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Sequence heterogeneity of the envelope-like domain in the Egyptian cotton Gossypium barbadense
Abdel Ghany A. Abdel Ghany, Essam A Zaki
African Journal of Biotechnology , 2003,
Abstract: Abbreviations; LTR: long terminal repeat, ORF: open-reading frame, PCR: polymerase chain reaction, RT: reverse transcriptase gene. The current study aimed to investigate the evolution of env-like sequences in the Egyptian cotton Gossypium barbadense. DNA sequence determination and analysis of env -like sequences revealed that these sequences are heterogeneous in G. barbadense. The observed sequence diversity, however, seems to preserve the coding information. Phylogenetic analysis demonstrated that plant env -like sequences group together, suggesting their monophyletic origin. Gossypium env-like sequences are, however, more closely related to elements present in other plant species. Our result suggests that env -like sequences in cotton have evolved under functional constraint and likely to play a role in the life cycle of these elements.
Mining, characterization, and exploitation of EST-derived microsatellites in Gossypium barbadense
YuanDa Lü,CaiPing Cai,Lei Wang,ShaoYan Lin,Liang Zhao,LiangLiang Tian,JunHong Lü,TianZhen Zhang,WangZhen Guo
Chinese Science Bulletin , 2010, DOI: 10.1007/s11434-010-3230-4
Abstract: Simple sequence repeats (SSRs) have been widely applied as molecular markers in genetic studies. However, the number of expressed sequence tags (ESTs) and SSR markers from Gossypium barbadense is fewer than those from other cotton species. In this study, EST-SSR distribution from G. barbadense was characterized and new G. barbadense-derived EST-SSR markers were determined on the basis of the ESTs obtained by randomly sequencing 2 cDNA libraries associated with fiber development in G. barbadense. By mining 9697 non-redundant ESTs, a total of 638 SSR loci derived from 595 ESTs were observed. In G. barbadense, the frequency of ESTs containing SSRs was 6.13%, with an average of 1 SSR in every 10.4 kb of EST sequence. Furthermore, trinucleotide was found to be the most abundant repeat type among 2–6-nucleotide repeat types. It accounted for 26.6% of the total, followed by the hexanucleotide (26.0%) and pentanucleotide repeats (25.9%). Among all the repeat motifs, (AAG)n accounted for the highest proportion. EST-SSR primer pairs were developed using the Primer3 program, and the redundant primers were removed using the virtual PCR approach. As a result, 380 non-redundant EST-SSR primer pairs were developed and used to detect polymorphisms between the mapping parents G. hirsutum ‘TM-1’ and G. barbadense ‘Hai7124’ for constructing linkage groups in cultivated allotetraploid cotton. Out of these, 98 (25.8%) primer pairs detected polymorphisms. Finally, 95 polymorphic loci from 82 primer pairs were integrated into the backbone genetic map; of these, 42 were mapped into the A subgenome and 53 into the D subgenome. The present work provided the foundation for constructing saturated genetic maps and conducting comparative genomic studies on different cotton species.
Evaluation of the antimalarial activity of the aqueous leaf extract of Gossypium barbadense (Malvaeceae) in mice  [cached]
Olanrewaju A. Salako,Olufunsho Awodele
Drugs and Therapy Studies , 2012, DOI: 10.4081/dts.2012.e2
Abstract: Some medicinal plants have been shown to have antimalarial activity when used as combination therapy. Gossypium barbadense has been used by herbal medicine practitioners in combination with other herbs, and as a monotherapy in the treatment of malarial infection. The study was, therefore, aimed at evaluating the antimalarial effect of the aqueous leaf extract of G. barbadense using mice infected with P. berghei. The suppressive effect was evaluated by administering 25 mice divided into five groups with 250, 500, and 1,000 mg/kg of aqueous leaf extract of G. barbadense, 5 mg/kg of chloroquine, and 10 mL/kg of distilled water, respectively, starting from the day of inoculation with P. berghei for four days. The curative effect was evaluated by administering 25 mice divided into five groups as above with treatment starting 72 h post inoculation with P. berghei. The results indicate that the aqueous leaf extract of G. barbadense, when used alone as monotherapy, has a non-significant (P ≥ 0.05) but slight suppressive antimalarial activity (23%) when compared with that of chloroquine (100%). The curative model also revealed that aqueous leaf extract of G. barbadense showed no significant antimalarial activity. It can be concluded that the use of aqueous leaf extract of G. barbadense as monotherapy for malaria has no significant therapeutic effect. Therefore, it is not recommended to be used alone to manage malaria infection as practiced by some herbal medicine practitioners.
Studies of new EST-SSRs derived from Gossypium barbadense
YanXin Zhang,ZhongXu Lin,Wu Li,LiLi Tu,YiChun Nie,XianLong Zhang
Chinese Science Bulletin , 2007, DOI: 10.1007/s11434-007-0399-2
Abstract: Existing cotton EST-SSR markers are mostly derived from Gossypium arboreum and Gossypium hirsutum, but EST-SSR markers from Gossypium barbadense are scarce. One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G. barbadense cv. Pima3–79. Among the SSRs, trinucleotide AAG appeared at a high frequency of 11.76%. 36 accessions (consisting of 13 diploids of the A genome, 11 diploids of the D genome and 12 allotetraploids of the AD genome) were employed to test new EST-SSRs. 76 EST-SSRs were successfully amplified, and 313 polymorphic fragments were yielded, with an average of 4.11 fragments per primer pair. The PIC ranged from 0.17 to 0.95 with an average of 0.53. Based on Jaccard’s genetic similarity coefficient, these 36 accessions were clustered into three groups. 21 EST-SSRs exhibited polymorphisms in BC1 population ((Emian22 × Pima3–79) × Emian22), 24 polymorphic loci were generated, while 22 of the 24 polymorphic loci were integrated with our interspecific BC1 backbone genetic linkage map, and anchored in 12 chromosomes. This study effectively proved that EST-SSRs from G. barbadense are valuable for genetic diversity analysis and genetic mapping.
Amplified fragment length polymorphism (AFLP) and genealogy analysis of the introgressed lines from Gossypium hirsutum × Gossypium barbadense varieties
Z Liu, Y Zhang, J Peng, K Deng, S Dong, Z Ren
African Journal of Biotechnology , 2010,
Abstract: In this study, amplified fragment length polymorphism (AFLP) technique was used to analyze the genealogical relationship of 7 introgressed cotton varieties from the hybridization of upland (Gossypium hirsutum L) and sea-island cottons (Gossypium barbadense L). Ten pairs of primer combinations with high polymorphism and resolution were selected from 64 primers. These 10 primer combinations resulted in a total of 480 bands, of which 374 bands (77.9%) were polymorphic and 51 bands (10.6%) were specific. Cluster analyses showed that 7 varieties of cottons were divided into two groups. Our results suggested that interspecific hybridization is feasible to broaden germplasm of upland cotton and AFLP technique could be applied for the identification of variety purity and genealogical relationship.
Genetic Diversity in the Environmental Conditioning of Gossypium hirsutum and Gossypium barbadense Cultivars  [PDF]
John J. Burke
American Journal of Plant Sciences (AJPS) , 2017, DOI: 10.4236/ajps.2017.83036
Abstract: Enzyme adaptations to temperature occur constantly as temperature patterns modulate diurnally and seasonally. These adaptations entail qualitative and/or quantitative metabolic changes that often provide a competitive advantage, impact adjustment to new environments, and effect the survival of the species. Changes in isozymes or allozymes, changes in enzyme concentration, modification by substrate and effectors, and metabolic regulation of enzyme function without changing enzyme composition are all possible strategies for adaptation to changes in temperature. The degree of adaptation among cotton cultivars to a specific thermal regime may be difficult to determine from phenotypic responses of the plants. The present study evaluated the thermal sensitivity of Gossypium hirsutum L. and Gossypium barbadense L. cultivars following growth under distinct thermal environments. The metabolic fitness of Gossypium hirsutum L. and Gossypium barbadense L. cultivars showed that the Gossypium hirsutum L. cultivars grown in a 28°C/20°C day/night cycle tended to be better equipped to cope with a 16 h - 38°C treatment than the same cultivars grown in a 38°C/32°C day/night cycle. The Gossypium barbadense L. cultivars, on the other hand, grown in a 38°C/32°C day/night cycle tended to be equipped to cope with a 16 h - 38°C treatment than the same cultivars grown in a 28°C/20°C day/night cycle. The Gossypium hirsutum L. line TX 303 is an exception to these general trends as its responses were similar to the Gossypium barbadense L. St. Vincent and Pima S-7 cottons.
DNA Sequences of RAPD Fragments in the Egyptian cotton Gossypium barbadense
Abdel Ghany A. Abdel Ghany, Essam A. Zaki
African Journal of Biotechnology , 2003,
Abstract: Random Amplified Polymorphic DNAs (RAPDs) is a DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. Despite the fact that the RAPD technique has become a very powerful tool and has found use in numerous applications, yet, the nature of molecular variation(s) uncovered by the RAPD technique is still unclear. The aim of the following study, therefore, was to investigate the molecular nature of RAPD DNA fragments in four Gossypium barbadense cultivars. Five RAPD DNA fragments, generated by improved RAPD-PCR technique, and representing polymorphic and nonpolymorphic bands were analyzed at the molecular level using DNA sequence analysis. Nonpolymorphic RAPD DNA fragments showed homologies to previously characterized plant structural genes. Comparative nucleotide sequence analysis of two comigrating nonpolymorphic fragments revealed that these two DNA sequences are highly similar to each other, indicating that similarity of fragment size is a good predicator of homology. Polymorphic RAPD DNA fragments, on the other hand, showed homologies to middle and high-repetitive DNA sequences. These results promote the initiative to integrate these RAPD markers in cotton breeding applications, and DNA fingerprinting. (African Journal of Biotechnology: 2003 2(5): 129-132)
Generation, Annotation and Analysis of First Large-Scale Expressed Sequence Tags from Developing Fiber of Gossypium barbadense L  [PDF]
Daojun Yuan, Lili Tu, Xianlong Zhang
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022758
Abstract: Background Cotton fiber is the world's leading natural fiber used in the manufacture of textiles. Gossypium is also the model plant in the study of polyploidization, evolution, cell elongation, cell wall development, and cellulose biosynthesis. G. barbadense L. is an ideal candidate for providing new genetic variations useful to improve fiber quality for its superior properties. However, little is known about fiber development mechanisms of G. barbadense and only a few molecular resources are available in GenBank. Methodology and Principal Findings In total, 10,979 high-quality expressed sequence tags (ESTs) were generated from a normalized fiber cDNA library of G. barbadense. The ESTs were clustered and assembled into 5852 unigenes, consisting of 1492 contigs and 4360 singletons. The blastx result showed 2165 unigenes with significant similarity to known genes and 2687 unigenes with significant similarity to genes of predicted proteins. Functional classification revealed that unigenes were abundant in the functions of binding, catalytic activity, and metabolic pathways of carbohydrate, amino acid, energy, and lipids. The function motif/domain-related cytoskeleton and redox homeostasis were enriched. Among the 5852 unigenes, 282 and 736 unigenes were identified as potential cell wall biosynthesis and transcription factors, respectively. Furthermore, the relationships among cotton species or between cotton and other model plant systems were analyzed. Some putative species-specific unigenes of G. barbadense were highlighted. Conclusions/Significance The ESTs generated in this study are from the first large-scale EST project for G. barbadense and significantly enhance the number of G. barbadense ESTs in public databases. This knowledge will contribute to cotton improvements by studying fiber development mechanisms of G. barbadense, establishing a breeding program using marker-assisted selection, and discovering candidate genes related to important agronomic traits of cotton through oligonucleotide array. Our work will also provide important resources for comparative genomics, polyploidization, and genome evolution among Gossypium species.
Development of Agrobacterium-Mediated Virus-Induced Gene Silencing and Performance Evaluation of Four Marker Genes in Gossypium barbadense  [PDF]
Jinhuan Pang, Yue Zhu, Qing Li, Jinzhi Liu, Yingchuan Tian, Yule Liu, Jiahe Wu
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073211
Abstract: Gossypium barbadense is a cultivated cotton species and possesses many desirable traits, including high fiber quality and resistance to pathogens, especially Verticillium dahliae (a devastating pathogen of Gossypium hirsutum, the main cultivated species). These elite traits are difficult to be introduced into G. hirsutum through classical breeding methods. In addition, genetic transformation of G. barbadense has not been successfully performed. It is therefore important to develop methods for evaluating the function and molecular mechanism of genes in G. barbadense. In this study, we had successfully introduced a virus-induced gene silencing (VIGS) system into three cultivars of G. barbadense by inserting marker genes into the tobacco rattle virus (TRV) vector. After we optimized the VIGS conditions, including light intensity, photoperiod, seedling age and Agrobacterium strain, 100% of plants agroinfiltrated with the GaPDS silencing vector showed white colored leaves. Three other marker genes, GaCLA1, GaANS and GaANR, were employed to further test this VIGS system in G. barbadense. The transcript levels of the endogenous genes in the silenced plants were reduced by more than 99% compared to control plants; these plants presented phenotypic symptoms 2 weeks after inoculation. We introduced a fusing sequence fragment of GaPDS and GaANR gene silencing vectors into a single plant, which resulted in both photobleaching and brownish coloration. The extent of silencing in plants agroinfiltrated with fusing two-gene-silencing vector was consistent with plants harboring a single gene silencing vector. The development of this VIGS system should promote analysis of gene function in G. barbadense, and help to contribute desirable traits for breeding of G. barbadense and G. hirsutum.
Phylogenetic and molecular evolutionary analyses of gypsy group retrotransposon families in the Egyptian cotton Gossypium barbadense
Abdel Ghany A Abdel Ghany, Essam A Zaki
African Journal of Biotechnology , 2003,
Abstract: Gypsy group retrotransposons in the Egyptian cotton, Gossypium barbadense, was examined by phylogenetic and molecular evolutionary analyses. DNA sequences of gypsy group retrotransposons in two G. barbadense cultivars revealed that these sequences are heterogeneous and represent two distinct families. Sequence variation between these families seems to preserve coding information of the reverse transcriptase domain. The high ratio of synonymous to nonsynonymous changes indicates that the reverse transcriptase domain of these families is evolving under purifying selection. Our phylogenetic analysis revealed that the closest relatives of cotton retroelements are found in other plants gypsy group retrotransposons. Cotton retroelements-encoded transcripts were detected in their related respective young seedlings using RNA slot-blot hybridization, suggesting their transcriptional activity. The wide distribution of gypsy group retrotransposons and the detection of their encoded transcripts illustrate their active role in the Gossypium genome.
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