Natural variations in a pectin acetylesterase gene, <i>MdPAE10</i>, contribute to prolonged apple fruit shelf life

Wu, Bei; Shen, Fei; Chen, Chi Jie; Liu, Li; Wang, Xuan; Zheng, Wen Yan; Deng, Yang; Wang, Ting; Huang, Zhen Yu; Xiao, Chen; Zhou, Qian; Wang, Yi; Wu, Ting; Xu, Xuefeng; Han, Zhen; Zhang, Xin Zhong

doi:10.1002/tpg2.20084

Cited by 18 publications

(7 citation statements)

References 66 publications

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“…Similarly, Valenzuela-Riffo and Morales-Quintana (2020) illustrated the binding mechanism of EXPA2 in strawberry cultivars during fruit softening. According to Wu et al (2021), the pectin acetylesterase gene enhanced the fruit softening in apple; similarly, in our results, the low firm 'P69' consisted of a higher expression level of pectin acetylesterase. Moreover, in strawberry, the silencing of pectate lyase and ß-galactosidase enhanced fruit firmness by influencing pectin metabolism (Salentijn et al, 2003;Paniagua et al, 2016).…”

Section: Discussionsupporting

confidence: 84%

Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

et al. 2021

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Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line ‘Wongyo 3115’, using long- and short-read sequencing technologies. The assembly of ‘Wongyo 3115’ produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the ‘Wongyo 3115’ reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the ‘BS F2’ populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the ‘Wongyo 3115’ genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of ‘BS F2’ obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.

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Section: Discussionsupporting

confidence: 84%

Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

et al. 2021

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“…For example, the overexpression of MdPAE10 encodes pectin acetylesterase and leads to a significant reduction in flesh firmness. In contrast, silencing MdPAE10 delays the decline of fruit firmness [ 73 ]. FaEG1 genes encoding endo-β-1, 4-glucanase are reported to be involved in the breakdown of cellulose and hemicellulose structures and play a role in cell wall restructuration during strawberry fruit softening [ 74 ].…”

Section: Cell Wall Metabolism and Structure Remodelingmentioning

confidence: 99%

Molecular and Genetic Events Determining the Softening of Fleshy Fruits: A Comprehensive Review

Peng

Liu

et al. 2022

IJMS

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Fruit softening that occurs during fruit ripening and postharvest storage determines the fruit quality, shelf life and commercial value and makes fruits more attractive for seed dispersal. In addition, over-softening results in fruit eventual decay, render fruit susceptible to invasion by opportunistic pathogens. Many studies have been conducted to reveal how fruit softens and how to control softening. However, softening is a complex and delicate life process, including physiological, biochemical and metabolic changes, which are closely related to each other and are affected by environmental conditions such as temperature, humidity and light. In this review, the current knowledge regarding fruit softening mechanisms is summarized from cell wall metabolism (cell wall structure changes and cell-wall-degrading enzymes), plant hormones (ETH, ABA, IAA and BR et al.), transcription factors (MADS-Box, AP2/ERF, NAC, MYB and BZR) and epigenetics (DNA methylation, histone demethylation and histone acetylation) and a diagram of the regulatory relationship between these factors is provided. It will provide reference for the cultivation of anti-softening fruits.

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“…Unfortunately, the empirical predictive power of these four functional markers were limited, with 15% of the observed variation in initial firmness and 18% in softening rate; therefore, their large-scale use for MAS was doubtful (Nybom et al, 2013). The genotypes of commonly used markers on MdACS1 (MD15G1302200) and MdACO1 (MD15G1205100) did not segregate in the 'Zisai Pearl' 9 'Red Fuji' population (Wu et al, 2020), which offered opportunity to map more QTLs. Ethylene production, however, varied with types of firmness and crispness retainability (Figure 1e,f).…”

Section: Discussionmentioning

confidence: 99%

“…Each bulked DNA sample was sequenced to obtain 309 genome coverage using a pairedend 150-bp read strategy (Illumina X10, Illumin a, USA). The parental cultivars have been re-sequenced previously (Shen et al, 2019;Wu et al, 2020). The re-sequencing data were processed, and QTLs were identified using the BSATOS software package (https://github.com/maypoleflyn/BSATOS) (Shen et al, 2019).…”

Section: Bsa-seq and Qtl Identificationmentioning

confidence: 99%

Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL‐based genomics‐assisted prediction

Shen

Wang

et al. 2021

Plant Biotechnology Journal

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Retention of flesh texture attributes during cold storage is critical for the long-term maintenance of fruit quality. The genetic variations determining flesh firmness and crispness retainability are not well understood. The objectives of this study are to identify gene markers based on quantitative trait loci (QTLs) and to develop genomics-assisted prediction (GAP) models for apple flesh firmness and crispness retainability. Phenotype data of 2664 hybrids derived from three Malus domestica cultivars and a M. asiatica cultivar were collected in 2016 and 2017. The phenotype segregated considerably with high broad-sense heritability of 83.85% and 83.64% for flesh firmness and crispness retainability, respectively. Fifty-six candidate genes were predicted from the 62 QTLs identified using bulked segregant analysis and RNA-seq. The genotype effects of the markers designed on each candidate gene were estimated. The genomics-predicted values were obtained using pyramiding marker genotype effects and overall mean phenotype values. Fivefold cross-validation revealed that the prediction accuracy was 0.5541 and 0.6018 for retainability of flesh firmness and crispness, respectively. An 8-bp deletion in the MdERF3 promoter disrupted MdDOF5.3 binding, reduced MdERF3 expression, relieved the inhibition on MdPGLR3, MdPME2, and MdACO4 expression, and ultimately decreased flesh firmness and crispness retainability. A 3-bp deletion in the MdERF118 promoter decreased its expression by disrupting the binding of MdRAVL1, which increased MdPGLR3 and MdACO4 expression and reduced flesh firmness and crispness retainability. These results provide insights regarding the genetic variation network regulating flesh firmness and crispness retainability, and the GAP models can assist in apple breeding.

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Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life

Cited by 18 publications

References 66 publications

Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

Molecular and Genetic Events Determining the Softening of Fleshy Fruits: A Comprehensive Review

Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL‐based genomics‐assisted prediction

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