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  • Open Access


    Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing

    Luli Li1,2, Nigel G. Halford3, Huihui Wang4, Yingjie Zong1, Zhenzhu Guo1, Ruiju Lu1, Chenghong Liu1, Zhiwei Chen1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1275-1287, 2023, DOI:10.32604/phyton.2023.026946

    Abstract Barley (Hordeum vulgare L.) is an important economic crop for food, feed and industrial raw materials. In the present research, 112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing (GBS), and the genetic diversity and population structure were analyzed. The results showed that 210,268 Single Nucleotide Polymorphisms (SNPs) were present in total, and the average poly-morphism information content (PIC) was 0.1642. Genetic diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups, with morphological traits of row-type and adherence of the hulls the main distinguishing factors between groups. Genotypes… More >

  • Open Access


    Nitric oxide alleviates cadmium-impeded growth by limiting ROS accumulation in pea seedlings


    BIOCELL, Vol.46, No.12, pp. 2583-2593, 2022, DOI:10.32604/biocell.2022.021732


    Cadmium (Cd) causes oxidative stress, which leads to the oxidation of various biomolecules by the production of reactive oxygen species (ROS) to facilitate programmed cell death (PCD). The antioxidant defense system fails to detoxify ROS when it is produced in excess. Nitric oxide (NO), a gaseous free radical and a phytohormone, regulates various physiological processes of plants. Therefore, this work was undertaken to study the effects of the application of exogenous sodium nitroprusside (SNP, a NO donor) on growth parameters, oxidative stress, accumulation of secondary metabolites, and activities of antioxidant enzymes under Cd stress. Mild (50 µM) and severe (200… More >

  • Open Access


    Population Structure Analysis and Genome-Wide Association Study of Tea (Camellia sinensis (L.) K untze) Germplasm in Qiannan, China, Based on SLAFSeq Technology

    Fen Zhang1, Weili Tian1, Lu Cen1, Litang Lv2, Xiaofang Zeng1, Yulu Chen1, Yichen Zhao2,*, Yan Li1,*

    Phyton-International Journal of Experimental Botany, Vol.91, No.4, pp. 791-809, 2022, DOI:10.32604/phyton.2022.018104

    Abstract Duyun Maojian tea is a famous tea in China. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of 2 leaf traits of 123 tea plants in Qiannan, China. A total of 462,019 SLAF tags and 11,362,041 single-nucleotide polymorphism (SNP) loci were obtained. The results of phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 123 tea germplasms were clustered into three groups, and the heterozygosity rates for Groups I, II, and II were 0.206, 0.224, and 0.34, respectively. Generally, tea germplasms in… More >

  • Open Access


    Identification of Polymorphic Markers by High-Resolution Melting (HRM) Assay for High-Throughput SNP Genotyping in Maize

    Zhigang Shang1,2, Yongzhe Zhu3, Xinmei Guo1,2, Meiai Zhao1,4,*

    Phyton-International Journal of Experimental Botany, Vol.90, No.6, pp. 1711-1725, 2021, DOI:10.32604/phyton.2021.015048

    Abstract The development of next generation sequencing (NGS) and high throughput genotyping are important techniques for the QTL mapping and genetic analysis of different crops. High-resolution melting (HRM) is an emerging technology used for detecting single-nucleotide polymorphisms (SNPs) in various species. However, its use is still limited in maize. The HRM analysis was integrated with SNPs to identify three types of populations (NIL population, RIL population and natural population), and the useful tags were screened. The patterns of temperature-shifted melting curves were investigated from the HRM analysis, and compared these with the kit. Among all 48 pairs of primers, 10 pairs… More >

  • Open Access


    Transcriptome based high-throughput SSRs and SNPs discovery in the medicinal plant Lagenaria siceraria


    BIOCELL, Vol.45, No.2, pp. 371-386, 2021, DOI:10.32604/biocell.2021.013869

    Abstract Lagenaria siceraria (Molina) Standley has unique biological characteristics with high nutritional and medicinal values. It is an important pharmaceutical plant with various biologically active ingredients. Genetic improvement and deeper genomic studies require a rich resource of molecular markers. The application of next-generation sequencing technology, especially for transcriptome profiling, has greatly facilitated high throughput single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) discovery. In this study, we sequenced the transcriptome of three major cultivars of L. siceraria and obtained 64.88 GB of clean data. The assembled high-quality reads were clustered into 89,347 unigenes, which were annotated by non-redundant protein database,… More >

  • Open Access


    Genome-Wide Identification of Candidate Genes Associated with β-glucan Traits in a Hulled and Hulless Barley (Hordeum vulgare L.) Population

    Longhua Zhou1,2,#, Ting He1,2,#, Guimei Guo1,2, Jing Li1,2, Ruiju Lu1,2, Yingbo Li1,2,*, Chenghong Liu1,2,*

    Phyton-International Journal of Experimental Botany, Vol.89, No.4, pp. 987-997, 2020, DOI:10.32604/phyton.2020.011728

    Abstract Barley grain is a valuable source of β-glucan, which is an important component of dietary fiber with significant human health benefits. Although the genetic basis of β-glucan biosynthesis has been widely studied, a genome-wide association study (GWAS) is still required for a scan of the candidate genes related to the complex quantitative trait based on the high-quality barley reference genome. In this study, a GWAS was conducted using a population composed of 87 barley landraces (39 hulled and 48 hulless, β-glucan from 2.07% to 6.56%) with 191,098 nucleotide polymorphisms (SNPs) markers to cover the chromosomes with the highest density. The… More >

  • Open Access


    Association Analysis of the Growth of Black Poplar (Populus Nigra L.) Under Contrasting Nitrogen Levels

    Xihua Liu1, Changjun Ding2, Xiaohua Su2,*

    Phyton-International Journal of Experimental Botany, Vol.88, No.4, pp. 425-433, 2019, DOI:10.32604/phyton.2019.08285

    Abstract The European black poplar (Populus nigra L.) has been used as a germplasm resource for the breeding of new poplar varieties around the world. The identification and screening of its high nitrogen use efficiency genotypes could enable the breeding of new resource-efficient poplar varieties. The accessions were screened using MALDI-TOF MS genotyping technology for ammonium transporter (AMT) and nitrate transporters (NRT) genes against phenotypic data for seedling height and ground diameter traits, in both low and high nitrogen environments. Allele re-sequencing of seven genes related to root development was carried out using the minisequencing method. By cluster analysis, 101 accessions… More >

  • Open Access


    Association between preterm birth risk and polymorphism and expression of the DNA repair genes OGG1 and APE1 in Saudi women

    Arwa Osama NEMER1, Mohammad Saud AL ANAZI2, Ramesa Shafi BHAT1*, Arjumand S. WARSY3, Zeneb A BABAY4, Mohammad H. ADDAR4, Jilani SHAIK2, Sooad AL-DAIHAN1

    BIOCELL, Vol.42, No.1, pp. 1-6, 2018, DOI:10.32604/biocell.2018.07005

    Abstract Genomic instability and mutations caused by increases in oxidative stress during pregnancy can damage the fetoplacental unit and can upshot preterm birth. Oxidative damage to DNA may possibly be involved in etiology of preterm birth (PTB) which can be repaired by DNA repair gene. In the present study, we assessed the association of base excision repair gene family by analyzing the association of single nucleotide polymorphisms and genes expression in 8-oxoguanine glycosylase-1 (OGG1) and apurinic-apyrimidinic endonuclease 1 (APE1) genes with risk of preterm birth in Saudi women. We analyzed genotypes of four single nucleotide polymorphisms (SNPs) (rs1052133, rs293795, rs2072668 and… More >

  • Open Access


    XRCC1 Arg399Gln and Arg194Trp polymorphisms regulate XRCC1 expression and chemoresistance of non-small cell lung cancer cells

    Dairong LI1, Xianlu ZHUO1,2, Lumi HUANG1, Xiaohui JI1, Donglin WANG1

    BIOCELL, Vol.43, No.3, pp. 139-144, 2019, DOI:10.32604/biocell.2019.06460

    Abstract X-ray repair cross-complementing protein 1 (XRCC1) could repair cisplatin-induced DNA damage. XRCC1 Arg399Gln and Arg194Trp variants alter XRCC1 expression and function, leading to changes in cancer sensitivity to cisplatin treatment. This study aimed to investigate the effects of XRCC1 Arg399Gln and Arg194Trp polymorphisms on cell viability, apoptosis and XRCC1 expression in cisplatin-sensitive A549 and cisplatin-resistant A549/DDP nonsmall cell lung cancer (NSCLC) cells. Plasmids carrying XRCC1 Arg399Gln and Arg194Trp were constructed and transfected into A549 and A549/DDP cells. RT–PCR, Western blot, MTT assay, and flow cytometry analysis were performed to assess cell viability, apoptosis, and XRCC1 expression. Compared to control cells,… More >

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