Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil
Rice is a staple food for more than half of the world's population. In Brazil, this crop plays an important role in consumption, production and economy. Root system is a key trait for rice yield, as it is responsible for water uptake, absorption, transportation of nutrients from soil, and other...
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Elsevier
2025-05-01
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| Series: | Crop Design |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2772899425000011 |
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| author | Gabriel Brandão das Chagas Latóia Eduarda Maltzahn Josiane Vargas de Oliveira Maximino Viviane Kopp da Luz Ariano Martins de Magalhães Junior Antonio Costa de Oliveira Luciano Carlos da Maia Camila Pegoraro |
| author_facet | Gabriel Brandão das Chagas Latóia Eduarda Maltzahn Josiane Vargas de Oliveira Maximino Viviane Kopp da Luz Ariano Martins de Magalhães Junior Antonio Costa de Oliveira Luciano Carlos da Maia Camila Pegoraro |
| author_sort | Gabriel Brandão das Chagas |
| collection | DOAJ |
| description | Rice is a staple food for more than half of the world's population. In Brazil, this crop plays an important role in consumption, production and economy. Root system is a key trait for rice yield, as it is responsible for water uptake, absorption, transportation of nutrients from soil, and other vital functions. Root dry weight (RDW) and root length (RL) are related to crop yields. Understanding molecular basis of rice root traits is a strategy to help breeders develop genotypes with higheryield. However, few studies using Brazilian germplasm have been developed. Therefore, the objective of this research was to map genome regions responsible for root dry weight and length in adult rice plants grown in Southern of Brazil. Genome-wide association study (GWAS) was applied using 7098 single nucleotide polymorphism (SNPs) markers and a collection of 188 rice genotypes. Seven SNP markers for root length and four markers for root dry weight were detected. Genes encoding myeloblastosis (MYB) transcription factor, cinnamyl alcohol dehydrogenase, cyclin-dependent protein kinase (Cdk)-activating kinase were associated with root length. Amidst the genes related to root dry weight, those encoding cellulose synthase, lipid transfer protein, Receptor-like cytoplasmic kinase and CCCH-type zinc finger protein associated with drought tolerance were identified. This study provides insights of genetic control of rice root traits considering as a panel composed mainly of Brazilian genotypes. The rice breeders can apply this knowledge to guide for further research and develop new cultivars in Brazil. |
| format | Article |
| id | doaj-art-cacbf8e75b634558b1aceaea36923d4a |
| institution | OA Journals |
| issn | 2772-8994 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Crop Design |
| spelling | doaj-art-cacbf8e75b634558b1aceaea36923d4a2025-08-20T01:51:31ZengElsevierCrop Design2772-89942025-05-014210009510.1016/j.cropd.2025.100095Genome-wide association study identifies loci and candidate genes for root traits in rice grown in BrazilGabriel Brandão das Chagas0Latóia Eduarda Maltzahn1Josiane Vargas de Oliveira Maximino2Viviane Kopp da Luz3Ariano Martins de Magalhães Junior4Antonio Costa de Oliveira5Luciano Carlos da Maia6Camila Pegoraro7Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Campus Capão do Leão, CEP 96160-000, Capão do Leão, RS, BrazilUniversidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Campus Capão do Leão, CEP 96160-000, Capão do Leão, RS, BrazilUniversidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Campus Capão do Leão, CEP 96160-000, Capão do Leão, RS, BrazilUniversidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Campus Capão do Leão, CEP 96160-000, Capão do Leão, RS, BrazilEmbrapa Clima Temperado, Estação Experimental Terras Baixas, CEP 96001-970, Capão do Leão, RS, BrazilUniversidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Campus Capão do Leão, CEP 96160-000, Capão do Leão, RS, BrazilUniversidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Campus Capão do Leão, CEP 96160-000, Capão do Leão, RS, Brazil; Corresponding author. Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Campus Universitário S/N, 96160-000, Capão do Leão, Rio Grande do Sul, Brazil.Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Campus Capão do Leão, CEP 96160-000, Capão do Leão, RS, Brazil; Corresponding author. Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Campus Universitário S/N, 96160-000, Capão do Leão, Rio Grande do Sul, Brazil.Rice is a staple food for more than half of the world's population. In Brazil, this crop plays an important role in consumption, production and economy. Root system is a key trait for rice yield, as it is responsible for water uptake, absorption, transportation of nutrients from soil, and other vital functions. Root dry weight (RDW) and root length (RL) are related to crop yields. Understanding molecular basis of rice root traits is a strategy to help breeders develop genotypes with higheryield. However, few studies using Brazilian germplasm have been developed. Therefore, the objective of this research was to map genome regions responsible for root dry weight and length in adult rice plants grown in Southern of Brazil. Genome-wide association study (GWAS) was applied using 7098 single nucleotide polymorphism (SNPs) markers and a collection of 188 rice genotypes. Seven SNP markers for root length and four markers for root dry weight were detected. Genes encoding myeloblastosis (MYB) transcription factor, cinnamyl alcohol dehydrogenase, cyclin-dependent protein kinase (Cdk)-activating kinase were associated with root length. Amidst the genes related to root dry weight, those encoding cellulose synthase, lipid transfer protein, Receptor-like cytoplasmic kinase and CCCH-type zinc finger protein associated with drought tolerance were identified. This study provides insights of genetic control of rice root traits considering as a panel composed mainly of Brazilian genotypes. The rice breeders can apply this knowledge to guide for further research and develop new cultivars in Brazil.http://www.sciencedirect.com/science/article/pii/S2772899425000011GWASLinkage disequilibriumMappingOryza sativa L.Population structure |
| spellingShingle | Gabriel Brandão das Chagas Latóia Eduarda Maltzahn Josiane Vargas de Oliveira Maximino Viviane Kopp da Luz Ariano Martins de Magalhães Junior Antonio Costa de Oliveira Luciano Carlos da Maia Camila Pegoraro Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil Crop Design GWAS Linkage disequilibrium Mapping Oryza sativa L. Population structure |
| title | Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil |
| title_full | Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil |
| title_fullStr | Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil |
| title_full_unstemmed | Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil |
| title_short | Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil |
| title_sort | genome wide association study identifies loci and candidate genes for root traits in rice grown in brazil |
| topic | GWAS Linkage disequilibrium Mapping Oryza sativa L. Population structure |
| url | http://www.sciencedirect.com/science/article/pii/S2772899425000011 |
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