2023]
Abstract
Genetic selection for whole-plant water use efficiency (yield per transpiration; WUEplant ) in any crop-breeding programme requires high-throughput phenotyping of component traits of WUEplant such as intrinsic water use efficiency (WUEi ; CO2 assimilation rate per stomatal conductance). Measuring WUEi by gas exchange measurements is laborious and time consuming and may not reflect an integrated WUEi over the life of the leaf. Alternatively, leaf carbon stable isotope composition (δ13 Cleaf ) has been suggested as a potential time-integrated proxy for WUEi that may provide a tool to screen for WUEplant . However, a genetic link between δ13 Cleaf and WUEplant in a C4 species has not been well established. Therefore, to determine if there is a genetic relationship in a C4 plant between δ13 Cleaf and WUEplant under well watered and water-limited growth conditions, a high-throughput phenotyping facility was used to measure WUEplant in a recombinant inbred line (RIL) population created between the C4 grasses Setaria viridis and S. italica. Three quantitative trait loci (QTL) for δ13 Cleaf were found and co-localized with transpiration, biomass accumulation, and WUEplant . Additionally, WUEplant for each of the δ13 Cleaf QTL allele classes was negatively correlated with δ13 Cleaf , as would be predicted when WUEi influences WUEplant . These results demonstrate that δ13 Cleaf is genetically linked to WUEplant , likely to be through their relationship with WUEi , and can be used as a high-throughput proxy to screen for WUEplant in these C4 species.
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Affiliation(s)
- Patrick Z Ellsworth
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Max J Feldman
- Donald Danforth Plant Sciences Center, St. Louis, MO, USA
| | - Ivan Baxter
- Donald Danforth Plant Sciences Center, St. Louis, MO, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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4
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Onda Y, Inoue K, Sawada Y, Shimizu M, Takahagi K, Uehara-Yamaguchi Y, Hirai MY, Garvin DF, Mochida K. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20092348. [PMID: 31083584 PMCID: PMC6540107 DOI: 10.3390/ijms20092348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 12/27/2022] Open
Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses.
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Affiliation(s)
- Yoshihiko Onda
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Minami Shimizu
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yukiko Uehara-Yamaguchi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Masami Y Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - David F Garvin
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research Service, 1991 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan.
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Institute of Plant Science and Resource, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan.
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Abstract
To improve sustainability of agriculture, high yielding crop varieties with improved water use efficiency (WUE) are needed. Despite the feasibility of assessing WUE using different measurement techniques, breeding for WUE and high yield is a major challenge. Factors influencing the trait under field conditions are complex, including different scenarios of water availability. Plants with C3 photosynthesis are able to moderately increase WUE by restricting transpiration, resulting in higher intrinsic WUE (iWUE) at the leaf level. However, reduced CO2 uptake negatively influences photosynthesis and possibly growth and yield as well. The negative correlation of growth and WUE could be partly disconnected in model plant species with implications for crops. In this paper, we discuss recent insights obtained for Arabidopsis thaliana (L.) and the potential to translate the findings to C3 and C4 crops. Our data on Zea mays (L.) lines subjected to progressive drought show that there is potential for improvements in WUE of the maize line B73 at the whole plant level (WUEplant). However, changes in iWUE of B73 and Arabidopsis reduced the assimilation rate relatively more in maize. The trade-off observed in the C4 crop possibly limits the effectiveness of approaches aimed at improving iWUE but not necessarily efforts to improve WUEplant.
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Whitehead C, Ostos Garrido FJ, Reymond M, Simister R, Distelfeld A, Atienza SG, Piston F, Gomez LD, McQueen‐Mason SJ. A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon. THE NEW PHYTOLOGIST 2018; 218:974-985. [PMID: 29574807 PMCID: PMC5947151 DOI: 10.1111/nph.15089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/05/2018] [Indexed: 05/27/2023]
Abstract
The recalcitrance of secondary plant cell walls to digestion constrains biomass use for the production of sustainable bioproducts and for animal feed. We screened a population of Brachypodium recombinant inbred lines (RILs) for cell wall digestibility using commercial cellulases and detected a quantitative trait locus (QTL) associated with this trait. Examination of the chromosomal region associated with this QTL revealed a candidate gene that encodes a putative glycosyl transferase family (GT) 43 protein, orthologue of IRX14 in Arabidopsis, and hence predicted to be involved in the biosynthesis of xylan. Arabinoxylans form the major matrix polysaccharides in cell walls of grasses, such as Brachypodium. The parental lines of the RIL population carry alternative nonsynonymous polymorphisms in the BdGT43A gene, which were inherited in the RIL progeny in a manner compatible with a causative role in the variation in straw digestibility. In order to validate the implied role of our candidate gene in affecting straw digestibility, we used RNA interference to lower the expression levels of the BdGT43A gene in Brachypodium. The biomass of the silenced lines showed higher digestibility supporting a causative role of the BdGT43A gene, suggesting that it might form a good target for improving straw digestibility in crops.
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Affiliation(s)
- Caragh Whitehead
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
| | - Francisco J. Ostos Garrido
- Departamento de Mejora Genética VegetalInstituto de Agricultura Sostenible – Consejo Superior de Investigaciones CientíficasCórdobaSpain
| | - Matthieu Reymond
- Institut Jean‐Pierre BourginUMR 1318 INRA‐AgroParisTechINRA Centre de Versailles‐GrignonRoute de Saint‐Cyr78026VersaillesFrance
| | - Rachael Simister
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
| | - Assaf Distelfeld
- Deparment of Molecular Biology and Ecology of PlantsTel Aviv UniversityTel AvivIsrael
| | - Sergio G. Atienza
- Departamento de Mejora Genética VegetalInstituto de Agricultura Sostenible – Consejo Superior de Investigaciones CientíficasCórdobaSpain
| | - Fernando Piston
- Departamento de Mejora Genética VegetalInstituto de Agricultura Sostenible – Consejo Superior de Investigaciones CientíficasCórdobaSpain
| | - Leonardo D. Gomez
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
| | - Simon J. McQueen‐Mason
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
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7
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Wang J, Su K, Guo Y, Xing H, Zhao Y, Liu Z, Li K, Guo X. Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing. PLoS One 2017; 12:e0181728. [PMID: 28746364 PMCID: PMC5528875 DOI: 10.1371/journal.pone.0181728] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/06/2017] [Indexed: 12/30/2022] Open
Abstract
Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.
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Affiliation(s)
- Jiahui Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
| | - Huiyang Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
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Jiang Y, Wang X, Yu X, Zhao X, Luo N, Pei Z, Liu H, Garvin DF. Quantitative Trait Loci Associated with Drought Tolerance in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2017; 8:811. [PMID: 28567049 PMCID: PMC5434166 DOI: 10.3389/fpls.2017.00811] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/01/2017] [Indexed: 05/11/2023]
Abstract
The temperate wild grass Brachypodium distachyon (Brachypodium) serves as model system for studying turf and forage grasses. Brachypodium collections show diverse responses to drought stress, but little is known about the genetic mechanisms of drought tolerance of this species. The objective of this study was to identify quantitative trait loci (QTLs) associated with drought tolerance traits in Brachypodium. We assessed leaf fresh weight (LFW), leaf dry weight (LDW), leaf water content (LWC), leaf wilting (WT), and chlorophyll fluorescence (Fv/Fm) under well-watered and drought conditions on a recombinant inbred line (RIL) population from two parents (Bd3-1 and Bd1-1) known to differ in their drought adaptation. A linkage map of the RIL population was constructed using 467 single nucleotide polymorphism (SNP) markers obtained from genotyping-by-sequencing. The Bd3-1/Bd1-1 map spanned 1,618 cM and had an average distance of 3.5 cM between adjacent single nucleotide polymorphisms (SNPs). Twenty-six QTLs were identified in chromosome 1, 2, and 3 in two experiments, with 14 of the QTLs under well-watered conditions and 12 QTLs under drought stress. In Experiment 1, a QTL located on chromosome 2 with a peak at 182 cM appeared to simultaneously control WT, LWC, and Fv/Fm under drought stress, accounting for 11-18.7% of the phenotypic variation. Allelic diversity of candidate genes DREB2B, MYB, and SPK, which reside in one multi-QTL region, may play a role in the natural variation in whole plant drought tolerance in Brachypodium. Co-localization of QTLs for multiple drought-related traits suggest that the gene(s) involved are important regulators of drought tolerance in Brachypodium.
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Affiliation(s)
- Yiwei Jiang
- College of Agronomy, Resources, and Environment, Tianjin Agricultural UniversityTianjin, China
- Department of Agronomy, Purdue UniversityWest Lafayette, IN, United States
| | - Xicheng Wang
- Institute of Horticulture, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Xiaoqing Yu
- Department of Agronomy, Iowa State UniversityAmes, IA, United States
| | - Xiongwei Zhao
- Department of Agronomy, Purdue UniversityWest Lafayette, IN, United States
- Department of Crop Genetics and Breeding, Sichuan Agricultural UniversityChengdu, China
| | - Na Luo
- College of Life Sciences, South China Agricultural UniversityGuangzhou, China
| | - Zhongyou Pei
- College of Agronomy, Resources, and Environment, Tianjin Agricultural UniversityTianjin, China
| | - Huifen Liu
- College of Agronomy, Resources, and Environment, Tianjin Agricultural UniversityTianjin, China
| | - David F. Garvin
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, United States
- Plant Science Research Unit, United States Department of Agriculture, Agricultural Research ServiceSt. Paul, MN, United States
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9
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Des Marais DL, Lasky JR, Verslues PE, Chang TZ, Juenger TE. Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon. THE NEW PHYTOLOGIST 2017; 214:132-144. [PMID: 27864966 DOI: 10.1111/nph.14316] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/03/2016] [Indexed: 05/21/2023]
Abstract
An enduring question in plant physiology and evolution is how single genotypes of plants optimize performance in diverse, often highly variable, environments. We grew 35 natural accessions of the grass Brachypodium distachyon in four environments in the glasshouse, contrasting soil water deficit, elevated temperature and their interaction. We modeled treatment, genotype and interactive effects on leaf-level and whole-plant traits, including fecundity. We also assessed the relationship between glasshouse-measured traits and parameters related to climate at the place of origin. We found abundant genetic variation in both constitutive and induced traits related to plant-water relations. Most traits showed strong interaction between temperature and water availability, and we observed genotype-by-environment interaction for several traits. Notably, leaf free proline abundance showed a strong effect of genotype × temperature × water. We found strong associations between phenology, biomass and water use efficiency (WUE) with parameters describing climate of origin. Plants respond to multiple stressors in ways not directly predictable from single stressors, underscoring the complex and trait-specific mechanisms of environmental response. Climate-trait correlations support a role for WUE and phenology in local adaptation to climate in B. distachyon.
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Affiliation(s)
- David L Des Marais
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul E Verslues
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Trent Z Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Thomas E Juenger
- Department of Integrative Biology and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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10
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Viaud G, Loudet O, Cournède PH. Leaf Segmentation and Tracking in Arabidopsis thaliana Combined to an Organ-Scale Plant Model for Genotypic Differentiation. FRONTIERS IN PLANT SCIENCE 2017; 7:2057. [PMID: 28123392 PMCID: PMC5225094 DOI: 10.3389/fpls.2016.02057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/23/2016] [Indexed: 05/29/2023]
Abstract
A promising method for characterizing the phenotype of a plant as an interaction between its genotype and its environment is to use refined organ-scale plant growth models that use the observation of architectural traits, such as leaf area, containing a lot of information on the whole history of the functioning of the plant. The Phenoscope, a high-throughput automated platform, allowed the acquisition of zenithal images of Arabidopsis thaliana over twenty one days for 4 different genotypes. A novel image processing algorithm involving both segmentation and tracking of the plant leaves allows to extract areas of the latter. First, all the images in the series are segmented independently using a watershed-based approach. A second step based on ellipsoid-shaped leaves is then applied on the segments found to refine the segmentation. Taking into account all the segments at every time, the whole history of each leaf is reconstructed by choosing recursively through time the most probable segment achieving the best score, computed using some characteristics of the segment such as its orientation, its distance to the plant mass center and its area. These results are compared to manually extracted segments, showing a very good accordance in leaf rank and that they therefore provide low-biased data in large quantity for leaf areas. Such data can therefore be exploited to design an organ-scale plant model adapted from the existing GreenLab model for A. thaliana and subsequently parameterize it. This calibration of the model parameters should pave the way for differentiation between the Arabidopsis genotypes.
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Affiliation(s)
- Gautier Viaud
- Laboratory MICS, CentraleSupélec, University of Paris-SaclayChâtenay-Malabry, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
| | - Paul-Henry Cournède
- Laboratory MICS, CentraleSupélec, University of Paris-SaclayChâtenay-Malabry, France
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11
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Serial sequencing of isolength RAD tags for cost-efficient genome-wide profiling of genetic and epigenetic variations. Nat Protoc 2016; 11:2189-2200. [PMID: 27711051 DOI: 10.1038/nprot.2016.133] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Isolength restriction site-associated DNA (isoRAD) sequencing is a very simple but powerful approach that was originally developed for genome-wide genotyping at minimal labor and cost, and it has recently extended its applicability to allow quantification of DNA methylation levels. The isoRAD method is distinct from other genotyping-by-sequencing (GBS) methods because of its use of special restriction enzymes to produce isolength tags (32-36 bp), and sequencing of these uniform tags can bring many benefits. However, the relatively short tags produced by the original protocol are mostly suited to single-end (SE) sequencing (36-50 bp), and therefore they cannot efficiently match the gradually increased sequencing capacity of next-generation sequencing (NGS) platforms. To address this issue, we describe an advanced protocol that allows the preparation of five concatenated isoRAD tags for Illumina paired-end (PE) sequencing (100-150 bp). The configuration of the five concatenated tags is highly flexible, and can be defined by users to work with a desired combination of samples and/or restriction enzymes to suit specific research purposes. In comparison with the original protocol, the advanced protocol has an additional digestion and ligation step, and library preparation can be completed in ∼8 h.
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