A draft genome of sweet cherry (<i>Prunus avium</i> L.) reveals genome‐wide and local effects of domestication

Pinosio, Sara; Marroni, Fabio; Zuccolo, Andrea; Vitulo, Nicola; Mariette, Stéphanie; Sonnante, Gabriella; Aravanopoulos, Filippos; Ganopoulos, Ioannis; Palasciano, Marino; Vidotto, Michele; Magris, Gabriele; Iezzoni, Amy; Vendramin, Giovanni G.; Morgante, Michèle

doi:10.1111/tpj.14809

Cited by 30 publications

(16 citation statements)

References 72 publications

(97 reference statements)

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“…The differences for H o , H e , % of rare alleles, and inbreeding coefficient (Fis) between landraces and either early selection or modern breeding cultivars agreed with the loss of diversity associated with breeding [14,15,29]. These differences further highlight the potential of landraces as a source of novel genetic diversity in sweet cherry breeding.…”

Section: Genetic Diversity Estimationmentioning

confidence: 52%

SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe

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Blouin-Delmas

et al. 2021

Plants

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Sweet cherry (Prunus avium L.) is a temperate fruit species whose production might be highly impacted by climate change in the near future. Diversity of plant material could be an option to mitigate these climate risks by enabling producers to have new cultivars well adapted to new environmental conditions. In this study, subsets of sweet cherry collections of 19 European countries were genotyped using 14 SSR. The objectives of this study were (i) to assess genetic diversity parameters, (ii) to estimate the levels of population structure, and (iii) to identify germplasm redundancies. A total of 314 accessions, including landraces, early selections, and modern cultivars, were monitored, and 220 unique SSR genotypes were identified. All 14 loci were confirmed to be polymorphic, and a total of 137 alleles were detected with a mean of 9.8 alleles per locus. The average number of alleles (N = 9.8), PIC value (0.658), observed heterozygosity (Ho = 0.71), and expected heterozygosity (He = 0.70) were higher in this study compared to values reported so far. Four ancestral populations were detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA), and two of them (K1 and K4) could be attributed to the geographical origin of the accessions. A N-J tree grouped the 220 sweet cherry accessions within three main clusters and six subgroups. Accessions belonging to the four STRUCTURE populations roughly clustered together. Clustering confirmed known genealogical data for several accessions. The large genetic diversity of the collection was demonstrated, in particular within the landrace pool, justifying the efforts made over decades for their conservation. New sources of diversity will allow producers to face challenges, such as climate change and the need to develop more sustainable production systems.

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Section: Genetic Diversity Estimationmentioning

confidence: 52%

SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe

Barreneche

Concepcion

Blouin-Delmas

et al. 2021

Plants

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“…With markedly improved sequencing technologies, several important stone fruit species closely related to Chinese plum, including Japanese apricot (Prunus mume, 2n = 2x = 16) (Zhang et al, 2012), peach (Prunus persica, 2n = 2x = 16) (Verde et al, 2017), sweet cherry (Prunus avium, 2n = 2x = 16) (Pinosio et al, 2020;Shirasawa et al, 2017), almond (Prunus dulcis, 2n = 2x = 16) (Alioto et al, 2019;S anchez-P erez et al, 2019), and apricot (Prunus armeniaca, 2n = 29 = 16) (Jiang et al, 2019), have already been sequenced, which greatly contributes to our understanding of the structure of Prunus genomes in general and the rapid evolution of their genera. More recently, for the subgenus Prunophora, the genome architectures of a hexaploid European plum ('Improved French') and a diploid Chinese plum ('Sanyueli') have been dissected (Callahan et al, 2021;Fang et al, 2020;Liu et al, 2020b).…”

Section: Introductionmentioning

confidence: 99%

Chromosome‐scale genome assembly and population genomics provide insights into the adaptation, domestication, and flavonoid metabolism of Chinese plum

et al. 2021

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Globally, commercialized plum cultivars are mostly diploid Chinese plums (Prunus salicina Lindl.), also known as Japanese plums, and are one of the most abundant and variable fruit tree species. To advance Prunus genomic research, we present a chromosome-scale P. salicina genome assembly, constructed using an integrated strategy that combines Illumina, Oxford Nanopore, and high-throughput chromosome conformation capture (Hi-C) sequencing. The high-quality genome assembly consists of a 318.6-Mb sequence (contig N50 length of 2.3 Mb) with eight pseudo-chromosomes. The expansion of the P. salicina genome is led by recent segmental duplications and a long terminal repeat burst of approximately 0.2 Mya. This resulted in a significant expansion of gene families associated with flavonoid metabolism and plant resistance, which impacted fruit flavor and increased species adaptability. Population structure and domestication history suggest that Chinese plum may have originated from South China and provides a domestication route with accompanying genomic variations. Selection sweep and genetic diversity analysis enabled the identification of several critical genes associated with flowering time, stress tolerance, and flavonoid metabolism, demonstrating the essential roles of related pathways during domestication. Furthermore, we reconstructed and exploited flavonoid-anthocyanin metabolism using multi-omics analysis in Chinese plum and proposed a complete metabolic pathway. Collectively, our results will facilitate further candidate gene discovery for important agronomic traits in Chinese plum and provide insights into future functional genomic studies and DNA-informed breeding.

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“…The NGS technologies allow discovery of large numbers of SNPs for extensive genetic studies at relatively lowcast. The technologies include within-species diversity analysis; linkage map construction; and genome-wide association studies (GWAS), which have led to significant advances in plant genetics and breeding (Cao et al 2016;Li et al 2019;Pinosio et al 2020). The genus Prunus has shown conserved intraspecific and intragenic collinearity in the Rosaceae family, with the peach being considered a model species for the genus Prunus for multiple types of genetic research (Arús et al 2012;Carrasco et al 2018;Marti et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

Xiao

Shen

Zhang

et al. 2021

Tree Genetics & Genomes

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Chinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study, we constructed high-quality SNPs through whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. Phylogenetic analysis, principal component analysis, and population structure profiling indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China clustered with the other three groups. The genetic diversity indices including private allele number, observed heterozygosity, expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. Gene flow from the SCG to FG was also detected. Based on the distribution of wild resources, we concluded that the domestication center of origin of the Chinese plum was southwestern China. This study also provided genetic variation features and the population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants to improve Chinese plum varieties.

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A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication

Cited by 30 publications

References 72 publications

SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe

SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe

Chromosome‐scale genome assembly and population genomics provide insights into the adaptation, domestication, and flavonoid metabolism of Chinese plum

Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

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