A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum

ShaoHua, Yang; Li, Xueting; Huang, Fei; Huang, Yongji; Fan, Haosen; Wu, Jiayun; Wang, Qinnan; Deng, Zuhu; Ru-kai, Chen

doi:10.1371/journal.pone.0197458

Cited by 16 publications

(22 citation statements)

References 35 publications

(28 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A previous study using sweet potato has also shown that many PCR products have two or three bands after electrophoresis (Kou et al 2017). Sugarcane, an allopolyploid plant, also coexists with ancestral ITS sequences in some hybrid generations, resulting in three bands (Yang et al 2018).…”

Section: Discussionmentioning

confidence: 91%

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

et al. 2020

View full text Add to dashboard Cite

The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties ('Beniharuka', 'Annobeni', 'Pungwonmi', 'Hogammi') and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the 'Beniharuka', 'Pungwonmi', and 'Annobeni' sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.

show abstract

Section: Discussionmentioning

confidence: 91%

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

et al. 2020

View full text Add to dashboard Cite

show abstract

“…However, due to insufficient development and rational utilization of germplasm resources, as well as a long breeding cycle [ 7 ], sugarcane breeding is relatively slower than other crops. S. spontaneum is the most important wild sugarcane germplasm [ 57 ] and is a typical polyploid resource that is rich in resistance-related genes [ 58 ]. An in-depth study of the resistance of different ploidies of S. spontaneum and their rational use are thus of profound significance for accelerating sugarcane breeding.…”

Section: Discussionmentioning

confidence: 99%

Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum

Yang

Wang

et al. 2020

BMC Genomics

View full text Add to dashboard Cite

Background Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane varieties. Results A hypoploid clone 12–23 (2n = 54) and hyperploid clone 15–28 (2n = 92) of S. spontaneum were analysed under cold stress from morphological, physiological, and transcriptomic perspectives. Compared with clone 15–28, clone 12–23 plants had lower plant height, leaf length, internode length, stem diameter, and leaf width; depressed stomata and prominent bristles and papillae; and thick leaves with higher bulliform cell groups and thicker adaxial epidermis. Compared with clone 15–28, clone 12–23 showed significantly lower electrical conductivity, significantly higher water content, soluble protein content, and superoxide dismutase activity, and significantly higher soluble sugar content and peroxidase activity. Under cold stress, the number of upregulated genes and downregulated genes of clone 12–23 was higher than clone 15–28, and many stress response genes and pathways were affected and enriched to varying degrees, particularly sugar and starch metabolic pathways and plant hormone signalling pathways. Under cold stress, the activity of 6-phosphate glucose trehalose synthase, trehalose phosphate phosphatase, and brassinosteroid-signalling kinase and the content of trehalose and brassinosteroids of clone 12–23 increased. Conclusions Compared with hyperploid clone 15–28, hypoploid clone 12–23 maintained a more robust osmotic adjustment system through sugar accumulation and hormonal regulation, which resulted in stronger cold tolerance.

show abstract

“…technique for rapid identi cation of putative progeny. Over several decade, molecular markers had been developed by conventional methods such as random ampli ed polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), ampli ed fragment length polymorphism (AFLP), simple sequence repeats (SSR), inter simple sequence repeat (ISSR), and single nucleotide polymorphism (SNP) (Alix et al 1999;Cai et al 2005;Chen et al 2008;Govindaraj et al 2012;Nair and Mary 2006;Yang et al 2018). However, only limited molecular markers was used for identi cation of putative progeny between sugarcane and E. arundinaceus.…”

Section: Recent Advances In Molecular Biology Have Made Pcr-based Marmentioning

confidence: 99%

Efficient anchoring of Erianthus arundinaceus chromatin introgressed into sugarcane by specific molecular markers

Huang¹,

Wu²,

Li³

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for development of high-throughput E. arundinaceus-specific molecular markers at a reasonable cost. Results: In this study, we constructed a SSH library of E. arundinaceus. In total, 288 clones E. arundinaceus-specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E. arundinaceus chromosome repetitive sequence EaITS were developed as E. arundinaceus-specific molecular markers, namely Ea086-128, Ea009-257, and EaITS-278, covering all the E. arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F1, BC1, BC2, BC3, and BC4 progeny between sugarcane and E. arundinaceus. In addition, EaITS-278 was a 45S rDNA-bearing E. arundinaceus chromosome-specific molecular marker for rapid tracking the inherited status of this chromosome in sugarcane background. Three BC3 progeny had apparently lost the 45S rDNA-bearing E. arundinaceus chromosome. Conclusions: We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E. arundinaceus-specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane.

show abstract

A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum

Cited by 16 publications

References 35 publications

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum

Efficient anchoring of Erianthus arundinaceus chromatin introgressed into sugarcane by specific molecular markers

Contact Info

Product

Resources

About

A new method based on SNP of nrDNA-ITS to identify Saccharum spontaneum and its progeny in the genus Saccharum

Cited by 16 publications

References 35 publications

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs

Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum

Efficient anchoring of Erianthus&nbsp;arundinaceus chromatin introgressed into sugarcane by specific molecular markers

Contact Info

Product

Resources

About

Efficient anchoring of Erianthus arundinaceus chromatin introgressed into sugarcane by specific molecular markers