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

Li, Zhen; Lan, Yun; Gao, Zhiqi; Tian, Weijun; Ren, Xiaomin; Zhao, Yan

doi:10.3389/fpls.2022.837787

Cited by 5 publications

(5 citation statements)

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“…The SSR molecular markers have been widely used in crop genetic diversity analysis because of advantages such as their abundant quantity, codominance, simple detection, and stable results [ 19 , 20 ]. In the current work, 22 polymorphic SSR markers successfully assessed the genetic relationships and genetic diversity of 40 stock cultivars.…”

Section: Discussionmentioning

confidence: 99%

“…It has been discovered that SSRs are ubiquitous in genomes, with repeat units of 1–6 nt. As the most useful DNA marker system for variety identification and germplasm management, SSR molecular markers have several advantages due to their abundance, high polymorphism, multiple alleles, co-dominance, low-cost, and the ease of assay by PCR [ 17 , 18 ], which have been applied extensively in genetic analysis, such as the analysis of population structure and genetic diversity [ 19 , 20 ], QTL mapping [ 21 , 22 , 23 ], marker-assisted selection breeding [ 24 , 25 , 26 ], and DNA fingerprinting [ 27 , 28 ], etc. SSR molecular markers are rarely used in M. incana [ 11 , 14 ], which is largely due to the fact that SSR molecular markers have not been developed in M. incana .…”

Section: Introductionmentioning

confidence: 99%

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First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

Tan

Zhang

Chen

et al. 2023

Plants

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Stock (Matthiola incana (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of M. incana. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of M. incana. In this study, a high-quality genome of M. incana was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 M. incana varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on M. incana.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

Tan

Zhang

Chen

et al. 2023

Plants

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“…One hundred and three EST-SSR primer pairs were selected after polymorphism test. The methods used have been described in Li et al (2022) . The sequence data was deposited in the NCBI SRA (Sequence read archive) database ( ) (Accession numbers: , , , , , ).…”

Section: Methodsmentioning

confidence: 99%

“…The sequence data was deposited in the NCBI SRA (Sequence read archive) database ( ) (Accession numbers: , , , , , ). The sixteen pairs of EST-SSR primers used in the experiment were randomly selected from the 103 pairs of polymorphic primers developed and used in Russian wildrye genetic structure analysis by Li et al (2022) and synthesized by Sangon Biotech (Shanghai, China).…”

Section: Methodsmentioning

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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“…Thirty dense tillering (DT) plants and another thirty sparse tillering (ST) plants were selected from the same seventeen accessions. The RNA extraction, cDNA library construction and sequencing procedures were described in our previous publication [82].…”

Section: Rna Extraction Cdna Library Construction and Sequencingmentioning

confidence: 99%

Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology

Lan

Ren

et al. 2022

BMC Plant Biol

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Background Tillering is a complicated process in plant and is a significant trait that affects biomass and seed yield of bunch grass Psathyrostachys juncea, a typical perennial forage species. To clarify the regulatory mechanisms of tillering in P. juncea and to explore related candidate genes could be helpful to improve the seed and forage yield of perennial gramineous forages. We selected the tiller node tissues of P. juncea for transcriptome sequencing to determine the differentially expressed genes (DEG) between dense and sparse tillering genotypes. The metabolic pathway was studied, candidate genes were screened, and reference genes stability were evaluated. Results The results showed that approximately 5466 DEGs were identified between the two genotypes with dense and sparse tillers of P. juncea, which significantly differed in tiller number. Tillering regulation pathways analysis suggested that DEGs closely related to the biosynthesis of three plant hormones, namely auxin (IAA), cytokinin (CTK), and strigolactones (SLs), while “biosynthesis of lignin” and “nitrogen metabolism” have remarkable differences between the dense and sparse tillering genotypes. Meanwhile, the reference gene Actin1, having the best stability, was screened from twelve genes with highest expression level and was used in verification of ten tillering related candidate genes. Conclusions The tillering mechanism of perennial grass P. juncea was expounded by transcriptome analysis of tiller node tissues. We demonstrated that dense-tillering genotypes may be distinguished by their low expression patterns of genes involved in SL, IAA, and high expression patterns of genes involved in CTK biosynthesis at the tillering stage, and nitrogen metabolism and lignin biosynthesis can also affect the number of tillers. Furthermore, the expression level of ten tillering related candidate genes were verified using Actin1 as reference gene. These candidate genes provide valuable breeding resources for marker assisted selection and yield traits improvement of P. juncea.

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

Cited by 5 publications

References 67 publications

First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

First Report on Development of Genome-Wide Microsatellite Markers for Stock (Matthiola incana L.)

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

Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology

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