Fruit color is an important trait influencing the commercial value of eggplant fruits. Three dominant genes (D, P and Y) cooperatively control the anthocyanin coloration in eggplant fruits, but none has been mapped. In this study, two white-fruit accessions (19141 and 19147) and their F₂ progeny, with 9:7 segregation ratio of anthocyanin pigmented versus non-pigmented fruits, were used for mapping the D and P genes. A high-density genetic map was constructed with 5,270 SNPs spanning 1,997.98 cM. Three QTLs were identified, including two genes on chromosome 8 and one on chromosome 10. Gene expression analyses suggested that the SmANS on chromosome 8 and SmMYB1 on chromosome 10 were the putative candidate genes for P and D, respectively. We further identified (1) a SNP leading to a premature stop codon within the conserved PLN03176 domain of SmANS in 19141, (2) a G base InDel in the promoter region leading to an additional cis-regulatory element and (3) a 6-bp InDel within the R2-MYB DNA binding domain of SmMYB1, in 19147. Subsequently, these three variations were validated by PARMS technology as related to phenotypes in the F₂ population. Moreover, silencing of SmANS or SmMYB1 in the purple red fruits of F₁ (E3316) led to inhibition of anthocyanin biosynthesis in the peels. Conversely, overexpression of SmANS or SmMYB1 restored anthocyanin biosynthesis in the calli of 19141 and 19147 respectively. Our findings demonstrated the epistatic interactions underlying the white color of eggplant fruits, which can be potentially applied to breeding of eggplant fruit peel color.

Peel color is one of the most important appearance qualities of eggplant. The main pigment in the peel of green-fruited eggplant is chlorophyll, while white-fruited eggplant is a mutant of chlorophyll biosynthesis. A dominant gene Gv controls chlorophyll biosynthesis in eggplant peel, but none of its genes have been mapped. In this study, the white-peel inbred line 19141, the green-peel inbred line 19143, and their F₂ progeny with 3:1 segregation ratio of green-peel plants to white-peel plants, were used to map the Gv1 locus by whole genome re-sequencing combined with bulked segregant analysis (BSA). The Gv1 gene was mapped in a region spanning 7.66 Mb on chromosome 8, which was narrowed down to 173.2 kb interval by screening recombinant plants with InDel and SNP markers. Sixteen candidate genes were annotated in the above closely associated region. With the aid of RNA-Seq data, it was speculated that SmAPPR2-like is the candidate gene for Gv1. The results of cloning and sequencing of SmAPPR2-like showed that there might have been three types of mutation (large deletion, frameshift variant and premature stop codon) in white-peel accessions, and of these, the deletion mutation, such as that in inbred line 19141, was the most common. Based on the sequence difference of SmAPPR2-like, molecular markers were developed to distinguish the white and green-peel accessions in natural eggplant populations, and the other types of genetic variations of SmAPPR2-like leading to white-peel accessions were elucidated. The present study not only provided reliable markers for MAS (marker-assisted selection) breeding for eggplant peel color, but also paved the way for understanding the molecular mechanism of SmAPPR2-like on chlorophyll biosynthesis in eggplant fruit.

NBS-LRR genes constitute one of the largest resistance gene families in plants, which play key roles in resistance to pathogens. Although the identification and characterization of the NBS-LRR gene family has been extensively reported in various species, a comprehensive analysis in eggplant has not been previously documented. In this study, a total of 269 SmNBS genes were identified in the eggplant genome. Based on domain classification and phylogenetic analysis, SmNBSs were divided into three subgroups 231 CNLs (CC-NBS-LRR), 36 TNLs (TIR-NBS-LRR), and 2 RNLs (RPW8-NBS-LRR). Chromosomal mapping analysis revealed an uneven distribution of SmNBSs in clusters across chromosomes, with a predominant presence on chromosomes 10, 11, and 12. Structural analysis identified eight conserved motifs previously reported in SmNBSs, exhibiting high conservation in both amino acid sequences and their order. Evolutionary analysis demonstrated that tandem duplication events mainly contributed to the expansion of SmNBS. Subsequently, qRT-PCR analysis demonstrated that nine SmNBSs exhibited differential expression patterns in response to R. solanacearum stress, with EGP05874.1 potentially involved in the resistance response. In conclusion, this study provides a comprehensive insight into SmNBSs, which will enhance the research on eggplant disease resistance and facilitate the breeding of new disease-resistant varieties.

Eggplant ( Solanum melongena L.) is a globally important Solanaceae crop, yet trait-relevant genomic variants remain poorly characterized. Here, we perform population genomic analyses of 226 eggplant accessions sampled mainly from a major domestication center spanning Southeast Asia and South China, and find that genetic relationships closely track geographic origin. We generate chromosome-scale assemblies for 11 representative accessions using long-read sequencing and integrate six published genomes to build a pangenome resource. Using this resource, association scans identify a 12.4 Mb inversion on chromosome 10 segregating at 50.44% frequency that is strongly associated with fruit color, likely through hitchhiking with SmMYB1 . We also detect variants associated with bacterial wilt resistance, including a premature stop codon in SmCYP82D47 and copy number variations in SmEPS1 and SmRoq1 homologs. Together, our results illuminate the evolution and phenotypic impact of large structural variants and provide genomic resources for eggplant genetics and breeding.

Large structural variants (SVs) underlying important agronomic traits remain largely unexplored in Solanaceae crops. Eggplant (Solanum melongena L.) is a globally important horticultural crop worldwide, belonging to the Solanaceae family. Here, we first present population genomic analyses of a diversity panel of 201 eggplant accessions, largely representing genetic diversity from one of the main eggplant domestication centers, Southeast Asia. We revealed that genetic relationships are highly correlated with geographic origin. We then de novo generated the chromosome-scale genomes of nine representative accessions, plus five previously published assemblies, to construct a graph-based pangenome. With the aid of this resource in association scans, we identified a 12.4 Mb inversion at a high frequency (53.7%) within the population, which is associated with fruit color, likely the result of artificial selection favoring purple peel. We also discovered multiple mutations linked to bacterial wilt resistance, including a premature stop codon in SmCYP82D47 and copy number variations of SmEPS1 and SmRoq1 homologs. This study provides insights into the evolution and biology of large SVs in Solanaceae crops, as well as provides fundamental genomic resources accessible to genetic analyses and breeding in eggplant.