Front. Genet.
Sec. Plant Genomics
doi: 10.3389/fgene.2022.960007

Unveiling the genetic architecture for lodging resistance in rice (Oryza sativa. L) by genome-wide association analyses

  • 1Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, China
  • 2Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
  • 3College of Agronomy, Shandong Agricultural University, China
  • 4Islamia University of Bahawalpur, Pakistan
  • 5Precision Agriculture and Analytics Lab (PAAL), National Center for Big data and Cloud computing (NCBC), University of Agriculture Faisalabad, Pakistan
  • 6Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
  • 7Rice Research Institute, Guangxi Academy of Agricultural Sciences, China
Provisionally accepted:
The final, formatted version of the article will be published soon.

Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance-related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes further divided into two (indica and japonica) subpopulations was used to evaluate the lodging resistance and culm strength-related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mix linear model (MLM) was used for the whole population and two subpopulations, while a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in-silico and in-vitro expression analyses were conducted to validate the candidate three candidate genes in a pleiotropic QTL on chromosome 7. It validated the OsFBA2 as a candidate gene to contribute to the lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region of the candidate gene. Validation and introgression of alleles that are beneficial to induce culm strength may be employed in rice breeding for lodging resistance.

Keywords: GWAS, Association mapping, rice (Oryza sativa L.), Lodging resistance, Culm strength, Genetic architecture

Received: 02 Jun 2022; Accepted: 06 Jul 2022.

Copyright: © 2022 Rashid, Zhao, Azeem, Zhao, Ahmed, Atif, Pan, Zhu, Liang, Li, Zhang, Zhang and Li. 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.

* Correspondence: Dr. Muhammad Abdul Rehman Rashid, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100083, Beijing Municipality, China