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Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus

The Asparagus genus includes approximately 240 species, the most important of which is garden asparagus (Asparagus officinalis L.), as this is a vegetable crop cultivated worldwide for its edible spear. Along with garden asparagus, other species are also cultivated (e.g., Asparagus maritimus L.) or...

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Autores principales: Sala, Tea, Puglisi, Damiano, Ferrari, Luisa, Salamone, Filippo, Tassone, Maria Rosaria, Rotino, Giuseppe Leonardo, Fricano, Agostino, Losa, Alessia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10354869/
https://www.ncbi.nlm.nih.gov/pubmed/37476175
http://dx.doi.org/10.3389/fpls.2023.1187663
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author Sala, Tea
Puglisi, Damiano
Ferrari, Luisa
Salamone, Filippo
Tassone, Maria Rosaria
Rotino, Giuseppe Leonardo
Fricano, Agostino
Losa, Alessia
author_facet Sala, Tea
Puglisi, Damiano
Ferrari, Luisa
Salamone, Filippo
Tassone, Maria Rosaria
Rotino, Giuseppe Leonardo
Fricano, Agostino
Losa, Alessia
author_sort Sala, Tea
collection PubMed
description The Asparagus genus includes approximately 240 species, the most important of which is garden asparagus (Asparagus officinalis L.), as this is a vegetable crop cultivated worldwide for its edible spear. Along with garden asparagus, other species are also cultivated (e.g., Asparagus maritimus L.) or have been proposed as untapped sources of variability in breeding programs (e.g., Asparagus acutifolius L.). In the present work, we applied reduced-representation sequencing to examine a panel of 378 diverse asparagus genotypes, including commercial hybrids, interspecific lines, wild relatives of garden asparagus, and doubled haploids currently used in breeding programs, which enabled the identification of more than 200K single-nucleotide polymorphisms (SNPs). These SNPs were used to assess the extent of linkage disequilibrium in the diploid gene pool of asparagus and combined with preliminary phenotypic information to conduct genome-wide association studies for sex and traits tied to spear quality and production. Moreover, using the same phenotypic and genotypic information, we fitted and cross-validated genome-enabled prediction models for the same set of traits. Overall, our analyses demonstrated that, unlike the diversity detected in wild species related to garden asparagus and in interspecific crosses, cultivated and wild genotypes of A. officinalis L. show a narrow genetic basis, which is a contributing factor hampering the genetic improvement of this crop. Estimating the extent of linkage disequilibrium and providing the first example of genome-wide association study and genome-enabled prediction in this species, we concluded that the asparagus panel examined in the present study can lay the foundation for determination of the genetic bases of agronomically important traits and for the implementation of predictive breeding tools to sustain breeding.
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spelling pubmed-103548692023-07-20 Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus Sala, Tea Puglisi, Damiano Ferrari, Luisa Salamone, Filippo Tassone, Maria Rosaria Rotino, Giuseppe Leonardo Fricano, Agostino Losa, Alessia Front Plant Sci Plant Science The Asparagus genus includes approximately 240 species, the most important of which is garden asparagus (Asparagus officinalis L.), as this is a vegetable crop cultivated worldwide for its edible spear. Along with garden asparagus, other species are also cultivated (e.g., Asparagus maritimus L.) or have been proposed as untapped sources of variability in breeding programs (e.g., Asparagus acutifolius L.). In the present work, we applied reduced-representation sequencing to examine a panel of 378 diverse asparagus genotypes, including commercial hybrids, interspecific lines, wild relatives of garden asparagus, and doubled haploids currently used in breeding programs, which enabled the identification of more than 200K single-nucleotide polymorphisms (SNPs). These SNPs were used to assess the extent of linkage disequilibrium in the diploid gene pool of asparagus and combined with preliminary phenotypic information to conduct genome-wide association studies for sex and traits tied to spear quality and production. Moreover, using the same phenotypic and genotypic information, we fitted and cross-validated genome-enabled prediction models for the same set of traits. Overall, our analyses demonstrated that, unlike the diversity detected in wild species related to garden asparagus and in interspecific crosses, cultivated and wild genotypes of A. officinalis L. show a narrow genetic basis, which is a contributing factor hampering the genetic improvement of this crop. Estimating the extent of linkage disequilibrium and providing the first example of genome-wide association study and genome-enabled prediction in this species, we concluded that the asparagus panel examined in the present study can lay the foundation for determination of the genetic bases of agronomically important traits and for the implementation of predictive breeding tools to sustain breeding. Frontiers Media S.A. 2023-07-04 /pmc/articles/PMC10354869/ /pubmed/37476175 http://dx.doi.org/10.3389/fpls.2023.1187663 Text en Copyright © 2023 Sala, Puglisi, Ferrari, Salamone, Tassone, Rotino, Fricano and Losa https://creativecommons.org/licenses/by/4.0/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.
spellingShingle Plant Science
Sala, Tea
Puglisi, Damiano
Ferrari, Luisa
Salamone, Filippo
Tassone, Maria Rosaria
Rotino, Giuseppe Leonardo
Fricano, Agostino
Losa, Alessia
Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus
title Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus
title_full Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus
title_fullStr Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus
title_full_unstemmed Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus
title_short Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus
title_sort genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10354869/
https://www.ncbi.nlm.nih.gov/pubmed/37476175
http://dx.doi.org/10.3389/fpls.2023.1187663
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