Candidate genes and signatures of directional selection on fruit quality traits during apple domestication

Wedger, Marshall J.; Schumann, Abby C.; Gross, Briana L.

doi:10.1002/ajb2.1636

Cited by 7 publications

(10 citation statements)

References 69 publications

(106 reference statements)

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“…Moreover, according to the autochthone accessions from the different germplasm collections around the world, domestication and breeding could have caused diversity loss. Nevertheless, regardless of the many decades of domestication of Malus × domestica and its clonal propagation, there is no proof that domesticated apples have shown a genetic bottleneck in contrast with Malus × sieversii [ 77 , 78 ].…”

Section: Discussionmentioning

confidence: 99%

Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

Mignard

Forcada

Giménez

et al. 2023

Plants

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A basic knowledge of linkage disequilibrium and population structure is necessary in order to determine the genetic control and identify significant associations with agronomical and phytochemical compounds in apple (Malus × domestica Borkh). In this study, 186 apple accessions (Pop1), representing both Spanish native accessions (94) and non-Spanish cultivars (92) from the EEAD-CSIC apple core collection, were assessed using 23 SSRs markers. Four populations were considered: Pop1, Pop2, Pop3, and Pop4. The initial Pop1 was divided into 150 diploid (Pop2) and 36 triploid accessions (Pop3), while for the inter-chromosomal linkage disequilibrium and the association mapping analysis, 118 phenotype diploid accessions were considered Pop4. Thus, the average number of alleles per locus and observed heterozygosity for the overall sample set (Pop1) were 15.65 and 0.75, respectively. The population structure analysis identified two subpopulations in the diploid accessions (Pop2 and Pop4) and four in the triploids (Pop3). Regarding the Pop4, the population structure with K = 2 subpopulations segregation was in agreement with the UPGMA cluster analysis according to the genetic pairwise distances. Moreover, the accessions seemed to be segregated by their origin (Spanish/non-Spanish) in the clustering analysis. One of the two subpopulations encountered was quite-exclusively formed by non-Spanish accessions (30 out of 33). Furthermore, agronomical and basic fruit quality parameters, antioxidant traits, individual sugars, and organic acids were assessed for the association mapping analysis. A high level of biodiversity was exhibited in the phenotypic characterization of Pop4, and a total of 126 significant associations were found between the 23 SSR markers and the 21 phenotypic traits evaluated. This study also identified many new marker-locus trait associations for the first time, such as in the antioxidant traits or in sugars and organic acids, which may be useful for predictions and for a better understanding of the apple genome.

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Section: Discussionmentioning

confidence: 99%

Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

Mignard

Forcada

Giménez

et al. 2023

Plants

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“…Similarly, 21 misidentified and nine pure species PI accessions from the NPGS apple collection were tested for resistance levels to blue mold considering them to all be pure M. sieversii (Janisiewicz et al, 2008), and several accessions exhibiting moderate levels of resistance were hybrids and M. domestica in our results. Although Wedger et al (2021) used NPGS apple collection materials that were considered pure according to previous work (Gross et al, 2012), seven of the 15 M. sieversii individuals that study sampled from the NPGS were not pure species representatives according to the present analysis. In contrast, mapping population GMAL 4593 was created with parent PI 613981 (Desnoues et al, 2018), a M. sieversii pure species representative.…”

Section: Discussionmentioning

confidence: 99%

“…M. sieversii germplasm accessioned into the NPGS has been distributed as budwood of accessions resulting from imported budwood of wild trees considered “elites”, budwood of accessions grown from wild-collected seeds, and seed from crossing among wild accessions grown ex situ. These materials have subsequently been used to determine genetic relationships between M. domestica cultivars and M. sieversii ( Robinson et al., 2001 ; Gharghani et al., 2009 ; Nikiforova et al., 2013 ; Duan et al., 2017 ; Wedger et al., 2021 ), to evaluate phenotypic diversity of traits ( Janisiewicz et al., 2008 ; Fazio et al., 2009 ; Bassett et al., 2011 ; Jurick et al., 2011 ; Van Nocker et al., 2012 ; Fazio et al., 2014 ; Maguylo and Bassett, 2014 ; Harshman et al., 2017 ; Watts et al., 2021 ; Davies et al., 2022 ), and to identify QTLs and novel alleles ( Xu et al., 2012 ; Wisniewski et al., 2020 ; Singh et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions

et al. 2022

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The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species’ centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were compared with a dataset of more than 5000 unique M. domestica apple cultivars. Only 212 accessions (151 M. sieversii, 26 M. orientalis, and 35 M. sylvestris) were identified as “pure” species representatives because their DNA profiles did not exhibit genotypic signatures of recent hybridization with M. domestica. Twenty-one accessions (17 M. sieversii, 1 M. orientalis, and 3 M. sylvestris) previously labeled as wild species were instead fully M. domestica. Previously unrealized hybridization and admixture between wild species and M. domestica was identified in 230 accessions (215 M. sieversii, 9 M. orientalis, and 6 M. sylvestris). Among these species-mislabeled accessions, ‘Alexander’, ‘Gold Reinette’, ‘Charlamoff’, ‘Rosmarina Bianca’, and ‘King of the Pippins’ were the most frequently detected M. domestica parents or grandparents. These results have implications for collection management, including germplasm distribution, and might affect conclusions of previous research focused on these three progenitor species in the NPGS apple collection. Specifically, accessions received from the NPGS for breeding and genomics, genetics, and evolutionary biology research might not be truly representative of their previously assigned species.

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“…Several studies showed evidence of selection during apple domestication, e.g. , for fruit size ( Yao et al 2015 ; Duan et al 2017 ), fruit quality traits ( Wedger et al 2021 ), metabolite content ( Khan et al 2014 ) or disease-related genes ( Singh et al 2019 ). However, little information is available about the genomic consequences of the more recent apple improvement and the resulting genetic differences between genetic resources and modern cultivars.…”

Section: Discussionmentioning

confidence: 99%

Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple

Cazenave

Petit

Lateur

et al. 2021

G3 Genes|Genomes|Genetics

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Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e. genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and small increases in predictive ability could be obtained for some traits when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation.

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Candidate genes and signatures of directional selection on fruit quality traits during apple domestication

Cited by 7 publications

References 69 publications

Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm

DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions

Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple

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