Accessions with Hap. We later detected the expression level of Prupe. The expression level of this gene in the population with Hap. At the individual level, the expression pattern of Prupe. However, some accessions, such as 4, 14, 20, 21, 22, and 23, showed an opposite trend. This suggested that other loci were involved in this trait, as it is a QTL controlled by many gene loci When grouping accessions based on haplotypes, we found that in accessions with Hap.
The expression pattern of Prupe. This complex structural rearrangement interval may be the best candidate for the underlying cause of this allele-specific expression pattern. The ortholog in the apple was also confirmed to be closely associated with the fruit development period in a previous GWAS 51 ; this interval showed collinearity in apple, peach, apricot, and berry Thus, these genes may control fruit development using a conserved mechanism in these species.
The GWAS results on the maturity date trait were the same as those on the development period trait Fig. The arrow indicates the top associated SV. Double flowers with extra petals are important for artificial selection because of their attractive appearance and commercial value in several ornamental plants, such as peach.
Two distinct loci were described as the underlying genetic causes for the double flower traits in peach. Deletion of the miR target site in this gene is responsible for the dominant double-flower trait in Rosaceae 56 , However, to date, the Dl gene is still controversial.
S11 , which was located on a different scaffold from the Dl gene, which was located on chromosome 2. These two independent insertion events may prevent the transcription of the miRd precursor and result in decreased levels of mature miRd, and this decrease may lead to an increase in petal number, as the orthologs in other species and the target gene AP2 family were closely associated with petal number 58 , 59 , The arrow indicates the top associated LI.
The sequence represents mature miRd, and the dashed line represents its flanking sequence. Nectarine in peach is a key agricultural character affecting both appearance and ecological adaptation. The nectarine trait is recessive to normal peach, and the major gene controlling this trait is the MYB gene Prupe. A large insertion variant was discovered in the third exon of this gene and was shown to cause loss of function and the hairlessness phenotype 6.
S14a , where no proper candidate genes could be identified. S14d was located within the third exon of this MYB gene as previously reported 6. We further analyzed this insertion event in all nectarine accessions and found that all nectarine accessions from Gansu Province did not have this large insertion variant at this site.
To determine other variants responsible for hairlessness traits in accessions from Gansu Province, we first performed a SNP-based GWAS on this trait, but we defined other nectarine accessions with known LIs large insertion structural variants as hairy peaches.
Haplotyping analysis suggested that at least 3 haplotypes were responsible for the nectarine trait Fig. Another observation indicated that Hap. These observations suggested that the hairlessness trait originated from at least three independent mutation events. The arrow indicates the top associated SNP. In this GWAS, all nectarine accessions with the known LI large insertion structural variant were treated as normal peaches to identify a new genetic basis for hairlessness in some nectarine accessions without the LI large insertion structural variant.
The exon is represented by a blue box, and the intron is represented by a solid line. Flesh color white or yellow in peach affects fruit nutritional value and consumer preference.
White color is dominant to yellow color. The candidate gene Prupe. S15d , which was identified by a previous study 5.
A chromosome-grade genome assembly is valuable for identifying genetic variants and performing GWAS, providing new insights into the genetic architecture of key agronomic traits and genomic evolution In this study, we de novo assembled five species in the genus Prunus , demonstrated the utility of these genomes for the identification of structural variants, and provided a basis for functional genomics and comparative genomics in Prunus species.
GWAS is a versatile tool for identifying candidate genes and genetic architecture components for diseases and key agronomic and economic traits. Indeed, many studies have confirmed that this SNP-based approach was successful in discovering candidate genes 9 , 10 , 11 , 12 , However, this classic SNP-based approach was not very successful in peach, as few candidate genes and genetic architecture components were identified for traits in previous studies 16 , 17 and in this study.
After adjusting the GWAS approach, we identified a gene involved in fruit sugar content variance linked with nonacidity to some degree and a new allele for the nectarine trait from Gansu Province. Although selecting a sugar content variance-related gene in a GWAS of a nonacidity trait seemed improbable, this gene is located in a linkage interval harboring fruit sugar, acidity, and taste QTLs 40 , 41 , Additionally, Prupe. The allele frequency in the West and East populations suggested that this locus showed differential selection due to preferences for different tastes.
For the nectarine trait from Gansu Province, a new allele of the candidate gene Prupe. This finding suggested that the nectarine trait had multiple origins, similar to the fruit flesh color 5 , 61 and double flower traits in this study. This mechanism may be the universal mechanism for the adaptation of plants and natural or artificial selection.
We also used small indels as genetic markers to conduct GWASs, but this strategy was not successful in our study. Additionally, no causal indel was identified for any trait. One possibility is that allelic heterogeneity is poor in this analysis, such as in the case of fruit flesh color 5. The second possibility is that there was no casual indel for these traits or that the indel was not linked to any candidate genes or genetic architecture components.
One possible explanation is that the crossover and recombination rate could be extremely high in these flanking intervals if the SNP was not generated later than the SV or the flanking SNP was generated much later than the SV.
The third possibility may be that very low LD in the peach genome prevents the linkage of the SNPs with the SVs; this case may have occurred in maize, which has a similar LD value Furthermore, in some cases, the SNP is not linked with the candidate SV owing to a variety of mechanisms, such as mutation, genetic drift, and selection SV-based GWASs will provide a new approach to identify candidate genes and genetic architecture components for key traits.
The genetic basis for agronomic traits in plant species varies; thus, only one approach to identifying candidate genes for key traits is limiting. Thus, we used a combined SV-based GWAS approach to increase the success of identifying the underlying genetic architecture for traits. Using the SV-based approach DELs, DUPs, and INVs , we successfully identified a large inversion event responsible for flat shape in fruits and the premature abortion of fruits, as well as complex genomic rearrangements and tandem repeat events related to fruit development period and fruit maturity date traits.
As the genotyping of INSs at a large population scale cannot be performed to date to our knowledge, we adapted a simplified genotyping approach, although it decreased the power of GWAS detection. Using this approach, we identified transposable element insertion events as the underlying causal factors for double flower, nectarine, and flesh color traits.
All of these genes and candidate bases were lost in previous GWAS studies 16 , 17 , and we identified the top associated signals on these genes or very near them. These findings further indicated that INSs, especially transposable elements, are key genetic variants for many key agronomic traits, considering that transposable element events were responsible for three traits in this study and that transposable elements occur in the majority of the genome sequence.
We, fortunately, identified two independent transposable element events for double flowers, as only seven accessions with this phenotype were found in the accessions in our GWAS panel. We concluded that the success was because no accessions were derived from crosses of edible peach and ornamental peach.
Notably, the favorable traits of fruits and flowers were independently improved by breeders in the past. After we decreased this parameter to 0. Although a candidate PpCAD gene was previously identified, including this SNP 17 , the expression pattern of this gene between flat-type and round-type fruit during the fruit development period cannot explain the fruit shape difference However, the physical position, expression pattern, and transgenic phenotype of Prupe.
A Prupe. However, we found that this gene may not be a candidate gene for this trait based on three lines of evidence. First, the expression pattern suggested that this gene was not correlated with fruit ripening data not provided.
Second, the transgenic phenotype of the two alleles with and without small indels was not associated with fruit ripening data not provided. Third, the phylogenetic tree suggested that this gene may be related to the stress response However, these three lines of evidence except the transgenic phenotype, for which the identification is under way all supported Prupe.
The association of Prupe. Although a few genes and genetic architecture components were identified for some traits, the genetic architecture of many traits in this study was still not identified by the SV-based GWAS approach. Other types of variants, such as epigenetic footprints, may be the underlying genetic basis for some traits.
Allelic heterogeneity may also hinder the discovery of candidate genes and genetic architecture components. The environmental effect on phenotypes was not uniform. Further effort is still needed to identify and validate more candidate genes for these key traits. In summary, we de novo assembled five species in the genus Prunus and generated a useful sequence dataset, which will help promote Prunus functional genomics and comparative genomics in fruit species in the future.
The identified candidate genes and genetic architecture components by GWASs may provide targets for molecular marker selection and the improvement of key traits. Additionally, this comprehensive GWAS approach could be used in future deep sequencing studies to more precisely identify candidate genes and genetic architecture components for diseases and key traits in plants, animal species, and humans. Fresh leaflets were collected and stored in liquid nitrogen until DNA extraction and sequencing.
Filtered PacBio subreads were first assembled with Falcon v0. One copy of the contigs from heterozygous regions was retained by using redundant sequences v0. The resulting assembly was polished by aligning PacBio reads with Quiver 64 followed by running Pilon v1. The reads from the Hi-C library were aligned to the primary assembly using Bowtie2 The resulting bam files together with the contigs were used as input for Lachesis 67 with the cluster number set to 9 and the remaining parameters set as default.
The serial numbers of the chromosomes were manually adjusted in descending order of chromosome length Chr1-longest; Chr8-shortest. We generated RNA-Seq libraries from a mixture of leaves, phloem, fruit, and seeds and conducted full-length sequencing on the PacBio-Iso platform. The full-length transcripts were directly used to predict gene models with PASA Homology-based evidence was derived from protein sequences blasted against UniProt assemblies.
De novo prediction of gene models was performed using Augustus Complete and nonredundant gene models were combined using EvidenceModeler Repeated annotation of the assemblies was based on homology and de novo prediction strategies. The homology-based prediction was performed with RepeatMasker 71 using the RepBase database Phylogenetic tree construction was performed based on single-copy genes extracted from the gene family cluster analysis.
The maximum likelihood tree was constructed using PhyML software 74 with the default parameters. Among them, Prunus accessions were collected as described previously 3 , 17 , 29 , representing most ecotypes worldwide. The peach accessions newly sequenced in this study were collected from various regions in China and planted in the Peach Germplasm Repository, Shandong Agricultural University, China. These accessions included 5 accessions of P.
The samples were sequenced on the Illumina HiSeq platform. Nineteen agronomic traits were phenotyped in this study, including 11 qualitative and eight quantitative traits. The fruit traits were evaluated using fully matured fruits. All traits were analyzed in at least five fruits, flowers, leaves, and bark sections, which were collected from the tree that was sequenced for each accession. All agronomic traits considered here were characterized based on previously published plant genetic resource evaluation criteria The traits for the previously analyzed accessions were collected from previous papers 16 , 17 , 29 and books In this study, we analyzed a total of whole-genome sequences of peach accessions.
A total of peach accessions were sequenced in this study. The cultivated and wild peach accessions were sequenced unevenly from 3x to x. The public accessions were downloaded and mapped to the peach reference genome v2. The 18 wild relative accessions and 73 accessions with a low depth of sequencing were excluded from downstream analyses, and accessions were kept for SV calling and genotyping at a population scale. This pipeline was first used to call SVs for each accession to obtain a union of sites across all samples.
These variant sites were used to genotype each accession, and the resulting single samples were merged to generate a raw variant dataset. The genetic distance between two given accessions was calculated with dnadist in Phylip 83 v3. The population genetic structure was examined via an expectation-maximization algorithm, as implemented in the program Admixture The number of assumed genetic clusters K ranged from 2 to 9, with 10, iterations for each run. The first ten principal components of the PCA were included as the variance-covariance matrix for adjusting for population stratification based on 99, pruned SNPs.
The genome-wide significance thresholds of all the traits were determined using the Bonferroni test. According to a nominal level of 0. To identify the variant associated with hairlessness in nectarines without the previously reported LI, we considered all nectarine accessions with the LI as normal peaches and the remaining nectarines without LI events as the other class of phenotypes. The Manhattan plots and local plots were generated with the Sushi 88 and qqman 89 packages.
To analyze the allele-specific expression pattern of candidate genes, additional ripening fruit flesh tissue of eight peach cultivars at 80 days after full blooming was also collected.
These fruit flesh tissues were used to extract RNA. Reads were mapped onto the peach reference genome V2. To analyze the allele-specific expression pattern of Prupe. The allele-specific expression pattern of Prupe. The transcripts of each sample and expression levels of the genes were built and estimated by using Stringtie 92 with the default parameters. The reads were mapped against the peach reference V2. The expression patterns of Prupe. The CDS of Prupe. The transgenic lines T0 of Prupe.
Shulaev, V. Multiple models for Rosaceae genomics. Plant Physiol. Faust, M. Origin and dissemination of peach. Google Scholar. International Peach Genome, I. The high-quality draft genome of peach Prunus persica identifies unique patterns of genetic diversity, domestication, and genome evolution. Morgutti, S. Phytologist , — Falchi, R. Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach.
Plant J. Vendramin, E. A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach. PLoS One 9 , e Bielenberg, D. Sequencing and annotation of the evergrowing locus in peach [Prunus persica L. Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation.
Tree Genet. Genomes 4 , — Article Google Scholar. Chris Dardick, et al. PpeTAC1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. Atwell, S. Genome-wide association study of phenotypes in Arabidopsis thaliana inbred lines.
Nature , — Yano, K. This strain is a permissive background for the expression of most mutations, but is resilient to many tumors.
It also develops age-related hearing loss. The size of the genome is 2. You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser. Proteomes - Mus musculus Mouse Basket 0. Your basket is currently empty. Select a section on the left to see content. Solanaceae Genomics Resource September 14, - The chromosome-scale and haplotype-resolved genome assembly and annotation of a heterozygous tetraploid potato Otava is now available on SpudDB.
September 23, - The paper " Construction of a chromosome-scale long-read reference genome assembly for potato " describing the DM v6. The DM v6. May 22, - The Buell Lab at Michigan State University is pleased to make available an updated long-read chromosome-scale genome assembly v6. The genome assembly is available on the DM v6. March 14, - The haplotype resolved genome assembly and annotation of the heterozygous diploid potato RH is now available on SpudDB.
February 5, - The paper Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense , reveals residual heterozygosity been published in The Plant Journal. March 28, - A paper describing the resources, tools and data available in Spud DB has been published in the journal The Plant Genome.
DM v6. September 23, The paper " Construction of a chromosome-scale long-read reference genome assembly for potato " describing the DM v6. June 4, The genome annotation for the updated long-read chromosome-scale genome assembly v6. May 22, An updated and improved long-read chromosome-scale genome assembly v6. March 14, The haplotype resolved genome assembly and annotation of the heterozygous diploid potato RH is now available on SpudDB. February 5, The paper Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense , reveals residual heterozygosity been published in The Plant Journal.
February 1, The Buell Lab has released v4.
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