A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.)

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dc.creatorNavea, Ian Paul
dc.creatorMaung, Phyu Phyu
dc.creatorYang, Shiyi
dc.creatorHan, Jae-Hyuk
dc.creatorJing, Wen
dc.creatorShin, Na-Hyun
dc.creatorZhang, Wenhua
dc.creatorChin, Joong Hyoun
dc.date2023-08-18
dc.date2024-12-19T12:53:11Z
dc.date2024-12-19T12:53:11Z
dc.date.accessioned2026-06-27T04:08:13Z
dc.descriptionPhosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice.
dc.identifierhttps://hdl.handle.net/10568/163912
dc.identifier.urihttp://hdl.handle.net/123456789/22730
dc.languageen
dc.publisherFrontiers Media
dc.rightsOpen Access
dc.sourceNavea, Ian Paul; Maung, Phyu Phyu; Yang, Shiyi; Han, Jae-Hyuk; Jing, Wen; Shin, Na-Hyun; Zhang, Wenhua and Chin, Joong Hyoun. 2023. A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.). Front. Plant Sci., Volume 14
dc.subjectcandidate genes
dc.subjectquantitative trait loci
dc.subjecthaplotypes
dc.subjectphosphorus
dc.titleA meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice (Oryza sativa L.)
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)