Genome-wide association study of agronomic traits in rice cultivated in temperate regions
Background: Rice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying diversity in rice populations adapted to specific environmental conditions is a fu...
| Main Authors: | , , , |
|---|---|
| Format: | article |
| Language: | Inglés |
| Published: |
Springer Nature
2019
|
| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.11939/6176 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5086-y |
| _version_ | 1855032380272672768 |
|---|---|
| author | Reig-Valiente, Juan L. Marqués, Luis Talón, Manuel Domingo, Concha |
| author_browse | Domingo, Concha Marqués, Luis Reig-Valiente, Juan L. Talón, Manuel |
| author_facet | Reig-Valiente, Juan L. Marqués, Luis Talón, Manuel Domingo, Concha |
| author_sort | Reig-Valiente, Juan L. |
| collection | ReDivia |
| description | Background: Rice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor
contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying
diversity in rice populations adapted to specific environmental conditions is a fundamental resource for breeding. In
this study we have analysed a collection of japonica varieties adapted to temperate regions to perform association
studies with traits of high agronomical interest such as heading date, plant height, number of panicles, panicle
length and number of grains per panicle.
Results: We have performed a genome wide association study using a panel of 1713 SNPs that, based on previous
linkage disequilibrium estimations, provides a full coverage of the whole genome. We have found a total of 43
SNPs associated with variations in the different traits. The identified SNPs were distributed across the genome
except in chromosome 12, where no associated SNPs were found. The inspection of the vicinity of these markers
also revealed a set of genes associated with physiological functions strongly linked to agronomic traits. Of special
relevance are two genes involved in gibberellin homeostasis that are associated with plant height and panicle
length. We also detected novel associated sites with heading date, panicle length and number of grain per panicle.
Conclusion: We have identified loci associated with important agronomic traits among cultivars adapted to
temperate conditions. Some of these markers co-localized with already known genes or QTLs, but the association
also provided novel molecular markers that can be of help to elucidate the complicated genetic mechanism
controlling important agronomic traits, as flowering regulation in the non-dependent photoperiod pathway. The
detected associated markers may provide important tools for the genetic improvement of rice cultivars in
temperate regions. |
| format | article |
| id | ReDivia6176 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | ReDivia61762025-04-25T14:46:23Z Genome-wide association study of agronomic traits in rice cultivated in temperate regions Reig-Valiente, Juan L. Marqués, Luis Talón, Manuel Domingo, Concha Heading date GWAS F30 Plant genetics and breeding Cultivated varieties Agronomic characters Abies Genomes Rice Crop yield Background: Rice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying diversity in rice populations adapted to specific environmental conditions is a fundamental resource for breeding. In this study we have analysed a collection of japonica varieties adapted to temperate regions to perform association studies with traits of high agronomical interest such as heading date, plant height, number of panicles, panicle length and number of grains per panicle. Results: We have performed a genome wide association study using a panel of 1713 SNPs that, based on previous linkage disequilibrium estimations, provides a full coverage of the whole genome. We have found a total of 43 SNPs associated with variations in the different traits. The identified SNPs were distributed across the genome except in chromosome 12, where no associated SNPs were found. The inspection of the vicinity of these markers also revealed a set of genes associated with physiological functions strongly linked to agronomic traits. Of special relevance are two genes involved in gibberellin homeostasis that are associated with plant height and panicle length. We also detected novel associated sites with heading date, panicle length and number of grain per panicle. Conclusion: We have identified loci associated with important agronomic traits among cultivars adapted to temperate conditions. Some of these markers co-localized with already known genes or QTLs, but the association also provided novel molecular markers that can be of help to elucidate the complicated genetic mechanism controlling important agronomic traits, as flowering regulation in the non-dependent photoperiod pathway. The detected associated markers may provide important tools for the genetic improvement of rice cultivars in temperate regions. 2019-04-08T10:31:51Z 2019-04-08T10:31:51Z 2018 article publishedVersion Reig-Valiente, J.L.; Marqués, L.; Talón, M. and Domingo, C. (2018) Genome-wide association study of agronomic traits in rice cultivated in temperate regions. BMC Genomics 19:706. http://hdl.handle.net/20.500.11939/6176 10.1186/s12864-018-5086-y https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5086-y en info:eu-repo/grantAgreement/MICINN/Programa Nacional de Cooperación Público-Privada/IPT-2011-1244-010000 info:eu-repo/grantAgreement/MINECO/Programa Estatal de I+D+i Orientada a los Retos de la Sociedad/RTA2014–00058-C03–00 programa INNPACTO del Ministerio de Economía y Competitividad (IPT-2011-1244-010000), INIA (RTA2014–00058-C03–00) Fondo Social Europeo (beca 01/14-FSE-0) Springer Nature electronico |
| spellingShingle | Heading date GWAS F30 Plant genetics and breeding Cultivated varieties Agronomic characters Abies Genomes Rice Crop yield Reig-Valiente, Juan L. Marqués, Luis Talón, Manuel Domingo, Concha Genome-wide association study of agronomic traits in rice cultivated in temperate regions |
| title | Genome-wide association study of agronomic traits in rice cultivated in temperate regions |
| title_full | Genome-wide association study of agronomic traits in rice cultivated in temperate regions |
| title_fullStr | Genome-wide association study of agronomic traits in rice cultivated in temperate regions |
| title_full_unstemmed | Genome-wide association study of agronomic traits in rice cultivated in temperate regions |
| title_short | Genome-wide association study of agronomic traits in rice cultivated in temperate regions |
| title_sort | genome wide association study of agronomic traits in rice cultivated in temperate regions |
| topic | Heading date GWAS F30 Plant genetics and breeding Cultivated varieties Agronomic characters Abies Genomes Rice Crop yield |
| url | http://hdl.handle.net/20.500.11939/6176 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5086-y |
| work_keys_str_mv | AT reigvalientejuanl genomewideassociationstudyofagronomictraitsinricecultivatedintemperateregions AT marquesluis genomewideassociationstudyofagronomictraitsinricecultivatedintemperateregions AT talonmanuel genomewideassociationstudyofagronomictraitsinricecultivatedintemperateregions AT domingoconcha genomewideassociationstudyofagronomictraitsinricecultivatedintemperateregions |