Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis

Abstract

The success of rice (Oryza sativa L.) germination and survival under submerged conditions is mainly determined by the rapid growth of the coleoptile to reach the water surface. Previous reports have shown the presence of genetic variability within rice accessions in the levels of flooding tolerance during germination or anaerobic germination (AG). Although many studies have focused on the physiological mechanisms of oxygen stress, few studies have explored the breadth of natural variation in AG tolerance‐related traits in rice. In this study, we evaluated the coleoptile lengths of a geographically diverse rice panel of 241 accessions, including global accessions along with elite breeding lines and released cultivars from the United States, under the normal and flooded conditions in laboratory and greenhouse environments. A genome‐wide association study (GWAS) was performed using a 7K single‐nucleotide polymorphism (SNP) array and the phenotypic data of normal coleoptile length, flooded coleoptile length, flooding tolerance index, and survival at 14 d after seeding (DAS). Out of the 30 significant GWAS quantitative trait loci (QTL) regions identified, 14 colocalized with previously identified candidate genes of AG tolerance, whereas 16 were potentially novel. Two rice accessions showing contrasting phenotypic responses to AG stress were selected for the transcriptomics study. The combined approach of GWAS and transcriptomics analysis identified 77 potential candidate genes related to AG tolerance. The findings of our study may assist rice improvement programs in developing rice cultivars with robust tolerance under flooding stress during germination and the early seedling stage.

Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

“…In the region of qPP4 , the annotated gene was CTB2 ( Figure 6 a,b). The CTB2 gene, which encodes a UDP-glucose sterol glucosyltransferase, is responsible for cold tolerance in rice at the booting stage [ 35 ]. To understand how the CTB2 sequence may affect the PP phenotype, we analyzed the SNPs in the genomic coding region of CTB2 across the 302 varieties, which revealed five major haplotypes, two SNPs in the coding region and seven SNPs in the intron region ( Figure 6 b).…”

“…The seeds of each accession were harvested individually after maturity. The harvested seeds were dried in a hot air dryer at 37 °C for 5 days and then stored at room temperature for three months [ 35 ].…”

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

“…Although earlier research has primarily delved into the physiological aspects of oxygen stress, only few investigations have explored the broad spectrum of natural variation in traits related to anaerobic germination tolerance in rice. Thapa et al (2022) conducted a GWAS analysis on a rice diversity panel comprising 241 accessions, revealing 30 significant marker-trait associations (MTAs). Among these MTAs, 14 colocalized with previously detected genes linked to anaerobic germination tolerance, while 16 were novel discoveries.…”

“…Thapa et al. (2022) conducted a GWAS analysis on a rice diversity panel comprising 241 accessions, revealing 30 significant marker‐trait associations (MTAs). Among these MTAs, 14 colocalized with previously detected genes linked to anaerobic germination tolerance, while 16 were novel discoveries.…”

Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress

“…Many studies on QTL mapping and genome wide association studies (GWAS) on AG tolerance in rice have been reported [10][11][12][13][14][15][16][17][18][19][20][21][22]. Notably, a gene underlying one of the QTLs, qAG-9-2, has been cloned as trehalose-6-phosphate-phosphatase (OsTPP7), which is involved in starch mobilization during germination [23].…”