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

Giulio Mangino,Andrea Arrones,Mariola Plazas,Jaime Prohens,Pietro Gramazio,Torsten Pook,Santiago Vilanova

doi:10.3389/fpls.2022.847789

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.

Highlights

Multi-parent experimental populations are of great interest for the genetic dissection of quantitative traits and for the development of new recombinant materials for plant breeding (Huang et al, 2015)
Multi-parent advanced generation inter-cross (MAGIC) populations are already available in model species, such as Arabidopsis thaliana and in several crops, such as cereals, pulses, and vegetables (Kover et al, 2009; Bandillo et al, 2013; Pascual et al, 2015; Huynh et al, 2018), and have demonstrated their power to dissect the structure of complex traits (Dell’Acqua et al, 2015; Stadlmeier et al, 2018)
Seven accessions of eggplant and one of the wild relative S. incanum were selected as founder parents (A-H) for the construction of the eggplant MAGIC population (S3MEGGIC)

Summary

Introduction

Multi-parent experimental populations are of great interest for the genetic dissection of quantitative traits and for the development of new recombinant materials for plant breeding (Huang et al, 2015). Despite their complex management and resources requirement, multi-parent advanced generation intercross (MAGIC) populations represent powerful next-generation mapping tools by combining a high genetic diversity and recombination with a low population structure (Arrones et al, 2020; Scott et al, 2020). Apart from being of great interest for genetic analysis, interspecific MAGIC populations can be useful for broadening the genetic base of crops and provide new variation for breeding multiple traits, including those related to adaption to climate change (Gramazio et al, 2020a). The potential of interspecific MAGIC populations for plant breeding has largely remained unexploited (Arrones et al, 2020)

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