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

Zheng, Yonghua; Zhang, Zongyu; Wan, Yiyang; Tian, Jiao-Yang; Xie, Wengang

doi:10.3390/plants9101371

Cited by 7 publications

(7 citation statements)

References 66 publications

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“…GenAlEx 6.503 ( Peakall and Smouse, 2010 ) was used to calculate the number of alleles (Na), number of effective alleles (Ne), and Shannon’s information index (I). The polymorphic information (PIC) and expected heterozygosity (He) were calculated based on the formula of PIC = 1 − p 2 − q 2 , where p and q are frequency of present/absent band; He = 1 − Σ pi 2 , where pi is frequency of the i -th allele ( Zhang et al, 2019 ; Zheng et al, 2020 ). The Nei genetic distance (GD) matrix was obtained by Freetree ( Hampl et al, 2001 ), the UPGMA (unweighted pair-group method with arithmetic means) dendrogram was constructed, and the visualization was performed on Figtree ( Hampl et al, 2001 ).…”

Section: Methodsmentioning

confidence: 99%

Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera

Xiong

Yang²,

Xiong³

et al. 2022

Front. Plant Sci.

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As a typical psammophyte of the Triticeae, Kengyilia melanthera possesses high feeding potential and great utilization values in desertification control in the Qinghai-Tibet Plateau. However, few gene function and genetic studies have been performed in K. melanthera. In this study, single-molecule real-time sequencing technology was used to obtain the full-length transcriptome sequence of K. melanthera, following the functional annotation of transcripts and prediction of coding sequences (CDSs), transcription factors (TFs), and long noncoding RNA (lncRNA) sequences. Meanwhile, a total of 42,433 SSR loci were detected, with 5′-UTRs having the most SSR loci and trinucleotide being the most abundant type. In total, 108,399 SSR markers were designed, and 300 SSR markers were randomly selected for diversity verification of K. melanthera. A total of 49 polymorphic SSR markers were used to construct the genetic relationships of 56 K. melanthera accessions, among which 21 SSR markers showed good cross-species transferability among the related species. In conclusion, the full-length transcriptome sequence of the K. melanthera will assist gene prediction and promote molecular biology and genomics research, and the polymorphic SSR markers will promote molecular-assisted breeding and related research of K. melanthera and its relatives.

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Section: Methodsmentioning

confidence: 99%

Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera

Xiong

Yang²,

Xiong³

et al. 2022

Front. Plant Sci.

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“…EST-SSR is the identification of SSR by electronic screening using existing EST sequences, followed by PCR detection ( Zheng et al, 2020 ). Using EST to develop SSR avoids the cloning and sequencing steps in the process of developing SSR primers, makes full use of existing data, and reduces the development costs ( Fan M. et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski

Lan

Gao

et al. 2022

Front. Plant Sci.

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Psathyrostachys juncea is a perennial forage grass which plays an important role in soil and water conservation and ecological maintenance in cold and dry areas of temperate regions. In P. juncea, a variety of biotic and abiotic stress related genes have been used in crop improvement, indicating its agronomic, economic, forage, and breeding value. To date, there have been few studies on the genetic structure of P. juncea. Here, the genetic diversity and population structure of P. juncea were analyzed by EST-SSR molecular markers to evaluate the genetic differentiation related to tillering traits in P. juncea germplasm resources. The results showed that 400 simple sequence repeat (SSR) loci were detected in 2,020 differentially expressed tillering related genes. A total of 344 scored bands were amplified using 103 primer pairs, out of which 308 (89.53%) were polymorphic. The Nei’s gene diversity of 480 individuals was between 0.092 and 0.449, and the genetic similarity coefficient was between 0.5008 and 0.9111, with an average of 0.6618. Analysis of molecular variance analysis showed that 93% of the variance was due to differences within the population, and the remaining 7% was due to differences among populations. Psathyrostachys juncea materials were clustered into five groups based on population genetic structure, principal coordinate analysis and unweighted pair-group method with arithmetic means (UPGMA) analysis. The results were similar between clustering methods, but a few individual plants were distributed differently by the three models. The clustering results, gene diversity and genetic similarity coefficients showed that the overall genetic relationship of P. juncea individuals was relatively close. A Mantel test, UPGMA and structural analysis also showed a significant correlation between genetic relationship and geographical distribution. These results provide references for future breeding programs, genetic improvement and core germplasm collection of P. juncea.

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“…The results of SSR markers can be verified by PCR, and the working cycle can be greatly shortened ( Nadeem et al, 2014 ; Li et al, 2019 ; Zhong et al, 2021 ). EST-SSR is the identification of SSR by electronic screening using existing EST sequences, followed by PCR detection ( Zhang et al, 2020 ). Using EST to develop SSR avoids the cloning and sequencing steps in the process of developing SSR primers, makes full use of existing data, and reduces development costs ( Fan et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye

Gao

Lan

et al. 2022

PeerJ

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Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is widely distributed in the high latitude areas of Eurasia. It plays an important role in grassland ecosystem maintenance, as well as being a valuable palatable forage species for livestock and wildlife. Russian wildrye germplasm has rich phenotypic and genetic diversity and has potential for improvement through crossbreeding. In this study, fifteen Russian wildrye hybrid combinations were produced and one F1 population with 123 putative hybrids was obtained by crossing two individual plants with significant differences in nutritional characteristics and reproductive tiller number. Twelve phenotypic traits of the F1 population were measured for three consecutive years, and ten of the twelve traits were in line with the genetic characteristics of quantitative traits. Hybrid superiority was revealed among F1 hybrids in both nutritional and reproductive traits. One non-recurrent parent plant with the highest PCA-synthesis score was selected and used to make a backcross with the ‘BOZOISKY SELECT’ male parent, and 143 putative BC1 hybrids were obtained. Sixteen pairs of EST-SSR primers were randomly selected from polymorphic primers derived from different expressed tiller trait related genes. Three primer pairs that amplified both the paternal and maternal characteristic band were used to assess the purity of the F1 population, and three primer pairs (with one shared primer pair) were used to identify the BC1 population. The hybrid purity was 96.75% for the F1 population and 95.80% for the BC1 population, and the results were confirmed by self-fertility test through bagging isolation. The genetic similarity coefficients between the F1 progeny and the male parent ranged from 0.500 to 0.895, and those between the BC1 progeny and the male parent ranged from 0.667 to 0.939. A subset of individuals in the BC1 population had closer genetic distance to the recurrent parent, and genetic variation within the BC1 population decreased compared to the F1 population.

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

Cited by 7 publications

References 66 publications

Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera

Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera

EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski

Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye

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