Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population

Hein Zaw; Chitra Raghavan; Arnel Pocsedio; B P Mallikarjuna Swamy; Mona Liza Jubay; Rakesh Kumar Singh; Justine Bonifacio; Ramil Mauleon; Jose E Hernandez; Merlyn S Mendioro; Glenn B Gregorio; Hei Leung

doi:10.1038/s41598-019-55357-7

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Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population

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Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population

Hein Zaw, Chitra Raghavan, Arnel Pocsedio, B P Mallikarjuna Swamy, Mona Liza Jubay, Rakesh Kumar Singh, Justine Bonifacio, Ramil Mauleon, Jose E Hernandez, Merlyn S Mendioro, …

Scientific reports, Vol.9, 19605

20/12/2019

DOI: https://doi.org/10.1038/s41598-019-55357-7

PMCID: PMC6925145

PMID: 31862941

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Abstract

Bayes Theorem

Chromosome Mapping

Chromosomes, Plant

Crosses, Genetic

Edible Grain - genetics

Edible Grain - growth & development

Flowers

Genetic Association Studies

Genome, Plant

Genotype

Oryza - genetics

Oryza - growth & development

Phenotype

Polymorphism, Single Nucleotide

Quantitative Trait Loci

Species Specificity

Plant sciences

Genetics

Identification of Quantitative Trait Loci (QTL) has been a challenge for complex traits due to the use of populations with narrow genetic base. Most of QTL mapping studies were carried out from crosses made within the subspecies, either indica × indica or japonica × japonica. In this study we report advantages of using Multi-parent Advanced Generation Inter-Crosses global population, derived from a combination of eight indica and eight japonica elite parents, in QTL discovery for yield and grain quality traits. Genome-wide association study and interval mapping identified 38 and 34 QTLs whereas Bayesian networking detected 60 QTLs with 22 marker-marker associations, 32 trait-trait associations and 65 marker-trait associations. Notably, nine known QTLs/genes qPH1/OsGA20ox2, qDF3/OsMADS50, PL, QDg1, qGW-5b, grb7-2, qGL3/GS3, Amy6/Wx gene and OsNAS3 were consistently identified by all approaches for nine traits whereas qDF3/OsMADS50 was co-located for both yield and days-to-flowering traits on chromosome 3. Moreover, we identified a number of candidate QTLs in either one or two analyses but further validations will be needed. The results indicate that this new population has enabled identifications of significant QTLs and interactions for 16 traits through multiple approaches. Pyramided recombinant inbred lines provide a valuable source for integration into future breeding programs.

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Title: Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
Creators: Hein Zaw - International Rice Research Institute
Chitra Raghavan - International Rice Research Institute
Arnel Pocsedio - International Rice Research Institute
B P Mallikarjuna Swamy - International Rice Research Institute
Mona Liza Jubay - International Rice Research Institute
Rakesh Kumar Singh - International Center for Biosaline Agriculture
Justine Bonifacio - International Rice Research Institute
Ramil Mauleon - International Rice Research Institute
Jose E Hernandez - University of the Philippines Los Baños
Merlyn S Mendioro - University of the Philippines Los Baños
Glenn B Gregorio - University of the Philippines Los Baños
Hei Leung - International Rice Research Institute
Publication Details: Scientific reports, Vol.9, 19605
Publisher: Nature Publishing Group
Grant note: A-2015-163 / Council of Agriculture
Identifiers: 991013098100102368
Academic Unit: Faculty of Science and Engineering
Language: English
Resource Type: Journal article

Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population

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