Rambutan (Nephelium lappaceum L.) is a popular tropical fruit with a unique flavor and an economically valuable plant within the Sapindaceae family. MADS-box transcription factors are widely present in all eukaryotes and affect the morphogenesis, growth, and development of various plant organs. In this study, 75 MADS-box genes in rambutan were successfully characterized. Among them, 50 were identified as type I, including 24 Mα-type, 10 Mβ-type, and 16 Mγ-type genes. Twenty five were identified as type II, including 19 MIKC^C and six MIKC* type genes. These NlMADS genes were randomly located on 16 chromosomes based on chromosomal mapping. Synteny analysis indicated the occurrence of seven pairs of tandem duplication and seven pairs of segmental duplication events. Prediction of cis-acting elements demonstrated the involvement of MADS-box genes in plant growth and development, hormone response, and stress response. RNA-seq data showed that most rambutan MADS-box genes were highly expressed in flowers and aril development, particularly within the MIKC^C-type group. Notably, NlMADS4, NlMADS30, and NlMADS69 showed specific high expression during aril development, suggesting their critical role in this process. Furthermore, MIKC^C-type MADS-box members displayed higher expression levels across different tissues, indicating their importance during plant growth and development. Protein-predicted regulatory networks suggested potential close interactions between MIKC^C-type proteins in rambutan. The GO term enrichment analysis showed that the majority of genes might be involved in floral organ development (GO:0048437), embryo sac development (GO:0009553), and plant ovule development (GO:0048481). This paper conducted a comprehensive analysis of the rambutan MADS-box family for the first time, which will provide valuable insights into the molecular mechanisms governing flower and aril development in rambutan and other Sapindaceae species with aril structures.

Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties to raise the output. However, complex correlation patterns among quantitative traits with genetic interactions bring a challenge for vegetable soybean breeding. Here, a genome-wide association study (GWAS) was applied for six yield-related traits with 188 vegetable soybean accessions. A total of 81 SNPs were identified for pod length, plant height, pods number, pod thickness, pod width, and seed weight per plant by Blink model. Among these significant SNPs, 79 were novel SNPs, while 2 overlapped with previously reported SNPs. A total of 220 genes were found in 100 kb upstream and downstream regions of significant SNPs, of which 17 genes were functional proteins. Among these function proteins, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed as significant haplotype variations, which encode MYB-related transcription factor, auxin-responsive family protein, F-box protein and CYP450, respectively. In addition, the relative expression with four candidate genes in the V030 and V071 (Among them, the plant height, pod number and fresh pod weight of V030 were lower than V071 strains) vegetable soybean were significantly different and these genes could be involved in plant growth and development via various pathways. Therefore, we proposed four genes from vegetable soybean germplasm that could be the key candidate genes for pod yield and plant height and these studies will accelerate the process of high-yield vegetable soybean breeding.

Lychee (Litchi chinensis Sonn.), longan (Dimocarpus longan Lour.), and rambutan (Nephelium lappaceum L.) are popular tropical fruits in the family Sapindaceae, known for their succulent arils—specialized seed appendage with significant biological and commercial value. Despite their agricultural relevance, the molecular mechanisms underlying aril development in these species remain poorly understood. We conducted RNA-sequencing to profile transcriptomes during aril development, complemented by in-situ hybridization to validate the spatial expression of LcLBD1. OrthoFinder identified species-specific and shared differentially expressed genes (DEGs), while functional enrichment analyses (GO, KEGG) and transcriptional network modeling elucidated regulatory pathways. After detailed analyses of transcriptomes, species-specific and shared DEGs were identified across lychee, longan, and rambutan using OrthoFinder. Members of the bHLH and MYB gene families were implicated in early aril development. Species-specific DEGs were primarily enriched in metabolic pathways. From shared DEGs, we identified ten transcription factors (AGL8, AP3, SHP1, WOX13, LBD1, LBD3, OBP1, SPL2, SPL3, and SPL9) and three genes (IAA8, CSLD5, and CYCD3;2) as key regulators. Interestingly, in-situ hybridization localized LcLBD1 expression to funicle and small aril cells, suggesting roles in cell differentiation and division. We have identified ten transcription factors and three genes affecting aril development in lychee, longan, and rambutan, and validated the expression of LcLBD1 in funicle and aril cells. These results offer a new perspective on the molecular mechanism of aril development and lay the groundwork for future research into the functions and regulatory mechanisms of candidate genes.