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Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar

Rice (Oryza sativa L.) is a staple food of Madagascar, where per capita rice consumption is among the highest worldwide. Rice in Madagascar is mainly grown on smallholder farms on soils with low fertility and in the absence of external inputs such as mineral fertilizers. Consequently, rice productiv...

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Autores principales: Pariasca-Tanaka, Juan, Rakotondramanana, Mbolatantely Fahazavana, Tojo Mangaharisoa, Sarah, Ranaivo, Harisoa Nicole, Tanaka, Ryokei, Wissuwa, Matthias
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9116655/
https://www.ncbi.nlm.nih.gov/pubmed/35584097
http://dx.doi.org/10.1371/journal.pone.0262707
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author Pariasca-Tanaka, Juan
Rakotondramanana, Mbolatantely Fahazavana
Tojo Mangaharisoa, Sarah
Ranaivo, Harisoa Nicole
Tanaka, Ryokei
Wissuwa, Matthias
author_facet Pariasca-Tanaka, Juan
Rakotondramanana, Mbolatantely Fahazavana
Tojo Mangaharisoa, Sarah
Ranaivo, Harisoa Nicole
Tanaka, Ryokei
Wissuwa, Matthias
author_sort Pariasca-Tanaka, Juan
collection PubMed
description Rice (Oryza sativa L.) is a staple food of Madagascar, where per capita rice consumption is among the highest worldwide. Rice in Madagascar is mainly grown on smallholder farms on soils with low fertility and in the absence of external inputs such as mineral fertilizers. Consequently, rice productivity remains low and the gap between rice production and consumption is widening at the national level. This study evaluates genetic resources imported from the IRRI rice gene bank to identify potential donors and loci associated with low soil fertility tolerance (LFT) that could be utilized in improving rice yield under local cultivation conditions. Accessions were grown on-farm without fertilizer inputs in the central highlands of Madagascar. A Genome-wide association study (GWAS) identified quantitative trait loci (QTL) for total panicle weight per plant, straw weight, total plant biomass, heading date and plant height. We detected loci at locations of known major genes for heading date (hd1) and plant height (sd1), confirming the validity of GWAS procedures. Two QTLs for total panicle weight were detected on chromosomes 5 (qLFT5) and 11 (qLFT11) and superior panicle weight was conferred by minor alleles. Further phenotyping under P and N deficiency suggested qLFT11 to be related to preferential resource allocation to root growth under nutrient deficiency. A donor (IRIS 313–11949) carrying both minor advantageous alleles was identified and crossed to a local variety (X265) lacking these alleles to initiate variety development through a combination of marker-assisted selection with selection on-farm in the target environment rather than on-station as typically practiced.
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spelling pubmed-91166552022-05-19 Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar Pariasca-Tanaka, Juan Rakotondramanana, Mbolatantely Fahazavana Tojo Mangaharisoa, Sarah Ranaivo, Harisoa Nicole Tanaka, Ryokei Wissuwa, Matthias PLoS One Research Article Rice (Oryza sativa L.) is a staple food of Madagascar, where per capita rice consumption is among the highest worldwide. Rice in Madagascar is mainly grown on smallholder farms on soils with low fertility and in the absence of external inputs such as mineral fertilizers. Consequently, rice productivity remains low and the gap between rice production and consumption is widening at the national level. This study evaluates genetic resources imported from the IRRI rice gene bank to identify potential donors and loci associated with low soil fertility tolerance (LFT) that could be utilized in improving rice yield under local cultivation conditions. Accessions were grown on-farm without fertilizer inputs in the central highlands of Madagascar. A Genome-wide association study (GWAS) identified quantitative trait loci (QTL) for total panicle weight per plant, straw weight, total plant biomass, heading date and plant height. We detected loci at locations of known major genes for heading date (hd1) and plant height (sd1), confirming the validity of GWAS procedures. Two QTLs for total panicle weight were detected on chromosomes 5 (qLFT5) and 11 (qLFT11) and superior panicle weight was conferred by minor alleles. Further phenotyping under P and N deficiency suggested qLFT11 to be related to preferential resource allocation to root growth under nutrient deficiency. A donor (IRIS 313–11949) carrying both minor advantageous alleles was identified and crossed to a local variety (X265) lacking these alleles to initiate variety development through a combination of marker-assisted selection with selection on-farm in the target environment rather than on-station as typically practiced. Public Library of Science 2022-05-18 /pmc/articles/PMC9116655/ /pubmed/35584097 http://dx.doi.org/10.1371/journal.pone.0262707 Text en © 2022 Pariasca-Tanaka et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Pariasca-Tanaka, Juan
Rakotondramanana, Mbolatantely Fahazavana
Tojo Mangaharisoa, Sarah
Ranaivo, Harisoa Nicole
Tanaka, Ryokei
Wissuwa, Matthias
Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar
title Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar
title_full Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar
title_fullStr Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar
title_full_unstemmed Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar
title_short Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar
title_sort phenotyping of a rice (oryza sativa l.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in madagascar
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9116655/
https://www.ncbi.nlm.nih.gov/pubmed/35584097
http://dx.doi.org/10.1371/journal.pone.0262707
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