Development of SSR and SNP markers for identifying opium poppy

Zhang, Yanjun; Wang, Jing; Yang, Lulu; Niu, Jiaxin; Huang, Ruoqi; Yuan, Fang; Liang, Qiong

doi:10.1007/s00414-022-02810-4

Cited by 8 publications

(5 citation statements)

References 21 publications

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“…Molecular markers, such as SSR, SNP, and indel, are widely used in molecular identification, molecular marker-assisted selection, and genetic selection in animals and plants ( Jiang et al, 2019 ; Zhang et al, 2022 ). In this study, we detected 22,780 SSRs in 16,163 sequences.…”

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome analysis of Zanthoxylum nitidum (Roxb.) DC.

Zhu

Huang

Wei

et al. 2023

PeerJ

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Zanthoxylum nitidum (Roxb.) DC. (Z. nitidum) is a type of Chinese Dao-di herb, also called Liangmianzhen, which is widely used to treat arthralgia, rheumatic arthralgia, and stomach pain. However, genomic resources for Z. nitidum are still scarce. This study provides transcriptomic resources for Z. nitidum by applying single-molecule real-time (SMRT) sequencing technology. In total, 456,109 circular consensus sequencing (CCS) reads were generated with a mean length of 2,216 bp from Z. nitidum roots, old stems, young branches, leaves, flowers, and fruits. Of these total reads, 353,932 were full-length nonchimeric (FLNC) reads with an average length of 1,996 bp. A total of 16,163 transcripts with a mean length of 1,171 bp were acquired. Of these transcripts, 14,231 (88%) were successfully annotated using public databases. Across all the 16,163 transcripts, we identified 6,255 long non-coding RNAs (lncRNAs) and 22,780 simple sequence repeats (SSRs). Furthermore, 3,482 transcription factors were identified. Among the SSR loci, 1–3 nucleotide repeats were dominant, occupying 99.36% of the total SSR loci, with mono-, di-, and tri-nucleotide repeats accounting for 61.80%, 19.89%, and 5.02% of the total SSR loci, respectively. A total of 36 out of 100 randomly selected primer pairs were verified to be positive, 20 of which showed polymorphism. These findings enrich the genetic resources available for facilitating future studies and research on relevant topics such as population genetics in Z. nitidum.

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Section: Discussionmentioning

confidence: 99%

Full-length transcriptome analysis of Zanthoxylum nitidum (Roxb.) DC.

Zhu

Huang

Wei

et al. 2023

PeerJ

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“…For this purpose, a Pscp1 variable number of tandem repeat (VNTR) markers derived from a variant region of the chloroplast genome [20] as well as SNP markers [21] were developed and validated. Different Papaver species were also distinguished using many SSR markers [22]. SSR markers were also used for ecological studies and analyses of the genetic diversity within P. rhoeas L. in agricultural ecosystems [23].…”

Section: Discussionmentioning

confidence: 99%

New Set of EST-STR Markers for Discrimination of Related Papaver somniferum L. Varieties

Kaňuková,

Ondreičková,

Mihálik

et al. 2023

Life

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Papaver somniferum L. is cultivated for its edible seeds and for the production of alkaloids. A serious problem in seed trade and processing is the intentional mixing of excellent food-quality seeds with non-food-grade-quality seeds. Tracking the correct or illegitimate handling of seeds requires an efficient method for discrimination and individualization of poppy varieties. As in human and animal forensics, DNA variable regions containing short tandem repeats (STRs) located either in non-coding DNA or in gene sequences (EST-STRs) are preferred markers for discrimination between genotypes. Primers designed for 10 poppy EST-STR loci not analyzed so far were tested for their discriminatory ability on a set of 23 related P. somniferum L. genotypes. Thirty-three EST-STR alleles were identified together. Their polymorphic information content (PIC) values were in the range of 0.175–0.649. The PI value varied in the range of 0.140–0.669, and the cumulative PI was 1.2 × 10−5. PIsibs values varied between 0.436 and 0.820 and the cumulative value was lower (5.0 × 10−3). All analyzed genotypes were distinguished mutually, each with its own unique EST-STR profile. These newly developed EST-STR markers more effectively discriminated P. somniferum L. genotypes, even those genotypes whose DNA profiles were previously identical.

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“…Based on these features, chloroplast genome SSRs are mainly used in population genetic variation and gene flow analyses [43][44][45] and are considered valuable markers. The significance and applicability of cpSSR markers have been reported in various other Papaveroideae species, such as using cpSSR markers to assess the population genetics of opium poppy [46]. In this study, the numbers, types, and distribution of cpSSRs were analyzed in D. leptopodum and related chloroplast genomes.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

Wang

et al. 2022

BMC Genomics

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Background Dicranostigma leptopodum (Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown. Here, we sequenced and analyzed the chloroplast genome of D. leptopodum to discover its genome structure, organization, and phylogenomic position within the subfamily Papaveroideae. Results The chloroplast genome size of D. leptopodum was 162,942 bp, and D. leptopodum exhibited a characteristic circular quadripartite structure, with a large single-copy (LSC) region (87,565 bp), a small single-copy (SSC) region (18,759 bp) and a pair of inverted repeat (IR) regions (28,309 bp). The D. leptopodum chloroplast genome encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The dynamics of the genome structures, genes, IR contraction and expansion, long repeats, and single sequence repeats exhibited similarities, with slight differences observed among the eight Papaveroideae species. In addition, seven interspace regions and three coding genes displayed highly variable divergence, signifying their potential to serve as molecular markers for phylogenetic and species identification studies. Molecular evolution analyses indicated that most of the genes were undergoing purifying selection. Phylogenetic analyses revealed that D. leptopodum formed a clade with the tribe Chelidonieae. Conclusions Our study provides detailed information on the D. leptopodum chloroplast genome, expanding the available genomic resources that may be used for future evolution and genetic diversity studies.

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Development of SSR and SNP markers for identifying opium poppy

Cited by 8 publications

References 21 publications

Full-length transcriptome analysis of Zanthoxylum nitidum (Roxb.) DC.

Full-length transcriptome analysis of Zanthoxylum nitidum (Roxb.) DC.

New Set of EST-STR Markers for Discrimination of Related Papaver somniferum L. Varieties

Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae

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