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Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping

BACKGROUND: Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice p...

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Autores principales: Edzesi, Wisdom Mawuli, Dang, Xiaojing, Liu, Erbao, Bandoh, William Kwame Nuako, Gakpetor, Patience Mansa, Ofori, Daniel Aninagyei, Hong, Delin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930352/
https://www.ncbi.nlm.nih.gov/pubmed/36792993
http://dx.doi.org/10.1186/s12863-023-01107-8
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author Edzesi, Wisdom Mawuli
Dang, Xiaojing
Liu, Erbao
Bandoh, William Kwame Nuako
Gakpetor, Patience Mansa
Ofori, Daniel Aninagyei
Hong, Delin
author_facet Edzesi, Wisdom Mawuli
Dang, Xiaojing
Liu, Erbao
Bandoh, William Kwame Nuako
Gakpetor, Patience Mansa
Ofori, Daniel Aninagyei
Hong, Delin
author_sort Edzesi, Wisdom Mawuli
collection PubMed
description BACKGROUND: Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method. RESULTS: Among the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (r (GCC−FSC) = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC. CONCLUSION: Not every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-023-01107-8.
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spelling pubmed-99303522023-02-16 Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping Edzesi, Wisdom Mawuli Dang, Xiaojing Liu, Erbao Bandoh, William Kwame Nuako Gakpetor, Patience Mansa Ofori, Daniel Aninagyei Hong, Delin BMC Genom Data Research BACKGROUND: Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting, and competition from urbanization is making this traditional method of rice production unsustainable in the long term. In the present study, we mined favorable alleles for mesocotyl elongation length (MEL) by combining the phenotypic data of 543 rice accessions with genotypic data of 262 SSR markers through association mapping method. RESULTS: Among the 543 rice accessions studied, we found 130 accessions could elongate mesocotyl length under dark germination condition. A marker-trait association analysis based on a mixed linear model revealed eleven SSR markers were associated with MEL trait with p-value less than 0.01. Among the 11 association loci, seven were novel. In total, 30 favorable marker alleles for MEL were mined, and RM265-140 bp showed the highest phenotypic effect value of 1.8 cm with Yuedao46 as the carrier accession. The long MEL group of rice accessions had higher seedling emergence rate than the short MEL group in the field. The correlation coefficient (r (GCC−FSC) = 0.485**) between growth chamber condition (GCC) and field soil condition (FSC) showed positive relationship and highly significant (P < 0.01) indicating that the result obtained in GCC could basically represent that obtained under FSC. CONCLUSION: Not every genotype of the rice possesses the ability to elongate its mesocotyl length under dark or deep sowing condition. Mesocotyl elongation length is a quantitative trait controlled by many gene loci, and can be improved by pyramiding favorable alleles dispersed at different loci in different germplasm into a single genotype. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-023-01107-8. BioMed Central 2023-02-15 /pmc/articles/PMC9930352/ /pubmed/36792993 http://dx.doi.org/10.1186/s12863-023-01107-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Edzesi, Wisdom Mawuli
Dang, Xiaojing
Liu, Erbao
Bandoh, William Kwame Nuako
Gakpetor, Patience Mansa
Ofori, Daniel Aninagyei
Hong, Delin
Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping
title Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping
title_full Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping
title_fullStr Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping
title_full_unstemmed Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping
title_short Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping
title_sort screening germplasm and detecting qtls for mesocotyl elongation trait in rice (oryza sativa l.) by association mapping
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930352/
https://www.ncbi.nlm.nih.gov/pubmed/36792993
http://dx.doi.org/10.1186/s12863-023-01107-8
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