Improving plant resistance to Verticillium wilt (VW), which causes massive losses in Gossypium hirsutum, is a global challenge.  Crop plants need to efficiently allocate their limited energy resources to maintain a balance between growth and defense.  However, few transcriptional regulators specifically respond to Verticillium dahliae and the underlying mechanism has not been identified in cotton.  In this study, we found that the that expression of most R2R3-MYB members in cotton is significantly changed by V. dahliae infection relative to the other MYB types.  One novel R2R3-MYB transcription factor (TF) that specifically responds to V. dahliae, GhMYB3D5, was identified.  GhMYB3D5 was not expressed in 15 cotton tissues under normal conditions, but it was dramatically induced by V. dahliae stress.  We functionally characterized its positive role and underlying mechanism in VW resistance.  Upon V. dahliae infection, the up-regulated GhMYB3D5 bound to the GhADH1 promoter and activated GhADH1 expression.  In addition, GhMYB3D5 physically interacted with GhADH1 and further enhanced the transcriptional activation of GhADH1.  Consequently, the transcriptional regulatory module GhMYB3D5-GhADH1 then promoted lignin accumulation by improving the transcriptional levels of genes related to lignin biosynthesis (GhPAL, GhC4H, Gh4CL, and GhPOD/GhLAC) in cotton, thereby enhancing cotton VW resistance.  Our results demonstrated that the GhMYB3D5 promotes defense-induced lignin accumulation, which can be regarded as an effective way to orchestrate plant immunity and growth. 

^{Eukaryotic genomes are hierarchically packaged into cell nucleus, affecting gene regulation.  The genome is organized into multiscale structural units, including chromosome territories, compartments, topologically associating domains (TADs), and DNA loops.  The identification of these hierarchical structures has benefited from the development of experimental approaches, such as 3C-based methods (Hi-C, ChIA-PET, etc.), imaging tools (2D-FISH, 3D-FISH, Cryo-FISH, etc.) and ligation-free methods (GAM, SPRITE, etc.).  In recent two decades, numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms, such as regulating enhancer activity and promoter-enhancer interactions.  However, there are relatively few studies about the 3D genome in livestock species.  Therefore, studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.  In this review, we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies, drawing inspiration to explore the 3D genomics of livestock species.  We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.}

Structural variation is an important source of genetic variation in wheat and have been important in the evolution of the wheat’s genome. Few studies have examined the relationship between structural variations and agronomy and drought tolerance. The present study identified structural chromosome variations (SCVs) in a doubled haploid (DH) population and backcross introgression lines (BC₅F₃) derived from Jinmai 47 and Jinmai 84 using fluorescence in situ hybridization.  There are one simple translocation, 10 present/absent variations (PAVs), and one copy number variation (CNV) between Jinmai 47 and Jinmai 84, which distributed in 10 chromosomes.  Eight SCVs were associated with 15 agronomic traits. A PAV recombination occurred on chromosome 2A, which was associated with grain number per spike (GNS). The 1BL/1RS translocation and PAV.2D were associated with significant reductions in plant height, deriving from the effects on LI2-LI4 and UI, LI2-LI4, respectively.  PAV.2D was also contributed to an increase of 3.13% for GNS, 1BL/1RS significantly increased spikelet number, grain length (GL), and grain thickness (GT). The effect of PAV.4A.1 on GL, PAV.6A on spike length (SL) and thousand-grain weight (TGW), PAV.6B on SL, GT and TGW were identified and verified. PAVs on chromosomes 2A, 6A, 1D, 2D, and a CNV on chromosome 4B were associated with the drought tolerance coefficients.  Additive and interaction effects among SCVs were observed. Many previously cloned key genes and yield-related QTL were found in polymorphic regions of PAV.2B, PAV.2D, and CNV.4B.  Altogether, this study confirmed the genetic effect of SCVs on agronomy and drought tolerance, and identification of these SCVs will facilitate genetic improvement of wheat through marker-assisted selection.

Pesticide resistance greatly limits control efficacy after the long-term application of pesticides. The two-spotted spider mite, Tetranychus urticae Koch, is a notorious agricultural pest worldwide that is resistant to various pesticides, including abamectin. While some studies of abamectin resistance have investigated target resistance related to glutamate-gated chloride channels (GluCls), studies on the metabolic resistance mechanisms are still limited. In this study, we identified an ABCC subfamily gene, TuABCC4, that was overexpressed in resistant populations of T. urticae, based on the analysis of previously obtained transcriptomic and RNA-seq data. No consistent nonsynonymous mutations in the TuABCC4 gene were found between the susceptible and resistant populations, although TuABCC4 expression was significantly increased in all the resistant populations that were studied. Synergistic experiments with the inhibitor verapamil and gene expression analysis of the susceptible and resistant populations confirmed the key role of TuABCC4 in abamectin resistance. In addition, an increase in the expression of the TuABCC4 gene was shown by RNA interference and genetic association analysis to be closely related to the resistance of T. urticae to abamectin. In conclusion, overexpression of TuABCC4 was shown to be involved in abamectin resistance in T. urticae. These results can help us to better understand the molecular basis of pest resistance to abamectin.

Improving rice yield and nitrogen use efficiency (NUE) are crucial challenges for coordinating food production and environmental health. However, little is known about the physiological mechanisms underlying the synergistic effects of high yield and NUE in rice. Using two near-isogenic rice lines (named DEP1 and dep1), a two-year field experiment was conducted to assess agronomic characteristics and the physiological characteristics of carbon and nitrogen translocation under three nitrogen levels. Compared with DEP1, dep1 had higher grain yield, grain filling percentage, nitrogen (N) uptake, and NUE. More non-structural carbohydrates (NSCs) and N in the stems were translocated to grains during grain filling in dep1 than in DEP1. Furthermore, stem NSC translocation was significantly positively correlated with grain yield, while stem N translocation was significantly positively correlated with NUE. Key carbon metabolism enzyme activities (α-amylase, β-amylase and sucrose-phosphate synthase in stems, and sucrose synthase, ADP-glucose pyrophosphorylase and starch synthase in grains) and stem sucrose transporter gene (OsSUT1 and OsSWEET13) expression were higher in dep1 than in DEP1. This contributed to high stem NSC translocation. Higher N translocation in the stems occurred due to the higher expression of OsNPF2.4. Moreover, the higher values of root morphological traits (root dry weight, root surface area, root length and root volume) and structural characteristics (stele diameter, cortical thickness and vessel section area) in dep1 explained its high nitrogen uptake. In addition, higher expression of OsNADH-GOGAT1 and OsGS1.3 promoted the assimilation of ammonium and contributed to higher nitrogen uptake in dep1. The application of N reduced carbon translocation but enhanced N translocation by regulating the corresponding metabolic enzyme activities and gene expression. Overall, these findings highlighted the roles of nitrogen uptake, and carbon and nitrogen translocation from stems as crucial characteristics for synergistically improving yield and NUE in the dep1 rice line.

Japanese encephalitis (JE) is a zoonotic mosquito-borne viral disease caused by the Japanese encephalitis virus (JEV). The virus is transmitted among adult pigs, causing abortion in sows and orchitis in boars. Vaccination remains the most effective strategy for the prevention and control of this disease. Studies have shown that genotype I (GI) JEV has replaced GIII JEV as the dominant strain in many Asian countries. However, all currently licensed JE vaccines, including the widely used SA14-14-2 live attenuated vaccine, are derived from the GIII strain. It has been reported that GIII-based vaccines do not provide complete protection against the GI strain. In this study, we conducted vaccination-challenge protection assays in mice and boars to evaluate the protective efficacy of live attenuated GI (SD12-F120) derived vaccines against challenge by a homologous genotype. In mice, immunisation with the vaccine induced a potent viral-neutralising response against the homologous GI JEV SD12 strain. The SD12-F120 vaccine provided complete protection against lethal challenge by SD12, whilst also attenuating viraemia. JEV was not detected in the blood, oronasal swabs, or testicles of boars receiving the SD12-F120 vaccine. Vaccination induced high levels of neutralising antibodies against the homologous GI strain in boars, with titers as high as 64. Histopathological analysis showed that interstitial cells of the boar testis and spermatogonia at all levels were well preserved in the vaccine-immunised group, effectively suppressing the occurrence of orchitis. These results showed that the SD12-F120 vaccine provides boars complete protection against challenge by SD12, whilst also protecting against viraemia and testicular damage. Our findings indicate that SD12-F120 is a promising live-attenuated vaccine candidate for controlling the spread of GI JEV.