SNP development and diversity analysis for Ginkgo biloba based on transcriptome sequencing

Wu, Yaqiong; Zhou, Qi; Huang, Shujing; Wang, Guibin; Li, Xu

doi:10.1007/s00468-018-1803-z

Cited by 16 publications

(9 citation statements)

References 49 publications

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“…SNP markers have been used to evaluate diversity within many species, including Populus trichocarpa [ 31 ], Vitis vinifera [ 32 ], and Ginkgo biloba [ 33 ]. SNPs derived from transcriptome sequencing is a more efficient strategy for characterizing diversity in non-model or massive-genome species, since the sequences are detected on the coding regions rather than on the entire genome.…”

Section: Discussionmentioning

confidence: 99%

A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield

et al. 2020

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Background: Masson pine (Pinus massoniana Lamb.), the dominant native coniferous species in southern China, is commercially important for supplying timber and oleoresin. However, knowledge of the genetic variability of masson pine germplasm is still limited. In this study, the genetic diversity and population structure of masson pine germplasm were assessed using 204 wild accessions from 10 main distribution regions using 94,194 core singlenucleotide polymorphisms (SNPs) obtained from transcriptome sequencing data. Results: The average expected heterozygosity was 0.2724, implying abundant genetic diversity within masson pine germplasm. Analysis of molecular variance (AMOVA) revealed that 3.29% of the variation was sourced from genetic differentiation. Structure analysis identified two geographically distinct groups. Discriminant analysis of principal components (DAPC) showed that one of those groups was further divided into two clusters. Sichuan and Chongqing provenance is the geographical origin, which diffused outward along two different lines. Oleoresin yield is reflected in the evolution of the two groups, and exhibits two different trends along the two lines of diffusion. The oleoresin yield may be associated with the genes of chitinase, CYP720B, cytochrome P450, ABC transporter, and AP2/ethylene-responsive transcription factor (ERF) based on SNPs and expression. Conclusions: SNP markers from transcriptome sequencing are highly capable of evaluating genetic diversity within different species, as well as the genetic control of objective traits. The functions of these genes will be verified in future studies, and those genes strongly associated with oleoresin yield will be used to improve yields by means of early genotype selection and genetic engineering.

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Section: Discussionmentioning

confidence: 99%

A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield

et al. 2020

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“…As a multifunctional tree species, ginkgo has important economic and medicinal values [20] and has attracted researchers’ attention with many studies have been reported on the origin and evolution, cytology, molecular biology, tree breeding and medicinal value of ginkgo [19, 21–25]. Ginkgo is also a popular ornamental species and widely cultivated worldwide [24]. However, there are few studies on its ornamental characteristics [26].…”

Section: Introductionmentioning

confidence: 99%

Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L

Guo

Wang

et al. 2019

BMC Plant Biol

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BackgroundLong noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood.ResultsIn this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks.ConclusionsThis study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.

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“…The SNP markers have been used to evaluate diversity within many species, such as Populus trichocarpa [31], Vitis vinifera [32], Ginkgo biloba [33]. SNPs called from transcriptome sequencing is a more efficient strategy for characterizing diversity in non-model or massive-genome species, since the sequences are detected on the coding regions rather than the whole genome.…”

Section: Discussionmentioning

confidence: 99%

A Transcriptomic Variation Map Provides Insights into The Genetic Basis of Pinus massoniana Evolution and Association of Oleoresin Yield

Liu

Xie

Liu

et al. 2020

Preprint

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Background: Masson pine (Pinus massoniana Lamb.), the dominant native coniferous species in South China, is commercially important for timber and oleoresin. However, knowledge of the genetic variability of the masson pine germplasm is still scarce. Here, the genetic diversity and population structure of masson pine germplasm were assessed using 204 wild accessions from 10 main distribution regions by 94,194 core SNPs obtained from transcriptome sequencing data. Results: The average expected heterozygosity was 0.2724, implying abundant genetic diversity within masson pine germplasm. Analysis of molecular variance (AMOVA) revealed that 3.29% variation sourced from the genetic differentiation. Structure analysis identified two geographically distinct groups. Discriminant analysis of principal components (DAPC) showed one geographically distinct group was divided two clusters furtherly. Sichuan and Chongqing provenance is the geographical origin, and diffuses outward along two lines. Oleoresin yield might be reflected by the evolution, and exhibits two different changing trends between two diffusing line. It may be associated with the genes of chitinase, CYP720B, Cytochrome P450, ABC transporter and AP2/ERF based on SNPs and expression. Conclusions: SNP markers by transcriptome sequencing have a strong power in evaluating genetic diversity within species and the genetic control of objective trait. The function of these genes will be verified and the strong associated genes with oleoresin yield will be used in the improvement of oleoresin yield by early genotype selection or genetic engineering.

show abstract

SNP development and diversity analysis for Ginkgo biloba based on transcriptome sequencing

Cited by 16 publications

References 49 publications

A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield

A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield

Transcriptional profiling of long noncoding RNAs associated with leaf-color mutation in Ginkgo biloba L

A Transcriptomic Variation Map Provides Insights into The Genetic Basis of Pinus massoniana Evolution and Association of Oleoresin Yield

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