Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat (Fagopyrum esculentum)

Liu, Yang; Fang, Xiaomei; Tang, Tian; Wang, Yudong; Wu, Yangping; Luo, Jinyu; Wu, Haotian; Wang, Yingqian; Zhang, Jian; Ruan, Renwu; Zhou, Meiliang; Zhang, Kaixuan; Yi, Zelin

doi:10.3390/plants11060742

Cited by 8 publications

(3 citation statements)

References 56 publications

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“…Unigene-derived SSR markers have been widely used in studies of genetic diversity and population genetics, especially for phylogenetically related species [56][57][58]. In this study, polymorphic SSR markers of U. lagopodioides were developed using NGS technology.…”

Section: Discussionmentioning

confidence: 99%

Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae)

2023

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Background Uraria Desv. belongs to the tribe Desmodieae (Fabaceae), a group of legume plants, some of which have medicinal properties. However, due to a lack of genomic information, the interspecific relationships, genetic diversity, population genetics, and identification of functional genes within Uraria species are still unclear. Results Using RNA-Seq, a total of 66,026 Uraria lagopodioides unigenes with a total sequence content of 52,171,904 bp were obtained via de novo assembly and annotated using GO, KEGG, and KOG databases. 17,740 SSRs were identified from a set of 66,026 unigenes. Cross-species amplification showed that 54 out of 150 potential unigene-derived SSRs were transferable in Uraria, of which 19 polymorphic SSRs were developed. Cluster analysis based on polymorphisms successfully distinguished seven Uraria species and revealed their interspecific relationships. Seventeen samples of seven Uraria species were clustered into two monophyletic clades, and phylogenetic relationships of Uraria species based on unigene-derived SSRs were consistent with classifications based on morphological characteristics. Conclusions Unigenes annotated in the present study will provide new insights into the functional genomics of Uraria species. Meanwhile, the unigene-derived SSR markers developed here will be invaluable for assessing the genetic diversity and evolutionary history of Uraria and relatives.

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Section: Discussionmentioning

confidence: 99%

Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae)

2023

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“…The application of transcriptome sequencing technology has resulted in a rapid increase in the number of EST and EST-SSR markers in many plants, including tiger lily ( Sun et al, 2022 ), common buckwheat ( Liu et al, 2022 ), vegetable soybean ( Zhang et al, 2013 ), and Chrysanthemum morifolium Ramat ( Fan et al, 2022 ). However, there have been relatively few reports describing EST-SSR molecular markers in A. esculentus .…”

Section: Discussionmentioning

confidence: 99%

Development and Application of Fruit Color-Related Expressed Sequence Tag-Simple Sequence Repeat Markers in Abelmoschus esculentus on the Basis of Transcriptome Sequencing

Luo

Liu

et al. 2022

Front. Plant Sci.

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Abelmoschus esculentus is a medicinal and edible plant that contains large amounts of active ingredients, including anthocyanins, polysaccharides, flavonoids, and terpenoids. However, because of a relative lack of molecular research, there are few molecular markers applicable for this plant species. In this study, on the basis of A. esculentus fruit color-related transcriptome sequencing data, we analyzed the patterns of simple sequence repeats (SSRs) in differentially expressed genes (DEGs) and revealed the biological processes and metabolic pathways associated with the related genes. We also designed primers for SSR loci to develop SSR molecular markers. Primers were synthesized using a DEG associated with a protein–protein interaction network. Polymorphic SSR markers were screened for the subsequent examination of A. esculentus germplasm resources and fruit color association analysis. The results indicated that 24.98% of the unigenes contained SSR motifs. Single-base (mononucleotide) repeats were the main SSRs, followed by trinucleotide and dinucleotide repeats. We selected 47 expressed sequence tag (EST)-SSR primer pairs for the genotyping of 153 A. esculentus varieties/lines. We ultimately obtained 21 EST-SSR markers suitable for genotyping. A generalized linear model-based association analysis detected two EST-SSR markers significantly associated with A. esculentus fruit color. In conclusion, several EST-SSR and SSR molecular markers in A. esculentus were developed in this study. The fruit color-associated markers may be useful for the molecular marker-assisted breeding of new A. esculentus varieties.

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“…EST-SSR markers developed from transcriptome data have the characteristics of co-dominant inheritance, high polymorphism, good reproducibility, clear bands, convenient statistics, and cost saving. Moreover, since EST-SSRs are derived from expressed gene regions, they can directly reflect the diversity of related genes and are, therefore, widely used in plant genetic breeding and germplasm resource conservation and development [11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

The Diversity of Melia azedarach L. from China Based on Transcriptome-Developed SSR Marker

Cai

Yang

et al. 2022

Forests

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Melia azedarach L. is a native tree species that can be used in a comprehensive way and is widely distributed in all provinces south of the Yellow River in China. Genetic diversity analysis of different M. azedarach germplasm sources is an important basic work for the selection, evaluation, and genetic improvement of M. azedarach germplasm resources. In this study, 100 pairs of SSR primers were designed and synthesized based on M. azedarach transcriptome data, and 16 pairs of reliable SSR primers were finally selected. The developed primers were used to analyze the genetic diversity of M. azedarach from 15 sources in 10 provinces in East, Central, and South China. The results showed that the frequency of the M. azedarach transcriptome SSR loci was high, and the distribution density was high. There were 15 sources of M. azedarach genetic diversity at a moderate level, and genetic variation was mainly present within the sources. The present study further enriches the existing SSR marker database of the M. azedarach family and can provide a reference for genetic diversity analysis and molecularly assisted breeding of M. azedarach plants at the genomic level.

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Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat (Fagopyrum esculentum)

Cited by 8 publications

References 56 publications

Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae)

Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae)

Development and Application of Fruit Color-Related Expressed Sequence Tag-Simple Sequence Repeat Markers in Abelmoschus esculentus on the Basis of Transcriptome Sequencing

The Diversity of Melia azedarach L. from China Based on Transcriptome-Developed SSR Marker

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