Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental Pennisetum Rich. (Poaceae)

Guo, Yidi; Liu, Lingyun; Yue, Yuesen; Fan, Xing; Teng, Wan; Zhang, Hui; Kang, Guolian; Guan, Jin; Chang, Zhihui; Teng, Ke

doi:10.3390/agronomy12071683

Cited by 5 publications

(3 citation statements)

References 42 publications

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“…57 SSR markers distributed across 14 chromosomes of the chayote genome were randomly selected, and primers were designed using Primer 5.0 software (Supplementary Table 1). The specific parameters were: PCR product length of 100–250 bp, primer length of 18–24 bp, annealing temperature of 50–60℃, and GC content of 40–60% [ 40 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Cheng,

Su,

Guo

et al. 2024

BMC Plant Biol

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Background Chayote is a high economic crop in the Cucurbitaceae family, playing an important role in food production, disease treatment and the production of degradable materials in industries. Due to the harsh environment, such as high temperature, drought and frost, some chayote resources are gradually disappearing. It is crucial to collect, characterize, and conserve chayote resources. However, the genetic diversity of chayote resources in China has not been studied so far. Results In this study, we collected 35 individuals of chayote from 14 provinces in China. Subsequently, we found 363,156 SSR motifs from the chayote genome and designed 57 pairs of SSR primers for validation. Out of these, 48 primer pairs successfully amplified bands, with 42 of them showing polymorphism. These 42 primer pairs detected a total of 153 alleles, averaging 3.64 alleles per locus. The polymorphic information content ranged from 0.03 to 0.78, with an average value of 0.41, indicating a high level of polymorphism. Based on the analysis using STRUCTURE, PCoA, and UPGMA methods, the 35 chayote individuals were divided into two major clusters. Through further association analysis, 7 significantly associated SSR markers were identified, including four related to peel color and three related to spine. Conclusions These molecular markers will contribute to the analysis of genetic diversity and genetic breeding improvement of chayote in the future.

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Section: Methodsmentioning

confidence: 99%

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Cheng,

Su,

Guo

et al. 2024

BMC Plant Biol

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“…It was observed that SSR analysis demonstrated significant gene expression in the investigations aimed at identifying genetic diversity in different species (Guo et al 2022, Randazzo et al 2019, Singh et al 2020, Xiong et al, 2019. It was reported that when the genetic composition of the indigenous plant Centaurea corymbosa was analyzed, SSR analysis employing six microsatellite loci indicated a significant divergence across populations.…”

Section: Table 2 Correlation Matrix Of Sinapis Arvensis Populations B...mentioning

confidence: 99%

Genetic diversity of Sinapis arvensis L. (wild mustard) in Türkiye determined by microsatellite markers

Güzel,

Kaya Altop

2024

Bitki Koruma Bülteni

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Herbicides are heavily used to manage Sinapis arvensis, mostly a self-fertilizing weed that poses issues in wheat fields. Cross-fertilization may lead to genetic differentiation of this species. The aim of this study was to identify the genetic diversity of individuals collected from wheat fields across various regions in Turkey. The degree of genetic variation in wild mustard populations was evaluated using 5 simple sequence repeat (SSR) markers in samples taken from 30 different locations in Türkiye. Populations were analyzed using UPGMA (unweighted pair group method with arithmetic mean) and principal component analysis (PCA). The mean genetic diversity (GD) and polymorphism information content (PIC) values were 0.752 and 0.844, respectively. Results showed high genetic variability among individual genotypes within geographic locations. The populations were categorized into two major groups, as indicated by the UPGMA dendrogram generated using Average Linkage. There was no apparent geographic isolation among the genotypes of the studied wild mustard, which displayed a high degree of variability. It is recognized that the primary source of this condition is the adaptability of wild mustard seeds dispersed through various methods across different locations. Despite being a predominantly self-pollinating species, they may also employ some cross-pollination mechanisms. In conclusion, SSR markers prove useful in determining genetic diversity in outcrossing species, especially in cases where no prior genotypic information is available. The study suggests that genetic diversity is maintained in wild mustard populations even with rotational farming practices and the use of herbicides.

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“…Rubrum ( Liu et al., 2022 ) and Pennisetum alopecuroides cv. 'Little Bunny' ( Guo et al., 2022 ). In this study, P. alopecuroides cv.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level reference genome assembly provides insights into the evolution of Pennisetum alopecuroides

Teng,

Guo,

Liu

et al. 2023

Front. Plant Sci.

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Pennisetum alopecuroides is an important forage grass resource, which plays a vital role in ecological environment improvement. Therefore, the acquisition of P. alopecuroides genome resources is conducive to the study of the adaptability of Pennisetum species in ecological remediation and forage breeding development. Here we assembled a P. alopecuroides cv. 'Liqiu' genome at the chromosome level with a size of approximately 845.71 Mb, contig N50 of 84.83Mb, and genome integrity of 99.13% as assessed by CEGMA. A total of 833.41-Mb sequences were mounted on nine chromosomes by Hi-C technology. In total, 60.66% of the repetitive sequences and 34,312 genes were predicted. The genomic evolution analysis showed that P. alopecuroides cv. 'Liqiu' was isolated from Setaria 7.53–13.80 million years ago and from Cenchrus 5.33–8.99 million years ago, respectively. The whole-genome event analysis showed that P. alopecuroides cv. 'Liqiu' underwent two whole-genome duplication (WGD) events in the evolution process, and the duplication events occurred at a similar time to that of Oryza sativa and Setaria viridis. The completion of the genome sequencing of P. alopecuroides cv. 'Liqiu' provides data support for mining high-quality genetic resources of P. alopecuroides and provides a theoretical basis for the origin and evolutionary characteristics of Pennisetum.

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Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental Pennisetum Rich. (Poaceae)

Cited by 5 publications

References 42 publications

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Genome-wide development of simple sequence repeats markers and genetic diversity analysis of chayote

Genetic diversity of Sinapis arvensis L. (wild mustard) in Türkiye determined by microsatellite markers

Chromosome-level reference genome assembly provides insights into the evolution of Pennisetum alopecuroides

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