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Zhang Q.,CAS Wuhan Botanical Garden | Zhang Q.,University of Chinese Academy of Sciences | Li J.,CAS Wuhan Botanical Garden | Zhao Y.,Hebei Academy of Agricultural and Forestry science | And 2 more authors.
Plant Molecular Biology Reporter | Year: 2012

China, one of the primary centers of genetic diversity for the genus Malus, is very rich in wild apple germplasm. In this study, genetic diversity in 29 Malus accessions, including 12 accessions from 7 Chinese Malus species, 4 Chinese landraces, and 13 introduced apple cultivars, was assessed using a set of 19 single-locus simple sequence repeat (SSR) markers distributed across all 17 linkage groups of the apple genome. The number of alleles detected at each locus ranged from 2 to 11, with an average of 5.3 per SSR marker. In some accessions, 16 unique alleles were identified. Ten out of these 16 unique alleles (62.5%) were detected exclusively in wild species, indicating that these Chinese wild apple species have considerable genetic diversity and can be used in breeding programs to increase the genetic diversity of apple cultivars. Using 19 SSRs, an unweighted pair-group method with arithmetic average cluster analysis was conducted, and the resulting dendrogram revealed that all cultivars, except for Ef{cyrillic}peMeBckoe, were clustered together in the same group. The Russian cultivar Ef{cyrillic}peMeBckoe was closely related to the Chinese crabapple Baihaitang (M. prunifolia), with a high similarity coefficient value of 0.94. Of the two M. sieversii accessions used, one accession showed a close relationship to apple cultivars, while the other accession was closely related to wild apple species, suggesting the presence of a wider genetic diversity in Chinese M. sieversii species. The influence of SSR marker selection on genetic diversity analysis in this Malus collection was also discussed. © 2011 Springer-Verlag. Source

Anderson E.,Gregory Environmental | Arundale R.,Urbana University | Maughan M.,Urbana University | Oladeinde A.,Urbana University | And 2 more authors.
Biofuels | Year: 2011

Miscanthus × giganteus is a highly productive, sterile, rhizomatous, C4 perennial grass that should be considered as a feedstock for bioenergy production. Here, we review the current state of research and the future of M. × giganteus biomass production. Since the 1980s, the grass has been studied and used in Europe to produce heat and electricity via combustion. Since 2005, the US government has encouraged research using herbaceous feedstocks for conversion to ethanol for use as transportation fuel. M. × giganteus is being widely studied in the USA because of its potential to produce large quantities of biomass. This review examines the taxonomy and genetics, growth and development, physiology and agronomy, and modeled and potential 'real-world' yields of M. × giganteus in Europe and the USA. In addition, the invasiveness and the future perspective of M. × giganteus utility and research in the USA are also considered. © 2011 Future Science Ltd. Source

Vyakaranam K.V.,Rutgers University | Ashokan B.K.,Rutgers University | Kokini J.L.,Rutgers University | Kokini J.L.,Gregory Environmental
Journal of Food Engineering | Year: 2012

The effect of paddle element geometry, specifically a systematic change in stagger angle, on the velocity distribution of a Newtonian corn syrup was evaluated in the mixing region of a 2″ Readco continuous processor using 3D FEM simulations. Local velocities and regions of backflow were compared for three configurations of the paddle elements in the mixing region consisting of nine pairs of paddle elements with the central three being in a neutral (FLAT), staggered 45° forward (45F) or staggered 45° reverse (45R) configuration. The total material flow rate through the mixer was independent of the paddle element stagger but increased with screw speed when the mixer was operated with the barrel fully filled. The stagger angle variation caused only local disturbances in axial flow. The overall magnitudes of velocity were highest for the FLAT configuration followed by 45F and 45R. The local X and Y velocity components in the region of stagger showed no significant variation with paddle element stagger while the Z velocity component varied significantly in this region. Increased forward flow was seen for the 45F configuration while significant local backflow was seen for the 45R configuration at all positions of the paddle element rotation. The FLAT configuration had greater levels of pressure in the intermeshing region, suggesting a squeeze flow while there were not significant variations in pressure for the 45F and 45R configurations, suggesting a predominantly conveying/leakage flow in the axial direction. Variation in local flows is critical to good mixing. © 2011 Elsevier Ltd. All rights reserved. Source

Han Y.,CAS Wuhan Botanical Garden | Zheng D.,Gregory Environmental | Vimolmangkang S.,Gregory Environmental | Khan M.A.,Gregory Environmental | And 2 more authors.
Journal of Experimental Botany | Year: 2011

A total of 355 simple sequence repeat (SSR) markers were developed, based on expressed sequence tag (EST) and bacterial artificial chromosome (BAC)-end sequence databases, and successfully used to construct an SSR-based genetic linkage map of the apple. The consensus linkage map spanned 1143cM, with an average density of 2.5cM per marker. Newly developed SSR markers along with 279 SSR markers previously published by the HiDRAS project were further used to integrate physical and genetic maps of the apple using a PCR-based BAC library screening approach. A total of 470 contigs were unambiguously anchored onto all 17 linkage groups of the apple genome, and 158 contigs contained two or more molecular markers. The genetically mapped contigs spanned ∼421Mb in cumulative physical length, representing 60.0% of the genome. The sizes of anchored contigs ranged from 97kb to 4.0Mb, with an average of 995kb. The average physical length of anchored contigs on each linkage group was ∼24.8Mb, ranging from 17.0Mb to 37.73Mb. Using BAC DNA as templates, PCR screening of the BAC library amplified fragments of highly homologous sequences from homoeologous chromosomes. Upon integrating physical and genetic maps of the apple, the presence of not only homoeologous chromosome pairs, but also of multiple locus markers mapped to adjacent sites on the same chromosome was detected. These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple. © 2011 The Author. Source

Zhang Q.,CAS Wuhan Botanical Garden | Zhang Q.,University of Chinese Academy of Sciences | Ma B.,CAS Wuhan Botanical Garden | Ma B.,University of Chinese Academy of Sciences | And 16 more authors.
BMC Genomics | Year: 2012

Background: Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome.Results: A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation.Conclusions: This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding community in marker-assisted breeding, and for performing comparative genomic studies in Rosaceae. © 2012 Zhang et al.; licensee BioMed Central Ltd. Source

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