The identification of superior haplotypes and haplotype combinations is essential for haplotype-based breeding (HBB), which provides selection targets for genomics-assisted breeding. In this study, genotypes of 42 functional genes in rice were analyzed by targeted capture sequencing in a panel of 180 Indica rice accessions. In total, 69 SNPs/Indels in seven genes were detected to be associated with grain length (GL), grain width (GW), ratio of grain length–width (L/W) and thousand-grain weight (TGW) using candidate gene-based association analysis, including BG1 and GS3 for GL, GW5 for GW, BG1 and GW5 for L/W, and AET1, SNAC1, qTGW3, DHD1 and GW5 for TGW. Furthermore, two haplotypes were identified for each of the seven genes according to these associated SNPs/Indels, and the amount of genetic variation explained by different haplotypes ranged from 3.24% to 27.66%. Additionally, three, three and eight haplotype combinations for GL, L/W and TGW explained 25.38%, 5.5% and 22.49% of the total genetic variation for each trait, respectively. Further analysis showed that Minghui63 had the superior haplotype combination Haplotype Combination 4 (HC4) for TGW. The most interesting finding was that some widely used restorer lines derived from Minghui63 also have the superior haplotype combination HC4, and our breeding varieties and lines using the haplotype-specific marker panel also confirmed that the TGW of the lines was much higher than that of their sister lines without HC4, suggesting that TGW-HC4 is the superior haplotype combination for TGW and can be utilized in rice breeding.

Resistant starch (RS) shows several health benefits. Enhancing the RS content of wheat is of major commercial importance. However, knowledge regarding the RS synthesis mechanism in wheat remains limited. In this study, the dynamic accumulation of RS during the filling process in two wheat (Triticum aestivum L.) genotypes with contrasting RS contents (H242, high RS content; H189, low RS content) were investigated. The results demonstrate that beyond 25 days after pollination (DAP), the RS content of H189 was relatively stable, but that of H242 continued to increase. Secondary accumulation was observed in the high-RS-content wheat genotype. A comparative transcriptome analysis between H242 and H189 at 20 DAP and 35 DAP showed that the differentially expressed genes were mainly involved in glycerolipid metabolism, glycerophospholipid metabolism and glucuronate interconversions. Furthermore, weighted gene coexpression network analysis suggested that lipid metabolic pathways such as the glycerophospholipid metabolism pathway might be involved in RS synthesis, and lipid-related genes upregulated beyond 25 DAP resulted in RS secondary accumulation. This work provides insight into the characteristics and mechanisms of RS synthesis.