Editorial: Mining and utilization of favorable gene resources in rice

COPYRIGHT © 2023 Wang, Li, Ishikawa and Luo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 19 September 2023 DOI 10.3389/fpls.2023.1289069

low-temperature germinability without any harmful phenotype.As a new allele of the BR receptor hfr131 affected rice plant height through the dn-type internode elongation pattern, which had not been reported previously in any BR biosynthesis-or OsBRI1defective mutants.These findings suggest that the SNPs polymorphism may confer new functions to the known genes, and the discovery of new alleles is helpful to expand the diversity of gene function and mechanism.
Genome-wide association study facilitates mining of loci associated with complex agronomic traits Complex agronomic traits of crops involve complex genetic loci, and genome-wide association study (GWAS) can significantly improve the identification efficiency of potential QTLs.Li et al. conducted GWAS using 211 rice accessions to determine salt tolerance germinability indices.A total of 43 QTLs were identified, 18 of which were co-localized with previous studies.According to the RNA-seq and haplotype analysis, rice varieties with elite haplotypes in LOC_Os03g13560, LOC_Os03g13840 and LOC_Os03g14180 genes had high salt tolerance germinability.Dai et al. detected high-quality loci responsible for high seed vigor from 346 diverse accessions.By GWAS, 51 significant SNPs were identified, which were further validated using chromosome segment substitution lines.Integrating gene expression, gene annotation, and haplotype analysis, 21 strong candidate genes were identified.The functions of LOC_Os01g11270 and LOC_Os01g55240 were further verified by CRISPR/Cas9.Xu et al. combined GWAS and linkage mapping to analyze the candidate intervals for seedling salinity tolerance of 295 japonica rice varieties.After identifying the lead SNP (Chr12_20864157), the candidate gene LOC_Os12g34450 was obtained by haplotype analysis, qRT-PCR, and sequence analysis.
Salt tolerant germinability, high seed vigor and seedling salinity tolerance correspond to the key problems affecting the yield of rice in agricultural production.By GWAS, these works verified the known genetic loci and found new functional genes, which provided a promising resource for solving the problems.In addition, the integration of multiple methods (chromosome segment substitution, linkage mapping, RNA-seq database, haplotype analysis, CRISPR/Cas9, etc.) can validate the results of GWAS and help identify candidate genes.

Functional expansion of key gene resources via phylogenetic analysis and reverse genetics
Functional expansion of known key genes is another effective pathway for favorable gene resources.Papain-like cysteine proteases (PLCPs) play a crucial role in plant growth and development.Li et al. constructed CRISPR/Cas9 lines and showed that a PLCP, an oryzain alpha chain precursor (OCP), negatively regulated resistance to blast disease.OCP interacted with OsRACK1A or OsSNAP32 and influenced the expression of many resistance-related genes.Zheng et al.'s work was based on the cell cycle-associated transcription factors E2F (E2 promoter binding factor), and their downstream target gene the mismatch repair-related gene OsMSHs (Mutated S homologue).They systematically categorized six rice E2Fs, and constructed four msh mutants using the CRISPR-Cas9 technique.This study elucidated the mechanism of E2F and MSH for enhancing cadmium stress tolerance in rice.Zeng et al. focused on the glutamate-like receptor (GLR) genes, which play a crucial role in signal transduction and communication.An integrated approach involving phylogenetic analysis, phenotypic and functional characterization and comprehensive population genetic analyses was employed to understand the functionalities of 26 rice GLR genes.The results suggested that natural variations at most rice GLR loci had potential value in improving the productivity and tolerance to abiotic stresses.These studies expand our understanding of these known key gene functions, and genes in related biological processes and molecular networks are also worthy for the further exploration of effective gene resources.
Finally, one review article from Zhong et al. presented a comprehensive review on the recent breakthroughs in rice yield traits and molecular design breeding in China.The authors believed that the further mining of genes and gene regulatory networks, development and utilization of molecular markers, establishment of the high-throughput and low-cost genotype detection system, and rational aggregation of high-quality genes (genes related to yield traits, stress resistance traits and quality traits) to breed new varieties with high yield and superior quality, will be an inevitable trend in future rice research.

Perspectives
In summary, this Research Topic brought recent advances in the mining and utilization of rice germplasm resource.These studies indicated the new situations in the exploration of favorable gene resources.For example, crop yield breeding needs to balance the influence of environmental stress, and molecular design breeding needs to consider the pleiotropy between genes and complex regulatory networks among genes.Overcoming these problems will open the way to achieve a further breakthrough in the current yield level.