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

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Abstract

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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Most cited references 38

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Author and article information

Contributors

Wisdom Mawuli Edzesi: wedzesi@csir-forig.org.gh

Xiaojing Dang: dangxj@aaas.org.cn

Erbao Liu: liuerbao@ahau.edu.cn

William Kwame Nuako Bandoh: wbandoh@csir-forig.org.gh

Patience Mansa Gakpetor: pmgakpetor@csir-forig.org.gh

Daniel Aninagyei Ofori: dofori@csir-forig.org.gh

Delin Hong: delinhong@njau.edu.cn

Journal

Journal ID (nlm-ta): BMC Genom Data

Journal ID (iso-abbrev): BMC Genom Data

Title: BMC Genomic Data

Publisher: BioMed Central (London )

ISSN (Electronic): 2730-6844

Publication date (Electronic): 15 February 2023

Publication date PMC-release: 15 February 2023

Publication date Collection: 2023

Volume: 24

Electronic Location Identifier: 8

Affiliations

[1 ]GRID grid.27871.3b, ISNI 0000 0000 9750 7019, State Key Laboratory of Crop Genetics and Germplasm Enhancement, , Nanjing Agricultural University, ; Nanjing, 210095 China

[2 ]GRID grid.423756.1, ISNI 0000 0004 1764 1672, Council for Scientific and Industrial Research, , Forestry Research Institute of Ghana, ; P. O. Box UP 63, KNUST, Fumesua, Kumasi, Ashanti Region Ghana

[3 ]GRID grid.469521.d, ISNI 0000 0004 1756 0127, Institute of Rice Research, , Anhui Academy of Agricultural Sciences, ; Hefei, 230031 China

[4 ]GRID grid.411389.6, ISNI 0000 0004 1760 4804, College of Agriculture, , Anhui Agricultural University, ; Hefei, 230036 China

Article

Publisher ID: 1107

DOI: 10.1186/s12863-023-01107-8

PMC ID: 9930352

PubMed ID: 36792993

SO-VID: df617de9-f50c-40f0-9d8f-3a36e196e11b

License:

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/. The Creative Commons Public Domain Dedication waiver ( http://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.

History

Date received : 9 September 2022

Date accepted : 23 January 2023

Funding

Funded by: National Natural Science Foundation of China

Award ID: 31671658

Award Recipient : Wisdom Mawuli Edzesi

Funded by: doctoral found of Educational Ministry

Award ID: B0201300662

Award Recipient : Wisdom Mawuli Edzesi

Funded by: China national “863” program

Award ID: 2010AA101301

Award Recipient : Wisdom Mawuli Edzesi

Custom metadata

Keywords: dry direct seeding rice,mesocotyl elongation length,association mapping,favorable marker allele,simple sequence repeat

Data availability:

Keywords: dry direct seeding rice, mesocotyl elongation length, association mapping, favorable marker allele, simple sequence repeat

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Genome-wide association study (GWAS) with high-throughput SNP chip DNA markers identified novel genetic factors for mesocotyl elongation and seedling emergence in rice ( Oryza sativa L.) using multiple GAPIT models
Authors: Nkulu Rolly Kabange, Simon Alibu, Youngho Kwon …

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

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Abstract

Background

Results

Conclusion

Supplementary Information

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Climate Change: Open Access

Most cited references 38

Inference of Population Structure Using Multilocus Genotype Data

TASSEL: software for association mapping of complex traits in diverse samples.

Rapid isolation of high molecular weight plant DNA.

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Cited by 1

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