Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice

Jyothi Badri; Revadi Padmashree; Chandrappa Anilkumar; Akshay Mamidi; Subhakara Rao Isetty; Avsr Swamy; Raman Menakshi Sundaram

doi:10.3389/fpls.2023.1298083

Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice

Front Plant Sci. 2024 Jan 22:14:1298083. doi: 10.3389/fpls.2023.1298083. eCollection 2023.

Authors

Jyothi Badri¹, Revadi Padmashree¹, Chandrappa Anilkumar², Akshay Mamidi^{1

3}, Subhakara Rao Isetty¹, Avsr Swamy¹, Raman Menakshi Sundaram¹

Affiliations

¹ Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India.
² Crop Improvement Section, ICAR-National Rice Research Institute (ICAR-NRRI), Cuttack, India.
³ Department of Genetics and Plant Breeding, College of Agriculture, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India.

Abstract

Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (p< 0.0001) for culm strength traits. Two novel major effect marker-trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the indica background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice.

Keywords: Epistatic interactions; association mapping; candidate gene; culm strength; genotyping by sequencing (GBS); lodging resistance; marker trait associations (MTAs).

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The research was conducted as part of ICAR-Indian Institute of Rice Research (ICAR-IIRR)- Institute/IRC Project-GEY/CI/BR/25: “Broadening the genetic base of indica rice and modify plant type by introgressing traits from Tropical japonica” and funding support from ICAR-IIRR and DBT project BT/PR32853/AGIII/103/1159/2019- “Development of Haplotype based Near Isogenic Lines (Haplo-NILs) for Enhanced Genetic Gain in Rice”.