2024 Vol. 23 No. 7 Previous Issue   
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Crop Science
Genetic analysis and fine mapping of a grain size QTL in the small-grain sterile rice line Zhuo201S
Bin Lei, Jiale Shao, Feng Zhang, Jian Wang, Yunhua Xiao, Zhijun Cheng, Wenbang Tang, Jianmin Wan
2024, 23(7): 2155-2163.  DOI: 10.1016/j.jia.2023.07.026
Abstract ( )   PDF in ScienceDirect  
The development and application of the small-grain rice sterile line Zhuo201S (Z201S) has demonstrated its potential for mechanized hybrid rice seed production, leading to significant cost reductions.  However, the molecular mechanism responsible for the small-grain size characteristic of Z201S remains unclear.  In this study, we conducted a genetic analysis using near-isogenic lines constructed from Z210S, a small-grain rice sterile line, and R2115, a normal-grain variety.  The results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain number.  Through mapping, we localized the causal gene to the short arm of chromosome 2, within a 113 kb physical region delimited by the molecular markers S2-4-1 and LB63.  Transgenic analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene, suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.
Identification of P-type plasma membrane H+-ATPases in common wheat and characterization of TaHA7 associated with seed dormancy and germination
Bingli Jiang, Wei Gao, Yating Jiang, Shengnan Yan, Jiajia Cao, Litian Zhang, Yue Zhang, Jie Lu, Chuanxi Ma, Cheng Chang, Haiping Zhang
2024, 23(7): 2164-2177.  DOI: 10.1016/j.jia.2023.07.023
Abstract ( )   PDF in ScienceDirect  
The P-type plasma membrane (PM) H+-ATPases (HAs) are crucial for plant development, growth, and defense.  The HAs have been thoroughly characterized in many different plants.  However, despite their importance, the functions of HAs in germination and seed dormancy (SD) have not been validated in wheat.  Here, we identified 28 TaHA genes (TaHA1-28) in common wheat, which were divided into five subfamilies.  An examination of gene expression in strong- and weak-SD wheat varieties led to the discovery of six candidate genes (TaHA7/-12/-14/-16/-18/-20).  Based on a single nucleotide polymorphism (SNP) mutation (C/T) in the TaHA7 coding region, a CAPS marker (HA7) was developed and validated in 168 wheat varieties and 171 Chinese mini-core collections that exhibit diverse germination and SD phenotypes.  We further verified the roles of the two allelic variations of TaHA7 in germination and SD using wheat mutants mutagenized with ethyl methane sulphonate (EMS) in ‘Jimai 22’ and ‘Jing 411’ backgrounds, and in transgenic Arabidopsis lines.  TaHA7 appears to regulate germination and SD by mediating gibberellic acid (GA) and abscisic acid (ABA) signaling, metabolism, and biosynthesis.  The results presented here will enable future research regarding the TaHAs in wheat.

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize
Peng Liu, Langlang Ma, Siyi Jian, Yao He, Guangsheng Yuan, Fei Ge, Zhong Chen, Chaoying Zou, Guangtang Pan, Thomas Lübberstedt, Yaou Shen
2024, 23(7): 2178-2195.  DOI: 10.1016/j.jia.2023.06.032
Abstract ( )   PDF in ScienceDirect  

Genetic transformation has been an effective technology for improving the agronomic traits of maize.  However, it is highly reliant on the use of embryonic callus (EC) and shows a serious genotype dependence.  In this study, we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline (MQ2Gpipe).  Based on the induction rate of EC (REC), these inbred lines were categorized into three subpopulations.  The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.  By integrating a genome-wide selective signature screen and region-based association analysis, we revealed 95.23 Mb of selective regions and 43 REC-associated variants.  These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.  In total, 103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.  These genes mainly participate in regulation of the cell cycle, regulation of cytokinesis, and other functions, among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.  Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci, implying a potential synergistic selection of REC and leaf size during modern maize breeding.

Genetic analysis and candidate gene identification of salt tolerancerelated traits in maize
Hui Fang, Xiuyi Fu, Hanqiu Ge, Mengxue Jia, Jie Ji, Yizhou Zhao, Zijian Qu, Ziqian Cui, Aixia Zhang, Yuandong Wang, Ping Li, Baohua Wang
2024, 23(7): 2196-2210.  DOI: 10.1016/j.jia.2024.02.009
Abstract ( )   PDF in ScienceDirect  
Soil salinization poses a threat to maize production worldwide, but the genetic mechanism of salt tolerance in maize is not well understood.  Therefore, identifying the genetic components underlying salt tolerance in maize is of great importance.  In the current study, a teosinte-maize BC2F7 population was used to investigate the genetic basis of 21 salt tolerance-related traits.  In total, 125 QTLs were detected using a high-density genetic bin map, with one to five QTLs explaining 6.05–32.02% of the phenotypic variation for each trait.  The total phenotypic variation explained (PVE) by all detected QTLs ranged from 6.84 to 63.88% for each trait.  Of all 125 QTLs, only three were major QTLs distributed in two genomic regions on chromosome 6, which were involved in three salt tolerance-related traits.  In addition, 10 pairs of epistatic QTLs with additive effects were detected for eight traits, explaining 0.9 to 4.44% of the phenotypic variation.  Furthermore, 18 QTL hotspots affecting 3–7 traits were identified.  In one hotspot (L5), a gene cluster consisting of four genes (ZmNSA1, SAG6, ZmCLCg, and ZmHKT1;2) was found, suggesting the involvement of multiple pleiotropic genes.  Finally, two important candidate genes, Zm00001d002090 and Zm00001d002391, were found to be associated with salt tolerance-related traits by a combination of linkage and marker-trait association analyses.  Zm00001d002090 encodes a calcium-dependent lipid-binding (CaLB domain) family protein, which may function as a Ca2+ sensor for transmitting the salt stress signal downstream, while Zm00001d002391 encodes a ubiquitin-specific protease belonging to the C19-related subfamily.  Our findings provide valuable insights into the genetic basis of salt tolerance-related traits in maize and a theoretical foundation for breeders to develop enhanced salt-tolerant maize varieties.

Heterogeneous population distribution enhances resistance to wheat lodging by optimizing the light environment
Yibo Hu, Feng Qin, Zhen Wu, Xiaoqin Wang, Xiaolong Ren, Zhikuan Jia, Zhenlin Wang, Xiaoguang Chen, Tie Cai
2024, 23(7): 2211-2226.  DOI: 10.1016/j.jia.2023.07.006
Abstract ( )   PDF in ScienceDirect  

Lodging is still the key factor that limits continuous increases in wheat yields today, because the mechanical strength of culms is reduced due to low-light stress in populations under high-yield cultivation.  The mechanical properties of the culm are mainly determined by lignin, which is affected by the light environment.  However, little is known about whether the light environment can be sufficiently improved by changing the population distribution to inhibit culm lodging.  Therefore, in this study, we used the wheat cultivar “Xinong 979” to establish a low-density homogeneous distribution treatment (LD), high-density homogeneous distribution treatment (HD), and high-density heterogeneous distribution treatment (HD-h) to study the regulatory effects and mechanism responsible for differences in the lodging resistance of wheat culms under different population distributions.  Compared with LD, HD significantly reduced the light transmittance in the middle and basal layers of the canopy, the net photosynthetic rate in the middle and lower leaves of plants, the accumulation of lignin in the culm, and the breaking resistance of the culm, and thus the lodging index values increased significantly, with lodging rates of 67.5% in 2020–2021 and 59.3% in 2021–2022.  Under HD-h, the light transmittance and other indicators in the middle and basal canopy layers were significantly higher than those under HD, and the lodging index decreased to the point that no lodging occurred.  Compared with LD, the activities of phenylalanine ammonia-Lyase (PAL), 4-coumarate: coenzyme A ligase (4CL), catechol-O-methyltransferase (COMT), and cinnamyl-alcohol dehydrogenase (CAD) in the lignin synthesis pathway were significantly reduced in the culms under HD during the critical period for culm formation, and the relative expression levels of TaPAL, Ta4CL, TaCOMT, and TaCAD were significantly downregulated.  However, the activities of lignin synthesis-related enzymes and their gene expression levels were significantly increased under HD-h compared with HD.  A partial least squares path modeling analysis found significant positive effects between the canopy light environment, the photosynthetic capacity of the middle and lower leaves of plants, lignin synthesis and accumulation, and lodging resistance in the culms.  Thus, under conventional high-density planting, the risk of wheat lodging was significantly higher.  Accordingly, the canopy light environment can be optimized by changing the heterogeneity of the population distribution to improve the photosynthetic capacity of the middle and lower leaves of plants, promote lignin accumulation in the culm, and enhance lodging resistance in wheat.  These findings provide a basis for understanding the mechanism responsible for the lower mechanical strength of the culm under high-yield wheat cultivation, and a theoretical basis and for developing technical measures to enhance lodging resistance.

The environment, especially the minimum temperature, affects summer maize grain yield by regulating ear differentiation and grain development
Jing Chen, Baizhao Ren, Bin Zhao, Peng Liu, Jiwang Zhang
2024, 23(7): 2227-2241.  DOI: 10.1016/j.jia.2023.06.034
Abstract ( )   PDF in ScienceDirect  

Ear differentiation, grain development and their interaction with factors in the growing environment, such as temperature, solar radiation and precipitation, greatly influence grain number and grain weight, and ultimately affect summer maize production.  In this study, field experiments involving different sowing dates were conducted over three years to evaluate the effects of temperature factors, average solar radiation and total precipitation on the growth process, ear differentiation, fertilization characteristics, grain filling and yield of summer maize varieties with different growth durations.  Four hybrids were evaluated in Huang-Huai-Hai Plain (HHHP), China from 2018 to 2020 with five different sowing dates.  The results showed that the grain yield formation of summer maize was strongly impacted by the environment from the silking (R1) to milking (R3) stage.  Average minimum temperature (ATmin) was the key environmental factor that determined yield.  Reductions in the length of the growing season (r=–0.556, P<0.01) and the total floret number on ear (R2=0.200, P<0.001) were found when ATmin was elevated from the emerging (VE) to R1 stage.  Both grain-filling rate (R2=0.520, P<0.001) and the floret abortion rate on ear (R2=0.437, P<0.001) showed quadratic relationships with ATmin from the R1 to physiological maturity (R6) stage, while the number of days after the R1 stage (r=–0.756, P<0.01) was negatively correlated with ATmin.  An increase in ATmin was beneficial for the promotion of yield when it did not exceeded a certain level (above 23°C during the R1–R3 stage and 20–21°C during the R1-R6 stage).  Enhanced solar radiation and precipitation during R1–R6 increased the grain-filling rate (R2=0.562, P<0.001 and R2=0.229, P<0.05, respectively).  Compared with short-season hybrids, full-season hybrids showed much greater suitability for a critical environment.  The coordinated regulation of ATmin, ear differentiation and grain development at the pre- and post-silking stages improved maize yield by increasing total floret number and grain-filling rate, and by reducing the floret abortion rate on ear. 

Increasing root-lower characteristics improves drought tolerance in cotton cultivars at the seedling stage
Congcong Guo, Hongchun Sun, Xiaoyuan Bao, Lingxiao Zhu, Yongjiang Zhang, Ke Zhang, Anchang Li, Zhiying Bai, Liantao Liu, Cundong Li
2024, 23(7): 2242-2254.  DOI: 10.1016/j.jia.2023.07.013
Abstract ( )   PDF in ScienceDirect  
Drought is an important abiotic stress factor in cotton production.  The root system architecture (RSA) of cotton shows high plasticity which can alleviate drought-related stress under drought stress (DS) conditions; however, this alleviation is cultivar dependent.  Therefore, this study estimated the genetic variability of RSA in cotton under DS.  Using the paper-based growth system, we assessed the RSA variability in 80 cotton cultivars at the seedling stage, with 0 and 10% polyethylene glycol 6000 (PEG6000) as the control (CK) and DS treatment, respectively.  An analysis of 23 above-ground and root traits in the 80 cotton cultivars revealed different responses to DS.  On the 10th day after DS treatment, the degree of variation in the RSA traits under DS (5–55%) was greater than that of CK (5–49%).  The 80 cultivars were divided into drought-tolerant cultivars (group 1), intermediate drought-tolerant cultivars (group 2), and drought-sensitive cultivars (group 3) based on their comprehensive evaluation values of drought resistance.  Under DS, the root length-lower, root area-lower, root volume-lower, and root length density-lower were significantly reduced by 63, 71, 76, and 4% in the drought-sensitive cultivars compared to CK.  Notably, the drought-tolerant cultivars maintained their root length-lower, root area-lower, root volume-lower, and root length density–lower attributes.  Compared to CK, the root diameter (0–2 mm)-lower increased by 21% in group 1 but decreased by 3 and 64% in groups 2 and 3, respectively, under DS.  Additionally, the drought-tolerant cultivars displayed a plastic response under DS that was characterized by an increase in the root-lower characteristics.  Drought resistance was positively correlated with the root area-lower and root length density-lower.  Overall, the RSA of the different cotton cultivars varied greatly under DS.  Therefore, important root traits, such as the root-lower traits, provide great insights for exploring whether drought-tolerant cotton cultivars can effectively withstand adverse environments.
Physiological and transcriptome analyses of Chinese cabbage in response to drought stress
Lin Chen, Chao Li, Jiahao Zhang, Zongrui Li, Qi Zeng, Qingguo Sun, Xiaowu Wang, Limin Zhao, Lugang Zhang, Baohua Li
2024, 23(7): 2255-2269.  DOI: 10.1016/j.jia.2024.03.067
Abstract ( )   PDF in ScienceDirect  

Chinese cabbage is an important leafy vegetable crop with high water demand and susceptibility to drought stress.  To explore the molecular mechanisms underlying the response to drought, we performed a transcriptome analysis of drought-tolerant and -sensitive Chinese cabbage genotypes under drought stress, and uncovered core drought-responsive genes and key signaling pathways.  A co-expression network was constructed by a weighted gene co-expression network analysis (WGCNA) and candidate hub genes involved in drought tolerance were identified.  Furthermore, abscisic acid (ABA) biosynthesis and signaling pathways and their drought responses in Chinese cabbage leaves were systemically explored.  We also found that drought treatment increased the antioxidant enzyme activities and glucosinolate contents significantly.  These results substantially enhance our understanding of the molecular mechanisms underlying drought responses in Chinese cabbage.

Melatonin and dopamine alleviate waterlogging stress in apples by recruiting beneficial endophytes to enhance physiological resilience
Yang Cao, Peihua Du, Yuwei Shang, Jiahao Ji, Leiqing Tan, Xue Zhang, Jizhong Xu, Bowen Liang
2024, 23(7): 2270-2291.  DOI: 10.1016/j.jia.2023.12.012
Abstract ( )   PDF in ScienceDirect  
Melatonin and dopamine can potentially prevent waterlogging stress in apples.  The current study investigated the mechanism by which melatonin and dopamine alleviate apple waterlogging stress.  This study demonstrated that melatonin and dopamine alleviated waterlogging by removing reactive oxygen species (ROS), and that the nitric oxide (NO) content and nitrate reductase (NR) activity were significantly correlated.  Melatonin and dopamine were also found to recruit different candidate beneficial endophytes (melatonin: Novosphingobium, Propionivibrio, and Cellvibrio; dopamine: Hydrogenophaga, Simplicispira, Methyloversatilis, Candidatus_Kaiserbacteria, and Humicola), and these endophytes were significantly and positively correlated with plant growth.  Network analyses showed that melatonin and dopamine significantly affected the endophytic bacterial and fungal communities under waterlogging stress.  The metabolomic results showed that melatonin and dopamine led to waterlogging resistance by upregulating the abundance of beneficial substances such as amino acids, flavonoids, coumarins, and organic acids.  In addition, melatonin and dopamine regulated the physicochemical properties of the soil, which altered the endophyte community and affected plant growth.  The co-occurrence network demonstrated close and complex relationships among endophytes, metabolites, soil, and the plants.  Our results demonstrate that melatonin and dopamine alleviate waterlogging stress in apples by recruiting beneficial endophytes to enhance physiological resilience.  This study provides new insights into how melatonin and dopamine alleviate stress and a theoretical basis for synergistic beneficial microbial resistance to waterlogging stress.

Quantitative trait loci identification reveals zinc finger protein CONSTANS-LIKE 4 as the key candidate gene of stigma color in watermelon (Citrullus lanatus)
Shuang Pei, Zexu Wu, Ziqiao Ji, Zheng Liu, Zicheng Zhu, Feishi Luan, Shi Liu
2024, 23(7): 2292-2305.  DOI: 10.1016/j.jia.2024.03.070
Abstract ( )   PDF in ScienceDirect  

Stigma color is a critical agronomic trait in watermelon that plays an important role in pollination.  However, there are few reports on the regulation of stigma color in watermelon.  In this study, a genetic analysis of the F2 population derived from ZXG1553 (P1, with orange stigma) and W1-17 (P2, with yellow stigma) indicated that stigma color is a quantitative trait and the orange stigma is recessive compared with the yellow stigma.  Bulk segregant analysis sequencing (BSA-seq) revealed a 3.75 Mb segment on chromosome 6 that is related to stigma color.  Also, a major stable effective QTL Clqsc6.1 (QTL stigma color) was detected in two years between cleaved amplified polymorphic sequencing (CAPS) markers Chr06_8338913 and Chr06_9344593 spanning a ~1.01 Mb interval that harbors 51 annotated genes.  Cla97C06G117020 (annotated as zinc finger protein CONSTANS-LIKE 4) was identified as the best candidate gene for the stigma color trait through RNA-seq, quantitative real-time PCR (qRT-PCR), and gene structure alignment analysis among the natural watermelon panel.  The expression level of Cla97C06G117020 in the orange stigma accession was lower than in the yellow stigma accessions with a significant difference.  A nonsynonymous SNP site of the Cla97C06G117020 coding region that causes amino acid variation was related to the stigma color variation among nine watermelon accessions according to their re-sequencing data.  Stigma color formation is often related to carotenoids, and we also found that the expression trend of ClCHYB (annotated as β-carotene hydroxylase) in the carotenoid metabolic pathway was consistent with Cla97C06G117020, and it was expressed in low amounts in the orange stigma accession.  These data indicated that Cla97C06G117020 and ClCHYB may interact to form the stigma color.  This study provides a theoretical basis for gene fine mapping and mechanisms for the regulation of stigma color in watermelon. 

Plant Protection
Sensitivity and resistance risk analysis of Didymella bryoniae populations to fluopyram
Zhiwen Wu, Xiaowei Cai, Xuewei Mao, Mingguo Zhou, Yiping Hou
2024, 23(7): 2306-2317.  DOI: 10.1016/j.jia.2023.11.044
Abstract ( )   PDF in ScienceDirect  
Fluopyram is an succinate dehydrogenase inhibitors (SDHI) fungicide that has been registered in China to control gummy stem blight (GSB) in watermelons for many years.  However, whether the field pathogens of GSB are still sensitive to fluopyram or not is unknown.  Therefore, we collected 69 Didymella bryoniae isolates from the fields that usually use fluopyram to control GSB to determine the sensitivity change.  The EC50 (50% inhibition effect) values of fluopyram against Dbryoniae ranged from 0.0691 to 0.3503 μg mL–1 and the variation factor was 5.07.  The mean EC50 value was (0.1579±0.0669) μg mL–1 and the curve of sensitivity was unimodal.  No resistant strains were found in the isolates, which means that the pathogens were still sensitive to fluopyram.  The minimal inhibition concentration (MIC) of fluopyram against Dbryoniae was 3 μg mL–1.  Four low-resistant mutants and two medium-resistant mutants were obtained using fungicide taming and the resistance of mutants could be inherited stably.  The growth rate of mutants decreased significantly compared with that of wild-type strains while the biomass of most mutants was similar to that of wild-type strains.  The sensitivity of most resistant mutants to various stresses was increased compared with that of wild-type strains.  The virulence of mutants receded except for low-resistant mutant XN51FR-1, which had the same lesion area as XN51 on the watermelon leaves.  The results indicated that the fitness of resistant mutants was decreased compared with that of wild-type strains.  The cross-resistance assay indicated that fluopyram-resistant mutants were positive cross-resistant to all six SDHI fungicides in this test but were still sensitive to fluazinam and tebuconazole.  So the resistance risk of Dbryoniae to fluopyram was moderate.  In addition, we found that the SdhB gene of low-resistant mutant XN30FR-1 had three new point mutations at positions K258N, A259P, and H277N.  Medium-resistant mutant XN52FR-1 showed a mutation at position H277N and other mutants did not have any point mutation. 

Development of a stable attenuated double-mutant of tobacco mosaic virus for cross-protection
Wei Wang, Renfu Zhang, Haiyang Liu, Ruifeng Ding, Qiushi Huang, Ju Yao, Gemei Liang
2024, 23(7): 2318-2331.  DOI: 10.1016/j.jia.2024.02.019
Abstract ( )   PDF in ScienceDirect  

Tobacco (Nicotiana tabacum) and tomato (Solanum lycopersicum) are two major economic crops in China.  Tobacco mosaic virus (TMV; genus Tobamovirus) is the most prevalent virus infecting both crops.  Currently, some widely cultivated tobacco and tomato cultivars are susceptible to TMV and there is no effective strategy to control this virus.  Cross-protection can be a safe and environmentally friendly strategy to prevent viral diseases.  However, stable attenuated TMV mutants are scarce.  In this study, we found that the substitutions in the replicase p126, arginine at position 196 (R196) with aspartic acid (D), glutamic acid at position 614 (E614) with glycine (G), serine at position 643 (S643) with phenylalanine (F), or D at position 730 (D730) with S, significantly reduced the virulence and replication of TMV.  However, only the mutation of S643 to F reduced the RNA silencing suppression activity of TMV p126.  A double-mutant TMV-E614G-S643F induced no visible symptom and was genetically stable through six successive passages in tobacco plants.  Furthermore, our results showed that TMV-E614G-S643F double-mutant could provide effective protection against the wild-type TMV infection in tobacco and tomato plants.  This study reports a promising mild mutant for cross-protection to control TMV in tobacco and tomato plants.

Resistance development, cross-resistance, and fitness costs associated with Aphis gossypii resistance towards sulfoxaflor and acetamiprid in different geographical regions
Wei Wang, Renfu Zhang, Haiyang Liu, Ruifeng Ding, Qiushi Huang, Ju Yao, Gemei Liang
2024, 23(7): 2332-2345.  DOI: 10.1016/j.jia.2023.07.029
Abstract ( )   PDF in ScienceDirect  

Aphis gossypii has become increasingly difficult to manage due to its strong insecticide resistance.  In the laboratory, we established sulfoxaflor-resistant and acetamiprid-resistant strains in two A. gossypii populations with different basal insecticide resistance levels, and evaluated the effects of basal insecticide resistance on the resistance development and cross-resistance, as well as differences in fitness.  Under the same selection pressure, Yarkant A. gossypii (with low basal insecticide resistance) evolved resistance to sulfoxaflor and acetamiprid more quickly than Jinghe A. gossypii (with high basal insecticide resistance), and the evolution of A. gossypii resistance to sulfoxaflor developed faster than acetamiprid in both Yarkant and Jinghe, Xingjiang, China.  The sulfoxaflor-resistant strains selected from Yarkant and Jinghe developed significant cross-resistance to acetamiprid, imidacloprid, thiamethoxam and pymetrozine; while the acetamiprid-resistant strains developed significant cross-resistance to sulfoxaflor, imidacloprid, thiamethoxam, pymetrozine, and chlorpyrifos.  The relative fitness of A. gossypii decreased as the resistance to sulfoxaflor and acetamiprid developed.  The relative fitness levels of the sulfoxaflor-resistant strains (Yarkant-SulR and Jinghe-SulR) were lower than those of the acetamiprid-resistant strains (Yarkant-AceR and Jinghe-AceR).  In addition, the relative fitness levels of sulfoxaflor- and acetamiprid-resistant strains were lower in Jinghe than in Yarkant.  In summary, basal insecticide resistance of A. gossypii and insecticide type affected the evolution of resistance to insecticides in A. gossypii, as well as cross-resistance to other insecticides.  The sulfoxaflor- and acetamiprid-resistant A. gossypii strains had obvious fitness costs.  The results of this work will contribute to the insecticide resistance management and integrated management of A. gossypii.

The biosynthesis of alarm pheromone in the wheat aphid Rhopalo-siphum padi is regulated by hormones via fatty acid metabolism
Chengxian Sun, Yaoguo Qin, Julian Chen, Zhengxi Li
2024, 23(7): 2346-2361.  DOI: 10.1016/j.jia.2023.11.030
Abstract ( )   PDF in ScienceDirect  

Aphids are major insect pests in agriculture and forestry worldwide. Following attacks by natural enemies, many aphids release an alarm pheromone to protect their population. In most aphids, the main component of the aphid alarm pheromone (AAP) is the sesquiterpene hydrocarbon (E)-β-farnesene (EβF). However, the mechanisms behind its biosynthesis and regulation remain poorly understood. In this study, we used the bird cherry–oat aphid Rhopalosiphum padi, which is an important wheat aphid, to investigate the regulatory mechanisms of EβF biosynthesis. Our results showed that EβF biosynthesis occurs during the mature embryo period and the molting period of the 1st- and 2nd-instar nymphs. Triglycerides provide the prerequisite material for EβF production and release. Based on transcriptome sequencing, RNAi analysis, hormone treatments, and quantitative measurements, we found that the biosynthesis of EβF utilizes acetyl coenzyme A produced from fatty acid degradation, which can be suppressed by juvenile hormone but it is promoted by 20-hydroxyecdysone through the modulation of fatty acid metabolism. This is the first systemic study on the modulation of EβF production in aphids. The results of our study provide insights into the molecular regulatory mechanisms of AAP biosynthesis, as well as valuable information for designing potential aphid control strategies.

Animal Science · Veterinary Medicine
Dynamic transcriptome profiles and novel markers in bovine spermatogenesis revealed by single-cell sequencing
Yuan Gao, Fuxia Bai, Qi Zhang, Xiaoya An, Zhaofei Wang, Chuzhao Lei, Ruihua Dang
2024, 23(7): 2362-2378.  DOI: 10.1016/j.jia.2023.04.036
Abstract ( )   PDF in ScienceDirect  
Testicular development is an important biological process in male and requires interaction between the male germ cells and somatic cells. However, the mechanisms of testicular development in livestock, particularly in cattle, are poorly understood. Furthermore, cellular heterogeneity hinders the profiling of different cell types at different developmental stages. In this study, we first performed a single-cell transcriptomic study of the bovine testis development during puberty by using 10× genomics single-cell RNA sequencing (scRNA-seq). By collecting the scRNA-seq data from 11,083 cells from prepubertal and pubertal bovine testes, a high-resolution scRNA-seq atlas was described, identifying 9 somatic and 13 spermatogenic clusters. We also distinguished several stage-specific marker genes for bovine germ cells and somatic cells, such as GRAF2 and MORC1 for SSC (spermatogonial stem cells), HJURP and TCF19 for differentiating spermatogonia, ARSE for immature Sertoli, CLEC12B for mature Sertoli, LOC112441470 for Leydig. In conclusion, we have examined the transcription levels and constructed the single-cell developmental maps of germ cells and somatic cells during testicular development in Angus cattle. The datasets provided new insights into spermatogenesis and testicular somatic cell development in cattle.
Asymmetric expression of CA2 and CA13 linked to calcification in the bilateral mandibular condyles cause crossed beaks in chickens
Lei Shi, Yanyan Sun, Yunlei Li, Hao Bai, Jingwei Yuan, Hui Ma, Yuanmei Wang, Panlin Wang, Aixin Ni, Linlin Jiang, Pingzhuang Ge, Shixiong Bian, Yunhe Zong, Jinmeng Zhao, Adamu M. Isa, Hailai H. Tesfay, Jilan Chen
2024, 23(7): 2379-2390.  DOI: 10.1016/j.jia.2023.04.014
Abstract ( )   PDF in ScienceDirect  
Crossed beak is a complex mode of inheritance with prevalence ranging from 0.2 to 7.4% in at least 12 chicken strains worldwide. To reveal the intrinsic factors causing crossed beaks, genes expression patterns in bilateral mandibular condyle between affected and normal birds were characterized by RNA sequencing analysis in the present studies. Crossed beak was induced by short length of unilateral mandibular ramus, and a total of 110 differentially expressed genes were up- or down-regulated in the affected (short) mandibular condyle side as compared to the normal side. Carbonic anhydrase 2 (CA2) and Carbonic anhydrase 13 (CA13) were enriched in the carbonate dehydratase activity, and high-expressed in mandibular condyle and osteoblasts (P<0.05). However, both were low-expressed in short mandibular condyle side of affected birds (P<0.05). The carbonate dehydratase inhibitor experiments confirmed that there is positive association between the calcification and carbonic anhydrase isoenzymes. Quantitative analysis with cetylpyridinium chloride showed a decrease in calcification when the cells were transfected with an anti-CA13 shRNA. Our research suggested that CA2 and CA13 are down-calcified in shortside mandibular condyle, and caused mandibular ramus to grow slowly. CA2 and CA13 have the critical role in crossed beaks by regulating calcification of mandibular condyle.
Substitutions of stem-loop subdomains in internal ribosome entry site of Senecavirus A: Impacts on rescue of sequence-modifying viruses
Qianqian Wang, Jie Wang, Lei Zhang, Xiaoxiao Duan, Lijie Zhu, Youming Zhang, Yan Li, Fuxiao Liu
2024, 23(7): 2391-2406.  DOI: 10.1016/j.jia.2024.04.019
Abstract ( )   PDF in ScienceDirect  

Senecavirus A (SVA) has a positive-sense, single-stranded RNA genome. Its 5´ untranslated region harbors an internal ribosome entry site (IRES), comprising 10 larger or smaller stem-loop structures (including a pseudoknot) that have been demonstrated to be well conserved. However, it is still unclear whether each stem-loop subdomain, such as a single stem or loop, is also highly conserved. To clarify this issue in the present study, a set of 29 SVA cDNA clones were constructed by site-directed mutagenesis (SDM) on the IRES. The SDM-modified scenarios included: (1) stem-formed complementary sequences exchanging with each other; (2) loop transversion; (3) loop transition; and (4) point mutations. All cDNA clones were separately transfected into cells for rescuing viable viruses, whereas only four SVAs of interest could be recovered, and were genetically stable during 20 passages. One progeny grew significantly slower than the other three did. The dual-luciferase reporter assay showed that none of the SDM-modified IRESes significantly inhibited the IRES activity. Our previous study indicated that a single motif from any of the ten stem structures, if completely mutated, would cause the failure of virus recovery. Interestingly, our present study revealed three stem structures, whose individual complementary sequences could exchange with each other to rescue sequence-modifying SVAs. Moreover, one apical loop was demonstrated to have the ability to tolerate its own full-length transition, also having no impact on the recovery of sequence-modifying SVA. The present study suggested that not every stem-loop structure was strictly conserved in its conformation, while the full-length IRES itself was well conserved. This provides a new research direction on interaction between the IRES and many factors.

Genetic and pathogenic characterization of new infectious bronchitis virus strains in the GVI-1 and GI-19 lineages isolated in central China
Yuhan Yang, Dou Wang, Yaning Bai, Wenyan Huang, Shimin Gao, Xingchen Wu, Ying Wang, Jianle Ren, Jinxin He, Lin Jin, Mingming Hu, Zhiwei Wang, Zhongbing Wang, Haili Ma, Junping Li, Libin Liang
2024, 23(7): 2407-2420.  DOI: 10.1016/j.jia.2023.10.029
Abstract ( )   PDF in ScienceDirect  

Avian infectious bronchitis (IB) is a highly contagious infectious disease caused by infectious bronchitis virus (IBV), which is prevalent in many countries worldwide and causes serious harm to the poultry industry.  At present, many commercial IBV vaccines have been used for the prevention and control of IB; however, IB outbreaks occur frequently.  In this study, two new strains of IBV, SX/2106 and SX/2204, were isolated from two flocks which were immunized with IBV H120 vaccine in central China.  Phylogenetic and recombination analysis indicated that SX/2106, which was clustered into the GI-19 lineage, may be derived from recombination events of the GI-19 and GI-7 strains and the LDT3-A vaccine.  Genetic analysis showed that SX/2204 belongs to the GVI-1 lineage, which may have originated from the recombination of the GI-13 and GVI-1 strains and the H120 vaccine.  The virus cross-neutralization test showed that the antigenicity of SX/2106 and SX/2204 was different from H120.  Animal experiments found that both SX/2106 and SX/2204 could replicate effectively in the lungs and kidneys of chickens and cause disease and death, and H120 immunization could not provide effective protection against the two IBV isolates.  It is noteworthy that the pathogenicity of SX/2204 has significantly increased compared to the GVI-1 strains isolated previously, with a mortality rate up to 60%.  Considering the continuous mutation and recombination of the IBV genome to produce new variant strains, it is important to continuously monitor epidemic strains and develop new vaccines for the prevention and control of IBV epidemics.

Agro-ecosystem & Environment
Optimized NPK fertilizer recommendations based on topsoil available nutrient criteria for wheat in drylands of China
Wenjie Yang, Jie Yu, Yanhang Li, Bingli Jia, Longgang Jiang, Aijing Yuan, Yue Ma, Ming Huang, Hanbing Cao, Jinshan Liu, Weihong Qiu, Zhaohui Wang
2024, 23(7): 2421-2433.  DOI: 10.1016/j.jia.2023.11.049
Abstract ( )   PDF in ScienceDirect  

The optimized management of crop fertilization is very important for improving crop yield and reducing the consumption of chemical fertilizers. Critical nutrient values can be used for evaluating the nutritional status of a crop, and they reflect the nutrient concentrations above which the plant is sufficiently supplied for achieving the maximum potential yield. Based on on-farm surveys of 504 farmers and 60 field experimental sites in the drylands of China, we proposed a recommended fertilization method to determine nitrogen (N), phosphorus (P), and potassium (K) fertilizer input rates for wheat production, and then validated the method by a field experiment at 66 different sites in northern China. The results showed that wheat grain yield varied from 1.1 to 9.2 t ha−1, averaging 4.6 t ha−1, and it had a quadratic relationship with the topsoil (0−20 cm) nitrate N and soil available P contents at harvest. However, yield was not correlated with the inputs of N, P, and K fertilizers. Based on the relationship (exponential decay model) between 95–105% of the relative yield and topsoil nitrate N, available P, and available K contents at wheat harvest from 60 field experiments, the topsoil critical nutrient values were determined as 34.6, 15.6, and 150 mg kg−1 for soil nitrate N, available P, and available K, respectively. Then, based on five groups of relative yield (>125%, 115–125%, 105–115%, 95–105%, and <95%) and the model, the five groups of topsoil critical nutrient levels and fertilization coefficients (Fc) were determined. Finally, we proposed a new method for calculating the recommended fertilizer input rate as: Fr=Gy×Nr×Fc, where Fr is the recommended fertilizer (N/P/K) input rate; Gy is the potential grain yield; Nr is the N(NrN), P(NrP), and K(NrK) nutrient requirements for wheat to produce 1,000 kg of grain; and Fc is a coefficient for N(Nc)/P(Pc)/K(Kc) fertilizer. A 2-year validated experiment confirmed that the new method reduced N fertilizer input by 17.5% (38.5 kg N ha−1) and P fertilizer input by 43.5% (57.5 kg P2O5 ha−1) in northern China and did not reduce the wheat yield. This outcome can significantly increase the farmers’ benefits (by 7.58%, or 139 US$ ha−1).  Therefore, this new recommended fertilization method can be used as a tool to guide N, P, and K fertilizer application rates for dryland wheat production.

Excessive manure application stimulates nitrogen cycling but only weakly promotes crop yields in an acidic Ultisol: Results from a 20-year field experiment
Song Wan, Yongxin Lin, Hangwei Hu, Milin Deng, Jianbo Fan, Jizheng He
2024, 23(7): 2434-2445.  DOI: 10.1016/j.jia.2023.10.016
Abstract ( )   PDF in ScienceDirect  

Population growth and growing demand for livestock products produce large amounts of manure, which can be harnessed to maintain soil sustainability and crop productivity. However, the impacts of excessive manure application on crop yields, nitrogen (N)-cycling processes and microorganisms remain unknown. Here, we explored the effects of 20-year of excessive rates (18 and 27 Mg ha–1 yr–1) of pig manure application on peanut crop yields, soil nutrient contents, N-cycling processes and the abundance of N-cycling microorganisms in an acidic Ultisol in summer and winter, compared with none and a regular rate (9 Mg ha–1 yr–1) of pig manure application. Long-term excessive pig manure application, especially at the high-rate, significantly increased soil nutrient contents, the abundance of N-cycling functional genes, potential nitrification and denitrification activity, while it had a weaker effect on peanut yield and plant biomass. Compared with manure application, seasonality had a much weaker effect on N-cycling gene abundance. Random forest analysis showed that available phosphorus (AP) content was the primary predictor for N-cycling gene abundance, with significant and positive associations with all tested N-cycling genes. Our study clearly illustrated that excessive manure application would increase N-cycling gene abundance and potential N loss with relatively weak promotion of crop yields, providing significant implications for sustainable agriculture in the acidic Ultisols.

Nitrogen rhizodeposition from corn and soybean, and its contribution to the subsequent wheat crops
Sainan Geng, Lantao Li, Yuhong Miao, Yinjie Zhang, Xiaona Yu, Duo Zhang, Qirui Yang, Xiao Zhang, Yilun Wang
2024, 23(7): 2446-2457.  DOI: 10.1016/j.jia.2023.11.018
Abstract ( )   PDF in ScienceDirect  

Nitrogen (N) is a key factor in the positive response of cereal crops that follow leguminous crops when compared to gramineous crops in rotations, with the nonrecyclable rhizosphere-derived N playing an important role.  However, quantitative assessments of differences in the N derived from rhizodeposition (NdfR) between legumes and gramineous crops are lacking, and comparative studies on their contributions to the subsequent cereals are scarce.  In this study, we conducted a meta-analysis of NdfR from leguminous and gramineous crops based on 34 observations published worldwide.  In addition, pot experiments were conducted to study the differences in the NdfR amounts, distributions and subsequent effects of two major wheat (Triticum aestivum L.)-preceding crops, corn (Zea mays L.) and soybean (Glycine max L.), by the cotton wick-labelling method in the main wheat-producing areas of China.  The meta-analysis results showed that the NdfR of legumes was significantly greater by 138.93% compared to gramineous crops.  In our pot experiment, the NdfR values from corn and soybean were 502.32 and 944.12 mg/pot, respectively, and soybean was also significantly higher than corn, accounting for 76.91 and 84.15% of the total belowground nitrogen of the plants, respectively.  Moreover, in different soil particle sizes, NdfR was mainly enriched in the large macro-aggregates (>2 mm), followed by the small macro-aggregates (2–0.25 mm).  The amount and proportion of NdfR in the macro-aggregates (>0.25 mm) of soybean were 3.48 and 1.66 times higher than those of corn, respectively, indicating the high utilization potential of soybean NdfR.  Regarding the N accumulation of subsequent wheat, the contribution of soybean NdfR to wheat was approximately 3 times that of corn, accounting for 8.37 and 4.04% of the total N uptake of wheat, respectively.  In conclusion, soybean NdfR is superior to corn in terms of the quantity and distribution ratio of soil macro-aggregates.  In future field production, legume NdfR should be included in the nitrogen pool that can be absorbed and utilized by subsequent crops, and the role and potential of leguminous plants as nitrogen source providers in crop rotation systems should be fully utilized.

Comparison of CWSI and Ts-Ta-VIs in moisture monitoring of dryland crops (sorghum and maize) based on UAV remote sensing
Hui Chen, Hongxing Chen, Song Zhang, Shengxi Chen, Fulang Cen, Quanzhi Zhao, Xiaoyun Huang, Tengbing He, Zhenran Gao
2024, 23(7): 2458-2475.  DOI: 10.1016/j.jia.2024.03.042
Abstract ( )   PDF in ScienceDirect  

Monitoring agricultural drought using remote sensing data is crucial for precision irrigation in modern agriculture.  Utilizing unmanned aerial vehicle (UAV) remote sensing, we explored the applicability of an empirical crop water stress index (CWSI) based on canopy temperature and three-dimensional drought indices (TDDI) constructed from surface temperature (Ts), air temperature (Ta) and five vegetation indices (VIs) for monitoring the moisture status of dryland crops.  Three machine learning algorithms (random forest regression (RFR), support vector regression, and partial least squares regression) were used to compare the performance of the drought indices for vegetation moisture content (VMC) estimation in sorghum and maize.  The main results of the study were as follows: (1) Comparative analysis of the drought indices revealed that Ts-Ta-normalized difference vegetation index (TDDIn) and Ts-Ta-enhanced vegetation index (TDDIe) were more strongly correlated with VMC compared with the other indices.  The indices exhibited varying sensitivities to VMC under different irrigation regimes; the strongest correlation observed was for the TDDIe index with maize under the fully irrigated treatment (r=−0.93). (2) Regarding spatial and temporal characteristics, the TDDIn, TDDIe and CWSI indices showed minimal differences.  Over the experimental period, with coefficients of variation were 0.25, 0.18 and 0.24, respectively. All three indices were capable of effectively characterizing the moisture distribution in dryland maize and sorghum crops, but the TDDI indices more accurately monitored the spatial distribution of crop moisture after a rainfall or irrigation event.  (3) For prediction of the moisture content of single crops, RFR models based on TDDIn and TDDIe estimated VMC most accurately (R2>0.7), and the TDDIn-based model predicted VMC with the highest accuracy when considering multiple-crop samples, with R2 and RMSE of 0.62 and 14.26%, respectively. Thus, TDDI proved more effective than the CWSI in estimating crop water content.

Food Science
Effects of 1-methylcyclopropene on skin greasiness and quality of ‘Yuluxiang’ pear during storage at 20°C
Wanting Yu, Xinnan Zhang, Weiwei Yan, Xiaonan Sun, Yang Wang, Xiaohui Jia
2024, 23(7): 2476-2490.  DOI: 10.1016/j.jia.2024.03.017
Abstract ( )   PDF in ScienceDirect  

During storage at 20°C, specific pear cultivars may exhibit a greasy texture and decline in quality due to fruit senescence. Among these varieties, ‘Yuluxiang’ is particularly susceptible to peel greasiness, resulting in significant economic losses. Therefore, there is an urgent need for a preservative that can effectively inhibit the development of greasiness. Previous studies have demonstrated the efficacy of 1-methylcyclopropene (1- MCP) in extending the storage period of fruits. We hypothesize that it may also influence the occurrence of postharvest peel greasiness in the ‘Yuluxiang’ pears. In this study, we treated ‘Yuluxiang’ pears with 1-MCP. We stored them at 20°C while analyzing the composition and morphology of the surface waxes, recording enzyme activities related to wax synthesis, and measuring indicators associated with fruit storage quality and physiological characteristics. The results demonstrate that prolonged storage at 20°C leads to a rapid increase in skin greasiness, consistent with the observed elevations in L*, greasiness score, and the content of total wax and greasy wax components. Moreover, there were indications that cuticular waxes underwent melting, resulting in the formation of an amorphous structure. In comparison to controls, the application of 1-MCP significantly inhibited increments in L* values as well as grease scores while also reducing accumulation rates for oily waxes throughout most stages over its shelf period, additionally delaying transitions from flaky-wax structures towards their amorphous counterparts. During the initial 7 d of storage, several enzymes involved in the biosynthesis and metabolism of greasy wax components, including lipoxygenase (LOX), phospholipase D (PLD), and β-ketoacyl-CoA synthase (KCS), exhibited an increase followed by a subsequent decline. The activity of LOX during early shelf life (0–7 d) and the KCS activity during middle to late shelf life (14–21 d) were significantly suppressed by 1-MCP. Additionally, 1-MCP effectively maintained firmness, total soluble solid (TSS) and titratable acid (TA) contents, peroxidase (POD), and phenylalanine ammonia-lyase (PAL) activities while inhibiting vitamin C degradation and weight loss. Furthermore, it restrained polyphenol oxidase (PPO) activity, ethylene production, and respiration rate increase. These findings demonstrate that 1-MCP not only delays the onset of peel greasiness but also preserves the overall storage quality of ‘Yuluxiang’ pear at a temperature of 20°C. This study presents a novel approach for developing new preservatives to inhibit pear fruit peel greasiness and provides a theoretical foundation for further research on pear fruit preservation.

Low-fat microwaved peanut snacks production: Effect of defatting treatment on structural characteristics, texture, color, and nutrition
Bo Jiao, Xin Guo, Yiying Chen, Shah Faisal, Wenchao Liu, Xiaojie Ma, Bicong Wu, Guangyue Ren, Qiang Wang
2024, 23(7): 2491-2502.  DOI: 10.1016/j.jia.2024.03.069
Abstract ( )   PDF in ScienceDirect  

This study develops low-fat microwaved peanut snacks (LMPS) using partially defatted peanuts (PDP) with different defatting ratios, catering to people’s pursuit of healthy, low-fat cuisine.  The effects of defatting treatment on the structural characteristics, texture, color, and nutrient composition of LMPS were comprehensively explored.  The structural characteristics of LMPS were characterized using X-ray micro-computed tomography (Micro-CT) and scanning electron microscope (SEM).  The results demonstrated that the porosity, pore number, pore volume, brightness, brittleness, protein content, and total sugar content of LMPS all significantly increased (P<0.05) with the increase in the defatting ratio.  At the micro level, porous structure, cell wall rupture, and loss of intracellular material could be observed in LMPS after defatting treatments.  LMPS made from PDP with a defatting ratio of 64.44% had the highest internal pore structural parameters (porosity 59%, pore number 85.3×105, pore volume 68.23 mm3), the brightest color (L* 78.39±0.39), the best brittleness (3.64±0.21) mm–1), and the best nutrition (high protein content, (34.02±0.38)%; high total sugar content, (17.45±0.59)%; low-fat content, (27.58±0.85)%).  The study provides a theoretical basis for the quality improvement of LMPS.

Soybean maize strip intercropping: A solution for maintaining food security in China
Jiang Liu, Wenyu Yang
2024, 23(7): 2503-2506.  DOI: 10.1016/j.jia.2024.02.001
Abstract ( )   PDF in ScienceDirect  

The practice of intercropping leguminous and gramineous crops is used for promoting sustainable agriculture, optimizing resource utilization, enhancing biodiversity, and reducing reliance on petroleum products.  However, promoting conventional intercropping strategies in modern agriculture can prove challenging.  The innovative technology of soybean maize strip intercropping (SMSI) has been proposed as a solution.  This system has produced remarkable results in improving domestic soybean and maize production for both food security and sustainable agriculture.  In this article, we provide an overview of SMSI and explain how it differs from traditional intercropping.  We also discuss the core principles that foster higher yields and the prospects for its future development.