scholarly journals Efficient anchoring of Erianthus arundinaceus chromatin introgressed into sugarcane by specific molecular markers

2020 ◽  
Author(s):  
Yongji Huang ◽  
Jiayun Wu ◽  
Xueting Li ◽  
Fan Yu ◽  
Xuguang Hu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
High Throughput ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Distribution Patterns ◽  
Subtractive Hybridization ◽  
High Accuracy ◽  
Wild Relatives ◽  
45S Rdna ◽  
Erianthus Arundinaceus

Abstract Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for development of high-throughput E. arundinaceus-specific molecular markers at a reasonable cost. In this study, we constructed a SSH library of E. arundinaceus. In total, 288 clones E. arundinaceus-specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E. arundinaceus chromosome repetitive sequence EaITS were developed as E. arundinaceus-specific molecular markers, namely Ea086-128, Ea009-257, and EaITS-278, covering all the E. arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F1, BC1, BC2, BC3, and BC4 progeny between sugarcane and E. arundinaceus. In addition, EaITS-278 was a 45S rDNA-bearing E. arundinaceus chromosome-specific molecular marker for rapid tracking the inherited status of this chromosome in sugarcane background. Three BC3 progeny had apparently lost the 45S rDNA-bearing E. arundinaceus chromosome. We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E. arundinaceus-specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane.

scholarly journals Efficient anchoring of Erianthus arundinaceus chromatin introgressed into sugarcane by specific molecular markers

2020 ◽  
Author(s):  
Yongji Huang ◽  
Jiayun Wu ◽  
Xueting Li ◽  
Fan Yu ◽  
Xuguang Hu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
High Throughput ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Distribution Patterns ◽  
Subtractive Hybridization ◽  
High Accuracy ◽  
Wild Relatives ◽  
45S Rdna ◽  
Species Specific

Abstract Background: Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for development of high-throughput E. arundinaceus-specific molecular markers at a reasonable cost. Results: In this study, we constructed a SSH library of E. arundinaceus. In total, 288 clones E. arundinaceus-specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E. arundinaceus chromosome repetitive sequence EaITS were developed as E. arundinaceus-specific molecular markers, namely Ea086-128, Ea009-257, and EaITS-278, covering all the E. arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F1, BC1, BC2, BC3, and BC4 progeny between sugarcane and E. arundinaceus. In addition, EaITS-278 was a 45S rDNA-bearing E. arundinaceus chromosome-specific molecular marker for rapid tracking the inherited status of this chromosome in sugarcane background. Three BC3 progeny had apparently lost the 45S rDNA-bearing E. arundinaceus chromosome. Conclusions: We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E. arundinaceus-specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane.

scholarly journals Identification of a repetitive sequence belonging to a PPE gene of Mycobacterium tuberculosis and its use in diagnosis of tuberculosis

2006 ◽  
Vol 55 (8) ◽  
pp. 1071-1077 ◽  
Author(s):  
Ranjana Srivastava ◽  
D. Kumar ◽  
M. N. Waskar ◽  
Meera Sharma ◽  
V. M. Katoch ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Dna Hybridization ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Subtractive Hybridization ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Nucleotide Sequencing ◽  
Family Gene ◽  
Positive Hybridization

A repetitive sequence specific to Mycobacterium tuberculosis was isolated from a λgt11 library of M. tuberculosis by DNA–DNA hybridization using genomic DNA of M. tuberculosis as probe followed by subtractive hybridization with a cocktail of other mycobacterial DNA. This led to identification of CD192, a 1291 bp fragment of M. tuberculosis containing repetitive sequences, which produced positive hybridization signals with M. tuberculosis DNA within 30 min. Nucleotide sequencing revealed the presence of several direct and inverted repeats within the 1291 bp fragment that belonged to a PPE family gene (Rv0355) of M. tuberculosis. The use of CD192 as a DNA probe for the identification of M. tuberculosis in culture and clinical samples was investigated. The 1291 bp sequence was present in M. tuberculosis, Mycobacterium bovis and M. bovis BCG, but was not present in many of the other mycobacterial strains tested, including M. tuberculosis H37Ra. More than 300 clinical isolates of M. tuberculosis were probed with CD192, and the presence of the 1291 bp sequence was observed in all the clinical strains, including those lacking IS6110. The sequence displayed RFLP among the clinical isolates. A PCR assay was developed which detected M. tuberculosis with 100 % specificity from specimens of sputum, cerebrospinal fluid and pleural effusion from clinically diagnosed cases of tuberculosis.

scholarly journals High-Throughput Chlorophyll and Carotenoid Profiling Reveals Positive Associations with Sugar and Apocarotenoid Volatile Content in Fruits of Tomato Varieties in Modern and Wild Accessions

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 398
Author(s):  
Yusuke Aono ◽  
Yonathan Asikin ◽  
Ning Wang ◽  
Denise Tieman ◽  
Harry Klee ◽  
...  
Keyword(s):  
High Throughput ◽  
Fruit Color ◽  
Wild Relatives ◽  
Aroma Compounds ◽  
Soluble Solids ◽  
Sugar Production ◽  
Volatile Content ◽  
Factors Influencing ◽  
High Throughput Method ◽  
Wild Accessions

Flavor and nutritional quality has been negatively impacted during the course of domestication and improvement of the cultivated tomato (Solanum lycopersicum). Recent emphasis on consumers has emphasized breeding strategies that focus on flavor-associated chemicals, including sugars, acids, and aroma compounds. Carotenoids indirectly affect flavor as precursors of aroma compounds, while chlorophylls contribute to sugar production through photosynthesis. However, the relationships between these pigments and flavor content are still unclear. In this study, we developed a simple and high-throughput method to quantify chlorophylls and carotenoids. This method was applied to over one hundred tomato varieties, including S. lycopersicum and its wild relatives (S. l. var. cerasiforme and S. pimpinellifolium), for quantification of these pigments in fruits. The results obtained by integrating data of the pigments, soluble solids, sugars, and aroma compounds indicate that (i) chlorophyll-abundant varieties have relatively higher sugar accumulations and (ii) prolycopene is associated with an abundance of linear carotenoid-derived aroma compounds in one of the orange-fruited varieties, “Dixie Golden Giant”. Our results suggest the importance of these pigments not only as components of fruit color but also as factors influencing flavor traits, such as sugars and aroma.

scholarly journals Allelic effects and variations for key bread-making quality genes in bread wheat using high-throughput molecular markers

2019 ◽  
Vol 85 ◽  
pp. 305-309 ◽  
Author(s):  
Awais Rasheed ◽  
Hui Jin ◽  
Yonggui Xiao ◽  
Yan Zhang ◽  
Yuanfeng Hao ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Bread Wheat ◽  
High Throughput ◽  
Bread Making

scholarly journals Breeding for boron tolerance in lentil (Lens culinaris Medik.) using a high-throughput phenotypic assay and molecular markers

2018 ◽  
Vol 137 (4) ◽  
pp. 492-501 ◽  
Author(s):  
Matthew S. Rodda ◽  
Shimna Sudheesh ◽  
Muhammad Javid ◽  
Dianne Noy ◽  
Annathurai Gnanasambandam ◽  
...  
Keyword(s):  
Molecular Markers ◽  
High Throughput ◽  
Lens Culinaris ◽  
Boron Tolerance ◽  
Phenotypic Assay

Novel molecular markers for high-throughput sex characterization of Cynoglossus semilaevis

Aquaculture ◽  
2019 ◽  
Vol 513 ◽  
pp. 734331 ◽  
Author(s):  
Bo Zhang ◽  
Na Zhao ◽  
Yangyang Liu ◽  
Lei Jia ◽  
Yan Fu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
High Throughput ◽  
Cynoglossus Semilaevis

scholarly journals SpyCLIP: an easy-to-use and high-throughput compatible CLIP platform for the characterization of protein–RNA interactions with high accuracy

2019 ◽  
Vol 47 (6) ◽  
pp. e33-e33 ◽  
Author(s):  
Ya Zhao ◽  
Yao Zhang ◽  
Yilan Teng ◽  
Kai Liu ◽  
Yanqing Liu ◽  
...  
Keyword(s):  
High Throughput ◽  
High Accuracy

scholarly journals Evolutionary characterization of a Y chromosomal sequence conserved in the genus Mus

1988 ◽  
Vol 52 (2) ◽  
pp. 145-150 ◽  
Author(s):  
Yutaka Nishioka
Keyword(s):  
Related Species ◽  
Rattus Norvegicus ◽  
Phylogenetic Relationships ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Closely Related Species ◽  
Specific Hybridization ◽  
Male Specific ◽  
Chromosomal Sequence

SummaryThe extent of accumulation of mouse Y chromosomal repetitive sequences generally correlates with the known phylogenetic relationships in the genus Mus. However, we describe here a M. musculus Y chromosomal repetitive sequence, designated as ACClfl, whose accumulation patterns among eight Mus species do not correspond to their phylogenetic relationships. Although male-specific hybridization bands were present in all the species examined, significant accumulation (> 200 copies) in the Y chromosomes was found in M. minutoides (subgenus Nannomys), M. pahari (subgenus Coelomys) and M. saxicola (subgenus Pyromys) as well as in the three closely related species M. hortulanus, M. musculus and M. spretus that belong to the subgenus Mus. Unexpectedly, the Y chromosomes of M. caroli and M. cookii (both subgenus Mus) had considerably reduced amounts of ACClfl-related sequences. Furthermore, in rats (Rattus norvegicus) the major accumulation sites appear to be autosomal. These observations suggest that caution must be taken in the interpretation of data obtained with repetitive sequences that have evolved quickly.

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