Quantitative Trait Loci Mapping Identified Candidate Genes Involved in Plant Height Regulation in Rice

Abstract

Rice plant height is an agricultural trait closely related to biomass, lodging tolerance, and yield. Identifying quantitative trait loci (QTL) regions related to plant height regulation and developing strategies to screen potential candidate genes can improve agricultural traits in rice. In this study, a double haploid population (CNDH), derived by crossing ‘Cheongcheong’ and ‘Nagdong’ individuals, was used, and a genetic map was constructed with 222 single-sequence repeat markers. In the RM3482-RM212 region on chromosome 1, qPh1, qPh1-1, qPh1-3, qPh1-5, and qPh1-6 were identified for five consecutive years. The phenotypic variance explained ranged from 9.3% to 13.1%, and the LOD score ranged between 3.6 and 17.6. OsPHq1, a candidate gene related to plant height regulation, was screened in RM3482-RM212. OsPHq1 is an ortholog of gibberellin 20 oxidase 2, and its haplotype was distinguished by nine SNPs. Plants were divided into two groups based on their height, and tall and short plants were distinguished and clustered according to the expression level of OsPHq1. QTLs and candidate genes related to plant height regulation, and thus, biomass regulation, were screened and identified in this study, but the molecular mechanism of the regulation remains poorly known. The information obtained in this study will help develop molecular markers for marker-assisted selection and breeding through rice plant height control.

Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice (Oryza sativa L.)

“…Identified subpopulations are Sub-pop 1 (red color), Sub-pop 2 (green color) and Subpop 3 (navy blue color). The numbers in the X-axis stand for variety code corresponding to Table S1; Figure S3: Neighbor joining tree for the 518 accessions constructed using Nei's (1983) genetic distance; Figure S4: Relationship between D ′ value and genetic distance of syntenic marker pairs in subpopulations POP1, POP2 and POP3 represent subpopulation 1 to subpopulation 3, respectively; Supplementary Figure S5: Genome-wide association showing significant loci associated with PH and its component traits in 2021 and 2022; Table S1: Rice materials and their membership probabilities corresponding to each subpopulation; Table S2: Summary statistics for the 262 SSR markers used in this study; Table S3: Marker-trait association with p-value less than 0.05, proportion of phenotypic variance explained (PVE), marker position on chromosome derived from 262 markers and 518 Rice Accessions; Table S4: phenotypic effect of top two positive elite alleles significantly associated with the 8 traits and their carrier varieties; Table S5: The list for QTLs identified from this study and shared in previous studies [65,66]; Table S6: Favorable alleles carried by the superior parents for the 8 traits and corresponding phenotypic effect; Table S7: Parental combinations and numbers of elite alleles after combinations predicted for the 8 traits; Table S8: Information of QTLs detected for the eight traits of this study. Funding: Funding support was provided by a grant from the National Natural Science Foundation of China (31671658), a grant from the doctoral fund of the Educational Ministry (B0201300662) and a grant from the China national "863" program (2010AA101301).…”