scholarly journals Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1440
Author(s):  
Gunlayarat Bhusudsawang ◽  
Ratchanee Rattanawong ◽  
Thitaporn Phumichai ◽  
Wirulda Pootakham ◽  
Sithichoke Tangphatsornruang ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Single Molecule ◽  
Plant Cell Wall ◽  
Rubber Tree ◽  
Cost Effective ◽  
Tree Breeding ◽  
Snp Markers ◽  
Intron Length Polymorphism ◽  
Breeding Lines ◽  
Gene Based Markers

Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

scholarly journals Transcriptome Analysis of Distinct Cold Tolerance Strategies in the Rubber Tree (Hevea brasiliensis)

2018 ◽  
Author(s):  
Camila Campos Mantello ◽  
Lucas Boatwright ◽  
Carla Cristina da Silva ◽  
Erivaldo Jose Scaloppi ◽  
Paulo de Souza Gonçalves ◽  
...  
Keyword(s):  
Cold Tolerance ◽  
Hevea Brasiliensis ◽  
Amazon Basin ◽  
Rubber Tree ◽  
Tree Breeding ◽  
Snp Markers ◽  
Large Field ◽  
New Variety ◽  
Cold Response ◽  
Cold Temperatures

AbstractNatural rubber is an indispensable commodity used in approximately 40,000 products and is fundamental to the tire industry. Among the species that produce latex, the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg.], a species native to the Amazon rainforest, is the major producer of latex used worldwide. The Amazon Basin presents optimal conditions for rubber tree growth, but the occurrence of South American leaf blight, which is caused by the fungus Microcyclus ulei (P. Henn) v. Arx, limits rubber tree production. Currently, rubber tree plantations are located in scape regions that exhibit suboptimal conditions such as high winds and cold temperatures. Rubber tree breeding programs aim to identify clones that are adapted to these stress conditions. However, rubber tree breeding is time-consuming, taking more than 20 years to develop a new variety. It is also expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. Transcriptome sequencing using next-generation sequencing (RNA-seq) is a powerful tool to identify a full set of transcripts and for evaluating gene expression in model and non-model species. In this study, we constructed a comprehensive transcriptome to evaluate the cold response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes. Furthermore, we identified putative microsatellite (SSR) and single-nucleotide polymorphism (SNP) markers. Alternative splicing, which is an important mechanism for plant adaptation under abiotic stress, was further identified, providing an important database for further studies of cold tolerance.

scholarly journals Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

2021 ◽  
Vol 7 (6) ◽  
pp. 485
Author(s):  
Boxun Li ◽  
Yang Yang ◽  
Jimiao Cai ◽  
Xianbao Liu ◽  
Tao Shi ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Single Molecule ◽  
Rubber Tree ◽  
Gene Families ◽  
Gene Clusters ◽  
The Philippines ◽  
Tree Plantations ◽  
Comparative Genomic ◽  
Corynespora Cassiicola ◽  
Leaf Fall

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

scholarly journals Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments

2021 ◽  
Author(s):  
Brian P. Anton ◽  
Alexey Fomenkov ◽  
Victoria Wu ◽  
Richard J. Roberts
Keyword(s):  
Single Molecule ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Restriction Enzymes ◽  
Specific Sequence ◽  
Genome Wide ◽  
Cost Effective Alternative ◽  
Simple Column ◽  
Sequencing Platforms

ABSTRACTSingle-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that “write” these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.

scholarly journals Current trends in apple tree breeding (Malus Mill.)

2020 ◽  
pp. 5-11
Author(s):  
O. V. Kalinina ◽  
Yu. V. Burmenko ◽  
N. Yu. Svistunova
Keyword(s):  
Cost Effective ◽  
Tree Breeding ◽  
Industrial Sector ◽  
Crop Breeding ◽  
Relevant Today ◽  
Planting Material ◽  
Current Trends ◽  
Breeding Programmes ◽  
Apple Cultivars ◽  
Modern Breeding

Apples are among the most significant fruit crops in Russian horticulture. The wide variety, as well as the prominent economic potential of the crop, both enable its cultivation across many climate zones and bring orchard farming in general to the attention of investors in the agro-industrial sector. Breeders have met the rising challenges inherent in creating varieties that are superior in terms of productivity, abiotic- and biotic stress resistance, fruit quality and competitive fast-return capacity. In the present article, current research in apple breeding including methods for intensive selection is reviewed with a focus on breeding programmes for creating adaptive varieties having a high commercial and consumer value. Classical breeding can be complemented with modern techniques for an earlier selection of commercially valuable genotypes, identification of primary genotypes, as well as the creation of new donors and cultivars. The research achievements of leading national institutions in the development of apple varieties reflect additions to the Catalog of State-Permitted Cultivars of Agricultural Crops over the last decade. Most of the 422 permitted adapted apple cultivars are highly marketable due to having best-before-consumption dates in the winter. Despite current success in national orchard farming, further endeavours in crop breeding remain relevant today. Comprehensive research engaging genetics, physiology, phytopathology, virology, agrochemistry and nursery is essential for improving modern breeding programmes with the aim of supplying producers with high-quality planting material for a cost-effective, low pesticide, environmentallystable product.

scholarly journals Genome-wide identification of 5-methylcytosine sites in bacterial genomes by high-throughput sequencing of MspJI restriction fragments

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0247541
Author(s):  
Brian P. Anton ◽  
Alexey Fomenkov ◽  
Victoria Wu ◽  
Richard J. Roberts
Keyword(s):  
Single Molecule ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Restriction Enzymes ◽  
Specific Sequence ◽  
Genome Wide ◽  
Cost Effective Alternative ◽  
Simple Column ◽  
Sequencing Platforms

Single-molecule Real-Time (SMRT) sequencing can easily identify sites of N6-methyladenine and N4-methylcytosine within DNA sequences, but similar identification of 5-methylcytosine sites is not as straightforward. In prokaryotic DNA, methylation typically occurs within specific sequence contexts, or motifs, that are a property of the methyltransferases that “write” these epigenetic marks. We present here a straightforward, cost-effective alternative to both SMRT and bisulfite sequencing for the determination of prokaryotic 5-methylcytosine methylation motifs. The method, called MFRE-Seq, relies on excision and isolation of fully methylated fragments of predictable size using MspJI-Family Restriction Enzymes (MFREs), which depend on the presence of 5-methylcytosine for cleavage. We demonstrate that MFRE-Seq is compatible with both Illumina and Ion Torrent sequencing platforms and requires only a digestion step and simple column purification of size-selected digest fragments prior to standard library preparation procedures. We applied MFRE-Seq to numerous bacterial and archaeal genomic DNA preparations and successfully confirmed known motifs and identified novel ones. This method should be a useful complement to existing methodologies for studying prokaryotic methylomes and characterizing the contributing methyltransferases.

scholarly journals Genotyping Single-Nucleotide Polymorphisms by the Invader Assay with Dual-Color Fluorescence Polarization Detection

2001 ◽  
Vol 47 (8) ◽  
pp. 1373-1377 ◽  
Author(s):  
Tony M Hsu ◽  
Scott M Law ◽  
Shenghui Duan ◽  
Bruce P Neri ◽  
Pui-Yan Kwok
Keyword(s):  
Fluorescence Polarization ◽  
Cost Effective ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Clear Cut ◽  
Pcr Product ◽  
Invader Assay ◽  
Pcr Products ◽  
Incorporation Assay

Abstract Background: The PCR-Invader® assay is a robust, homogeneous assay that has been shown to be highly sensitive and specific in genotyping single-nucleotide polymorphism (SNP) markers. In this study, we introduce two changes to improve the assay: (a) we streamline the PCR-Invader method by assaying both alleles for each SNP in one reaction; and (b) we reduce the cost of the method by adopting fluorescence polarization (FP) as the detection method. Methods: PCR product was incubated with Invader oligonucleotide and two primary probes at 93 °C for 5 min. Signal probes corresponding to the cleaved flaps of the primary probes [labeled with fluorescein and 6-carboxytetramethylrhodamine (TAMRA) dye] and Cleavase® VIII enzyme (a flap endonuclease) were then added to the mixture. This reaction mixture was incubated at 63 °C for 5 min. FP measurements were made with a fluorescence plate reader. Results: Eighty-eight individuals were genotyped across a panel of 10 SNPs, using PCR product as template, for a total of 880 genotypes. An average “no call” rate of 3.2% was observed after first round of experiments. PCR products were remade in those samples that failed to produce any genotype in the first round, and all gave clear-cut genotypes. When the genotypes determined by the PCR-Invader assay and template-directed dye-terminator incorporation assay with FP were compared, they were in 100% concordance for all SNP markers and experiments. Conclusions: The improvements introduced in this study make PCR-Invader assay simpler and more cost-effective, and therefore more suitable for high-throughput genotyping.

scholarly journals A Sensitive and Cost-Effective Chemiluminescence ELISA for Measurement of Amyloid-β 1-42 Peptide in Human Plasma

2020 ◽  
Vol 78 (3) ◽  
pp. 1237-1244
Author(s):  
Pankaj D. Mehta ◽  
Bruce A. Patrick ◽  
David L. Miller ◽  
Patricia K. Coyle ◽  
Thomas Wisniewski
Keyword(s):  
Human Plasma ◽  
Single Molecule ◽  
Limit Of Detection ◽  
Sandwich Elisa ◽  
Amyloid Β ◽  
Cost Effective ◽  
Measurement Range ◽  
Rabbit Monoclonal Antibody ◽  
Low Levels ◽  
The Brain

Background: Amyloid-β42 (Aβ42) is associated with plaque formation in the brain of patients with Alzheimer’s disease (AD). Studies have suggested the potential utility of plasma Aβ42 levels in the diagnosis, and in longitudinal study of AD pathology. Conventional ELISAs are used to measure Aβ42 levels in plasma but are not sensitive enough to quantitate low levels. Although ultrasensitive assays like single molecule array or immunoprecipitation-mass spectrometry have been developed to quantitate plasma Aβ42 levels, the high cost of instruments and reagents limit their use. Objective: We hypothesized that a sensitive and cost-effective chemiluminescence (CL) immunoassay could be developed to detect low Aβ42 levels in human plasma. Methods: We developed a sandwich ELISA using high affinity rabbit monoclonal antibody specific to Aβ42. The sensitivity of the assay was increased using CL substrate to quantitate low levels of Aβ42 in plasma. We examined the levels in plasma from 13 AD, 25 Down syndrome (DS), and 50 elderly controls. Results: The measurement range of the assay was 0.25 to 500 pg/ml. The limit of detection was 1 pg/ml. All AD, DS, and 45 of 50 control plasma showed measurable Aβ42 levels. Conclusion: This assay detects low levels of Aβ42 in plasma and does not need any expensive equipment or reagents. It offers a preferred alternative to ultrasensitive assays. Since the antibodies, peptide, and substrate are commercially available, the assay is well suited for academic or diagnostic laboratories, and has a potential for the diagnosis of AD or in clinical trials.

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