Genome-wide quantitative trait loci mapping on Verticillium wilt resistance in 300 chromosome segment substitution lines from Gossypium hirsutum × Gossypium barbadense

Cotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistance to VW. However, multiple attempts to improve the VW resistance of the most widely cultivated upland cottons have made little significant progress. The introduction of chromosome segment substitution lines (CSSLs) provide the practical solutions for merging the superior genes related with high yield and wide adaptation from Gossypium hirsutum and VW resistance and the excellent fiber quality from Gossypium barbadense. In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed from CCRI36 (G. hirsutum) and Hai1 (G. barbadense) to conduct quantitative trait locus (QTL) mapping of VW resistance, and a total of 40 QTL relevant to VW disease index (DI) were identified. Phenotypic data were obtained from a 2-year investigation in two fields with two replications per year. All the QTL were distributed on 21 chromosomes, with phenotypic variation of 1.05%-10.52%, and 21 stable QTL were consistent in at least two environments. Based on a meta-analysis, 34 novel QTL were identified, while 6 loci were consistent with previously identified QTL. Meanwhile, 70 QTL hotspot regions were detected, including 44 novel regions. This study concentrates on QTL identification and screening for hotspot regions related with VW in the 300 CSSLs, and the results lay a solid foundation not only for revealing the genetic and molecular mechanisms of VW resistance but also for further fine mapping, gene cloning and molecular designing in breeding programs for resistant cotton varieties.

QTL mapping and genetic effect of chromosome segment substitution lines with excellent fiber quality from Gossypium hirsutum × Gossypium barbadense

Chromosome segment substitution lines (CSSLs) are ideal materials for identifying genetic effects. In this study, CSSL MBI7561 with excellent fiber quality that was selected from BC₄F_3:5 of CCRI45 (Gossypium hirsutum) × Hai1 (Gossypium barbadense) was used to construct 3 secondary segregating populations with 2 generations (BC₅F₂ and BC₅F_2:3). Eighty-one polymorphic markers related to 33 chromosome introgressive segments on 18 chromosomes were finally screened using 2292 SSR markers which covered the whole tetraploid cotton genome. A total of 129 quantitative trait loci (QTL) associated with fiber quality (103) and yield-related traits (26) were detected on 17 chromosomes, explaining 0.85-30.35% of the phenotypic variation; 39 were stable (30.2%), 53 were common (41.1%), 76 were new (58.9%), and 86 had favorable effects on the related traits. More QTL were distributed in the Dt subgenome than in the At subgenome. Twenty-five stable QTL clusters (with stable or common QTL) were detected on 22 chromosome introgressed segments. Finally, the 6 important chromosome introgressed segments (Seg-A02-1, Seg-A06-1, Seg-A07-2, Seg-A07-3, Seg-D07-3, and Seg-D06-2) were identified as candidate chromosome regions for fiber quality, which should be given more attention in future QTL fine mapping, gene cloning, and marker-assisted selection (MAS) breeding.

Transcriptomic and biochemical analysis of upland cotton (Gossypium hirsutum) and a chromosome segment substitution line from G. hirsutum × G. barbadense in response to Verticillium dahliae infection

BACKGROUND

Verticillium wilt (VW), also known as "cotton cancer," is one of the most destructive diseases in global cotton production that seriously impacts fiber yield and quality. Despite numerous attempts, little significant progress has been made in improving the VW resistance of upland cotton. The development of chromosome segment substitution lines (CSSLs) from Gossypium hirsutum × G. barbadense has emerged as a means of simultaneously developing new cotton varieties with high-yield, superior fiber, and resistance to VW.

RESULTS

In this study, VW-resistant investigations were first conducted in an artificial greenhouse, a natural field, and diseased nursery conditions, resulting in the identification of one stably VW-resistant CSSL, MBI8255, and one VW-susceptible G. hirsutum, CCRI36, which were subsequently subjected to biochemical tests and transcriptome sequencing during V991 infection (0, 1, and 2 days after inoculation). Eighteen root samples with three replications were collected to perform multiple comparisons of enzyme activity and biochemical substance contents. The findings indicated that VW resistance was positively correlated with peroxidase and polyphenol oxidase activity, but negatively correlated with malondialdehyde content. Additionally, RNA sequencing was used for the same root samples, resulting in a total of 77,412 genes, of which 23,180 differentially expressed genes were identified from multiple comparisons between samples. After Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the expression profiles identified using Short Time-series Expression Miner, we found that the metabolic process in the biological process, as well as the pathways of phenylpropanoid biosynthesis and plant hormone signal transduction, participated significantly in the response to VW. Gene functional annotation and expression quantity analysis indicated the important roles of the phenylpropanoid metabolic pathway and oxidation-reduction process in response to VW, which also provided plenty of candidate genes related to plant resistance.

CONCLUSIONS

This study concentrates on the preliminary response to V991 infection by comparing the VW-resistant CSSL and its VW-susceptible recurrent parent. Not only do our findings facilitate the culturing of new resistant varieties with high yield and superior performance, but they also broaden our understanding of the mechanisms of cotton resistance to VW.

Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and Chromosome Segment Substitution Lines from G. hirsutum × G. barbadense

Background

How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton.

Results

In total, 15 RNA-seq libraries were constructed and sequenced separately, generating 705.433 million clean reads with mean GC content of 45.13% and average Q30 of 90.26%. Through multiple comparisons between libraries, 1801 differentially expressed genes (DEGs) were identified, of which the 902 up-regulated DEGs were mainly involved in cell wall organization and response to oxidative stress and auxin, while the 898 down-regulated ones participated in translation, regulation of transcription, DNA-templated and cytoplasmic translation based on GO annotation and KEGG enrichment analysis. Subsequently, STEM software was performed to explicate the temporal expression pattern of DEGs. Two peroxidases and four flavonoid pathway-related genes were identified in the “oxidation-reduction process”, which could play a role in fiber development and quality formation. Finally, the reliability of RNA-seq data was validated by quantitative real-time PCR of randomly selected 20 genes.

Conclusions

The present report focuses on the similarities and differences of transcriptome profiles between the two CSSLs and the recurrent parent CCRI36 and provides novel insights into the molecular mechanism of fiber development, and into further exploration of the feasible contribution of G. barbadense substitution segments to fiber quality formation, which will lay solid foundation for simultaneously improving fiber yield and quality of upland cotton through CSSLs.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4077-8) contains supplementary material, which is available to authorized users.

Observation of a charged charmoniumlike structure in e+ e- → π+ π- J/ψ at sqrt[s] = 4.26 GeV

We study the process ee+ e- → π+ π- J/ψ at a center-of-mass energy of 4.260 GeV using a 525  pb(-1) data sample collected with the BESIII detector operating at the Beijing Electron Positron Collider. The Born cross section is measured to be (62.9±1.9±3.7)  pb, consistent with the production of the Y(4260). We observe a structure at around 3.9  GeV/c2 in the π(±)J/ψ mass spectrum, which we refer to as the Z(c)(3900). If interpreted as a new particle, it is unusual in that it carries an electric charge and couples to charmonium. A fit to the π(±)J/ψ invariant mass spectrum, neglecting interference, results in a mass of (3899.0±3.6±4.9)  MeV/c2 and a width of (46±10±20)  MeV. Its production ratio is measured to be R = (σ(e+ e- → π(±)Z(c)(3900)(∓) → π+ π- J/ψ)/σ(e+ e- → π+ π- J/ψ)) = (21.5±3.3±7.5)%. In all measurements the first errors are statistical and the second are systematic.

Observation of two new N* resonances in the decay ψ(3686)→ppπ0

Based on 106×10(6)ψ(3686) events collected with the BESIII detector at the BEPCII facility, a partial wave analysis of ψ(3686)→ppπ0 is performed. The branching fraction of this channel has been determined to be B(ψ(3686)→ppπ0)=(1.65±0.03±0.15)×10(-4). In this decay, 7 N* intermediate resonances are observed. Among these, two new resonances, N(2300) and N(2570) are significant, one 1/2+ resonance with a mass of 2300(-30-0)(+40+109)  MeV/c2 and width of 340(-30-58)(+30+110)  MeV/c2, and one 5/2- resonance with a mass of 2570(-10-10)(+19+34)  MeV/c2 and width of 250(-24-21)(+14+69)  MeV/c2. For the remaining 5 N* intermediate resonances [N(1440), N(1520), N(1535), N(1650) and N(1720)], the analysis yields mass and width values that are consistent with those from established resonances.

Evidence for the direct two-photon transition from ψ(3686) to J/ψ

The two-photon transition ψ(3686)→γγJ/ψ is studied in a sample of 1.06×10(8) ψ(3686) decays collected by the BESIII detector. The branching fraction is measured to be (3.1±0.6(stat)(-1.0)(+0.8)(syst))×10(-4) using J/ψ→e(+)e(-) and J/ψ→μ(+)μ(-) decays, and its upper limit is estimated to be 4.5×10(-4) at the 90% confidence level. This work represents the first measurement of a two-photon transition among charmonium states. The orientation of the ψ(3686) decay plane and the J/ψ polarization in this decay are also studied. In addition, the product branching fractions of sequential E1 transitions ψ(3686)→γχ(cJ) and χ(cJ)→γJ/ψ(J=0,1,2) are reported.

First observation of the M1 transition ψ(3686)→γη(c)(2S)

Using a sample of 106×10(6) ψ(3686) events collected with the BESIII detector at the BEPCII storage ring, we have made the first measurement of the M1 transition between the radially excited charmonium S-wave spin-triplet and the radially excited S-wave spin-singlet states: ψ(3686)→γη(c)(2S). Analyses of the processes ψ(3686)→γη(c)(2S) with η(c)(2S)→K(S)(0)K(±)π(∓) and K(+)K(-)π(0) give an η(c)(2S) signal with a statistical significance of greater than 10 standard deviations under a wide range of assumptions about the signal and background properties. The data are used to obtain measurements of the η(c)(2S) mass (M(η(c)(2S))=3637.6±2.9(stat)±1.6(syst) MeV/c(2)), width (Γ(η(c)(2S))=16.9±6.4(stat)±4.8(syst) MeV), and the product branching-fraction (B(ψ(3686)→γη(c)(2S))×B(η(c)(2S)→KKπ)=(1.30±0.20(stat)±0.30(syst))×10(-5)). Combining our result with a BABAR measurement of B(η(c)(2S)→KKπ), we find the branching fraction of the M1 transition to be B(ψ(3686)→γη(c)(2S))=(6.8±1.1(stat)±4.5(syst))×10(-4).

Measurements of the mass and width of the η(c) using the decay ψ(3686)→γη(c)

The mass and width of the lowest-lying S-wave spin singlet charmonium state, the η(c), are measured using a data sample of 1.06×10(8) ψ(3686) decays collected with the BESIII detector at the BEPCII storage ring. We use a model that incorporates full interference between the signal reaction, ψ(3686)→γη(c), and a nonresonant radiative background to describe the line shape of the η(c) successfully. We measure the η(c) mass to be 2984.3±0.6±0.6 MeV/c(2) and the total width to be 32.0±1.2±1.0 MeV, where the first errors are statistical and the second are systematic.

First observation of η(1405) decays into f(0)(980)π0

The decays J/ψ → γ π+ π- π0 and J/ψ → γ π0 π0 π0 are analyzed using a sample of 225×10(6) J/ψ events collected with the BESIII detector. The decay of η(1405) → f(0)(980)π0 with a large isospin violation is observed for the first time. The width of the f(0)(980) observed in the dipion mass spectra is anomalously narrower than the world average. Decay rates for three-pion decays of the η' are also measured precisely.

Spin-parity analysis of pp¯ mass threshold structure in J/ψ and ψ(3686) radiative decays

A partial wave analysis of the pp¯ mass-threshold enhancement in the reaction J/ψ→γpp¯ is used to determine its J(PC) quantum numbers to be 0(-+), its peak mass to be below threshold at M=1832(-5)(+19)(stat)(-17)(+18)(syst)±19(model) MeV/c(2), and its total width to be Γ<76 MeV/c(2) at the 90% C.L. The product of branching ratios is measured to be BR[J/ψ→γX(pp¯)]BR[X(pp¯)→pp¯]=[9.0(-1.1)(+0.4)(stat)(-5.0)(+1.5)(syst)±2.3(model)]×10(-5). A similar analysis performed on ψ(3686)→γpp¯ decays shows, for the first time, the presence of a corresponding enhancement with a production rate relative to that for J/ψ decays of R=[5.08(-0.45)(+0.71)(stat)(-3.58)(+0.67)(syst)±0.12(model)]%.

ηπ+ π- resonant structure around 1.8 GeV/c(2) and η(1405) in J/ψ → ωηπ+ π-

We present results of a study of the decay J/ψ → ωηπ+ π- using a sample of (225.2 ± 2.8) × 10(6) J/ψ events collected by the BESIII detector, and report the observation of a new process J/ψ → ωX(1870) with a statistical significance of 7.2σ, in which X(1870) decays to a(0)(±)(980)π±. Fitting to ηπ+ π- mass spectrum yields a mass M = 1877.3 ± 6.3(stat)(-7.4)(+3.4)(syst) MeV/c(2), a width Γ = 57 ± 12(stat)(-4)(+19)(syst) MeV/c(2), and a product branching fraction B(J/ψ → ωX) × B(X→a(0)(±)(980)π±) × B(a(0) (±)(980) → ηπ±) = [1.50 ± 0.26(stat)(-0.36)(+0.72) (syst)] × 10(-4). Signals for J/ψ → ωf(1)(1285) and J/ψ → ω η(1405) are also clearly observed and measured.

Observation of χ(c1) decays into vector meson pairs φφ, ωω, and ωφ

Using (106±4)×10⁻⁶ ψ(3686) events accumulated with the BESIII detector at the BEPCII e⁺e⁻ collider, we present the first measurement of decays of χ(c1) to vector meson pairs φφ, ωω, and ωφ. The branching fractions are measured to be (4.4±0.3±0.5)×10⁻⁴, (6.0±0.3±0.7)×10⁻⁴, and (2.2±0.6±0.2)×10⁻⁵, for χ(c1)→φφ, ωω, and ωφ, respectively, which indicates that the hadron helicity selection rule is significantly violated in χ(cJ) decays. In addition, the measurement of χ(cJ)→ωφ provides the first indication of the rate of doubly OZI-suppressed χ(cJ) decay. Finally, we present improved measurements for the branching fractions of χ(c0) and χ(c2) to vector meson pairs.

Confirmation of the X(1835) and observation of the resonances X(2120) and X(2370) in J/ψ→γπ+π-η'

With a sample of (225.2±2.8)×10(6) J/ψ events registered in the BESIII detector, J/ψ→γπ(+)π(-)η(') is studied using two η(') decay modes: η(')→π(+)π(-)η and η(')→γρ(0). The X(1835), which was previously observed by BESII, is confirmed with a statistical significance that is larger than 20σ. In addition, in the π(+)π(-)η(') invariant-mass spectrum, the X(2120) and the X(2370), are observed with statistical significances larger than 7.2σ and 6.4σ, respectively. For the X(1835), the angular distribution of the radiative photon is consistent with expectations for a pseudoscalar.

Evidence for ψ' decays into γπ0 and γη

The decays ψ'→γπ(0), γη and γη' are studied using data collected with the BESIII detector at the BEPCII e(+)e(-) collider. The processes ψ'→γπ(0) and ψ'→γη are observed for the first time with signal significances of 4.6σ and 4.3σ, respectively. The branching fractions are determined to be B(ψ'→γπ(0))=(1.58±0.40±0.13)×10(-6), B(ψ'→γη)=(1.38±0.48±0.09)×10(-6), and B(ψ'→γη')=(126±3±8)×10(-6), where the first errors are statistical and the second ones systematic.

Measurements of h(c)(1P(1)) in psi' decays

We present measurements of the charmonium state h(c)(1P(1)) made with 106x10(6) psi' events collected by BESIII at BEPCII. Clear signals are observed for psi'-->pi0 h(c) with and without the subsequent radiative decay h(c)-->gamma eta(c). First measurements of the absolute branching ratios B(psi'-->pi0 h(c)) = (8.4+/-1.3+/-1.0) x 10(-4) and B(h(c)-->gamma eta(c)) = (54.3+/-6.7+/-5.2)% are presented. A statistics-limited determination of the previously unmeasured h(c) width leads to an upper limit Gamma(h(c))<1.44 MeV (90% confidence). Measurements of M(h(c)) = 3525.40+/-0.13+/-0.18 MeV/c2 and B(psi'-->pi0 h(c)) x B(h(c)-->gamma eta(c)) = (4.58+/-0.40+/-0.50) x 10(-4) are consistent with previous results.

Functional consequences of the mutations in human cardiac troponin I gene found in familial hypertrophic cardiomyopathy

Functional consequences of the six mutations (R145G, R145Q, R162W, DeltaK183, G203S, K206Q) in cardiac troponin I (cTnI) that cause familial hypertrophic cardiomyopathy (HCM) were studied using purified recombinant human cTnI. The missense mutations R145G and R145Q in the inhibitory region of cTnI reduced the intrinsic inhibitory activity of cTnI without changing the apparent affinity for actin. On the other hand, the missense mutation R162W in the second troponin C binding region and the deletion mutation DeltaK183 near the second actin-tropomyosin region reduced the apparent affinity of cTnI for actin without changing the intrinsic inhibitory activity. Ca(2+) titration of a fluorescent probe-labeled human cardiac troponin C (cTnC) showed that only R162W mutation impaired the cTnC-cTnI interaction determining the Ca(2+) affinity of the N-terminal regulatory domain of cTnC. Exchanging the human cardiac troponin into isolated cardiac myofibrils or skinned cardiac muscle fibers showed that the mutations R145G, R145Q, R162W, DeltaK183 and K206Q induced a definite increase in the Ca(2+)-sensitivity of myofibrillar ATPase activity and force generation in skinned muscle fibers. Although the mutation G203S also showed a tendency to increase the Ca(2+) sensitivity in both myofibrils and skinned muscle fibers, no statistically significant difference compared with wild-type cTnI could be detected. These results demonstrated that most of the HCM-linked cTnI mutations did affect the regulatory processes involving the cTnI molecule, and that at least five mutations (R145G, R145Q, R162W, DeltaK183, K206Q) increased the Ca(2+) sensitivity of cardiac muscle contraction.

[Stereotactic conformal radiotherapy technology]

Body Stereotactic Conformal Radiotherapy technology was introduced in this paper. This discusses target localization, beam shape, treatment planning system and reproducibility.

Transmembrane Ca2+ gradient is essential for high anion transport activity of human erythrocytes

The role of a transmembrane Ca2+ gradient in anion transport by Band 3 of human resealed erythrocyte ghosts has been studied. The results show that a transmembrane Ca2+ gradient is essential for the conformation of erythrocyte Band 3 with higher anion transport activity. The dissipation of the transmembrane Ca2+ gradient by the ionophore A23187 inhibits the anion transport activity. The extent of this inhibition approaches 90% as the Ca2+ concentration on both sides of the ghost membrane is increased to 1.0 mM and half-maximum inhibitions is observed at 0.25 mM Ca2+. Addition of ATP (0.4 mM) to the resealing medium can partly reestablish the transmembrane Ca2+ gradient by activation of Ca(2+)-ATPase and alleviate the inhibition to some extent. N-ethylmaleimide, an inhibitor of erythrocyte Ca(2+)-ATPase, prevents such restoration. Electron micrographs reveal that numerous larger intramembranous particle can be observed on the P-faces of freeze-fractured resealed ghosts in the absence of a transmembrane Ca2+ gradient.

[Freeze-fracturing studies on human erythrocyte membranes effected by external pulsed electrical field]

Electron microscopic observations made on the freeze-fracturing replica of plasma membranes of human erythrocytes exposed to external pulsed electrical field have shown that under experimental conditions, some particles and fibers appear around the cells pulsed by higher intensities than 3 KV/cm. Electrophoretical analysis for the cell suspensions has proved that some of these particles and fibers are membrane proteins and membrane skeleton proteins escaped from cells. On account of this, the stability of cell membrane decreases and the cells are easy to change their shapes and to form pseudopodium like structures and protein free membrane lipids tend to form vesicular structure in cytoplasma. The changes of protein-protein interactions and protein-lipid interactions caused by electrical field are considered as the dominating mechanism of cell membrane electroporation. An argument about intramembrane particles (IMPS) and other possibilities of the contributions to IMPS, for instance, ice crystals formation which related to membrane hydrophilic or hydrophobic properties were discussed in this paper.