Genome‐wide association study of stem structural characteristics that extracted by a high‐throughput phenotypic analysis “LabelmeP rice” in rice

SUMMARY Stem is important for assimilating transport and plant strength; however, less is known about the genetic basis of its structural characteristics. In this study, a high‐throughput method, “LabelmeP rice” was developed to generate 14 traits related to stem regions and vascular bundles, which allows the establishment of a stem cross‐section phenotype dataset containing anatomical information of 1738 images from hand‐cut transections of stems collected from 387 rice germplasm accessions grown over two successive seasons. Then, the phenotypic diversity of the rice accessions was evaluated. Genome‐wide association studies identified 94, 83, and 66 significant single nucleotide polymorphisms (SNPs) for the assayed traits in 2 years and their best linear unbiased estimates, respectively. These SNPs can be integrated into 29 quantitative trait loci (QTL), and 11 of them were common in 2 years, while correlated traits shared 19. In addition, 173 candidate genes were identified, and six located at significant SNPs were repeatedly detected and annotated with a potential function in stem development. By using three introgression lines (chromosome segment substitution lines), four of the 29 QTLs were validated. LOC_Os01g70200, located on the QTL uq1.4 , is detected for the area of small vascular bundles (SVB) and the rate of large vascular bundles number to SVB number. Besides, the CRISPR/Cas9 editing approach has elucidated the function of the candidate gene LOC_Os06g46340 in stem development. In conclusion, the results present a time‐ and cost‐effective method that provides convenience for extracting rice stem anatomical traits and the candidate genes/QTL, which would help improve rice.