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

Ian Paul Navea; Phyu Phyu Maung; Shiyi Yang; Jae-Hyuk Han; Wen Jing; Na-Hyun Shin; Wenhua Zhang; Joong Hyoun Chin

doi:10.3389/fpls.2023.1226297

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

Front Plant Sci. 2023 Aug 18:14:1226297. doi: 10.3389/fpls.2023.1226297. eCollection 2023.

Authors

Ian Paul Navea^{1

2}, Phyu Phyu Maung^{1

2}, Shiyi Yang³, Jae-Hyuk Han^{1

4}, Wen Jing³, Na-Hyun Shin^{1

2}, Wenhua Zhang³, Joong Hyoun Chin^{1

2}

Affiliations

¹ Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea.
² Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea.
³ College of Life Sciences, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China.
⁴ The International Rice Research Institute-Korea Office, National Institute of Crop Science, Rural Development Administration, Iseo-myeon, Republic of Korea.

Abstract

Phosphorus 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.

Keywords: Meta-QTL analysis; Quantitative Trait Loci; candidate genes; phosphorus use efficiency; rice; superior haplotypes.

Grants and funding

Half of this work was supported by grants from the framework of the international cooperation program managed by the National Research Foundation of Korea (NRF-2021K1A3A1A61002988) and National Key R&D Program of China (2022YFE0198100). Half of this work was supported by the Rural Administration of Korea (PJ017008).