Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

Alvin D. Palanog; Chau Thanh Nha; Gwen Iris L. Descalsota-Empleo; Mark Ian Calayugan; Zin Mar Swe; Amery Amparado; Mary Ann Inabangan-Asilo; Jose E. Hernandez; Pompe C. Sta. Cruz; Teresita H. Borromeo; Antonio G. Lalusin; Ramil Mauleon; Kenneth L. McNally; B. P. Mallikarjuna Swamy

doi:10.3389/fpls.2023.1157507

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Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

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Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

Alvin D. Palanog, Chau Thanh Nha, Gwen Iris L. Descalsota-Empleo, Mark Ian Calayugan, Zin Mar Swe, Amery Amparado, Mary Ann Inabangan-Asilo, Jose E. Hernandez, Pompe C. Sta. Cruz, Teresita H. Borromeo, …

Frontiers in plant science, Vol.14

22/03/2023

DOI: https://doi.org/10.3389/fpls.2023.1157507

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Abstract

biofortification

candidate genes

micronutrients

QTL

rice

Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1, and qGW6.1, which can be used in rice genomics assisted breeding. A major QTL (qZn5.2) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R2. In all, 26 QTL clusters were identified on different chromosomes. qPH6.1 epistatically interacted with qZn5.1 and qGY6.2. Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.

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Title: Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits
Creators: Alvin D. Palanog - International Rice Research Institute
Chau Thanh Nha - Cant Ho University, Cant Ho, Vietnam
Gwen Iris L. Descalsota-Empleo - University of Southern Mindanao
Mark Ian Calayugan - University of the Philippines Los Baños
Zin Mar Swe - International Rice Research Institute
Amery Amparado - International Rice Research Institute
Mary Ann Inabangan-Asilo - International Rice Research Institute
Jose E. Hernandez - University of the Philippines Los Baños
Pompe C. Sta. Cruz - University of the Philippines Los Baños
Teresita H. Borromeo - University of the Philippines Los Baños
Antonio G. Lalusin - University of the Philippines Los Baños
Ramil Mauleon - International Rice Research Institute
Kenneth L. McNally - International Rice Research Institute
B. P. Mallikarjuna Swamy - International Rice Research Institute
Publication Details: Frontiers in plant science, Vol.14
Publisher: Frontiers Media S.A
Identifiers: 991013099087802368
Copyright: © 2023 Palanog, Nha, Descalsota-Empleo, Calayugan, Swe, Amparado, Inabangan-Asilo, Hernandez, Sta. Cruz, Borromeo, Lalusin, Mauleon, McNally and Swamy. This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
Academic Unit: Faculty of Science and Engineering
Language: English
Resource Type: Journal article

Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits

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