Fig 1.
Frequency distribution of grain chalkiness in the CSSL population.
(a) The percentage of grain with chalkiness (PGC) and (b) degree of endosperm chalkiness (DEC). The arrows indicate the mean of ZS97.
Fig 2.
Bin mapping of grain chalkiness QTLs.
The bin effects on PGC (a) and DEC (b) along the whole genome in the NIP/ZS97 CSSL population. The green and black bars on the x-axis represent the chromosomes. The -log scale of P values are plotted on the y-axis. The dotted lines indicate the threshold with P = 0.01.
Table 1.
The common QTLs identified for both PGC and DEC in the ZS/NIP CSSL population using the SNP bin markers.
Fig 3.
(a) The schematic bins on chromosome 8 defined by SNP genotyping of the CSSL population, where one bin contains an introduced qPGC8–2 (ISA1). (b) Grain chalkiness in the three genotypic classes in a CSSL-derived segregation population. Means and standard deviations of grain chalkiness for the three genotypes by the gene marker DE2 are given inside the panel.
Fig 4.
Suppression of ISA1 causes chalky grains.
(a) The gene ISA1 model showing INDEL and SNP differences between ZS97 and NIP; the exons (rectangles) and introns (lines connecting the exons) are illustrated; the RNAi target domain is indicated by a short bold line above the model. (b) Box plot for PGC levels of 31 NIP type and 73 ZS type varieties at the InDel (the middle line indicates the median, the box indicates the range of the 25th to 75th percentiles of the total data, the whiskers indicate the interquartile range). (c) Quantitative RT-PCR showing the repressed ISA1 expression in the RNAi line, where the Actin gene was used as an internal control. The (d) grain appearances and (e) PGC difference in the ISA1-RNAi line and the control. Asterisks (**) indicate mean values are significantly different at P < 0.01.
Fig 5.
Suppressed ISA1 influences the expressions of starch synthesis related genes in the rice panicle.
Differential expressions of eight starch-related genes between the RNAi line and the control, with the identification numbers based on the rice genome database (http://www.plantbiology.msu.edu); the Actin gene was used as an internal control for the semi-quantitative RT-PCR.
Fig 6.
Evaluation of the NILs with contrasting ISA1 alleles.
(a) The trial with four sowing dates (A1–A4) in 2010. (b) The trial with three sowing dates (B1–B3) in 2011. ISA-N and ISA-Z represent the ISA1 alleles from NIP and ZS97, respectively. Different letters (a, b, c, and d) above the bars indicate significant differences at P < 0.01 using Duncan’s test.