Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.)
Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.00769/full |
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| author | Kornelia Gudys Kornelia Gudys Justyna Guzy-Wrobelska Agnieszka Janiak Michał A. Dziurka Agnieszka Ostrowska Katarzyna Hura Barbara Jurczyk Katarzyna Żmuda Daria Grzybkowska Joanna Śróbka Wojciech Urban Jolanta Biesaga-Koscielniak Maria Filek Janusz Koscielniak Krzysztof Mikołajczak Piotr Ogrodowicz Karolina Krystkowiak Karolina Krystkowiak Anetta Kuczyńska Paweł Krajewski Iwona Szarejko |
| author_facet | Kornelia Gudys Kornelia Gudys Justyna Guzy-Wrobelska Agnieszka Janiak Michał A. Dziurka Agnieszka Ostrowska Katarzyna Hura Barbara Jurczyk Katarzyna Żmuda Daria Grzybkowska Joanna Śróbka Wojciech Urban Jolanta Biesaga-Koscielniak Maria Filek Janusz Koscielniak Krzysztof Mikołajczak Piotr Ogrodowicz Karolina Krystkowiak Karolina Krystkowiak Anetta Kuczyńska Paweł Krajewski Iwona Szarejko |
| author_sort | Kornelia Gudys |
| collection | DOAJ |
| description | Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs), followed by their prioritization based on Gene Ontology (GO) enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin up-regulated RNAs, nitric oxide synthase, ATP sulfurylases, and proteins involved in regulation of flowering time. This global approach may be proposed for identification of new CGs that underlies QTLs responsible for complex traits. |
| first_indexed | 2024-12-14T18:13:10Z |
| format | Article |
| id | doaj.art-42362fbf87994c0db4bb607ef1bb4ad4 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-14T18:13:10Z |
| publishDate | 2018-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-42362fbf87994c0db4bb607ef1bb4ad42022-12-21T22:52:14ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-06-01910.3389/fpls.2018.00769326641Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.)Kornelia Gudys0Kornelia Gudys1Justyna Guzy-Wrobelska2Agnieszka Janiak3Michał A. Dziurka4Agnieszka Ostrowska5Katarzyna Hura6Barbara Jurczyk7Katarzyna Żmuda8Daria Grzybkowska9Joanna Śróbka10Wojciech Urban11Jolanta Biesaga-Koscielniak12Maria Filek13Janusz Koscielniak14Krzysztof Mikołajczak15Piotr Ogrodowicz16Karolina Krystkowiak17Karolina Krystkowiak18Anetta Kuczyńska19Paweł Krajewski20Iwona Szarejko21Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDepartment of Botany and Nature Protection, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDepartment of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDepartment of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDepartment of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, PolandDepartment of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, PolandDepartment of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, PolandDepartment of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, PolandDepartment of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, PolandDepartment of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDepartment of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDepartment of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDepartment of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, PolandDepartment of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, PolandDepartment of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, PolandDepartment of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, PolandDepartment of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, PolandDepartment of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, PolandDepartment of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, PolandDepartment of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, PolandDepartment of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, PolandDepartment of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, PolandDrought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs), followed by their prioritization based on Gene Ontology (GO) enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin up-regulated RNAs, nitric oxide synthase, ATP sulfurylases, and proteins involved in regulation of flowering time. This global approach may be proposed for identification of new CGs that underlies QTLs responsible for complex traits.https://www.frontiersin.org/article/10.3389/fpls.2018.00769/fullbarleydrought tolerancefunction mapQTLQTL hotspotCG prioritization |
| spellingShingle | Kornelia Gudys Kornelia Gudys Justyna Guzy-Wrobelska Agnieszka Janiak Michał A. Dziurka Agnieszka Ostrowska Katarzyna Hura Barbara Jurczyk Katarzyna Żmuda Daria Grzybkowska Joanna Śróbka Wojciech Urban Jolanta Biesaga-Koscielniak Maria Filek Janusz Koscielniak Krzysztof Mikołajczak Piotr Ogrodowicz Karolina Krystkowiak Karolina Krystkowiak Anetta Kuczyńska Paweł Krajewski Iwona Szarejko Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.) Frontiers in Plant Science barley drought tolerance function map QTL QTL hotspot CG prioritization |
| title | Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.) |
| title_full | Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.) |
| title_fullStr | Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.) |
| title_full_unstemmed | Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.) |
| title_short | Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.) |
| title_sort | prioritization of candidate genes in qtl regions for physiological and biochemical traits underlying drought response in barley hordeum vulgare l |
| topic | barley drought tolerance function map QTL QTL hotspot CG prioritization |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.00769/full |
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