Genetic diversity and apple leaf spot disease resistance characterization assessed by SSR markers

Klabunde, Gustavo H F; Junkes, Camila F.O.; Tenfen, Sarah Z.A.; Dantas, Adriana Cibele de Mesquita; Furlan, Carla Regina Costa; Mantovani, Adelar; Denardi, Frederico; Boneti, José Itamar da Silva; Nodari, Rubens Onofre

doi:10.1590/1984-70332016v16n3a29

Cited by 6 publications

(4 citation statements)

References 33 publications

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“…Although there are variations detected among individuals, the sequences of SSRs are generally conservative. The molecular polymorphisms based on SSRs have shown significant values for the genetic studies of biological stress resistance and marker-assisted molecular breeding ( 66 , 67 ). For example, SSR markers were used to identify loci associated with soybean Phytophthora resistance, and SSR markers associated with blast resistance and sheath blight resistance were detected in a total of 91 rice cultivars ( 68 , 69 ).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis reveals the effect of cold storage time on the expression of genes related to oxidative metabolism in Chinese black truffle

Zhang,

Yang,

Yao

et al. 2024

Front. Nutr.

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Chinese black truffle (Tuber indicum) is a hypogenous fungus of great value due to its distinctive aroma. In this study, both transcriptome and physicochemical analyses were performed to investigate the changes of nutrients and gene expression in truffle fruiting bodies during cold storage. The results of physicochemical analysis revealed the active metabolism of fruiting bodies in cold storage, showing the decreased contents of protein and soluble sugar, the variations in both polyphenol oxidase activity and total phenol content, and the detrimental effect of reactive oxygen species production caused by heavy metals (cadmium and lead) in truffles. Transcriptome analysis identified a total of 139,489 unigenes. Down-regulated expression of genes encoding the catalase-like domain-containing protein (katE), glutaredoxin protein (GRX), a copper/zinc superoxide dismutase (Sod_Cu), and aspartate aminotransferase (AAT) affected the degradation metabolism of intracellular oxides. Ribulose-5-phosphate-3-epimerase (RPE) was a key enzyme in response to oxidative stress in truffle cells through the pentose phosphate pathway (PPP). A total of 51,612 simple sequence repeats were identified, providing valuable resources for further genetic diversity analysis, molecular breeding, and genetic map-ping in T. indicum. Transcription factors GAL4 and SUF4-like protein were involved in glucose metabolism and histone methylation processes, respectively. Our study provided a fundamental characterization of the physicochemical and molecular variations in T. indicum during the cold storage at 4°C, providing strong experimental evidence to support the improvement of storage quality of T. indicum.

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Section: Discussionmentioning

confidence: 99%

Transcriptome analysis reveals the effect of cold storage time on the expression of genes related to oxidative metabolism in Chinese black truffle

Zhang,

Yang,

Yao

et al. 2024

Front. Nutr.

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“…These sequences are conservative, but there will be differences between individuals, which results in site polymorphism can be used in molecular marker-assisted breeding, which is of great significance to the study of plant resistance genetic breeding. At present, SSR markers have been well applied in molecular genetic testing of different resistant plants such as apples [ 54 ]. Sun et al used SSR markers to identify 4 resistance sites related to phytophthora sojae resistance through association analysis [ 55 ].…”

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

et al. 2022

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Background Potato (Solanum tuberosum L.) is one of the world's most important crops, the cultivated potato is frost-sensitive, and low-temperature severely influences potato production. However, the mechanism by which potato responds to low-temperature stress is unclear. In this research, we apply a combination of second-generation sequencing and third-generation sequencing technologies to sequence full-length transcriptomes in low-temperature-sensitive cultivars to identify the important genes and main pathways related to low-temperature resistance. Results In this study, we obtained 41,016 high-quality transcripts, which included 15,189 putative new transcripts. Amongst them, we identified 11,665 open reading frames, 6085 simple sequence repeats out of the potato dataset. We used public available genomic contigs to analyze the gene features, simple sequence repeat, and alternative splicing event of 24,658 non-redundant transcript sequences, predicted the coding sequence and identified the alternative polyadenylation. We performed cluster analysis, GO, and KEGG functional analysis of 4518 genes that were differentially expressed between the different low-temperature treatments. We examined 36 transcription factor families and identified 542 transcription factors in the differentially expressed genes, and 64 transcription factors were found in the AP2 transcription factor family which was the most. We measured the malondialdehyde, soluble sugar, and proline contents and the expression genes changed associated with low temperature resistance in the low-temperature treated leaves. We also tentatively speculate that StLPIN10369.5 and StCDPK16 may play a central coordinating role in the response of potatoes to low temperature stress. Conclusions Overall, this study provided the first large-scale full-length transcriptome sequencing of potato and will facilitate structure–function genetic and comparative genomics studies of this important crop.

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“…(Table 1). The choice of SSR primers was based on the literature data (Klabunde et al 2016, Hawerroth et al 2018) and sampling genomic regions from 12 of the 17 chromosomes of apple species. The PCR reactions were made using multiplex panels, as detailed in Table 1.…”

Section: Polymerase Chain Reaction (Pcr) Conditionsmentioning

confidence: 99%

Pedigree testing for the SCS425 Luiza apple cultivar

Brancher,

Kvitschal,

Bosetto

et al. 2023

Crop Breed. Appl. Biotechnol.

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According to literature, the apple cultivar SCS425 Luiza is a hybrid of Imperatriz ♀ and Cripps Pink ♂ ; however, molecular analysis of gametophytic selfincompatibility alleles showed the presence of an unexpected allele in SCS425 Luiza. This raised doubts about the fidelity of the pedigree. Thus, this study aimed to investigate the real genealogy of the SCS425 Luiza cultivar via fingerprint analysis. A total of 19 pairs of SSR primers covering 12 of the 17 chromosomes were used. 'Imperatriz' was tested as the female parent, and either 'Cripps Pink' or 'Baronesa' was tested as the presumed male parents. The results excluded 'Cripps Pink' as the male parent because most of the markers showed alleles of exclusion with Likelihood ratio (LR) value equal to zero. In contrast, when Baronesa was tested as the male parent, all alleles followed the expected segregation with very high LR values (>10.000). Therefore, it is concluded that the correct genealogy of the SCS425 Luiza cultivar is Imperatriz ♀ and Baronesa ♂ .

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Genetic diversity and apple leaf spot disease resistance characterization assessed by SSR markers

Abstract: Abstract:Among the cultivation problems of apple production in Brazil, Apple Leaf Spot (ALS)

Cited by 6 publications

References 33 publications

Transcriptome analysis reveals the effect of cold storage time on the expression of genes related to oxidative metabolism in Chinese black truffle

Transcriptome analysis reveals the effect of cold storage time on the expression of genes related to oxidative metabolism in Chinese black truffle

Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature

Pedigree testing for the SCS425 Luiza apple cultivar

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