Rice yield is determined by source, sink, and flow and the coordination of these factors. However, the genetic base of the sink-flow is still unknown. We conducted on genome-wide association to detect quantitative trait loci (QTL) related to sink size (the number of rachis branches and spikelet number in rachis branches) and flow vascular bundle (large and small vascular bundles number in panicle neck and second internode) using 440 germplasm resources. The accessions exhibited marked variation

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... in all traits and demonstrated complex phenotypic correlations. A total of 138 QTL affecting the 8 traits were detected using 3,188,500 high-quality single nucleotide polymorphism markers. Sixteen QTL clusters simultaneously affected flow and sink traits, which might explain the genetic base of significant correlations between flow and sink traits. The nine candidate genes in two consistent chromosomal regions simultaneously affecting multiple vascular bundle and sink size traits by performing gene-based association analysis and haplotype analysis. Among them, D2 (LOC_Os01g10040) and Gn1a (LOC_Os01g10110) for qPLVN1.1, qSLVN1.1, and qPRN1.2 and OsPIN5b (LOC_Os08g41720) for qPLVN8, qSLVN8, qSSVN8, and qSTSN8.2 were considered the most likely candidate genes based on functional annotations. The results provide useful information for improving rice yield potential via balancing sink–flow relationships by marker-assisted selection.