Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development

Peng, Fred Y.; Reid, Karen E.; Liao, Nancy; Schlosser, James; Lijavetzky, Diego; Holt, Robert A.; Zapater, José Miguel Martı́nez; Jones, Steven J.M.; Marra, Marco A.; Bohlmann, Jörg; Lund, Steven T.

doi:10.1016/j.gene.2007.07.016

Cited by 48 publications

(36 citation statements)

References 44 publications

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“…These tools include full genome sequences for grape (Jaillon et al, 2007) and papaya (Ming et al, 2008) and large EST collections for apple (Malus domestica; Newcomb et al, 2006), tomato (Fei et al, 2004), and grape (Peng et al, 2007). In kiwifruit, a large database of EST sequences has also become (Varughese et al, 1992).…”

Section: Discussionmentioning

confidence: 99%

Mapping, Complementation, and Targets of the Cysteine Protease Actinidin in Kiwifruit

et al. 2011

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Cysteine proteases (CPs) accumulate to high concentration in many fruit, where they are believed to play a role in fungal and insect defense. The fruit of Actinidia species (kiwifruit) exhibit a range of CP activities (e.g. the Actinidia chinensis variety YellowA shows less than 2% of the activity of Actinidia deliciosa variety Hayward). A major quantitative trait locus for CP activity was mapped to linkage group 16 in a segregating population of A. chinensis. This quantitative trait locus colocated with the gene encoding actinidin, the major acidic CP in ripe Hayward fruit encoded by the ACT1A-1 allele. Sequence analysis indicated that the ACT1A locus in the segregating A. chinensis population contained one functional allele (A-2) and three nonfunctional alleles (a-3, a-4, and a-5) each containing a unique frameshift mutation. YellowA kiwifruit contained two further alleles: a-6, which was nonfunctional because of a large insertion, and a-7, which produced an inactive enzyme. Site-directed mutagenesis of the act1a-7 protein revealed a residue that restored CP activity. Expression of the functional ACT1A-1 cDNA in transgenic plants complemented the natural YellowA mutations and partially restored CP activity in fruit. Two consequences of the increase in CP activity were enhanced degradation of gelatin-based jellies in vitro and an increase in the processing of a class IV chitinase in planta. These results provide new insight into key residues required for CP activity and the in vivo protein targets of actinidin.

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Section: Discussionmentioning

confidence: 99%

Mapping, Complementation, and Targets of the Cysteine Protease Actinidin in Kiwifruit

et al. 2011

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“…To date, little information is available regarding the molecular biology of the seed. Analysis of expressed sequence tags (ESTs) is a rapid and effective method to identify novel genes or to investigate gene expression in different tissues, organs and plants [14,15]. Furthermore, EST libraries and databases could provide valuable resources for functional genomic studies [16].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome (ESTs) of Avocado “Native” Mexicano Early Seed Development Shows Abundance of Regulatory, Antioxidant and Defense Genes

Suárez-Rodríguez¹,

Sánchez-Albarrán²,

HuberLeón-Corona³

et al. 2017

Advances in Seed Biology

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Avocado native "Mexicano" (Persea americana var drymifolia) has been a really important species in agricultural and indigenous medicine. In the agricultural world, it has been the germplasm source for the generation of economically important cultivars like Hass and it is the main source of rootstocks for the world production of Hass avocado fruit. In spite of its importance, little is known about the molecular network of seed-fruit development. The aim of this work was to know the expressed genes (ESTs) during the early avocado native "Mexicano" seed development. Using total RNA we constructed cDNA libraries of fourth months seed development, sequencing, assembling and bioinformatic analysis was made. For validation, a semi-quantitative PCR experiments with the most abundant genes were made. About 5005 ESTs from the 5' representing 1653 possible unigenes were isolated. After assembling process, we have 171 genes that are closely related to Nelumbo nucifera sequences. The transcriptome is dominating by one bHLH transcription factor, three metallothioneins and snakin, suggesting its main role in seed development. Until now, there are no molecular studies in avocado seed development.

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“…In 2001, there were fewer than 400 ESTs from V. vinifera L. that were deposited in GenBank (Moser et al, 2005), but this number rose rapidly to 195,434 by July 1, 2006 (Peng et al, 2007) and 446,664 by July 1, 2012. Establishing sets of ESTs from different cultivars is important for molecular genetics and genomics because some nucleotide variations exist among cultivars.…”

Section: Introductionmentioning

confidence: 99%

Characterization of EST-derived and non-EST simple sequence repeats in an F1 hybrid population of Vitis vinifera L.

Kayesh¹,

Bilkish²,

Liu³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Among different classes of molecular markers, expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping in F 1 hybrid populations of Vitis vinifera L. Recently, because of the availability of an enormous amount of data for ESTs in the public domain, the emphasis has shifted from genomic SSRs to EST-SSRs, which belong to transcribed regions of the genome and may have a role in gene expression or function. The objective of this study was to assess the polymorphisms among 94 F 1 hybrids from "Early Rose" and "Red Globe" using 25 EST-derived and 25 non-EST SSR markers. A total collection of 362,375 grape ESTs that were retrieved from the National Center for Biotechnology Information (NCBI) and 2522 EST-SSR sequences were identified. From them, 205 primer pairs were randomly selected, including 176 pairs that were EST-derived and 29 non-EST SSR primer pairs, for polymerase chain reaction amplification. A total Characterization of EST and non-EST SSRs in grapevine of 131 alleles were amplified using 50 pairs of primers; 78 alleles were amplified using EST-derived SSR primers and 53 were from non-EST SSR primers. At most, 6 and 5 alleles were amplified by EST-derived and non-EST SSR primers, respectively. The EST-derived SSR markers showed a maximum polymorphic information content (PIC) value of 1 and a minimum of 0.33 while non-EST SSR markers had maximum and minimum PIC values of 1 and 0.25, respectively. The average PIC value was 0.56 for EST-derived SSR markers and 0.45 for non-EST SSR markers.

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Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development

Cited by 48 publications

References 44 publications

Mapping, Complementation, and Targets of the Cysteine Protease Actinidin in Kiwifruit

Mapping, Complementation, and Targets of the Cysteine Protease Actinidin in Kiwifruit

Transcriptome (ESTs) of Avocado “Native” Mexicano Early Seed Development Shows Abundance of Regulatory, Antioxidant and Defense Genes

Characterization of EST-derived and non-EST simple sequence repeats in an F1 hybrid population of Vitis vinifera L.

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