Detection and mapping of homologous and homoeologous segments in homoeologous groups of allotetraploid cotton by BAC-FISH

<p>Abstract</p> <p>Background</p> <p>Cotton, as an allopolyploid species, contains homoeologous A and D subgenomes. The study of the homoeologous (duplicated) segments or chromosomes can facilitate insight into the evolutionary process of polyploidy and the development of genomic resources. Fluorescence <it>in situ </it>hybridization (FISH) using bacterial artificial chromosome (BAC) clones as probes has commonly been used to provide a reliable cytological technique for chromosome identification. In polyploids, it also presents a useful approach for identification and localization of duplicated segments. Here, two types of BACs that contained the duplicated segments were isolated and analyzed in tetraploid cotton by FISH.</p> <p>Results</p> <p>Homologous and homoeologous BACs were isolated by way of SSR marker-based selection and then used to develop BAC-FISH probes. Duplicated segments in homoeologous chromosomes were detected by FISH. The FISH and related linkage map results followed known reinforced the relationships of homoeologous chromosomes in allotetraploid cotton, and presented a useful approach for isolation of homoeologous loci or segments and for mapping of monomorphic loci. It is very important to find that the large duplicated segments (homologous BACs) do exist between homoeologous chromosomes, so the shot-gun approach for genome sequencing was unavailable for tetraploid cotton. However, without doubt, it will contain more information and promote the research for duplicated segments as well as the genome evolution in cotton.</p> <p>Conclusion</p> <p>These findings and the analysis method by BAC-FISH demonstrated the powerful nature and wide use for the genome and genome evolutionary researches in cotton and other polyploidy species.</p

Association mapping for salinity tolerance in cotton (Gossypium hirsutum L.) germplasm from US and diverse regions of China

Abstract Salinity affects cotton production worldwide. In our study, we assessed marker-trait associations for salinity tolerance in cotton using a set of 109 cotton variety germplasm (mainly from China and USA). Cotton varieties were screened for polymorphism with 250 SSR markers. Out of these 250 SSR markers, 98 were found to be polymorphic. Plant material was grown under normal versus saline (100mM and 200mM NaCl) conditions in greenhouse and data was collected for morpho-physiological traits at seedling stage. SSR markers linked with T 1 , T 2 , relative value of T 1 , and relative value of T 2 treatments only were considered associated with salinity tolerance. On the basis of overall performance of cultivars judged by relative values, cultivars Jian mian 13, Si mian 4 and Gan mian 8 were found to be salt tolerant, whereas, Ke yi 2, Yan mian 48 and Zhong mian suo 49 were found to be salt sensitive. STRUCTURE software identified 5 sub-populations in this cotton germplasm. These sub-populations consisted of 10-30 varieties. At r 2 &gt; 0.05, 3% SSR marker pairs showed significant pairwise linkage disequilibrium (LD). At the highly significant threshold of r 2 &gt; 0.1, 1.82% of SSR marker pairs were remained in LD. Genome-wide LD at r 2 &gt; 0.1 was reduced to ~4 -7 cM, indicating a strong potential for association mapping. Markers BNL3103 (D6), NAU478 (D8) and BNL3140 (D9) were associated with salt treatment. These markers can be utilized in molecular breeding of cotton for the release of salt tolerant cultivars

A preliminary analysis of genome structure and composition in Gossypium hirsutum

<p>Abstract</p> <p>Background</p> <p>Upland cotton has the highest yield, and accounts for > 95% of world cotton production. Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural, functional, and evolutionary studies of the species. Here, we employed GeneTrek and BAC tagging information approaches to predict the general composition and structure of the allotetraploid cotton genome.</p> <p>Results</p> <p>142 BAC sequences from <it>Gossypium hirsutum </it>cv. Maxxa were downloaded <url>http://www.ncbi.nlm.nih.gov</url> and confirmed. These BAC sequence analysis revealed that the tetraploid cotton genome contains over 70,000 candidate genes with duplicated gene copies in homoeologous A- and D-subgenome regions. Gene distribution is uneven, with gene-rich and gene-free regions of the genome. Twenty-one percent of the 142 BACs lacked genes. BAC gene density ranged from 0 to 33.2 per 100 kb, whereas most gene islands contained only one gene with an average of 1.5 genes per island. Retro-elements were found to be a major component, first an enriched LTR/gypsy and second LTR/copia. Most LTR retrotransposons were truncated and in nested structures. In addition, 166 polymorphic loci amplified with SSRs developed from 70 BAC clones were tagged on our backbone genetic map. Seventy-five percent (125/166) of the polymorphic loci were tagged on the D-subgenome. By comprehensively analyzing the molecular size of amplified products among tetraploid <it>G. hirsutum </it>cv. Maxxa, acc. TM-1, and <it>G. barbadense </it>cv. Hai7124, and diploid <it>G. herbaceum </it>var. <it>africanum </it>and <it>G. raimondii</it>, 37 BACs, 12 from the A- and 25 from the D-subgenome, were further anchored to their corresponding subgenome chromosomes. After a large amount of genes sequence comparison from different subgenome BACs, the result showed that introns might have no contribution to different subgenome size in <it>Gossypium</it>.</p> <p>Conclusion</p> <p>This study provides us with the first glimpse of cotton genome complexity and serves as a foundation for tetraploid cotton whole genomesequencing in the future.</p

Spin-Orbit induced phase-shift in Bi2_{2}Se3_{3} Josephson junctions

The transmission of Cooper pairs between two weakly coupled superconductors produces a superfluid current and a phase difference; the celebrated Josephson effect. Because of time-reversal and parity symmetries, there is no Josephson current without a phase difference between two superconductors. Reciprocally, when those two symmetries are broken, an anomalous supercurrent can exist in the absence of phase bias or, equivalently, an anomalous phase shift $\varphi_0$ can exist in the absence of a superfluid current. We report on the observation of an anomalous phase shift $\varphi_0$ in hybrid Josephson junctions fabricated with the topological insulator Bi$_2$Se$_3$ submitted to an in-plane magnetic field. This anomalous phase shift $\varphi_0$ is observed directly through measurements of the current-phase relationship in a Josephson interferometer. This result provides a direct measurement of the spin-orbit coupling strength and open new possibilities for phase-controlled Josephson devices made from materials with strong spin-orbit coupling

Quantum confinement effects in Pb Nanocrystals grown on InAs

In the recent work of Ref.\cite{Vlaic2017-bs}, it has been shown that Pb nanocrystals grown on the electron accumulation layer at the (110) surface of InAs are in the regime of Coulomb blockade. This enabled the first scanning tunneling spectroscopy study of the superconducting parity effect across the Anderson limit. The nature of the tunnel barrier between the nanocrystals and the substrate has been attributed to a quantum constriction of the electronic wave-function at the interface due to the large Fermi wavelength of the electron accumulation layer in InAs. In this manuscript, we detail and review the arguments leading to this conclusion. Furthermore, we show that, thanks to this highly clean tunnel barrier, this system is remarkably suited for the study of discrete electronic levels induced by quantum confinement effects in the Pb nanocrystals. We identified three distinct regimes of quantum confinement. For the largest nanocrystals, quantum confinement effects appear through the formation of quantum well states regularly organized in energy and in space. For the smallest nanocrystals, only atomic-like electronic levels separated by a large energy scale are observed. Finally, in the intermediate size regime, discrete electronic levels associated to electronic wave-functions with a random spatial structure are observed, as expected from Random Matrix Theory.Comment: Main 12 pages, Supp: 6 page

Exploring the Applicability of Building Energy Performance Certification Systems in Underground Stations in China

To improve the energy efficiency of underground metro stations, and in view of the absence of a comprehensive energy performance evaluation system for underground stations, this study introduced building Energy Performance Certification (EPC) tools into underground stations and conducted a comparative analysis of their applicability. The findings indicated that due to the unique characteristics of underground stations, China’s current EPC system was inapplicable to them. Specifically, (1) for basic items, although evaluation methods were available, due to the limited energy use data for the statistical method, the self-reference method was preferred, but its calculation encountered issues with missing reference values; (2) for prescribed items, the emphasis should be placed on the energy efficiency requirements of energy use systems rather than those of the thermal performance of envelopes; (3) for alternative items, the energy recovery measures related to the heat dissipation of trains and the piston wind should be addressed. Furthermore, a case study was conducted for verification of the proposed energy evaluation method, and the EPC system was updated based on the results of the comparison. The authors hope that this study will help improve China’s energy evaluation methods for underground stations and serve as a reference for expanding the EPC system to include public transportation buildings

Structure, expression differentiation and evolution of duplicated fiber developmental genes in Gossypium barbadense and G. hirsutum

<p>Abstract</p> <p>Background</p> <p>Both <it>Gossypium hirsutum </it>and <it>G. barbadense </it>probably originated from a common ancestor, but they have very different agronomic and fiber quality characters. Here we selected 17 fiber development-related genes to study their structures, tree topologies, chromosomal location and expression patterns to better understand the interspecific divergence of fiber development genes in the two cultivated tetraploid species.</p> <p>Results</p> <p>The sequence and structure of 70.59% genes were conserved with the same exon length and numbers in different species, while 29.41% genes showed diversity. There were 15 genes showing independent evolution between the A- and D-subgenomes after polyploid formation, while two evolved via different degrees of colonization. Chromosomal location showed that 22 duplicate genes were located in which at least one fiber quality QTL was detected. The molecular evolutionary rates suggested that the D-subgenome of the allotetraploid underwent rapid evolutionary differentiation, and selection had acted at the tetraploid level. Expression profiles at fiber initiation and early elongation showed that the transcripts levels of most genes were higher in Hai7124 than in TM-1. During the primary-secondary transition period, expression of most genes peaked earlier in TM-1 than in Hai7124. Homeolog expression profile showed that A-subgenome, or the combination of A- and D-subgenomes, played critical roles in fiber quality divergence of <it>G. hirsutum </it>and <it>G. barbadense</it>. However, the expression of D-subgenome alone also played an important role.</p> <p>Conclusion</p> <p>Integrating analysis of the structure and expression to fiber development genes, suggests selective breeding for certain desirable fiber qualities played an important role in divergence of <it>G. hirsutum </it>and <it>G. barbadense</it>.</p