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

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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.

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Most cited references 94

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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Yoav Benjamini, Yosef Hochberg (1995)

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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.

Pablo E. Cingolani, Adrian E. Platts, Le Lily Wang … (2012)

We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w(1118); iso-2; iso-3 strain and the reference y(1); cn(1) bw(1) sp(1) strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5'UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5' and 3' UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus. As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

M.A. DePristo, E Banks, R.E. Poplin … (2011)

Recent advances in sequencing technology make it possible to comprehensively catalogue genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (1) initial read mapping; (2) local realignment around indels; (3) base quality score recalibration; (4) SNP discovery and genotyping to find all potential variants; and (5) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We discuss the application of these tools, instantiated in the Genome Analysis Toolkit (GATK), to deep whole-genome, whole-exome capture, and multi-sample low-pass (~4×) 1000 Genomes Project datasets.

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Author and article information

Contributors

Giulio Mangino: URI : http://loop.frontiersin.org/people/467071/overview

Andrea Arrones: URI : http://loop.frontiersin.org/people/1608256/overview

Mariola Plazas: URI : http://loop.frontiersin.org/people/305857/overview

Torsten Pook: URI : http://loop.frontiersin.org/people/941529/overview

Jaime Prohens: URI : http://loop.frontiersin.org/people/31244/overview

Pietro Gramazio: URI : http://loop.frontiersin.org/people/170472/overview

Santiago Vilanova: URI : http://loop.frontiersin.org/people/780113/overview

Journal

Journal ID (nlm-ta): Front Plant Sci

Journal ID (iso-abbrev): Front Plant Sci

Journal ID (publisher-id): Front. Plant Sci.

Title: Frontiers in Plant Science

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-462X

Publication date (Electronic): 07 March 2022

Publication date Collection: 2022

Volume: 13

Electronic Location Identifier: 847789

Affiliations

[1] ¹Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València , Valencia, Spain

[2] ²Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València , Valencia, Spain

[3] ³Animal Breeding and Genetics Group, Department of Animal Sciences, Center for Integrated Breeding Research, University of Göttingen , Göttingin, Germany

Author notes

Edited by: Nunzio D’Agostino, University of Naples Federico II, Italy

Reviewed by: Monica Rodriguez, University of Sassari, Italy; Mark Chapman, University of Southampton, United Kingdom

*Correspondence: Pietro Gramazio, piegra@ 123456upv.es

Santiago Vilanova, sanvina@ 123456upvnet.upv.es

^†These authors have contributed equally to this work

This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

Article

DOI: 10.3389/fpls.2022.847789

PMC ID: 8940277

PubMed ID: 35330873

SO-VID: cbce0077-53c6-4013-8c68-c2f434828997

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

History

Date received : 03 January 2022

Date accepted : 20 January 2022

Page count

Figures: 6, Tables: 1, Equations: 0, References: 95, Pages: 15, Words: 10664

Funding

Funded by: Ministerio de Ciencia, Innovación y Universidades, doi 10.13039/100014440;

Award ID: FPU18/01742

Award ID: RTI2018-094592-B-I00

Award ID: FJC2019-038921-I/AEI/10.13039/501100011033

Award ID: IJC2019-039091-I/AEI/10.13039/501100011033

Funded by: Horizon 2020, doi 10.13039/501100007601;

Award ID: 677379

Funded by: Universitat Politècnica de València, doi 10.13039/501100004233;

Award ID: PAID-12-21

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

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Abstract

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Plant MYBs

Most cited references 94

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.

A framework for variation discovery and genotyping using next-generation DNA sequencing data

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