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.

Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F₂ plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC₁F₁-BC₃F₁ individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC₂F₁ generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H₂O₂, and O₂⁻, activated SA and JA signaling-dependent ISR, and displayed immune activation against Ralstonia solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.

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.