Many different chicken breeds are found around the world, their features vary among them, and they are valuable resources.  Currently, there is a huge lack of knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these breeds of chickens.  Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved chicken breeds.  The whole-genomes of 140 chickens from 7 Shandong native breeds and 20 introduced recessive white chickens from China were re-sequenced.  Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed geographically based clusters among the chickens.  Through genome-wide scans for selective sweeps, we identified thyroid stimulating hormone receptor (TSHR, reproductive traits, circadian rhythm), erythrocyte membrane protein band 4.1 like 1 (EPB41L1, body size), and alkylglycerol monooxygenase (AGMO, aggressive behavior), as major candidate breed-specific determining genes in chickens.  In addition, we used a machine learning classification model to predict chicken breeds based on the SNPs significantly associated with recourse characteristics, and the prediction accuracy was 92%, which can effectively achieve the breed identification of Laiwu Black chickens.  We provide the first comprehensive genomic data of the Shandong indigenous chickens.  Our analyses revealed phylogeographic patterns among the Shandong indigenous chickens and candidate genes that potentially contribute to breed-specific traits of the chickens.  In addition, we developed a machine learning-based prediction model using SNP data to identify chicken breeds.  The genetic basis of indigenous chicken breeds revealed in this study is useful to better understand the mechanisms underlying the resource characteristics of chicken.

Porcine reproductive and respiratory syndrome (PRRS) is recognized as one of the most infectious viral diseases of swine. Although Cluster of differentiation 163 (CD163) is identified as an essential receptor for mediating PRRS virus (PRRSV) infection, the important residues involved in infection on CD163 are still unclear. Therefore, it is very important to identify these key residues to study the mechanism of PRRSV infection and to generate anti-PRRSV pigs. In this study, we first generated immortalized porcine alveolar macrophage (IPAM) cell lines harboring 40-residues (residues 523–562, including R561 (arginine (R) at position 561)) deletion of CD163. PRRSV infection experiments showed that these IPAM cell lines were completely resistant to PRRSV infection. We then generated cloned pigs carrying CD163- R561A (an arginine (R) to alanine (A) substitution at position 561 of CD163). PRRSV challenge experiments in porcine alveolar macrophages (PAMs) isolated from the CD163-R561A pigs showed significantly lower susceptibility to PRRSV than that of CD163-R561 PAMs. Through this study, we show that CD163 523–562 contains essential residues for mediating PRRSV infection, and that CD163 R561 significantly contributes to PRRSV infection but is not essential for infection. These functional sites can therefore serve as new targets for understanding the mechanism of PRRSV infection. Furthermore, CD163-R561A pigs can be used as an important model for improving pig germplasm with resistance against PRRSV.

Although it is usually latent on citrus, apple, and pear, apple stem grooving virus (ASGV) poses a great risk to many sensitive cultivars.  Since severe leaf yellow mottle mosaic (LYMM) symptoms have been observed on Huangjinmiyou (HJY) pummelos (Citrus grandis cv. Huangjinmiyou), a commercial variety that is widely cultivated in South China, high throughput sequencing (HTS) was used to find potential pathogens and only three divergent ASGV variants were identified.  The three ASGV variants shared 81.03–82.34% genome-wide pairwise identities with each other, and were separately closest to other ASGV variants from different hosts and/or geographical regions, as indicated by viral phylogenies.  However, these new variants may have developed from viral interstrain interactions, based on the results of recombination analysis.  A large-scale survey using reverse transcription-PCR (RT-PCR) protocols designed for the three ASGV variants revealed a high incidence (92.7–100%) of ASGV in symptomatic HJY trees from 11 major citrus-producing regions in China.  None of ASGV were detected in asymptomatic trees.  Temperature treatments applied to the symptomatic HJY plants showed that ASGV is sensitive to high temperatures (30–35°C), at which not only the plants recovered, but also the viruses were not detected by RT-PCR, while at low temperatures (20–24°C), both the symptoms and viruses remained detectable.  These data show that ASGV is associated with the LYMM disease prevalent on HJY in China, and this is the significant basis especially of taking appropriate measures timely to manage the disease.  

In 2009, an emerging citrus viral disease caused by Citrus chlorotic dwarf-associated virus (CCDaV) was discovered in Yunnan Province of China.  However, the occurrence and spread of CCDaV in other citrus-growing provinces in China is unknown to date.  To better understand the distribution and molecular diversity of CCDaV in China, a total of 1 772 citrus samples were collected from 11 major citrus-growing provinces and were tested for CCDaV by PCR.  Among these, 134 citrus samples from Guangxi, Yunnan and Guangdong were tested positive for CCDaV, demonstrating that the occurrence and spread of CCDaV are increasing in China.  The complete genome sequences of 17 CCDaV isolates from different provinces and hosts were sequenced.  Comparisons of the whole-genome sequences of the 17 CCDaV isolates as well as the 15 isolates available in GenBank revealed that the sequence identity was about 99–100%, showing that the CCDaV isolates were highly conserved.  Phylogenetic studies showed that the 32 CCDaV isolates belonged to four different groups based on geographical origins and host species, and that CCDaV isolates from China and Turkey were clustered into different groups.  The results provide important information for clarifying the distribution and genetic diversity of CCDaV in China.

The effects of exogenous GSH (reduced glutathione) on photosynthetic characteristics, photosystem II efficiency, absorbed light energy allocation and the H₂O₂-scavenging system in chloroplasts of salt-stressed tomato (Solanum lycopersicum L.) seedlings were studied using hydroponic experiments in a greenhouse.  Application of exogenous GSH ameliorated saline-induced growth inhibition, the disturbed balance of Na⁺ and Cl⁻ ions and Na⁺/K⁺ ratios, and the reduction of the net photosynthetic rate (P_n).  GSH also increased the maximal photochemical efficiency of PSII (F_v/F_m), the electron transport rate (ETR), the photochemical quenching coefficient (q_P), and the non-photochemical quenching coefficient (NPQ).  In addition, GSH application increased the photochemical quantum yield (Y(II)) and relative deviation from full balance between the photosystems (β/α–1) and decreased the PSII excitation pressure (1–q_P) and quantum yield of non-regulated energy dissipation (Y(NO)) in leaves of salt-stressed tomatoes without BSO (L-buthionine-sulfoximine, an inhibitor of key GSH synthesis enzyme γ-glutamylcysteine synthetase) or with BSO.  Further, the addition of GSH depressed the accumulation of H₂O₂ and malondialdehyde (MDA), induced the redistribution of absorbed light energy in PSII reaction centers, and improved the endogenous GSH content, GSH/GSSH ratio and activities of H₂O₂-scavenging enzymes (including superoxidase dismutase (SOD), catalase (CAT), peroxidase (POD) and key enzymes in the AsA-GSH cycle and Grx system) in the chloroplasts of salt-stressed plants with or without BSO.  Therefore, GSH application alleviates inhibition of salt-induced growth and photosynthesis mainly by overcoming stomatal limitations, improving the PSII efficiency, and balancing the uneven distribution of light energy to reduce the risk of ROS generation and to mediate chloroplast redox homeostasis and the antioxidant defense system to protect the chloroplasts from oxidative damage.  Thus, GSH may be used as a potential tool for alleviating salt stress in tomato plants.

    A process-oriented methodology to conduct precise evaluation temporally and spatially on temperature suitability for potato growth was applied in China. Arable lands in China were gridded with 1 km×1 km geographic units, and potential potato phenology in each unit was automatically identified in terms of the potato planting initial temperature and effective accumulated temperature. A temperature thermal response coefficient model was used to compute a temperature suitability value for each day of potato phenology in each geographic unit. In addition, five temperature suitability ranking methods were applied to define suitable areas: (1) upper fourth quantile, (2) median, (3) expected value+1/4 standard deviation, (4) expected value+1/2 standard deviation, (5) expected value+1 standard deviation. A validation indicator was innovated to test the effectiveness of the five ranking methods. The results showed that from a strict degree point of view, the five methods sequence was as follows: 1=3>4>2>5, with a and c determined as the two best ranking methods. For methods 1 and 3, the suitable potato growing area was 1 of 57.76×10⁴ km². In addition, the suitable areas were spatially coincident with the main potato producing counties. The study output technically supports the proposal from China’s government that there is a large potential area to grow winter-ploughed potato in South China because the potential suitable area for growing potato is approximately 2×10⁷ ha. In southeast Heilongjiang and east Jilin, where it is hilly and mountainous, there are still some potentially suitable areas for potato growing accounting for nearly 2.32×10⁶ ha. The authors suggest to optimize the agricultural regionalization and layout in China and to adjust the cropping pattern structure.

The incorporation of straw in cultivated fields can potentially improve soil quality and crop yield. However, the presence of recalcitrant carbon compounds in straw slow its decomposition rate. The objective of this study was to determine the effects of different nitrogen sources, with and without the application of zinc, on straw decomposition and soil quality. Soils were treated with three different nitrogen sources, with and without zinc: urea (CO(NH2)2), ammonium sulfate ((NH4)2SO4), and ammonium chloride (NH4Cl). The combined treatments were as follows: maize (M) and wheat (W) straw incorporated into urea-, ammonium sulfate-, or ammonium chloride-treated soil (U, S, and C, respectively) with and without zinc (Z) (MU, MUZ, WU, WUZ; MS, MSZ, WS, WSZ; MC, MCZ, WC, WCZ, respectively); straw with zinc only (MZ, WZ); straw with untreated soil (MS, WS); and soil-only or control conditions (NT). The experiment consisted of 17 treatments with four replications. Each pot contained 150 g soil and 1.125 g straw, had a moisture content of 80% of the field capacity, and was incubated for 53 days at 25°C. The rates of CO2-C emission, cumulative CO2-C evolution, total CO2 production in the soils of different treatments were measured to infer decomposition rates. The total organic carbon (TOC), labile organic carbon (LOC), and soil microbial biomass in the soils of different treatments were measured to infer soil quality. All results were significantly different (P<0.05) with the exception of the labile organic carbon (LOC). The maize and wheat straw showed different patterns in CO2 evolution rates. For both straw types, Zn had a synergic effect with U, but an antagonistic effect with the other N sources as determined by the total CO2 produced. The MUZ treatment showed the highest decomposition rate and cumulative CO2 concentration (1 120.29 mg/pot), whereas the WACZ treatment had the lowest cumulative CO2 concentration (1 040.57 mg/pot). The addition of NH4Cl resulted in the highest total organic carbon (TOC) concentration (11.59 mg kg-1). The incorporation of wheat straw resulted in higher microbial biomass accumulation in soils relative to that of the maize straw application. The results demonstrate that mineral N sources can affect the ability of microorganisms to decompose straw, as well as the soil carbon concentrations.

Citrus tristeza virus (CTV) is one of the most important causal agents of citrus diseases and exists as numerous strains.CTV is replicated in phloem cells of plants within the family Rutaceae and is transmitted by a few of aphid species. CTVepidemics have caused death of millions of citrus trees in many regions all over the world, where the sour orange (Citrusaurantium) was used as rootstock. Also the production of grapefruit (C. paradisi) and sweet orange (C. sinensis) hasbeen affected by CTV strains. CTV gives uplift to three prominent syndromes, namely quick-decline (tristeza), stempittingand seedling-yellows. The disease is graft-transmissible in nature but not seed-transmitted. However, the tristezadisease in most citrus groves was a man-made problem created by the desire of horticulturists to introduce cultivars fromother citrus growing areas. The utmost importance of the disease called for review articles in numbers of plant protection,epidemiology books, citriculture and proceedings. This review collects the information with respects to disease history,distribution host range, virus isolates association, identification and detection, transmission and management; especiallyon the current status of CTV prevailing and controlling in Pakistan. It provides valuable information for CTV disease andits controlling approaches.

Since May 2006, a highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) variant characterizedby 30 amino acids deletion within its NSP2-coding region emerged and caused extensive economic losses to China’s pigindustry. To investigate the in vivo pathogenicity and immune responses of the newly emerging PRRSV, 3 groups of 60-d-old conventional piglets were inoculated intranasally with a representative strain of the HP-PRRSV variant HuN4 with3 different infection doses (3×103-3×105 TCID50). The results revealed that the virus variant caused severe disease inpiglets and the significant clinical characteristics consisted of persistently high fever (41.0-41.9ºC) and high morbidity andmortality (60-100%), the marked clinical signs of PRRS and severe histopathogenic damages in multiple organs. It inducedrapid and intense humoral immune responses and seroconversion was detected in most infected pigs at 7 d post-infection(DPI). The virus vigorously replicated in vivo and the highest virus average titer was 9.7 log copies mL-1 serum at 7 DPI.Elevated levels of IFN-γ and IL-10 cytokine production in serum in this study were also observed. Taken together, ourresults demonstrated that the HP-PRRSV variant HuN4 strain is highly pathogenic for piglets and suitable to be a referencestrain of highly virulent PRRSV for evaluating the efficacy of the new vaccines.

Apple fruit firmness is a crucial index for measuring the internal quality of apples, influencing palatability and determining storage and transportation capacity. The primary cause of decreased firmness during fruit development is the hydrolysis of cell wall polysaccharides. Xyloglucan endotransglycosylase/hydrolase (XTH) is a key enzyme involved in the depolymerization of cell wall polysaccharides, but its mechanism in the formation of fruit firmness remains unclear. Here, we identified the gene MdXTH2 by integrating metabolomic and transcriptomic data, and further analyzed its function and molecular mechanism in the formation of apple fruit firmness. The results showed a downward trend in both fruit firmness and cell wall components throughout fruit development. The contents of cell wall material, cellulose, and hemicellulose in various apple varieties exhibited significant positive correlations with firmness, with total correlation coefficients of 0.862, 0.884, and 0.891, respectively. Overexpression of MdXTH2 significantly increased fruit firmness in apple and tomato, inhibited fruit ripening, and significantly suppressed calli growth. The upstream transcription factor MdNAC72 of the MdXTH2 gene can promote the expression of fruit ripening-related genes. Furthermore, dual-luciferase, yeast one-hybrid, and electrophoretic mobility shift assay assays demonstrated that MdNAC72 down-regulated the transcription of MdXTH2 by binding to its promoter. In summary, these results provide a strategy for studying fruit quality regulation and a theoretical basis for breeding apple varieties with moderate firmness through genetic improvement.