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Context Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. Results Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. Conclusions Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice. Electronic supplementary material The online version of this article (10.1186/s12870-018-1504-1) contains supplementary material, which is available to authorized users.

Figure S5. QQ plots and Manhattan plots for panicle morphological traits for 2014 and 2015 in the full panel, indica and japonica subpanels. (a, i) Rachis length (RL); (b, j) primary branch number (PBN); (c, k) secondary branch number (SBN); (d, l) spikelet number (SpN); (e, m) primary branch length (PBL); (f, n) primary branch internode length (PBintL); (g, o) secondary branch length (SBL); (h, p) secondary branch internode length (SBintL) for 2014 and 2015, respectively (PDF 9355 kb)

Figure S3. Correlation between SpN and PBN traits in 2014 and 2015. In grey and orange are values for 2014 and 2015, respectively. The right panel indicates the value density for the two traits in 2014 (grey) and 2015 (orange). SpN: spikelet number. PBN: primary branch number. (PDF 123 kb)

Figure S1. The phenotype variation of indica and japonica subpanels in 2014 and 2015. Primary branch number (PBN), secondary branch number (SBN), spikelet number (SpN), primary branch length (PBL), primary internode length (PBintL), secondary branch length (SBL), secondary internode length (SBintL), tertiary branch number (TBN) and rachis length (RL). The values relating to length are in cm. Statistical significance (t test p values) between the two subpanels for the different panicle morphological traits is indicated (PDF 378 kb)

Figure S2. Correlation plots and PCA in the full panel, indica and japonica subpanels over the two years including flowering time (FT), plant height (PH), tiller number (TN) and efficient tiller number (eTN). (a) Correlation plots of the full panel in 2014 (left) and 2015 (right). (b) PCA of the full panel in 2014 (left) and 2015 (right). (c) Correlation plots of the indica (left) and the japonica (right) subpanels in 2014 (top) and 2015 (bottom). Primary branch number (PBN), secondary branch number (SBN), spikelet number (SpN), primary branch length (PBL), primary internode length (PBintL), secondary branch length (SBL), secondary internode length (SBintL), tertiary branch number (TBN) and rachis length (RL). (PDF 475 kb)

Figure S4 Heatmap clustering of the accessions related to panicle morphological traits in 2014 and 2015. In red and blue are the values for indica and japonica subpanels, respectively. Primary branch number (PBN), secondary branch number (SBN), spikelet number (SpN), primary branch length (PBL), primary internode length (PBintL), secondary branch length (SBL), secondary internode length (SBintL), tertiary branch number (TBN) and rachis length (RL). (PDF 271 kb)