Two adjacent NAC transcription factors regulate fruit maturity date and flavor in peach.

Although maturity date (MD) is an essential factor affecting fresh fruit marketing and has a pleiotropic effect on fruit taste qualities, the underlying mechanisms remain largely unclear. In this study, we functionally characterized two adjacent NAM-ATAF1/2-CUC2 (NAC) transcription factors (TFs), PpNAC1 and PpNAC5, both of which were associated with fruit MD in peach. PpNAC1 and PpNAC5 were found capable of activating transcription of genes associated with cell elongation, cell wall degradation and ethylene biosynthesis, suggesting their regulatory roles in fruit enlargement and ripening. Furthermore, PpNAC1 and PpNAC5 had pleiotropic effects on fruit taste due to their ability to activate transcription of genes for sugar accumulation and organic acid degradation. Interestingly, both PpNAC1 and PpNAC5 orthologues were found in fruit-producing angiosperms and adjacently arranged in all 91 tested dicots but absent in fruitless gymnosperms, suggesting their important roles in fruit development. Our results provide insight into the regulatory roles of NAC TFs in MD and fruit taste.

Allelic variation of MdMYB123 controls malic acid content by regulating MdMa1 and MdMa11 expression in apple.

Acidity is a key determinant of fruit organoleptic quality. Here, a candidate gene for fruit acidity, designated MdMYB123, was identified from a comparative transcriptome study of two Ma1Ma1 apple (Malus domestica) varieties, "Qinguan (QG)" and "Honeycrisp (HC)" with different malic acid content. Sequence analysis identified an A→T SNP, which was located in the last exon, resulting in a truncating mutation, designated mdmyb123. This SNP was significantly associated with fruit malic acid content, accounting for 9.5% of the observed phenotypic variation in apple germplasm. Differential MdMYB123- and mdmyb123-mediated regulation of malic acid accumulation was observed in transgenic apple calli, fruits, and plantlets. Two genes, MdMa1 and MdMa11, were up- and down-regulated in transgenic apple plantlets overexpressing MdMYB123 and mdmyb123, respectively. MdMYB123 could directly bind to the promoter of MdMa1 and MdMa11, and induce their expression. In contrast, mdmyb123 could directly bind to the promoters of MdMa1 and MdMa11, but with no transcriptional activation of both genes. In addition, gene expression analysis in 20 different apple genotypes based on SNP locus from "QG" × "HC" hybrid population confirmed a correlation between A/T SNP with expression levels of MdMa1 and MdMa11. Our finding provides valuable functional validation of MdMYB123 and its role in the transcriptional regulation of both MdMa1 and MdMa11, and apple fruit malic acid accumulation.

Polystyrene nanoplastics induce apoptosis, autophagy, and steroidogenesis disruption in granulosa cells to reduce oocyte quality and fertility by inhibiting the PI3K/AKT pathway in female mice.

BACKGROUND: Nanoplastics (NPs) are emerging pollutants that pose risks to living organisms. Recent findings have unveiled the reproductive harm caused by polystyrene nanoparticles (PS-NPs) in female animals, yet the intricate mechanism remains incompletely understood. Under this research, we investigated whether sustained exposure to PS-NPs at certain concentrations in vivo can enter oocytes through the zona pellucida or through other routes that affect female reproduction. RESULTS: We show that PS-NPs disrupted ovarian functions and decreased oocyte quality, which may be a contributing factor to lower female fertility in mice. RNA sequencing of mouse ovaries illustrated that the PI3K-AKT signaling pathway emerged as the predominant environmental information processing pathway responding to PS-NPs. Western blotting results of ovaries in vivo and cells in vitro showed that PS-NPs deactivated PI3K-AKT signaling pathway by down-regulating the expression of PI3K and reducing AKT phosphorylation at the protein level, PI3K-AKT signaling pathway which was accompanied by the activation of autophagy and apoptosis and the disruption of steroidogenesis in granulosa cells. Since PS-NPs penetrate granulosa cells but not oocytes, we examined whether PS-NPs indirectly affect oocyte quality through granulosa cells using a granulosa cell-oocyte coculture system. Preincubation of granulosa cells with PS-NPs causes granulosa cell dysfunction, resulting in a decrease in the quality of the cocultured oocytes that can be reversed by the addition of 17ß-estradiol. CONCLUSIONS: This study provides findings on how PS-NPs impact ovarian function and include transcriptome sequencing analysis of ovarian tissue. The study demonstrates that PS-NPs impair oocyte quality by altering the functioning of ovarian granulosa cells. Therefore, it is necessary to focus on the research on the effects of PS-NPs on female reproduction and the related methods that may mitigate their toxicity.

Origins and Genetic Characteristics of Egyptian Peach.

Peach (Prunus persica), a significant economic fruit tree in the Rosaceae family, is extensively cultivated in temperate and subtropical regions due to its abundant genetic diversity, robust adaptability, and high nutritional value. Originating from China over 4000 years ago, peaches were introduced to Persia through the Silk Road during the Han Dynasty and gradually spread to India, Greece, Rome, Egypt, Europe, and America. Currently grown in more than 80 countries worldwide, the expansion of peach cultivation in Egypt is mainly due to the development and utilization of peach varieties with low chilling requirements. These varieties exhibit unique phenotypic characteristics such as early maturity, reduced need for winter cold temperatures, low water requirements, and high economic value. In this study, a systematic analysis was conducted on the genetic characteristics and kinship relationships of peaches with low chilling requirements in Egypt. We conducted a comprehensive evolutionary and Identity-by-Descent (IBD) analysis on over 300 peach core germplasm resources, including Egyptian cultivars with low chilling requirements, to investigate their origin and genetic characteristics. The evolutionary analysis revealed that 'Bitter almond' is closely related to China's wild relative species Prunus tangutica Batal, while 'Early grand' shares one branch with Chinese ornamental peach cultivars, and 'Nemaguard' clusters with some ancient local varieties from China. The IBD analysis also indicated similar genetic backgrounds, suggesting a plausible origin from China. Similarly, the analysis suggested that 'Swelling' may have originated from the Czech Republic while 'Met ghamr' has connections to South Africa. 'Desert red', 'Early swelling', and 'Florida prince' are likely derived from Brazil. These findings provide valuable insights into the genetic characteristics of Egyptian peach cultivars. They offer a significant foundation for investigating the origin and spread of cultivated peaches worldwide and serve as a valuable genetic resource for breeding low chilling requirement cultivars, which is of considerable significance for the advancement of peach cultivation in Egypt.

A PpEIL2/3-PpNAC1-PpWRKY14 module regulates fruit ripening by modulating ethylene production in peach.

WRKY transcription factors play key roles in plant resistance to various stresses, but their roles in fruit ripening remain largely unknown. Here, we report a WRKY gene PpWRKY14 involved in the regulation of fruit ripening in peach. The expression of PpWRKY14 showed an increasing trend throughout fruit development. PpWRKY14 was a target gene of PpNAC1, a master regulator of peach fruit ripening. PpWRKY14 could directly bind to the promoters of PpACS1 and PpACO1 to induce their expression, and this induction was greatly enhanced when PpWRKY14 formed a dimer with PpNAC1. However, the transcription of PpNAC1 could be directly suppressed by two EIN3/EIL1 genes, PpEIL2 and PpEIL3. The PpEIL2/3 genes were highly expressed at the early stages of fruit development, but their expression was programmed to decrease significantly during the ripening stage, thus derepressing the expression of PpNAC1. These results suggested a PpEIL2/3-PpNAC1-PpWRKY14 module that regulates fruit ripening by modulating ethylene production in peach. Our results provided an insight into the regulatory roles of EIN3/EIL1 and WRKY genes in fruit ripening.

NUCKS1 promotes the progression of colorectal cancer via activating PI3K/AKT/mTOR signaling pathway.

Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 (NUCKS1) is highly expressed in a variety of malignant tumors and functions as an oncogene; however, its role in colorectal cancer (CRC) remains unclear. We aimed to explore the function and regulatory mechanisms of NUCKS1 and potential therapeutic agents targeting NUCKS1 in CRC. We knocked down and overexpressed NUCKS1 in CRC cells and explored its effects in vitro and in vivo. Flow cytometry, CCK-8, Western blotting, colony formation, immunohistochemistry, in vivo tumorigenic, and transmission electron microscopy analyses were performed to determine the effects of NUCKS1 on CRC cell function. LY294002 was used to examine the mechanism of NUCKS1 expression in CRC cells. Potential therapeutic agents for NUCKS1-high CRC patients were analyzed using the CTRP and PRISM datasets, and the function of selected agents was determined by CCK-8 and Western blotting. We revealed that NUCKS1 was highly expressed in CRC tissues and clinically correlated with poor prognosis in CRC patients. NUCKS1 knockdown induces cell cycle arrest, inhibits CRC cell proliferation, and promotes apoptosis and autophagy. These results were reversed when NUCKS1 was overexpressed. Mechanistically, NUCKS1 exerts a cancer-promoting function by activating the PI3K/AKT/mTOR signaling pathway. This was reversed when LY294002 was used to inhibit the PI3K/AKT pathway. Furthermore, we determined that mitoxantrone exhibited high drug sensitivity in NUCKS1-overexpressing CRC cells. This work demonstrated NUCKS1 plays a crucial role in CRC progression via the PI3K/AKT/mTOR signaling pathway. Additionally, mitoxantrone may be a potential therapeutic agent for CRC treatment. Therefore, NUCKS1 represents a promising anti-tumor therapeutic target.

Two R2R3-MYB genes cooperatively control trichome development and cuticular wax biosynthesis in Prunus persica.

The fruit surface has an enormous impact on the external appearance and postharvest shelf-life of fruit. Here, we report two functionally redundant genes, PpMYB25 and PpMYB26, involved in regulation of fruit skin texture in peach. PpMYB25 can activate transcription of PpMYB26 and they both induce trichome development and cuticular wax accumulation, resulting in peach fruit with a fuzzy and dull appearance. By contrast, nonfunctional mutation of PpMYB25 caused by an insertional retrotransposon in the last exon in nectarine fails to activate transcription of PpMYB26, resulting in nectarine fruit with a smooth and shiny appearance due to loss of trichome initiation and decreased cuticular wax accumulation. Secondary cell wall biosynthesis in peach fruit pubescence is controlled by a transcriptional regulatory network, including the master regulator PpNAC43 and its downstream MYB transcription factors such as PpMYB42, PpMYB46 and PpMYB83. Our results show that PpMYB25 and PpMYB26 coordinately regulate fruit pubescence and cuticular wax accumulation and their simultaneous perturbation results in the origin of nectarine, which is botanically classified as a subspecies of peach.

Which urban communities are susceptible to COVID-19? An empirical study through the lens of community resilience.

BACKGROUND: After the lockdown of Wuhan on January 23, 2020, the government used community-based pandemic prevention and control as the core strategy to fight the pandemic, and explored a set of standardized community pandemic prevention measures that were uniformly implemented throughout the city. One month later, the city announced its first lists of "high-risk" communities and COVID-19-free communities. Under the standardized measures of pandemic prevention and mitigation, why some communities showed a high degree of resilience and effectively avoided escalation, while the situation spun out of control in other communities? This study investigated: 1) key factors that affect the effective response of urban communities to the pandemic, and 2) types of COVID-19 susceptible communities. METHODS: This study employs the crisp-set qualitative comparative analysis method to explore the influencing variables and possible causal condition combination paths that affect community resilience during the pandemic outbreak. Relying on extreme-case approach, 26 high-risk communities and 14 COVID-19 free communities were selected as empirical research subjects from the lists announced by Wuhan government. The community resilience assessment framework that evaluates the communities' capacity on pandemic prevention and mitigation covers four dimensions, namely spatial resilience, capital resilience, social resilience, and governance resilience, each dimension is measured by one to three variables. RESULTS: The results of measuring the necessity of 7 single-condition variables found that the consistency index of "whether the physical structure of the community is favorable to virus transmission" reached 0.9, which constitutes a necessary condition for COVID-19 susceptible communities. By analyzing the seven condition configurations with high row coverage and unique coverage in the obtained complex solutions and intermediate solutions, we found that outbreaks are most likely to occur in communities populated by disadvantaged populations. However, if lacking spatial-, capital-, and governance resilience, middle-class and even wealthy communities could also become areas where COVID-19 spreads easily. CONCLUSIONS: Three types of communities namely vulnerable communities, alienated communities, and inefficient communities have lower risk resilience. Spatial resilience, rather than social resilience, constitutes the key influencing factor of COVID-19-susceptible communities, and the dual deficiencies of social resilience and governance resilience are the common features of these communities.

Genome-wide identification, characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh).

BACKGROUND: As an important group of the multidrug efflux transporter family, the multidrug and toxic compound extrusion (MATE) family has a wide range of functions and is distributed in all kingdoms of living organisms. However, only two MATE genes in apple have been analyzed and genome-wide comprehensive analysis of MATE family is needed. RESULTS: In this study, a total of 66 MATE (MdMATE) candidates encoding putative MATE transporters were identified in the apple genome. These MdMATE genes were classified into four groups by phylogenetic analysis with MATE genes in Arabidopsis. Synteny analysis reveals that whole genome duplication (WGD) and segmental duplication events played a major role in the expansion of MATE gene family in apple. MdMATE genes show diverse expression patterns in different tissues/organs and developmental stages. Analysis of cis-regulatory elements in MdMATE promoter regions indicates that the function of MdMATE genes is mainly related to stress response. Besides, the changes of gene expression levels upon different pathogen infections reveal that MdMATE genes are involved in biotic stress response. CONCLUSIONS: In this work, we systematically identified MdMATE genes in apple genome using a set of bioinformatics approaches. Our comprehensive analysis provided valuable resources for improving disease resistance in apple and further functional characterization of MATE genes in other species.

A 1.7-Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach.

Flat peaches have become popular worldwide due to their novelty and convenience. The peach flat fruit trait is genetically controlled by a single gene at the S locus, but its genetic basis remains unclear. Here, we report a 1.7-Mb chromosomal inversion downstream of a candidate gene encoding OVATE Family Protein, designated PpOFP1, as the causal mutation for the peach flat fruit trait. Genotyping of 727 peach cultivars revealed an occurrence of this large inversion in flat peaches, but absent in round peaches. Ectopic overexpression of PpOFP1 resulted in oval-shaped leaves and shortened siliques in Arabidopsis, suggesting its role in repressing cell elongation. Transcriptional activation of PpOFP1 by the chromosomal inversion may repress vertical elongation in flat-shaped fruits at early stages of development, resulting in the flat fruit shape. Moreover, PpOFP1 can interact with fruit elongation activator PpTRM17, suggesting a regulatory network controlling fruit shape in peach. Additionally, screening of peach wild relatives revealed an exclusive presence of the chromosomal inversion in P. ferganensis, supporting that this species is the ancestor of the domesticated peach. This study provides new insights into mechanisms underlying fruit shape evolution and molecular tools for genetic improvement of fruit shape trait in peach breeding programmes.

The MADS-box gene PpPI is a key regulator of the double-flower trait in peach.

Double flower is an invaluable trait in ornamental peach, but the mechanism underlying its development remains largely unknown. Here, we report the roles of ABCE model genes in double flower development in peach. A total of nine ABCE regulatory genes, including eight MADS-box genes and one AP2/EREBP gene, were identified in the peach genome. Subcellular localization assay showed that all the ABCE proteins were localized in the nucleus. Four genes, PpAP1, PpAP3, PpSEP3, and PpPI, showed a difference in expression levels between single and double flowers. Ectopic overexpression of PpPI increased petal number in Arabidopsis, while transgenic lines overexpressing PpAP3 or PpSEP3 were morphologically similar to wild-type. Ectopic overexpression of PpAP1 resulted in a significant decrease in the number of basal leaves and caused early flowering. These results suggest that PpPI is likely crucial for double flower development in peach. In addition, double flowers have petaloid sepals and stamens, and single flower could occasionally change to be double flower by converting stamens to petals in peach, suggesting that the double-flower trait is likely to have evolved from an ancestral single-flower structure. Our results provide new insights into mechanisms underlying the double-flower trait in peach.

The sucrose transporter MdSUT4.1 participates in the regulation of fruit sugar accumulation in apple.

BACKGROUND: Sugar content is an important determinant of fruit sweetness, but details on the complex molecular mechanism underlying fruit sugar accumulation remain scarce. Here, we report the role of sucrose transporter (SUT) family in regulating fruit sugar accumulation in apple. RESULTS: Gene-tagged markers were developed to conduct candidate gene-based association study, and an SUT4 member MdSUT4.1 was found to be significantly associated with fruit sugar accumulation. MdSUT4.1 encodes a tonoplast localized protein and its expression level had a negative correlation with fruit sugar content. Overexpression of MdSUT4.1 in strawberry and apple callus had an overall negative impact on sugar accumulation, suggesting that it functions to remobilize sugar out of the vacuole. In addition, MdSUT4.1 is located on chromosomal region harboring a previously reported QTL for sugar content, suggesting that it is a candidate gene for fruit sugar accumulation in apple. CONCLUSIONS: MdSUT4.1 is involved in the regulation of fruit sugar accumulation in apple. This study is not only helpful for understanding the complex mechanism of fruit sugar accumulation, but it also provides molecular tools for genetic improvement of fruit quality in breeding programs of apple.

Identification of EIL and ERF Genes Related to Fruit Ripening in Peach.

Peach (Prunus persica) is a climacteric fruit with a relatively short shelf life due to its fast ripening or softening process. Here, we report the association of gene families encoding ethylene insensitive-3 like (EIL) and ethylene response factor (ERF) with fruit ripening in peach. In total, 3 PpEILs and 12 PpERFs were highly expressed in fruit, with the majority showing a peak of expression at different stages. All three EILs could activate ethylene biosynthesis genes PpACS1 and PpACO1. One out of the 12 PpERFs, termed PpERF.E2, is a homolog of ripening-associated ERFs in tomato, with a consistently high expression throughout fruit development and an ability to activate PpACS1 and PpACO1. Additionally, four subgroup F PpERFs harboring the EAR repressive motif were able to repress the PpACO1 promoter but could also activate the PpACS1 promoter. Promoter deletion assay revealed that PpEILs and PpERFs could participate in transcriptional regulation of PpACS1 through either direct or indirect interaction with various cis-elements. Taken together, these results suggested that all three PpEILs and PpERF.E2 are candidates involved in ethylene biosynthesis, and EAR motif-containing PpERFs may function as activator or repressor of ethylene biosynthesis genes in peach. Our study provides an insight into the roles of EILs and ERFs in the fruit ripening process.

Analysis of sorbitol content variation in wild and cultivated apples.

BACKGROUND: Sorbitol is the major sugar alcohol in apple and its accumulation in fruit is associated with fruit sweetness. However, little is known about variation in sorbitol content in fruits of apple germplasm. In this study, we investigated sorbitol content in mature fruits of 243 apple cultivars and 20 wild relatives using high-performance liquid chromatography (HPLC). RESULTS: Sorbitol accumulation showed a significant variation in apple germplasm. Overall, cultivated fruits had significantly lower content of sorbitol than wild fruits. Fruit sorbitol concentration was significantly correlated with fruit size and acidity that are extensively domesticated traits. Hence, the variation in sorbitol accumulation between cultivated and wild fruits may be the indirect result of fruit size and acidity selection during domestication. Moreover, sorbitol content was maintained at low levels throughout fruit development, with a dramatic decrease at the middle stage. The SDH1 gene was highly expressed throughout fruit development, and its expression showed a significant correlation with fruit sorbitol concentration, suggesting its potential role in apple fruit sorbitol accumulation. CONCLUSIONS: The finding that there is a great variation in fruit sorbitol content among apple germplasm will be helpful for genetic improvement of fruit sorbitol content in apple breeding programs. © 2019 Society of Chemical Industry.

Hippo pathway functions as a downstream effector of AKT signaling to regulate the activation of primordial follicles in mice.

Clarifying the molecular mechanisms by which primordial follicles are initiated is crucial for the prevention and treatment of female infertility and ovarian dysfunction. The Hippo pathway has been proven to have a spatiotemporal correlation with the size of the primordial follicle pool in mice in our previous work. But the role and underlying mechanisms of the Hippo pathway in primordial follicle activation remain unclear. Here, the localization and expression of the core components were examined in primordial follicles before and after activation. And the effects of the Hippo pathway on primordial follicle activation were determined by genetically manipulating yes-associated protein 1 (Yap1), the key transcriptional effector. Furthermore, an AKT specific inhibitor (MK2206) was added to determine the interaction between the Hippo pathway and AKT, an important signaling regulator of ovarian function. Results showed that the core components of the Hippo pathway were localized in both primordial and primary follicles and the expression levels of them changed significantly during the initiation of primordial follicles. Yap1 knockdown suppressed primordial follicle activation, while its overexpression led to the opposite trend. MK2206 downregulated the ratio of P-MST/MST1 and upregulated the ratio of P-YAP1/YAP1 significantly, whereas Yap1-treatment had no influence on AKT. In addition, YAP1 upregulation partially rescued the suppression of the primordial follicle activation induced by MK2206. Our findings revealed that the Hippo-YAP1 regulates primordial follicular activation, which is mediated by AKT signaling in mice, thus providing direct and new evidence to highlight the role of Hippo signaling in regulating ovarian follicles development.

A Ma10 gene encoding P-type ATPase is involved in fruit organic acid accumulation in apple.

Acidity is one of the main determinants of fruit organoleptic quality. Here, comparative transcriptome analysis was conducted between two cultivars that showed a significant difference in fruit acidity, but contained homozygous non-functional alleles at the major gene Ma1 locus controlling apple fruit acidity. A candidate gene for fruit acidity, designated M10, was identified. The M10 gene encodes a P-type proton pump, P3A -ATPase, which facilitates malate uptake into the vacuole. The Ma10 gene is significantly associated with fruit malate content, accounting for ~7.5% of the observed phenotypic variation in apple germplasm. Subcellular localization assay showed that the Ma10 is targeted to the tonoplast. Overexpression of the Ma10 gene can complement the defect in proton transport of the mutant YAK2 yeast strain and enhance the accumulation of malic acid in apple callus. Moreover, its ectopic expression in tomato induces a decrease in fruit pH. These results suggest that the Ma10 gene has the capacity for proton pumping and plays an important role in fruit vacuolar acidification in apple. Our study provides useful knowledge towards comprehensive understanding of the complex mechanism regulating apple fruit acidity.

Two amino acid changes in the R3 repeat cause functional divergence of two clustered MYB10 genes in peach.

R2R3-MYB genes play a pivotal role in regulating anthocyanin accumulation. Here, we report two tandemly duplicated R2R3-MYB genes in peach, PpMYB10.1 and PpMYB10.2, with the latter showing lower ability to induce anthocyanin accumulation than the former. Site-directed mutation assay revealed two amino acid changes in the R3 repeat, Arg/Lys66 and Gly/Arg93, responsible for functional divergence between these two PpMYB10 genes. Anthocyanin-promoting activity of PpMYB10.2 was significantly increased by a single amino acid replacement of Arg93 with Gly93. However, either the Gly93 → Arg93 or Arg66 → Lys66 substitutions alone showed little impact on anthocyanin-promoting activity of PpMYB10.1, but simultaneous substitutions caused a significant decrease. Reciprocal substitution of Arg/Gly93 could significantly alter binding affinity to PpbHLH3, while the Arg66 → Lys66 substitution is predicted to affect the folding of the MYB DNA-binding domain, instead of PpbHLH3-binding affinity. Overall, the change of anthocyanin-promoting activity was accompanied with that of bHLH-binding affinity, suggesting that DNA-binding affinity of R2R3-MYBs depends on their bHLH partners. Our study is helpful for understanding of functional evolution of R2R3-MYBs and their interaction with DNA targets.

Assessment of calcium and zinc accumulation in cultivated and wild apples.

BACKGROUND: Apple is one of the staple fruits worldwide which are a good source of mineral nutrients. However, little is known about genetic variation for mineral nutrition in apple germplasm. In this study, the calcium and zinc contents in mature fruits of 378 apple cultivars and 39 wild relatives were assessed. Mineral concentrations were quantified using flame atomic absorption spectroscopy (FAAS). RESULTS: Both calcium and zinc accumulation showed great variation among accessions tested. Overall, wild fruits were significantly richer in zinc than cultivated fruits, while the average concentration of calcium was similar between cultivated and wild fruits. The difference in zinc concentration between wild and cultivated fruits may be an indirect result of artificial selection on fruit characteristics during apple domestication. Moreover, calcium concentration in fruit showed a decreasing trend throughout fruit development of apple, while zinc concentration in fruit displayed a complex variation pattern in the late stages of fruit development. CONCLUSION: The finding of a wild genetic variation for fruit calcium and zinc accumulation in apple germplasm could be helpful for future research on genetic dissection and improvement of calcium and zinc accumulation in apple fruit. © 2017 Society of Chemical Industry.

Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple.

Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphisms with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples. Linkage disequilibrium (LD) decays were observed quite rapidly in cultivated and wild apples, with an r2 -value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribution patterns of LD blocks were detected between domesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domestication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgression could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.