Genome-wide association study of nitrogen use efficiency and agronomic traits in upland rice

Rakotoson Tatiana, Dusserre Julie, Letourmy Philippe, Frouin Julien, Ratsimiala Ramonta Isabelle, Rakotoarisoa Noronirina Victorine, Cao Tuong-Vi, Vom Brocke Kirsten, Ramanantsoanirina Alain, Ahmadi Nourollah, Raboin Louis-Marie. 2021. Genome-wide association study of nitrogen use efficiency and agronomic traits in upland rice. Rice Science, 28 (4) : 379-390.

Url - éditeur : http://www.ricescience.org/EN/abstract/abstract9958.shtml

Quartile : Q1, Sujet : AGRONOMY / Quartile : Q1, Sujet : PLANT SCIENCES

Résumé : Genome-wide association study (GWAS) was performed for 16 agronomic traits including nitrogen use efficiency (NUE) and yield-related components using a panel of 190 mainly japonica rice varieties and a set of 38 390 single nucleotide polymorphism (SNP) markers. This panel was evaluated under rainfed upland conditions in Madagascar in two consecutive cropping seasons with two contrasted nitrogen input levels. Using another set of five grain traits, we identified previously known genes (GW5, GS3, Awn1 and Glabrous1), thus validating the pertinence and accuracy of our datasets for GWAS. A total of 369 significant associations were detected between SNPs and agronomic traits, gathered into 46 distinct haplotype groups and 28 isolated markers. Few association signals were identified for the complex quantitative trait NUE, however, larger number of quantitative trait loci (QTLs) were detected for its component traits, with 10 and 2 association signals for nitrogen utilization efficiency and nitrogen uptake efficiency, respectively. Several detected association signals co-localized with genes involved in nitrogen transport or nitrogen remobilization within 100 kb. The present study thus confirmed the potential of GWAS to identify candidate genes and new loci associated with agronomic traits. However, because of the quantitative and complex nature of NUE-related traits, GWAS might have not captured a large number of QTLs with limited effects.

Mots-clés Agrovoc : génome, caractère agronomique, utilisation des nutriments, riz pluvial, azote, locus des caractères quantitatifs, azote assimilable par la plante, polymorphisme à nucléotide unique

Mots-clés géographiques Agrovoc : Madagascar

Mots-clés libres : Genome-wide association study, Nitrogen use efficiency, Agronomic trait, Upland rice

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement hors UE : Fondazione Cariplo, Agropolis Fondation

Auteurs et affiliations

• Rakotoson Tatiana, Université d'Antananarivo (MDG)
• Dusserre Julie, CIRAD-PERSYST-UPR AIDA (FRA) ORCID: 0000-0002-4971-8799
• Letourmy Philippe, CIRAD-PERSYST-UPR AIDA (FRA) ORCID: 0000-0003-1040-0860
• Frouin Julien, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1591-0755
• Ratsimiala Ramonta Isabelle, Université d'Antananarivo (MDG)
• Rakotoarisoa Noronirina Victorine, Université d'Antananarivo (MDG)
• Cao Tuong-Vi, CIRAD-BIOS-UMR AGAP (BEN) ORCID: 0000-0002-7011-2003
• Vom Brocke Kirsten, CIRAD-BIOS-UMR AGAP (MDG)
• Ramanantsoanirina Alain, FOFIFA (MDG)
• Ahmadi Nourollah, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0072-6285
• Raboin Louis-Marie, CIRAD-PERSYST-UPR AIDA (BFA) ORCID: 0000-0002-8749-0406 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/598478/)

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