Leaf thickness is an important morphological trait in rice. Its association to the yield potential, as of now has not been documented because of the shortage of the equipment which could conveniently measure the leaf thickness in rice. In this study, the thickness of top three leaves of 208 cultivars had been determined by a nondestructive rice leaf thickness instrument for the research of the natural variation of leaves thickness and its association to yield traits in indica rice. The results showed that the flag leaf was the thickest, and the second leaf was thicker than the third leaf. Analysis of variance indicated the existence of wide genetic diversity of leaf thickness among the investigated indica rice genotypes. The tight correlation among the thicknesses of the top three leaves means that the leaf thickness traits share one genetic control system. Leaf thickness had a significant positive correlation with leaf length and a positive correlation with leaf width, indicated that thicker leaf was beneficial to increasing the single leaf area. The results of correlation analysis revealed that thicker leaf should be profitable to the leaf erection, higher numbers of grains per panicle and higher grains weight per panicle. However, the significantly negative correlation between leaf thickness and number of panicles per plant counteracted the profitability from increased grains weight per panicle, so that the correlations of the thicknesses of the top three leaves to yield and biomass were positive but not significantly. It has made great progress in the genetic improvement of leaves thickness in inbred indica rice breeding in Guangdong Province since 1990s.

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Leaf thickness is an important trait in rice ( Oryza sativa L.). It affects both photosynthesis and sink-resource efficiency. However, compared to leaf length and length width, reports seldom focused on leaf thickness due to the complicated measurement and minor difference. To identify the quantitative trait loci (QTL) and explore the genetic mechanism regulating the natural variation of leaf thickness, we crossed a high leaf thickness variety Aixiuzhan (AXZ) to a thin leaf thickness variety Yangdao No.6 (YD 6) and evaluated 585 F 2 individuals. We further use bulked sergeant analysis with whole-genome resequencing (BSA-seq) to identify five genomic regions, including chromosomes 1, 6, 9, 10, and 12. These regions represented significant allele frequency differentiation between thick and thin leaf thickness among the mixed pool offspring. Moreover, we conducted a linkage mapping using 276 individuals derived from the F 2 population. We fine-mapped and confirmed that chromosome 9 contributed the primary explanation of phenotypic variance. We fine-mapped the candidate regions and confirmed that the chromosome 9 region contributed to flag leaf thickness in rice. We observed the virtual cellular slices and found that the bundle sheath cells in YD 6 flag leaf veins are fewer than AXZ. We analyzed the potential regions on chromosome 9 and narrowed the QTL candidate intervals in the 928-kb region. Candidate genes of this major QTL were listed as potentially controlled leaf thickness. These results provide promising evidence that cloning leaf thickness is associated with yield production in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01275-y.