Genome-Wide Association Study of Root System Development at Seedling Stage in Rice

Abstract

Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular basis of root development through screening of root-related traits in rice germplasms is critical to future rice breeding programs. This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million high-quality single nucleotide polymorphisms (SNPs) were used as the genotype, with maximum root length (MRL) and total root weight (TRW) in seedlings used as the phenotype. Genome-wide association study (GWAS) combined with Principal Components Analysis (PCA) and Kinship matrix analysis identified four quantitative trait loci (QTLs) on chromosomes 3, 6, and 8. Two QTLs were linked to MRL and two were related to TRW. Analysis of Linkage Disequilibrium (LD) decay identified a 230 kb exploratory range for detection of candidate root-related genes. Candidates were filtered using RNA-seq data, gene annotations, and quantitative real-time PCR (qRT-PCR), and five previously characterized genes related to root development were identified, as well as four novel candidate genes. Promoter analysis of candidate genes showed that LOC_Os03g08880 and LOC_Os06g13060 contained SNPs with the potential to impact gene expression in root-related promoter motifs. Haplotype analysis of candidate genes revealed diverse haplotypes that were significantly associated with phenotypic variation. Taken together, these results indicate that LOC_Os03g08880 and LOC_Os06g13060 are strong candidate genes for root development functions. The significant haplotypes identified in this study will be beneficial in future breeding programs for root improvement.

Molecular Subtypes Based on the Stemness Index Predict Prognosis in Glioma Patients

“…In 2018, Malta et al (2018) proposed the conception of mRNAsi, which is considered as a more comprehensive index to uncover the characteristics of CSCs. Subsequently, mRNAsi was widely applied to reveal the stemness-related characteristics of different cancers, such as lung cancer ( Qin et al, 2020 ; Zhang et al, 2020a ), bladder cancer ( Pan et al, 2019 ), endometrial carcinoma ( Liu et al, 2020 ), medulloblastoma ( Lian et al, 2019 ), and breast cancer ( Pei et al, 2020 ). Moreover, mRNAsi was also used to identify the prognostic biomarkers and therapeutic targets associated with CSC characteristics of glioma ( Lvu et al, 2020 ; Xia et al, 2020 ).…”

Development and Validation of SNP and InDel Markers for Pod-Shattering Tolerance in Soybean

“…The haplotype analysis for Glyma.16g076600, Glyma.16g141200, and Glyma.16g141500 was carried out to assess genetic variations among soybean genotypes using the methods by Zhang et al [56] with some modifications. In 120 varieties and elite lines panels, one InDel and two SNPs markers were used for the haplotype analysis.…”

Global Identification and Characterization of C2 Domain-Containing Proteins Associated with Abiotic Stress Response in Rice (Oryza sativa L.)

“…A total of 137 varieties containing multiple major rice subspecies including temperate japonica (Tej); tropical japonica (Trj); indica (Ind); and aus and admixture (Adm) were collected from 28 countries [66]. Approximately 1.85 million high-quality SNPs were filtered from raw re-sequencing data, according to a previous study [67]. For SNP genotyping of OsC2DPs, only japonica and indica SNPs located at the promoter, UTR, intron, and exon of OsC2DPs formed a 2861 SNP set; the annotations were performed using website tools http://bioinfo.sibs.ac.cn/, accessed on 15 November 2021.…”