Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance

Abstract

Lodging can reduce grain yield and quality in cereal crops including rice (Oryza sativa L.). To achieve both high biomass production and lodging resistance, the breeding of new cultivars with strong culms is a promising strategy. However, little is known about the diversity of culm strength in temperate japonica rice and underlying genetic factors. Here, we report a wide variation of culm strength among 135 temperate japonica cultivars, and some landraces having the strongest culms among these cultivars. The genome-wide association study (GWAS) identified 55 quantitative trait loci for culm strength and morphological traits, and revealed several candidate genes. The superior allele of candidate gene for culm thickness, OsRLCK191, was found in many landraces but had not inherited to the modern improved cultivars. Our results suggest that landraces of temperate japonica rice have unutilized superior alleles for contributing future improvements of culm strength and lodging resistance.

Figure 1

Phenotypic diversities and relationships between traits. (a–d) Histogram and boxplot of the traits associated with culm strength. Red and blue bars indicate the results in 2018 and 2019, respectively. (a) Basal culm diameter. (b) Bending moment at breaking. (c) Bending moment. (d) Culm diameter of the 3rd internode. (e) Correlations among 14 traits. The numbers show the correlation coefficient value (R). The number on the diagonal indicates the correlation coefficient between 2 years. The upper triangle and lower triangle show the results of 2018 and 2019, respectively.

Figure 2

The component traits of culm strength among cultivars. (a) The relationships between section modulus and bending stress on 135 cultivars. The graphs on the left and right shows the results of 2018 and 2019, respectively. The curves indicate the bending moment at breaking. Red plots indicate the positions of the 4 cultivars focused on (b–d). (b–d) The section modulus, bending moment and bending moment at breaking of the 4 cultivars. Different letters indicate significant differences between both cultivars: P < 0.05 (Tukey's test). Each bar indicates the mean ± SD (n = 8, only “Hinohikari” in 2019 is n = 5). (e–h) Images of culm sections. Each picture indicates Koshihikari, Kameji, Omachi and Hinohikari, in order from the left.

Figure 3

The relationships between the traits and the year each cultivar was bred. Dotted lines indicate the regression lines. Red and blue plots or lines indicate the result of 2018 and 2019, respectively. (a) Bending moment at breaking. (b) Basal culm diameter. (c) Culm length.

Figure 4

Candidate region mapping based on GWAS in 2018 and 2019. DTH days to heading, CL culm length, PN panicle number, PL panicle length, SPN spikelet number per panicle, FLL flag leaf length, FLW flag leaf width, BCD basal culm diameter, BM bending moment at breaking, BS bending stress, YM Young’s modulus, FR flexural rigidity, CTD culm tissue density, 3rdCD culm diameter of 3rd internode.

Figure 5

The candidate region detected between 27 Mb and the terminal end of chromosome 5. (a) The Manhattan plot of GWAS for basal culm diameter in 2018. The red triangle indicates the candidate region on chromosome 5, and the same applies hereinafter. (b) The Manhattan plot of the gene-based association study for basal culm diameter in 2018. (c) The Manhattan plot of GWAS for basal culm diameter in 2019. (d) The Manhattan plot of the gene-based association study for basal culm diameter in 2019. (e) The Manhattan plot of GWAS for the culm diameter of the 3rd internode in 2019. The figure below is the enlarged view of the candidate region. (f) The Manhattan plot of the gene-based association study for the culm diameter of the 3rd internode in 2019. The figure below is the enlarged view of the candidate region. (g) The ratio of the cultivars bred before 1950 and after 1950 in each haplotype of LOC_Os05g51190 (1950 is included after 1950). The numbers on the graph indicate the numbers of cultivars included. (h) The culm diameter of the 3rd internode for the indicated haplotype of LOC_Os05g51190. Differences between the haplotypes were analysed by Welch’s t-test. (i) The DNA mutations in the coding region of LOC_Os05g51190.

Figure 6

The breeding history of the top 5 cultivars in the cultivation area in Japan and their relationships with landraces.