Fine mapping of two grain chalkiness QTLs sensitive to high temperature in rice

Abstract

Background: Grain chalkiness is one of important factors affected rice grain quality. It is known that chalkiness is affected by the high temperature during the seed filling period. Although a larger of QTLs for chalkiness were reported across all 12 chromosomes, only a few of the QTLs were fine mapped or cloned up to now. Here, we fine map two QTLs for chalkiness in two single-segment substitution lines (SSSLs), 11-09 with substitution segment from O. sativa and HP67-11 with substitution segment from O. glaberrima.

Results: The grain chalkiness of SSSLs 11-09 and HP67-11 was significantly lower than that in the recipient Huajingxian 74 (HJX74) in consecutive 8 cropping seasons. The regression correlation analysis showed that percentage of chalky grain (PCG) and percentage of chalky area (PCA) were significantly and positively correlated with percentage of grain chalkiness (PGC). Two QTLs for grain chalkiness were located on two chromosomes by substitution mapping. qPGC9 was mapped on chromosome 9 with an estimated interval of 345.6 kb. qPGC11 was located on chromosome 11 and delimited to a 432.1 kb interval in the O. sativa genome and a 332.9 kb interval in the O. glaberrima genome. qPGC11 is a QTL for grain chalkiness from O. glaberrima and was mapped in a new region of chromosome 11. The effect of two QTLs was incomplete dominance. The additive effects of two QTLs on chalkiness in second cropping season (SCS) were significantly greater than that in first cropping season (FCS).

Conclusions: qPGC11 is a new QTL for grain chalkiness. The two QTLs were fine mapped. The donor alleles of qPGC9 and qPGC11 were sensitive to the high temperature of FCS.

Keywords: Grain chalkiness; Grain quality; Heat stress; Rice; Single-segment substitution line; Substitution mapping.

Fig. 1

Grain chalkiness in HJX74 and SSSLs. a, Plant type of HJX74 and SSSLs 11–09 and HP67–11. Scale bar: 15 cm. b, Percentage of grain chalkiness (PGC) (%) in HJX74 and SSSLs. Data were presented as mean ± S.E. of eight cropping seasons. One-way ANOVA, two-tailed, Dunnett t-test was used to generate the differences. c, Chromosome locations of the two SSSLs. Physical distance (Mb) is shown as rulers on the right of chromosome. Black bars on the left of each chromosome represent the estimated length of substitution segments in the SSSLs. Chr. chromosome, Mb megabase

Fig. 2

Substitution mapping of qPGC9 for grain chalkiness. a, The head rice appearance of the HJX74 and 11–09. Scale bar: 1 cm. b, Substitution mapping of qPGC9. The positions of substitution segments and the PGC of 11–09 and its NILs are shown, with HJX74 as the control. The numbers under the chromosome are physical distance (Mb). White and black blocks represent the homozygous genotypes of HJX74 and 11–09, respectively. c, PGC effects of three genotypes of qPGC9 in an F₂ population. qpgc9/qpgc9 represents homozygous genotype of HJX74 (n = 38); qPGC9/qpgc9 represents heterozygous genotype of HJX74/11–09 (n = 68); qPGC9/qPGC9 represents homozygous genotype of 11–09 (n = 34). Significant difference analysis in b and c was by one-way ANOVA, Duncan, two-tailed. Values in the lines among different letters are different at 1% level of significance

Fig. 3

Substituted mapping of qPGC11 for grain chalkiness. a, The head rice appearance of the HJX74 and HP67–11. Scale bar: 1 cm. b, Substitution mapping of qPGC11. The positions of substitution segments and the PGC of HP67–11 and its NILs are shown, with HJX74 as the control. The numbers under the chromosome are physical distance (Mb). White and black blocks represent the homozygous genotypes of HJX74 and HP67–11, respectively. c, PGC effects of three genotypes of qPGC11 in an F₂ population. qpgc11/qpgc11 represents homozygous genotype of HJX74 (n = 26); qPGC11/qpgc11 represents heterozygous genotype of HJX74/HP67–11 (n = 49); qPGC11/qPGC11 represents homozygous genotype of HP67–11 (n = 30). Significance analysis in b and c was by one-way ANOVA, Duncan, two-tailed. Values in the lines among different letters are different at 1% level of significance

Fig. 4

Regression correlation analysis between PCG and PGC and between PCA and PGC of SSSLs 11–09 and HP67–11. R² represents the percentage of x contribution to y phenotype variation. PCG percentage of chalky grain, PCA percentage of chalky area, PGC percentage of grain chalkiness

Fig. 5

The difference of chalky traits between first cropping seasons (FCS) and second cropping seasons (SCS) in HJX74, 11–09 and HP67–11. PCG percentage of chalky grain (a). PCA Percentage of chalky area (b). PGC Percentage of grain chalkiness (c)

Fig. 6

The additive effects of qPGC9 and qPGC11 on grain chalkiness in first cropping seasons (FCS) and second cropping seasons (SCS). PCG percentage of chalky grain (a). PCA Percentage of chalky area (b). PGC Percentage of grain chalkiness (c)