Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes
Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold s...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1303651/full |
| _version_ | 1797390983343636480 |
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| author | Michael R. Schläppi Avery R. Jessel Aaron K. Jackson Huy Phan Melissa H. Jia Jeremy D. Edwards Georgia C. Eizenga |
| author_facet | Michael R. Schläppi Avery R. Jessel Aaron K. Jackson Huy Phan Melissa H. Jia Jeremy D. Edwards Georgia C. Eizenga |
| author_sort | Michael R. Schläppi |
| collection | DOAJ |
| description | Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype. |
| first_indexed | 2024-03-08T23:26:13Z |
| format | Article |
| id | doaj.art-e8313d200a4844419fe270a27e754ff7 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-08T23:26:13Z |
| publishDate | 2023-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-e8313d200a4844419fe270a27e754ff72023-12-14T17:22:55ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-12-011410.3389/fpls.2023.13036511303651Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genesMichael R. Schläppi0Avery R. Jessel1Aaron K. Jackson2Huy Phan3Melissa H. Jia4Jeremy D. Edwards5Georgia C. Eizenga6Department of Biological Sciences, Marquette University, Milwaukee, WI, United StatesDepartment of Biological Sciences, Marquette University, Milwaukee, WI, United StatesDale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United StatesDepartment of Biological Sciences, Marquette University, Milwaukee, WI, United StatesDale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United StatesDale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United StatesDale Bumpers National Rice Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Stuttgart, AR, United StatesDue to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.https://www.frontiersin.org/articles/10.3389/fpls.2023.1303651/fullAsian ricechilling tolerancegenome-wide association studyheading dateIndica riceJaponica rice |
| spellingShingle | Michael R. Schläppi Avery R. Jessel Aaron K. Jackson Huy Phan Melissa H. Jia Jeremy D. Edwards Georgia C. Eizenga Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes Frontiers in Plant Science Asian rice chilling tolerance genome-wide association study heading date Indica rice Japonica rice |
| title | Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes |
| title_full | Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes |
| title_fullStr | Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes |
| title_full_unstemmed | Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes |
| title_short | Navigating rice seedling cold resilience: QTL mapping in two inbred line populations and the search for genes |
| title_sort | navigating rice seedling cold resilience qtl mapping in two inbred line populations and the search for genes |
| topic | Asian rice chilling tolerance genome-wide association study heading date Indica rice Japonica rice |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1303651/full |
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