RNA-Seq analysis of Orobanche resistance in Nicotiana tabacum: development of molecular markers for breeding recessive tolerance from ‘Wika’ tobacco variety

Julio, Emilie; Malpica, A.; Cotucheau, J.; Bachet, S.; Volpatti, R.; Decorps, C.; Borne, François Dorlhac de

doi:10.1007/s10681-019-2544-9

Cited by 6 publications

(3 citation statements)

References 56 publications

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“…The conservation and maintenance of germplasm require detailed knowledge of existing genetic diversity. In this context, DNA markers have proven extremely useful in germplasm characterization [12][13][14] and genetic improvement [15][16][17][18][19], for systematic and evolutionary studies [8,[20][21][22], and in the detection of traits of economic importance [23][24][25]. Methods involving polymerase chain reaction (PCR)-based markers, such as inter-simple sequence repeats (ISSR), can detect polymorphism without sequencing the DNA of the target organisms, thereby affording simple, inexpensive and powerful methods for the assessment of genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure of an active germplasm collection of Annona squamosa L.

Sá

Lima

Viana

et al. 2022

Ecological Genetics and Genomics

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Section: Introductionmentioning

confidence: 99%

Genetic diversity and structure of an active germplasm collection of Annona squamosa L.

Sá

Lima

Viana

et al. 2022

Ecological Genetics and Genomics

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“…Zhang et al, used EST-SSR markers of Malus to research genetic diversity of 33 Chaenomeles germplasms and obtain exciting results 17 . With the development the next generation sequencing (NGS) technologies and algorithms for data processing, RNA-seq has become an e cient and economical approach for genomic and trascriptomic resources digging, and has been increasingly considered as an e cient tool to identify transcriptwide molecule markers and to solve the phylogeny relationships innon-model species [18][19][20][21] . Although few studies about transcriptome datasets for individual species, increasing attention has been given to comparative transcriptomes in genus Chaenomeles.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome provides strategy for phylogenetic analysis and SSR marker development in Chaenomeles

Shao

Huang²,

Zhang³

et al. 2021

Preprint

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The genus Chaenomeles has long been considered as an important ornamental, herbal and cash plant and widely cultivated in East Asian. Traditional researches of Chaenomeles mainly focus on evolutionary relationships on phenotypic level. In this study, we conducted RNA-seq for 10 Chaenomeles germplasms supplemented with one related species Docynia delavayi (D. delavay) by Illumina HiSeq2500 platform. After de novo assemblies, we have generated unigenes for each germplasm with numbers from 40 084 to 48 487. By pairwise comparison of the orthologous sequences, 9 659 othologus within the 11 germplasms were obtained, with 6 154 othologous genes identified as single-copy genes. The phylogenetic tree was visualized to reveal evolutionary relationship for these 11 germplasms. GO and KEGG analyses were performed for these common single-copy genes to compare the functional similarities and differences. Selective pressure analysis based on 6 154 common single-copy genes reveals that 45 genes were under positive pressure selection. Most of them involved in plant disease defense system building process. 292 genes containing simple sequence repeats (SSRs) were used to develop SSR markers and compare their function in secondary metabolism pathways. Finally, 10 primers were chosen as SSR markers candidates for Chaenomeles germplasms by comprehensive screening. Our research provides new methodology and reference for future related research in Chaemomeles and is also useful for improvement, breeding and selection project in other related species.

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“…Zhang et al used EST-SSR markers of Malus to research the genetic diversity of 33 Chaenomeles germplasms and obtained exciting results 17 . With the development of next-generation sequencing (NGS) technologies and algorithms for data processing, RNA-seq has become an efficient and economical approach for genomic and transcriptomic resource mining and has been increasingly considered an efficient tool to identify transcript-wide molecular markers and to solve phylogenetic relationships in non-model species 18 – 21 . Although few studies have examined transcriptome datasets for individual species, increasing attention has been given to comparative transcriptomes in the genus Chaenomeles .…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles

Shao

Huang

Zhang

et al. 2021

Sci Rep

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The genus Chaenomeles has long been considered an important ornamental, herbal and cash crop and is widely cultivated in East Asia. Traditional studies of Chaenomeles mainly focus on evolutionary relationships at the phenotypic level. In this study, we conducted RNA-seq on 10 Chaenomeles germplasms supplemented with one outgroup species, Docynia delavayi (D. delavayi), on the Illumina HiSeq2500 platform. After de novo assemblies, we generated from 40,084 to 49,571 unigenes for each germplasm. After pairwise comparison of the orthologous sequences, 9,659 orthologues within the 11 germplasms were obtained, with 6,154 orthologous genes identified as single-copy genes. The phylogenetic tree was visualized to reveal evolutionary relationships for these 11 germplasms. GO and KEGG analyses were performed for these common single-copy genes to compare their functional similarities and differences. Selective pressure analysis based on 6,154 common single-copy genes revealed that 45 genes were under positive selection. Most of these genes are involved in building the plant disease defence system. A total of 292 genes containing simple sequence repeats (SSRs) were used to develop SSR markers and compare their functions in secondary metabolism pathways. Finally, 10 primers were chosen as SSR marker candidates for Chaenomeles germplasms by comprehensive standards. Our research provides a new methodology and reference for future related research in Chaenomeles and is also useful for improvement, breeding and selection projects in other related species.

show abstract

RNA-Seq analysis of Orobanche resistance in Nicotiana tabacum: development of molecular markers for breeding recessive tolerance from ‘Wika’ tobacco variety

Cited by 6 publications

References 56 publications

Genetic diversity and structure of an active germplasm collection of Annona squamosa L.

Genetic diversity and structure of an active germplasm collection of Annona squamosa L.

Comparative transcriptome provides strategy for phylogenetic analysis and SSR marker development in Chaenomeles

Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles

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