Sorghum bicolor (L.) is one of the oldest crops cultivated by human beings which has been used in food and wine making. To understand the genetic diversity of sorghum breeding resources and further guide molecular-marker-assisted breeding, six yield-related traits were analyzed for 214 sorghum germplasm from all over the world, and 2,811,016 single-nucleotide polymorphisms (SNPs) markers were produced by resequencing these germplasms. After controlling Q and K, QTLs were found to be related to the traits using three algorisms. Interestingly, an important QTL was found which may affect multiple traits in this study. It was the most likely candidate gene for the gene SORBI_3008G116500, which was a homolog of Arabidopsis thaliana gene-VIP5 found by analyzing the annotation of the gene in the LD block. The haplotype analysis showed that the SORBI_3008G116500hap3 was the elite haplotype, and it only existed in Chinese germplasms. The traits were proven to be more associated with the SNPs of the SORBI_3008G116500 promoter through gene association studies. Overall, the QTLs and the genes identified in this study would benefit molecular-assisted yield breeding in sorghum.

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Background Heterosis has been widely used for breeding high-yield crops, changes crop breeding and agricultural production by increasing yield. Transcriptome profiles of sorghum spikes in hybrid Jinnuo 3 and its parents 10480A and L17R were performed by RNA sequencing technology at secondary branch and spikelet differentiation period. Results During above two differentiation period, there were 2,641 and 2,175 differentially expressed genes (DEGs) between Jinnuo 3 and 10480A, respectively. Meanwhile, there were 1,387 and 1,094 DEGs between Jinnuo 3 and L17R, respectively. These indicated that massive DEGs were existed between hybird and its parents, and a more similar expression pattern was presented between hybrid and male parent. Gene expression inheritance analysis showed that most of genes were expressed additively, suggesting that the complementary effect may play a foundation role in sorghum spike heterosis. Among non-additive expression genes, L17R-dominant genes were predominant, indicating that male parent may provide beneficial alleles with great contribution to heterosis. GO and KEGG analysis suggested that metabolic pathways, such as photosynthetic antenna protein, photosynthesis, carbon fixation in photosynthetic organisms, amino acid metabolism, glycolysis, and endoplasmic reticulum protein processing, would participate in yield heterosis formation in hybrid Jinnuo 3. Further analysis showed that photosynthesis-related genes PsbW, PsbR, Lhca2, Lhcb1 and LAX3, spike structure development-related genes MADS1, MADS7, MADS16 and MADS55, as well as stress resistance-related genes WRKY14, WRKY35, HSFB2C and HSP70, might play an important role in yield heterosis formation in hybrid Jinnuo 3. Conclusion Hybrids Jinnuo 3 increased yield by simultaneously increasing source (photosynthetic efficiency-related genes), library (spike development-related genes), and resistance (inresistance-related genes). This molecular mechanism could provide new clues for sorghum heterosis utilization and high-yield breeding.