Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement

Abstract

Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8-10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.

Keywords: ABA; GA; GWAS; japonica rice; plant hormones; pre-harvest sprouting.

Figure 1

Pre-harvest sprouting of temperate japonica rice harvested at 20 days after flowering on the Zeigler Experiment Station of the International Rice Research Institute, Philippines, in the 2019 dry season.

Figure 2

Comparison of pre-harvest sprouting resistance of the temperate and tropical japonica panels, between samples harvested at 20 (A) and 30 (B) days after flowering.

Figure 3

Principal component analysis showing genetic variation between indica (green), temperate japonica (light blue), and tropical japonica (dark blue).

Figure 4

Pre-harvest sprouting resistance variation of indica (black), tropical japonica (red), and temperate japonica (blue) rice sub-groups harvested at 30 days after flowering.

Figure 5

Genome-wide association analysis of pre-harvest sprouting (PHS) of Japonica rice accessions: (A) Manhattan plot generated through the general linear model (GLM) with principal components and mixed linear model (MLM) with kinship matrix and principal components. Points above the blue and red threshold lines indicate significant association at −log10(p) = 5 and 6, respectively. Arrows indicate two major loci used for haplotype analysis in Figure 5C. R_C and Sdr4 loci are major dormancy genes in rice; (B) quantile–quantile plots; and (C) haplotype effects on the phenotype trait.

Figure 6

Projected economic loss by pre-harvest sprouting (PHS) damages on temperate japonica rice production in California state of the U.S., Japan, and the Republic of Korea: (A) Mean PHS resistance (%) of 48 temperate japonica varieties from those three countries used in this study; and (B) Projected economic loss by PHS between 2021 and 2030. The level of severe stress is the same as PHS screening conditions used in this study, whereas mild stress level is half of severe stress.