Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Muñoz-Espinoza, Claudia; Génova, Alex Di; Correa, Juan; Silva, Romina; Maass, Alejandro; González-Agüero, Mauricio; Orellana, Ariel; Hinrichsen, Patricio

doi:10.1186/s12870-016-0789-1

Cited by 19 publications

(38 citation statements)

References 80 publications

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“…() recently discovered new quantitative trait loci for berry weight or seed traits in grapevine, and mapped in these quantitative trait loci genes related to cell wall modifications, water import, auxin and ethylene signaling, transcription control, and organ identity. Likewise, recently, genes involved in the same pathways have been found differentially expressed in grapevine seedless segregants during berry development (Muñoz‐Espinoza et al ., ), thus our results support the hypothetical role of these genes in berry weight and development.…”

Section: Resultssupporting

confidence: 86%

“…Similarly, we found polymorphisms related to seedlessness and berry size in genes involved in auxin/hormone response, berry growth and development. Noteworthy, association mapping studies and expression data revealed candidate genes for berry weight involved in such similar pathways (Muñoz‐Bertomeu et al ., ; Doligez et al ., ; Muñoz‐Espinoza et al ., ). Our present results support the proposed role of these pathways in such complex traits and highlight new hypothetical candidate genes for further investigation.…”

Section: Discussionmentioning

confidence: 97%

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Inter‐varietal structural variation in grapevine genomes

Cardone¹,

D’Addabbo

Alkan

et al. 2016

The Plant Journal

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Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties.

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 97%

Inter‐varietal structural variation in grapevine genomes

Cardone¹,

D’Addabbo

Alkan

et al. 2016

The Plant Journal

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“…Recently we reported and identified a group of candidate genes associated with berry size using transcriptomic data. The candidate genes encode for bHLH transcription factors, a GDSL esterase/lipase, a stilbene synthase, HSP17.9-D, among others [20]. Despite these findings, the genetic determinism and the molecular mechanisms behind berry development are complex and futher analysis and data are required to reveal their genetic architecture.…”

Section: Introductionmentioning

confidence: 99%

Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches

et al. 2020

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Background: Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. Results: Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotypephenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. Conclusions: We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.

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“…Transcriptome sequencing is an effective method for genome-wide detection of potential participants of complex traits [18][19][20][21][22][23][24][25][26][27]. Dozens of studies in the field of fruit development and nutrition have implemented sequencing technologies [28][29][30]. In view of these facts, the work presented here was performed to uncover the key phytonutrient-associated genes and their regulators in elm fruit.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways

Zhang¹,

Li²,

Wang³

et al. 2019

Forests

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Plant fruit is an important source of natural active phytonutrients that are profitable for human health. Elm (Ulmus pumila) fruit is considered as natural plant food in China that is rich in nutrients. In the present study, high-throughput RNA sequencing was performed in U. pumila edible fruits and leaves and 11,386 unigenes were filtered as dysregulated genes in fruit samples, including 5231 up- and 6155 downregulated genes. Hundreds of pathways were predicted to participate in seed development and phytonutrient biosynthesis in U. pumila by GO, MapMan, and KEGG enrichment analysis, including “seed maturation”, “glycine, serine, and threonine metabolism” and “phenylpropanoid biosynthesis”. ABA-mediated glucose response-related ethylene-activated signaling pathway (e.g., ABI4) were supposed to associate with elm fruit development; unsaturated fatty acids pathway (e.g., ACX2 and SAD) were predicted to participate in determination of fatty acid composition in elm fruit; flavonoid and coumarins biosynthesis (e.g., CYP98A3 and CCoAOMT1) were demonstrated to correlate with the bioactivity of elm fruits in human cancer and inflammation resistance. To provide more information about fruit developmental status, the qRT-PCR analysis for key genes of “phenylpropanoid biosynthesis” and “alpha-Linolenic acid metabolism” were conducted in samples of young fruits, ripe fruit, old fruit, and leaves. Two biosynthetic pathways for unsaturated fatty acid and Jasmonic acid (JA) were deduced to be involved in fruit development in U. pumila and the phenylpropanoid glycoside, syringin, was speculated to accumulate in the early development stages of elm fruit. Our transcriptome data supports molecular clues for seed development and biologically active substances in elm fruits.

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Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Cited by 19 publications

References 80 publications

Inter‐varietal structural variation in grapevine genomes

Inter‐varietal structural variation in grapevine genomes

Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches

Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways

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