Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant

Abstract

Multi-parent advanced generation inter-cross (MAGIC) populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3 Magic EGGplant InCanum, S3MEGGIC; 8-way), constituted by the 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanin presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-insensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence single-nucleotide polymorphisms (SNPs) confirmed a low residual heterozygosity (6.87%), a lack of genetic structure in the S3MEGGIC population, and no differentiation among subpopulations carrying a cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of the founder genomes, suggesting a cryptic selection in favour or against specific parental genomes. Genome-wide association study (GWAS) analysis for PA, FA, and PUC detected strong associations with two myeloblastosis (MYB) genes similar to MYB113 involved in the anthocyanin biosynthesis pathway, and with a COP1 gene which encodes for a photo-regulatory protein and may be responsible for the PUC trait. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1 compared with the tomato genome. Parental genotypes for the three genes were in agreement with the identification of the candidate genes performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.

SoyMAGIC: An Unprecedented Platform for Genetic Studies and Breeding Activities in Soybean

“…In fact, intensification of the genetic variation across the genome of RILs was because of the way that the population is developed. Similar results were reported for multi-parent populations of other plant crops such as rice, maize, cowpea, and eggplant, confirming the competence of multi-parent populations in reshuffling of genome and improving the recombination level ( Dell’Acqua et al, 2015 ; Huynh et al, 2018 ; Ponce et al, 2020 ; Mangino et al, 2022 ). Since the eight parents were all completely inbred lines, the plants in each F 1 set were homogeneously heterozygous.…”

Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette

“…been developed, allowing the identification of candidate genes for anthocyanin pigmentation in eggplant fruits with greater accuracy and statistical robustness (Mangino et al, 2022).…”

“…A total of 420 S3 individuals from the eggplant S3MEGGIC multi-parent advanced generation inter-cross (MAGIC) population developed by Mangino et al (2022) were used to identify candidate genes associated with the chlorophyll pigmentation in the fruit peel. The S3MEGGIC population, which is the first and so far the only MAGIC population in eggplant, was obtained by inter-crossing one wild S. incanum accession and seven S. melongena accessions.…”

“…The genotyping data of the 420 S3MEGGIC individuals, assessed by the Single Primer Enrichment Technology (SPET) eggplant probes available (Barchi et al, 2019a), was retrieved from Mangino et al (2022). Combining both phenotypic and genotypic data, a Genome-Wide Association Study (GWAS) was performed using the Trait Analysis by aSSociation, Evolution and Linkage (TASSEL) software (ver.…”

Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant

“…In the past decade, especially in recent years, remarkable progress has been made in the molecular genetic research of anthocyanin accumulation in eggplant. A number of QTLs related to anthocyanin accumulation have been mapped on all eggplant chromosomes except chromosome E04 [ 23 , 34 , 37 , 38 ], and some anthocyanin metabolism-related genes have been identified using the approaches of reversed genetics, including transcriptomic or proteomic analysis [ 39 , 40 , 41 ] and homologous or candidate gene analysis [ 42 , 43 , 44 , 45 ]. However, as many genes/QTLs are involved in the control of anthocyanin accumulation, the genetic basis and regulatory mechanism underlying the anthocyanin metabolism in eggplant is still far from being clarified.…”