Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

B P Mallikarjuna Swamy; Noraziyah Abd Aziz Shamsudin; Site Noorzuraini Abd Rahman; Ramil Mauleon; Wickneswari Ratnam; Ma Teressa Sta Cruz; Arvind Kumar

doi:10.1186/s12284-017-0161-6

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Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

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Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

B P Mallikarjuna Swamy, Noraziyah Abd Aziz Shamsudin, Site Noorzuraini Abd Rahman, Ramil Mauleon, Wickneswari Ratnam, Ma Teressa Sta Cruz and Arvind Kumar

Rice (New York, N.Y.), Vol.10, 21

18/05/2017

DOI: https://doi.org/10.1186/s12284-017-0161-6

PMCID: PMC5436998

PMID: 28523639

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Abstract

Association mapping

Genetic diversity

Drought

Genes

Background The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. Results The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5–20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. Conclusion The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.

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Title: Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)
Creators: B P Mallikarjuna Swamy - International Rice Research Institute
Noraziyah Abd Aziz Shamsudin - National University of Malaysia
Site Noorzuraini Abd Rahman - International Rice Research Institute
Ramil Mauleon - International Rice Research Institute
Wickneswari Ratnam - Universiti Kebangsaan Malaysia
Ma Teressa Sta Cruz - International Rice Research Institute
Arvind Kumar - International Rice Research Institute
Publication Details: Rice (New York, N.Y.), Vol.10, 21
Publisher: Springer New York LLC
Identifiers: 991013099080702368
Copyright: © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).
Academic Unit: Faculty of Science and Engineering
Language: English
Resource Type: Journal article

Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

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