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Haider S, Bibi K, Munyaneza V, Zhang H, Zhang W, Ali A, Ahmad IA, Mehran M, Xu F, Yang C, Yang J, Ding G. Drought-induced adaptive and ameliorative strategies in plants. CHEMOSPHERE 2024; 364:143134. [PMID: 39168385 DOI: 10.1016/j.chemosphere.2024.143134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/01/2024] [Accepted: 08/18/2024] [Indexed: 08/23/2024]
Affiliation(s)
- Sharjeel Haider
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China
| | - Khadija Bibi
- Department of Botany, Faculty of Sciences, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Venuste Munyaneza
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China
| | - Hao Zhang
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China
| | - Wen Zhang
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ayaz Ali
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China
| | - Iftikhar Ali Ahmad
- Key Laboratory of Soil Health Diagnostic and Green Remediation, Ministry of Ecology and Environment, College of Resource and Environment, Huazhong Agricultural University, China
| | - Muhammad Mehran
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China
| | - Fangsen Xu
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China
| | - Chunlei Yang
- Hubei Academy of Tobacco Science, Wuhan, 430030, China.
| | - Jinpeng Yang
- Hubei Academy of Tobacco Science, Wuhan, 430030, China
| | - Guangda Ding
- College of Resources and Environment/Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, China.
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Riehl JFL, Cole CT, Morrow CJ, Barker HL, Bernhardsson C, Rubert‐Nason K, Ingvarsson PK, Lindroth RL. Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen ( Populus tremuloides Michx.). Ecol Evol 2023; 13:e10541. [PMID: 37780087 PMCID: PMC10534199 DOI: 10.1002/ece3.10541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023] Open
Abstract
Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.
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Affiliation(s)
| | | | - Clay J. Morrow
- Department of Forest and Wildlife EcologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Hilary L. Barker
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Present address:
Office of Student SuccessWisconsin Technical College SystemMadisonWisconsinUSA
| | - Carolina Bernhardsson
- Department of Ecology and Environmental ScienceUmeå UniversityUmeåSweden
- Present address:
Department of Organismal Biology, Center for Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Kennedy Rubert‐Nason
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- Present address:
Division of Natural SciencesUniversity of Maine at Fort KentFort KentMaineUSA
| | - Pär K. Ingvarsson
- Department of Plant BiologySwedish University of Agricultural Sciences, Uppsala BioCenterUppsalaSweden
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Gao J, Jebrane M, Terziev N, Daniel G. The contribution of G-layer glucose in Salix clones for biofuels: comparative enzymatic and HPLC analysis of stem cross sections. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:25. [PMID: 35248127 PMCID: PMC8898495 DOI: 10.1186/s13068-022-02123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/19/2022] [Indexed: 11/17/2022]
Abstract
Background Interest on the use of short rotation willow as a lignocellulose resource for liquid transport fuels has increased greatly over the last 10 years. Investigations have shown the advantages and potential of using Salix spp. for such fuels but have also emphasized the wide variations existing in the compositional structure between different species and genotypes in addition to their effects on overall yield. The present work studied the importance of tension wood (TW) as a readily available source of glucose in 2-year-old stems of four Salix clones (Tora, Björn, Jorr, Loden). Studies involved application of a novel approach whereby TW-glucose and residual sugars and lignin were quantified using stem cross sections with results correlated with HPLC analyses of milled wood. Compositional analyses were made for four points along stems and glucose derived from enzyme saccharification of TW gelatinous (G) layers (G-glucose), structural cell wall glucose (CW-glucose) remaining after saccharification and total glucose (T-glucose) determined both theoretically and from HPLC analyses. Comparisons were also made between presence of other characteristic sugars as well as acid-soluble and -insoluble lignin. Results Preliminary studies showed good agreement between using stem serial sections and milled powder from Salix stems for determining total sugar and lignin. Therefore, sections were used throughout the work. HPLC determination of T-glucose in Salix clones varied between 47.1 and 52.8%, showing a trend for higher T-glucose with increasing height (Björn, Tora and Jorr). Using histochemical/microscopy and image analysis, Tora (24.2%) and Björn (28.2%) showed greater volumes of % TW than Jorr (15.5%) and Loden (14.0%). Total G-glucose with enzyme saccharification of TW G-layers varied between 3.7 and 14.7% increasing as the total TW volume increased. CW-glucose measured after enzyme saccharification showed mean values of 41.9–49.1%. Total lignin between and within clones showed small differences with mean variations of 22.4–22.8% before and 22.4–24.3% after enzyme saccharification. Calculated theoretical and quantified values for CW-glucose at different heights for clones were similar with strong correlation: T-glucose = G-glucose + CW-glucose. Pearson’s correlation displayed a strong and positive correlation between T-glucose and G-glucose, % TW and stem height, and between G-glucose with % TW and stem height. Conclusions The use of stem cross sections to estimate TW together with enzyme saccharification represents a viable approach for determining freely available G-glucose from TW allowing comparisons between Salix clones. Using stem sections provides for discrete morphological/compositional tissue comparisons between clones with results consistent with traditional wet chemical analysis approaches where entire stems are milled and analyzed. The four clones showed variable TW and presence of total % G-glucose in the order Björn > Tora > Jorr > Loden. Calculated in terms of 1 m3, Salix stems Tora and Björn would contain ca. 0.24 and 0.28 m3 of tension wood representing a significant amount of freely available glucose. Graphical Abstract ![]()
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Akpertey A, Anim-Kwapong E, Adu-Gyamfi PKK, Ofori A. Genetic variability for vigor and yield of robusta coffee ( Coffea canephora) clones in Ghana. Heliyon 2022; 8:e10192. [PMID: 36033278 PMCID: PMC9400079 DOI: 10.1016/j.heliyon.2022.e10192] [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: 12/06/2021] [Revised: 05/21/2022] [Accepted: 07/28/2022] [Indexed: 11/15/2022] Open
Abstract
Effectiveness of plant improvement programs, especially in perennial crops like coffee, may be improved by knowing the level of genetic variation which exist within a breeding population coupled with the knowledge of estimates of genetic parameters for key agronomic traits. Thus, this study was conducted to evaluate C. canephora clones for growth (stem diameter, number of laterals and span) and yield traits; estimate genetic parameters of these traits; and determine the phenotypic and genetic associations between these traits to guide future crop improvement efforts. The productivity of 56 coffee clones was assessed from 2012 to 2020 in a clonal experiment planted in a randomized complete block design with three replicates. Each plot consisted of eight plants spaced at 2 × 3 m at the Cocoa Research Institute of Ghana. There were significant (p < 0.001) differences among clones for all the traits assessed. Broad sense heritability was low-to-moderate for all the traits evaluated with the highest (0.34) observed for cumulative yield (CY). Cumulative yield was genetically correlated (p < 0.001) with span and number of laterals (NOL). For the growth traits, NOL was the most strongly associated with CY (rg = 0.49, p < 0.001). The results revealed that selection based on early years’ yield (MY1) could be as effective as selection based on CY (rg = 0.87, p < 0.001). Our findings indicate that there is significant genetic variation among the test clones for the parameters assessed and presents a good opportunity for future variety development.
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Affiliation(s)
- Abraham Akpertey
- Cocoa Research Institute of Ghana, P. O. Box 8, New Tafo-Akim, ER, Ghana
| | | | | | - Atta Ofori
- Cocoa Research Institute of Ghana, P. O. Box 8, New Tafo-Akim, ER, Ghana
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Wilkerson DG, Taskiran B, Carlson CH, Smart LB. Mapping the sex determination region in the Salix F1 hybrid common parent population confirms a ZW system in six diverse species. G3 GENES|GENOMES|GENETICS 2022; 12:6554199. [PMID: 35333299 PMCID: PMC9157088 DOI: 10.1093/g3journal/jkac071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/17/2022] [Indexed: 11/24/2022]
Abstract
Within the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing 6 Salix species (Salix viminalis, Salix suchowensis, Salix integra, Salix koriyanagi, Salix udensis, and Salix alberti) to common male and female Salix purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S.suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra × S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop.
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Affiliation(s)
- Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
| | - Bircan Taskiran
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
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Sallam A, Eltaher S, Alqudah AM, Belamkar V, Baenziger PS. Combined GWAS and QTL mapping revealed candidate genes and SNP network controlling recovery and tolerance traits associated with drought tolerance in seedling winter wheat. Genomics 2022; 114:110358. [PMID: 35398246 DOI: 10.1016/j.ygeno.2022.110358] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/04/2022] [Accepted: 03/27/2022] [Indexed: 01/14/2023]
Abstract
To date, very little research on drought tolerance has been conducted at the seedling stage in winter wheat. In this study, two types of traits, namely tolerance and recovery traits, associated with drought tolerance were scored in biparental mapping population (BPP) and association mapping population (A-set). The results of this study revealed no or weak significant correlation between the two types of traits. Based on GWAS and QTL mapping analyses, all QTLs associated with recovery traits were completely different from those associated with tolerance traits except one QTL in each population that was found to be associated with one tolerance trait and one recovery trait. The analysis of SNP and gene networks confirmed the results of combined GWAS and QTL mapping. One SNP marker located on the 2B chromosome (S2B_26494801) was found to be associated with recovery traits in both populations. The results of this study provided new information on understanding and improving drought tolerance in winter wheat.
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Affiliation(s)
- Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt; Resources Genetics and Reproduction, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany.
| | - Shamseldeen Eltaher
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), Egypt
| | - Ahmad M Alqudah
- Department of Agroecology, Aarhus University at Flakkebjerg, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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Hallingbäck HR, Pucholt P, Ingvarsson PK, Rönnberg-Wästljung AC, Berlin S. Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis. BMC Genomics 2021; 22:710. [PMID: 34600471 PMCID: PMC8487499 DOI: 10.1186/s12864-021-08021-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/14/2021] [Indexed: 01/24/2023] Open
Abstract
Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher’s exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08021-2.
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Affiliation(s)
- Henrik R Hallingbäck
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden.,Present Address: Skogforsk (The Forestry Research Institute of Sweden), Uppsala Science Park, SE-751 83, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
| | - Ann Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden.
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Box 7080, SE-750 07, Uppsala, Sweden
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Guevara-Escudero M, Osorio AN, Cortés AJ. Integrative Pre-Breeding for Biotic Resistance in Forest Trees. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10102022. [PMID: 34685832 PMCID: PMC8541610 DOI: 10.3390/plants10102022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 05/18/2023]
Abstract
Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations' persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen-host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes.
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Affiliation(s)
- Melisa Guevara-Escudero
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Angy N. Osorio
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Andrés J. Cortés
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
- Main Address: Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia
- Correspondence:
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Cortés AJ, Restrepo-Montoya M, Bedoya-Canas LE. Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate. FRONTIERS IN PLANT SCIENCE 2020; 11:583323. [PMID: 33193532 PMCID: PMC7609427 DOI: 10.3389/fpls.2020.583323] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/29/2020] [Indexed: 05/02/2023]
Abstract
Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line in the fields of plant science and genetic improvement for tolerance to abiotic stress. Specifically, exploring the genomic basis of local adaptation is imperative for assessing the conditions under which trees will successfully adapt in situ to global climate change. However, this knowledge has scarcely been used in conservation and forest tree improvement because woody perennials face major research limitations such as their outcrossing reproductive systems, long juvenile phase, and huge genome sizes. Therefore, in this review we discuss predictive genomic approaches that promise increasing adaptive selection accuracy and shortening generation intervals. They may also assist the detection of novel allelic variants from tree germplasm, and disclose the genomic potential of adaptation to different environments. For instance, natural populations of tree species invite using tools from the population genomics field to study the signatures of local adaptation. Conventional genetic markers and whole genome sequencing both help identifying genes and markers that diverge between local populations more than expected under neutrality, and that exhibit unique signatures of diversity indicative of "selective sweeps." Ultimately, these efforts inform the conservation and breeding status capable of pivoting forest health, ecosystem services, and sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history may affect the adaptive relevant genetic variation available for adaptation to environmental change. Encouraging "big data" approaches (machine learning-ML) capable of comprehensively merging heterogeneous genomic and ecological datasets is becoming imperative, too.
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, Rionegro, Colombia
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Manuela Restrepo-Montoya
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Larry E. Bedoya-Canas
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
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Different genetic basis for alcohol dehydrogenase activity and plasticity in a novel alcohol environment for Drosophila melanogaster. Heredity (Edinb) 2020; 125:101-109. [PMID: 32483318 DOI: 10.1038/s41437-020-0323-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 11/08/2022] Open
Abstract
Phenotypic plasticity is known to enhance population persistence, facilitate adaptive evolution and initiate novel phenotypes in novel environments. How plasticity can contribute or hinder adaptation to different environments hinges on its genetic architecture. Even though plasticity in many traits is genetically controlled, whether and how plasticity's genetic architecture might change in novel environments is still unclear. Because much of gene expression can be environmentally influenced, each environment may trigger different sets of genes that influence a trait. Using a quantitative trait loci (QTL) approach, we investigated the genetic basis of plasticity in a classic functional trait, alcohol dehydrogenase (ADH) activity in D. melanogaster, across both historical and novel alcohol environments. Previous research in D. melanogaster has also demonstrated that ADH activity is plastic in response to alcohol concentration in substrates used by both adult flies and larvae. We found that across all environments tested, ADH activity was largely influenced by a single QTL encompassing the Adh-coding gene and its known regulatory locus, delta-1. After controlling for the allelic variation of the Adh and delta-1 loci, we found additional but different minor QTLs in the 0 and 14% alcohol environments. In contrast, we discovered no major QTL for plasticity itself, including the Adh locus, regardless of the environmental gradients. This suggests that plasticity in ADH activity is likely influenced by many loci with small effects, and that the Adh locus is not environmentally sensitive to dietary alcohol.
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Ohlsson JA, Hallingbäck HR, Jebrane M, Harman-Ware AE, Shollenberger T, Decker SR, Sandgren M, Rönnberg-Wästljung AC. Genetic variation of biomass recalcitrance in a natural Salix viminalis (L.) population. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:135. [PMID: 31171936 PMCID: PMC6545741 DOI: 10.1186/s13068-019-1479-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/25/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Salix spp. are high-productivity crops potentially used for lignocellulosic biofuels such as bioethanol. In general, pretreatment is needed to facilitate the enzymatic depolymerization process. Biomass resistance to degradation, i.e., biomass recalcitrance, is a trait which can be assessed by measuring the sugar released after combined pretreatment and enzymatic hydrolysis. We have examined genetic parameters of enzymatic sugar release and other traits related to biorefinery use in a population of 286 natural Salix viminalis clones. Furthermore, we have evaluated phenotypic and genetic correlations between these traits and performed a genomewide association mapping analysis using a set of 19,411 markers. RESULTS Sugar release (glucose and xylose) after pretreatment and enzymatic saccharification proved highly variable with large genetic and phenotypic variations, and chip heritability estimates (h 2) of 0.23-0.29. Lignin syringyl/guaiacyl (S/G) ratio and wood density were the most heritable traits (h 2 = 0.42 and 0.59, respectively). Sugar release traits were positively correlated, phenotypically and genetically, with biomass yield and lignin S/G ratio. Association mapping revealed seven marker-trait associations below a suggestive significance threshold, including one marker associated with glucose release. CONCLUSIONS We identified lignin S/G ratio and shoot diameter as heritable traits that could be relatively easily evaluated by breeders, making them suitable proxy traits for developing low-recalcitrance varieties. One marker below the suggestive threshold for marker associations was identified for sugar release, meriting further investigation while also highlighting the difficulties in employing genomewide association mapping for complex traits.
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Affiliation(s)
- Jonas A. Ohlsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik R. Hallingbäck
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07 Uppsala, Sweden
- Department of Plant Physiology and Forest Genetics, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Mohamed Jebrane
- Department of Forest Biomaterials and Technology/Wood Science, Swedish University of Agricultural Sciences, Box 7008, 750 07 Uppsala, Sweden
| | - Anne E. Harman-Ware
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- Center for Bioenergy Innovation, National Renewable Energy Laboratory, Golden, CO USA
| | - Todd Shollenberger
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07 Uppsala, Sweden
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