Genome-wide sequence comparison and development of InDel and SNP markers to facilitate localized rice breeding

Juan Pariasca-Tanaka; Yoshiaki Ueda; Katsuhiko Kondo; M. Asaduzzaman Prodhan; Toavintsoa Rajonandraina; Harisoa Nicole Ranaivo; Mbolatantely Fahazavana Rakotondramanana; Hiroki Saito; Lam Thi Dinh; Matthias Wissuwa

doi:10.1016/j.cpb.2025.100469

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Genome-wide sequence comparison and development of InDel and SNP markers to facilitate localized rice breeding

Journal article

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Genome-wide sequence comparison and development of InDel and SNP markers to facilitate localized rice breeding

Juan Pariasca-Tanaka, Yoshiaki Ueda, Katsuhiko Kondo, M. Asaduzzaman Prodhan, Toavintsoa Rajonandraina, Harisoa Nicole Ranaivo, Mbolatantely Fahazavana Rakotondramanana, Hiroki Saito, Lam Thi Dinh and Matthias Wissuwa

Current plant biology, Vol.42, 100469

2025

DOI: https://doi.org/10.1016/j.cpb.2025.100469

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Abstract

Genome-wide comparison

Madagascar

Oryza sativa L

Whole-genome re-sequencing

X265

Rice (Oryza sativa L.) is the staple crop for over half of the world's population and selection in different environmental and climatic conditions has led to the development of numerous local rice cultivars. In a changing environment, these local cultivars may need to be adapted to emerging stresses. Whole-genome sequences are available only for a small fraction of existing rice cultivars, limiting the opportunity for genomics-based marker-assisted selection (MAS) in most local cultivars. To efficiently develop locally-adapted rice cultivars resilient to adverse environmental conditions, our objective was to develop a pipeline for the analysis of re-sequencing data and the development of low-cost allele-specific markers that can be implemented in developing countries. This study focused on three rice cultivars (X265, F160, and Nerica4) commonly grown in Madagascar. We provide whole-genome sequencing data and identify sequence variations compared to publicly available sequences, followed by the development of simple PCR-based InDel and SNP markers. Their effectiveness in distinguishing different alleles at the Ghd7 locus controlling heading date was demonstrated, enabling us to employ these markers for MAS in a breeding population developed between X265 and a donor “Liu He Xi He”. In addition, we developed PCR-based SNP markers for the same population on qLFT-5, a quantitative trait locus for low-fertility tolerance in which the donor allele increases total panicle weight under low-input conditions. This study presents a practical pipeline for the utilization of next generation sequencing-derived large-scale data to accelerate low-cost marker development for MAS in rice and other crop species. •Rice varieties popular in Madagascar were re-sequenced and variants were identified.•Practical markers useful for local breeders were designed and validated.•Multi-varietal comparison suggested a key amino acid critical for heading date.•This study suggests paths for decentralized breeding approach for local cultivars.

Details

Title: Genome-wide sequence comparison and development of InDel and SNP markers to facilitate localized rice breeding
Authors/Creators: Juan Pariasca-Tanaka - Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi 1-1, Tsukuba, Ibaraki, Japan
Yoshiaki Ueda - Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi 1-1, Tsukuba, Ibaraki, Japan
Katsuhiko Kondo - Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi 1-1, Tsukuba, Ibaraki, Japan
M. Asaduzzaman Prodhan - Murdoch University, School of Veterinary Medicine
Toavintsoa Rajonandraina - University of Antananarivo
Harisoa Nicole Ranaivo - Rice Research Department, National Center for Applied Research on Rural Development (FOFIFA), BP 1690, Tsimbazaza, Antananarivo, Madagascar
Mbolatantely Fahazavana Rakotondramanana - Rice Research Department, National Center for Applied Research on Rural Development (FOFIFA), BP 1690, Tsimbazaza, Antananarivo, Madagascar
Hiroki Saito - Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), Maezato 1091-1, Ishigaki, Okinawa, Japan
Lam Thi Dinh - Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi 1-1, Tsukuba, Ibaraki, Japan
Matthias Wissuwa - Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi 1-1, Tsukuba, Ibaraki, Japan
Publication Details: Current plant biology, Vol.42, 100469
Publisher: Elsevier B.V.
Identifiers: 991005838794407891
Murdoch Affiliation: School of Veterinary Medicine
Language: English
Resource Type: Journal article

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