Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

Gwen Iris L. Descalsota; B. P. Mallikarjuna Swamy; Hein Zaw; Mary Ann Inabangan-Asilo; Amery Amparado; Ramil Mauleon; Prabhjit Chadha-Mohanty; Emily C. Arocena; Chitra Raghavan; Hei Leung; Jose E. Hernandez; Antonio B. Lalusin; Merlyn S. Mendioro; Ma. Genaleen Q. Diaz; Russell Reinke

doi:10.3389/fpls.2018.01347

Back

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

Journal article

Open access

Peer reviewed

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

Gwen Iris L. Descalsota, B. P. Mallikarjuna Swamy, Hein Zaw, Mary Ann Inabangan-Asilo, Amery Amparado, Ramil Mauleon, Prabhjit Chadha-Mohanty, Emily C. Arocena, Chitra Raghavan, Hei Leung, …

Frontiers in plant science, Vol.9, 1347

20/09/2018

DOI: https://doi.org/10.3389/fpls.2018.01347

PMCID: PMC6158342

PMID: 30294335

Files and links (2)

pdf

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification3.68 MBDownload View

Published (Version of record)CC BY V4.0, Open Access

url

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for BiofortificationView

Published (Version of record)CC BY V4.0, Open

Metrics

40 File views/ downloads

12 Record Views

55 Times Cited - Web of Science

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites

Abstract

Bayesian network

biofortification

GWAS

MAGIC

Plant Science

rice

Xanthomonas oryzae

The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH1.1 and Zn7.1 were consistently identified in all the four environments, ten QTLs qDF3.1, qDF6.2 qDF9.1 qPH5.1 qGL3.1, qGW3.1, qGW11.1, and qZn6.2 were detected in two environments, while two major loci qBLB11.1 and qBLB5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.

Details

Title: Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification
Creators: Gwen Iris L. Descalsota - International Rice Research Institute
B. P. Mallikarjuna Swamy - International Rice Research Institute
Hein Zaw - International Rice Research Institute
Mary Ann Inabangan-Asilo - International Rice Research Institute
Amery Amparado - International Rice Research Institute
Ramil Mauleon - International Rice Research Institute
Prabhjit Chadha-Mohanty - International Rice Research Institute
Emily C. Arocena - Philippine Rice Research Institute
Chitra Raghavan - International Rice Research Institute
Hei Leung - International Rice Research Institute (Phillipines)
Jose E. Hernandez - University of the Philippines Los Baños
Antonio B. Lalusin - University of the Philippines Los Baños
Merlyn S. Mendioro - University of the Philippines Los Baños
Ma. Genaleen Q. Diaz - University of the Philippines Los Baños
Russell Reinke - International Rice Research Institute
Publication Details: Frontiers in plant science, Vol.9, 1347
Publisher: Frontiers Media S.A
Identifiers: 991013099200302368
Copyright: Copyright © 2018 Descalsota, Swamy, Zaw, Inabangan-Asilo, Amparado, Mauleon, Chadha-Mohanty, Arocena, Raghavan, Leung, Hernandez, Lalusin, Mendioro, Diaz and Reinke. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) https://creativecommons.org/licenses/by/4.0/.
Academic Unit: Faculty of Science and Engineering
Language: English
Resource Type: Journal article

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

Files and links (2)

Metrics

UN Sustainable Development Goals (SDGs)

Abstract

Details

Southern Cross University Social media