EST-SSR marker characterization based on RNA-sequencing of Lolium multiflorum and cross transferability to related species

Pan, Ling; Huang, Ting; Yang, Zhongfu; Tang, Lu; Cheng, Yajuan; Wang, Jianping; Ma, Xiao; Zhang, Xinquan

doi:10.1007/s11032-018-0775-4

Cited by 18 publications

(17 citation statements)

References 28 publications

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“…In molecular ecology and evolutionary studies, universal markers allow comparison of genetic characters among related species 40,41 . In genera or families containing many economically important species, transferable, universal markers can decrease the time and effort required for marker development 42,43 . While the transferability for low-throughput microsatellite (SSR) markers is relatively good, ranging from 27% to 77% in the different taxa of plants and animals 44 , the transferability of high-throughput SNP genetic markers have been as low as 2% 17,45 .…”

Section: Discussionmentioning

confidence: 99%

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

et al. 2020

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Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linkedread de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those~20 million years divergent.

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Section: Discussionmentioning

confidence: 99%

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

et al. 2020

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“…SSRs are well known and widely used in studies of the genetic diversity and population structure of species [44][45][46] . Compared with gSSRs, EST-SSRs are functional molecular markers with the advantages of easier and more efficient development, lower cost and more interspecific transferability [15][16][17] . Furthermore, EST-SSRs can be used directly to obtain gene expression data due to their close link to functional genes 14 .…”

Section: Discussionmentioning

confidence: 99%

“…SSR markers are divided into two types, namely, expressed sequence tag (EST)-SSRs and genomic SSRs (gSSRs), which originate from RNA transcriptome sequencing and arbitrary genome sequencing, respectively. Compared with than gSSRs, EST-SSRs are functional molecular markers with the advantages of easier and more efficient development, lower cost and more interspecific transferability [15][16][17][18] . EST-SSRs developed from transcriptome sequences have also been used in studies of related species 19,20 .…”

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confidence: 99%

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Zang

Xie³

et al. 2020

Sci Rep

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Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

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“…In this study, mono-nucleotide repeats were the most abundant SSR motifs (41.92%), followed by tri-nucleotide (34.87%), which was the same as in Melilotus [ 46 ]. However, di-nucleotide repeats are the most abundant SSR motifs in tall fescue [ 34 ] and Lolium multiflorum [ 47 ], tri-nucleotide repeats are the most abundant SSR motifs in E. sibiricus [ 48 ] and Medicago sativa [ 49 ].…”

Section: Discussionmentioning

confidence: 99%

Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing

Zheng

Zhang

Wan

et al. 2020

Plants

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Elymus sibiricus L. is an important cold-season grass with excellent cold and drought tolerance, good palatability, and nutrition. Flowering time is a key trait that affects forage and seed yield. Development of EST-SSR (expressed sequence tag simple sequence repeat) markers based on flowering genes contributes to the improvement of flowering traits. In the study, we detected 155 candidate genes related to flowering traits from 10,591 unigenes via transcriptome sequencing in early- and late-flowering genotypes. These candidate genes were mainly involved in the photoperiodic pathway, vernalization pathway, central integrator, and gibberellin pathway. A total of 125 candidate gene-based EST-SSRs were developed. Further, 15 polymorphic EST-SSRs closely associated to 13 candidate genes were used for genetic diversity and population structure analysis among 20 E. sibiricus accessions, including two contrasting panels (early-flowering and late-flowering). Among them, primer 28366, designed from heading date 3a (HD3a), effectively distinguished early- and late-flowering genotypes using a specifically amplified band of 175 bp. The polymorphic information content (PIC) value ranged from 0.12 to 0.48, with an average of 0.25. The unweighted pair group method analysis (UPGMA) cluster and structure analysis showed that the 20 E. sibiricus genotypes with similar flowering times tended to group together. These newly developed EST-SSR markers have the potential to be used for molecular markers assisted selection and germplasm evaluation of flowering traits in E. sibiricus.

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EST-SSR marker characterization based on RNA-sequencing of Lolium multiflorum and cross transferability to related species

Cited by 18 publications

References 28 publications

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing

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