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2024 Vol. 23 No. 1 Previous Issue    Next Issue

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Review
Crop Science
Horticulture
Plant Protection
Animal Science · Veterinary Medicine
Agro-ecosystem & Environment
Food Science
Agricultural Economics and Management
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Flower organ development in rice is closely related to yield, and its identity is mainly determined by A-, B-, C- and E-class genes, with the majority encoding MADS-box transcription factors. However, the regulatory mechanisms of these floral organ signature genes during flower development remains to be clarified. In this study, we successfully identified SPW2, which ecodes a plant-specific EMF1- like protein that involved in the H3K27me3 modification as an important component of the PRC2 complex. We demonstrated that SPW2 can mediate the process of H3K27me3 modification of pistil- related genes，OsMADS3, OsMADS13, OsMADS58, and DL, to regulate their expression in non- pistil organs of spikelets in rice, which expands our understanding of the molecular mechanism by which SPW2 regulates floral organ identity genes through epigenetic regulation. The cover photo illustrates the abnormal phenotypes of spw2, provided by professor Li Yunfeng’s research group from Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, China.


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Review

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Advances in DNA methylation and its role in cytoplasmic male sterility in higher plants Atiqur RAHMAN, Md. Hasan Sofiur RAHMAN, Md. Shakil UDDIN, Naima SULTANA, Shirin AKHTER, Ujjal Kumar NATH, Shamsun Nahar BEGUM, Md. Mazadul ISLAM, Afroz NAZNIN, Md. Nurul AMIN, Sharif AHMED, Akbar HOSAIN 2024, 23(1): 1-19.  DOI: 10.1016/j.jia.2023.04.045 Abstract ( )   PDF in ScienceDirect   The impact of epigenetic modifications like DNA methylation on plant phenotypes has expanded the possibilities for crop development.  DNA methylation plays a part in the regulation of both the chromatin structure and gene expression, and the enzyme involved, DNA methyltransferase, executes the methylation process within the plant genome.  By regulating crucial biological pathways, epigenetic changes actively contribute to the creation of the phenotype.  Therefore, epigenome editing may assist in overcoming some of the drawbacks of genome editing, which can have minor off-target consequences and merely facilitate the loss of a gene’s function.  These drawbacks include gene knockout, which can have such off-target effects.  This review provides examples of several molecular characteristics of DNA methylation, as well as some plant physiological processes that are impacted by these epigenetic changes in the plants.  We also discuss how DNA alterations might be used to improve crops and meet the demands of sustainable and environmentally-friendly farming.

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Assessment of molecular markers and marker-assisted selection for drought tolerance in barley (Hordeum vulgare L.) Akmaral Baidyussen, Gulmira Khassanova, Maral Utebayev, Satyvaldy Jatayev, Rystay Kushanova, Sholpan Khalbayeva, Aigul Amangeldiyeva, Raushan Yerzhebayeva, Kulpash Bulatova, Carly Schramm, Peter Anderson, Colin L. D. Jenkins, Kathleen L. Soole, Yuri Shavrukov 2024, 23(1): 20-38.  DOI: 10.1016/j.jia.2023.06.012 Abstract ( )   PDF in ScienceDirect   This review updates the present status of the field of molecular markers and marker-assisted selection (MAS), using the example of drought tolerance in barley.  The accuracy of selected quantitative trait loci (QTLs), candidate genes and suggested markers was assessed in the barley genome cv. Morex.  Six common strategies are described for molecular marker development, candidate gene identification and verification, and their possible applications in MAS to improve the grain yield and yield components in barley under drought stress.  These strategies are based on the following five principles: (1) Molecular markers are designated as genomic ‘tags’, and their ‘prediction’ is strongly dependent on their distance from a candidate gene on genetic or physical maps; (2) plants react differently under favourable and stressful conditions or depending on their stage of development; (3) each candidate gene must be verified by confirming its expression in the relevant conditions, e.g., drought; (4) the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield; and (5) the small number of molecular markers realized for MAS in breeding, from among the many studies targeting candidate genes, can be explained by the complex nature of drought stress, and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.

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3D genome organization and its study in livestock breeding Jie Cheng, Xiukai Cao, Shengxuan Wang, Jiaqiang Zhang, Binglin Yue, Xiaoyan Zhang, Yongzhen Huang, Xianyong Lan, Gang Ren, Hong Chen 2024, 23(1): 39-58.  DOI: 10.1016/j.jia.2023.04.007 Abstract ( )   PDF in ScienceDirect   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.

Crop Science

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SUPER WOMAN 2 (SPW2) maintains organ identity in spikelets by inhibiting the expression of floral homeotic genes OsMADS3, OsMADS58, OsMADS13, and DROOPING LEAF ZHUANG Hui, LAN Jin-song, YANG Qiu-ni, ZHAO Xiao-yu, LI Yu-huan, ZHI Jing-ya, SHEN Ya-lin, HE Guang-hua, LI Yun-feng 2024, 23(1): 59-76.  DOI: 10.1016/j.jia.2023.07.010 Abstract ( )   PDF in ScienceDirect   Flower organ identity in rice is mainly determined by the A-, B-, C- and E-class genes, with the majority encoding MADS-box transcription factors.  However, few studies have investigated how the expression of these floral organ identity genes is regulated during flower development.  In this study, we identified a gene named SUPER WOMAN 2 (SPW2), which is necessary for spikelet/floret development in rice by participating in the regulation of the expression of pistil identity genes such as OsMADS3, OsMADS13, OsMADS58 and DL.  In the spw2 mutant, ectopic stigma/ovary-like tissues were observed in the non-pistil organs, including sterile lemma, lemma, palea, lodicule, and stamen, suggesting that the identities of these organs were severely affected by mutations in SPW2.  SPW2 was shown to encode a plant-specific EMF1-like protein that is involved in H3K27me3 modification as an important component of the PRC2 complex.  Expression analysis showed that the SPW2 mutation led to the ectopic expression of OsMADS3, OsMADS13, OsMADS58, and DL in non-pistil organs of the spikelet.  The ChIP-qPCR results showed significant reductions in the levels of H3K27me3 modification on the chromatin of these genes.  Thus, we demonstrated that SPW2 can mediate the process of H3K27me3 modification of pistil-related genes to regulate their expression in non-pistil organs of spikelets in rice.  The results of this study expand our understanding of the molecular mechanism by which SPW2 regulates floral organ identity genes through epigenetic regulation.

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Genetic dissection and validation of a major QTL for grain weight on chromosome 3B in bread wheat (Triticum aestivum L.) Simin Liao, Zhibin Xu, Xiaoli Fan, Qiang Zhou, Xiaofeng Liu, Cheng Jiang, Liangen Chen, Dian Lin, Bo Feng, Tao Wang 2024, 23(1): 77-92.  DOI: 10.1016/j.jia.2023.04.023 Abstract ( )   PDF in ScienceDirect   Grain weight is one of the key components of wheat (Triticum aestivum L.) yield.  Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.  A recombinant inbred line (RIL) population derived from a cross between W7268 and Chuanyu 12 (CY12) was employed to detect quantitative trait loci (QTLs) for thousand-grain weight (TGW), grain length (GL), grain width (GW), and the ratio of grain length to width (GLW) in six environments.  Seven major QTLs, QGl.cib-2D, QGw.cib-2D, QGw.cib-3B, QGw.cib-4B.1, QGlw.cib-2D.1, QTgw.cib-2D.1 and QTgw.cib-3B.1, were consistently identified in at least four environments and the best linear unbiased estimation (BLUE) datasets, and they explained 2.61 to 34.85% of the phenotypic variance.  Significant interactions were detected between the two major TGW QTLs and three major GW loci.  In addition, QTgw.cib-3B.1 and QGw.cib-3B were co-located, and the improved TGW at this locus was contributed by GW.  Unlike other loci, QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike (GNS).  They were further validated in advanced lines using Kompetitive Allele Specific PCR (KASP) markers, and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.  Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.  According to gene annotation, spatial expression patterns, ortholog analysis and sequence variation, the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.  Collectively, the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.

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Coupling of reduced inorganic fertilizer with plant-based organic fertilizer as a promising fertilizer management strategy for colored rice in tropical regions Tingcheng Zhao, Aibin He, Mohammad Nauman Khan, Qi Yin, Shaokun Song, Lixiao Nie 2024, 23(1): 93-107.  DOI: 10.1016/j.jia.2023.04.035 Abstract ( )   PDF in ScienceDirect   Colored rice is a type of high-quality, high-added-value rice that has attracted increasing attention in recent years. The use of large amounts of inorganic nitrogen fertilizer in rice fields results in low fertilizer use efficiency and high environmental pollution.  Organic fertilizer is a promising way to improve soil quality and sustain high yields.  However, most studies focus on the effect of animal-based organic fertilizers.  The effects of different ratios of plant-based organic fertilizer and inorganic fertilizer on the grain yield and quality of colored rice have rarely been reported.  Therefore, a two-year field experiment was conducted in 2020 and 2021 to study the effects of replacing inorganic N fertilizers with plant-based organic fertilizers on the yield, nitrogen use efficiency (NUE), and anthocyanin content of two colored rice varieties in a tropical region in China.  The experimental treatments included no nitrogen fertilization (T1), 100% inorganic nitrogen fertilizer (T2), 30% inorganic nitrogen fertilizer substitution with plant-based organic fertilizer (T3), 60% inorganic nitrogen fertilizer substitution with plant-based organic fertilizer (T4), and 100% plant-based organic fertilizer (T5).  The total nitrogen provided to all the treatments except T1 was the same at 120 kg ha–1.  Our results showed that the T3 treatment enhanced the grain yield and anthocyanin content of colored rice by increasing nitrogen use efficiency compared with T2.  On average, grain yields were increased by 9 and 8%, while the anthocyanin content increased by 16 and 10% in the two colored rice varieties under T3 across the two years, respectively, as compared with T2.  Further study of the residual effect of partial substitution of inorganic fertilizers showed that the substitution of inorganic fertilizer with plant-based organic fertilizer improved the soil physio-chemical properties, and thus increased the rice grain yield, in the subsequent seasons.  The highest grain yield of the subsequent rice crop was observed under the T5 treatment.  Our results suggested that the application of plant-based organic fertilizers can sustain the production of colored rice with high anthocyanin content in tropical regions, which is beneficial in reconciling the relationship between rice production and environmental protection.

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Effect of chemical regulators on the recovery of leaf physiology, dry matter accumulation and translocation, and yield-related characteristics in winter wheat following dry-hot wind Yanan Xu, Yue Wu, Yan Han, Jiqing Song, Wenying Zhang, Wei Han, Binhui Liu, Wenbo Bai 2024, 23(1): 108-121.  DOI: 10.1016/j.jia.2023.04.019 Abstract ( )   PDF in ScienceDirect   Dry-hot wind stress causes losses in wheat productivity in major growing regions worldwide, especially winter wheat in the Huang-Huai-Hai Plain of China, and both the occurrence and severity of such events are likely to increase with global climate change.  To investigate the recovery of physiological functions and yield formation using a new non-commercial chemical regulator (NCR) following dry-hot wind stress, we conducted a three-year field experiment (2018–2021) with sprayed treatments of tap water (control), monopotassium phosphate (CKP), NCR at both the jointing and flowering stages (CFS), and NCR only at the jointing stage (FSJ) or flowering stage (FSF).  The leaf physiology, biomass accumulation and translocation, grain-filling process, and yield components in winter wheat were assessed.  Among the single spraying treatments, the FSJ treatment was beneficial for the accumulation of dry matter before anthesis, as well as larger increases in the maximum grain-filling rate and mean grain-filling rate.  The FSF treatment performed better in maintaining a high relative chlorophyll content as indicated by the SPAD value, and a low rate of excised leaf water loss in flag leaves, promoting dry matter accumulation and the contribution to grain after anthesis, prolonging the duration of grain filling, and causing the period until the maximum grain-filling rate reached earlier.  The CFS treatment was better than any other treatments in relieving the effects of dry-hot wind.  The exogenous NCR treatments significantly increased grain yields by 12.45–18.20% in 2018–2019, 8.89–13.82% in 2019–2020, and 8.10–9.00% in 2020–2021.  The conventional measure of the CKP treatment only increased grain yield by 6.69% in 2020–2021.  The CFS treatment had the greatest mitigating effect on yield loss under dry-hot wind stress, followed by the FSF and FSJ treatments, and the CKP treatment only had a minimal effect.  In summary, the CFS treatment could be used as the main chemical control measure for wheat stress resistance and yield stability in areas with a high incidence of dry-hot wind.  This treatment can effectively regulate green retention and the water status of leaves, promote dry matter accumulation and efficient translocation, improve the grain-filling process, and ultimately reduce yield losses.

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Grain yield and N uptake of maize in response to increased plant density under reduced water and nitrogen supply conditions Jingui Wei, Qiang Chai, Wen Yin, Hong Fan, Yao Guo, Falong Hu, Zhilong Fan, Qiming Wang 2024, 23(1): 122-140.  DOI: 10.1016/j.jia.2023.05.006 Abstract ( )   PDF in ScienceDirect   The development of modern agriculture requires the reduction of water and chemical N fertilizer inputs.  Increasing the planting density can maintain higher yields, but also consumes more of these restrictive resources.  However, whether an increased maize density can compensate for the negative effects of reduced water and N supply on grain yield and N uptake in the arid irrigated areas remains unknown.  This study is part of a long-term positioning trial that started in 2016.  A split-split plot field experiment of maize was implemented in the arid irrigated area of northwestern China in 2020 to 2021.  The treatments included two irrigation levels: local conventional irrigation reduced by 20% (W1, 3,240 m3 ha–1) and local conventional irrigation (W2, 4,050 m3 ha–1); two N application rates: local conventional N reduced by 25% (N1, 270 kg ha–1) and local conventional N (360 kg ha–1); and three planting densities: local conventional density (D1, 75,000 plants ha–1), density increased by 30% (D2, 97,500 plants ha–1), and density increased by 60% (D3, 120,000 plants ha–1).  Our results showed that the grain yield and aboveground N accumulation of maize were lower under the reduced water and N inputs, but increasing the maize density by 30% can compensate for the reductions of grain yield and aboveground N accumulation caused by the reduced water and N supply.  When water was reduced while the N application rate remained unchanged, increasing the planting density by 30% enhanced grain yield by 13.9% and aboveground N accumulation by 15.3%.  Under reduced water and N inputs, increasing the maize density by 30% enhanced N uptake efficiency and N partial factor productivity, and it also compensated for the N harvest index and N metabolic related enzyme activities.  Compared with W2N2D1, the N uptake efficiency and N partial factor productivity increased by 28.6 and 17.6% under W1N1D2.  W1N2D2 had 8.4% higher N uptake efficiency and 13.9% higher N partial factor productivity than W2N2D1.  W1N2D2 improved urease activity and nitrate reductase activity by 5.4% at the R2 (blister) stage and 19.6% at the V6 (6th leaf) stage, and increased net income and the benefit:cost ratio by 22.1 and 16.7%, respectively.  W1N1D2 and W1N2D2 reduced the nitrate nitrogen and ammoniacal nitrogen contents at the R6 stage in the 40–100 cm soil layer, compared with W2N2D1.  In summary, increasing the planting density by 30% can compensate for the loss of grain yield and aboveground N accumulation under reduced water and N inputs.  Meanwhile, increasing the maize density by 30% improved grain yield and aboveground N accumulation when water was reduced by 20% while the N application rate remained constant in arid irrigation areas.

Horticulture

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Functional prediction of tomato PLATZ family members and functional verification of SlPLATZ17 Min Xu, Zhao Gao, Dalong Li, Chen Zhang, Yuqi Zhang, Qian He, Yingbin Qi, He Zhang, Jingbin Jiang, Xiangyang Xu, Tingting Zhao 2024, 23(1): 141-154.  DOI: 10.1016/j.jia.2023.08.003 Abstract ( )   PDF in ScienceDirect   PLATZ is a novel zinc finger DNA-binding protein that plays an important role in regulating plant growth and development and resisting abiotic stress.  However, there has been very little research on the function of this family gene in tomatoes, which limits its application in germplasm resource improvement.  Therefore, the PLATZ gene family was identified and analyzed in tomato, and its roles were predicted and verified to provide a basis for in-depth research on SlPLATZ gene function.  In this study, the PLATZ family members of tomato were identified in the whole genome, and 19 SlPLATZ genes were obtained.  Functional prediction was conducted based on gene and promoter structure analysis and RNA-seq-based expression pattern analysis.  SlPLATZ genes that responded significantly under different abiotic stresses or were significantly differentially expressed among multiple tissues were screened as functional gene resources.  SlPLATZ17 was selected for functional verification by experiment-based analysis.  The results showed that the downregulation of SlPLATZ17 gene expression reduced the drought and salt tolerance of tomato plants.  Tomato plants overexpressing SlPLATZ17 had larger flower sizes and long, thin petals, adjacent petals were not connected at the base, and the stamen circumference was smaller.  This study contributes to understanding the functions of the SlPLATZ family in tomato and provides a reference for functional gene screening.

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High-throughput screening system of citrus bacterial canker-associated transcription factors and its application to the regulation of citrus canker resistance Jia Fu, Jie Fan, Chenxi Zhang, Yongyao Fu, Baohang Xian, Qiyuan Yu, Xin Huang, Wen Yang, Shanchun Chen, Yongrui He, Qiang Li 2024, 23(1): 155-165.  DOI: 10.1016/j.jia.2023.11.011 Abstract ( )   PDF in ScienceDirect   One of the main diseases that adversely impacts the global citrus industry is citrus bacterial canker (CBC), caused by the bacteria Xanthomonas citri subsp. citri (Xcc).  Response to CBC is a complex process, with both protein-DNA as well as protein–protein interactions for the regulatory network.  To detect such interactions in CBC resistant regulation, a citrus high-throughput screening system with 203 CBC-inducible transcription factors (TFs), were developed.  Screening the upstream regulators of target by yeast-one hybrid (Y1H) methods was also performed.  A regulatory module of CBC resistance was identified based on this system.  One TF (CsDOF5.8) was explored due to its interactions with the 1-kb promoter fragment of CsPrx25, a resistant gene of CBC involved in reactive oxygen species (ROS) homeostasis regulation.  Electrophoretic mobility shift assay (EMSA), dual-LUC assays, as well as transient overexpression of CsDOF5.8, further validated the interactions and transcriptional regulation.  The CsDOF5.8–CsPrx25 promoter interaction revealed a complex pathway that governs the regulation of CBC resistance via H2O2 homeostasis.  The high-throughput Y1H/Y2H screening system could be an efficient tool for studying regulatory pathways or network of CBC resistance regulation.  In addition, it could highlight the potential of these candidate genes as targets for efforts to breed CBC-resistant citrus varieties.

Plant Protection

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A novel pathogen Fusarium cuneirostrum causing common bean (Phaseolus vulgaris) root rot in China Dong Deng, Wenqi Wu, Canxing Duan, Suli Sun, Zhendong Zhu 2024, 23(1): 166-176.  DOI: 10.1016/j.jia.2023.01.010 Abstract ( )   PDF in ScienceDirect   Several fungal pathogens cause root rot of common bean, among which Fusarium spp. are the most common pathogens causing Fusarium root rot (FRR) worldwide.  FRR has been becoming an increasingly severe disease of common bean in China, but the species of Fusarium spp. have remained unclear.  Thus, this study was performed to identify the pathogen causing common bean root rot in Liangcheng County, Inner Mongolia, China.  Nineteen Fusarium-like isolates were obtained after pathogen isolation and purification.  The pathogenicity test indicated that eight isolates caused severe disease symptoms on common bean, while 11 other isolates were not pathogenic.  The eight pathogenic isolates, FCL1–FCL8, were identified as Fusarium cuneirostrum by morphological characterization and phylogenetic analysis using partial sequences of EF-1α, ITS, 28S, and IGS regions.  Host range test showed that the representative F. cuneirostrum isolate FCL3 was also pathogenic to mung bean, while not pathogenic to adzuki bean, chickpea, cowpea, faba bean, pea, and soybean.  Moreover, 50 common bean and 50 mung bean cultivars were screened for resistance to FRR, and seven highly resistant or resistant cultivars of common bean were identified, while no resistant cultivars of mung bean were screened.  This study revealed that F. cuneirostrum was one of common bean FRR pathogens in Inner Mongolia and it could induce mung bean root rot as well.  To our knowledge, this is the first report of F. cuneirostrum causing FRR of common bean in China.

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Effect of mutations on acetohydroxyacid synthase (AHAS) function in Cyperus difformis L. Xiaotong Guo, Xiangju Li, Zheng Li, Licun Peng, Jingchao Chen, Haiyan Yu, Hailan Cui 2024, 23(1): 177-186.  DOI: 10.1016/j.jia.2023.04.009 Abstract ( )   PDF in ScienceDirect   Cyperus difformis L. is a troublesome weed in paddy fields and has attracted attention due to its resistance to acetohydroxyacid synthase (AHAS) inhibitors.  It was found that the amino acid mutation in AHAS was the primary cause for the resistance of Cyperus difformis.  However, the effect of different mutations on AHAS function is not clear in Cyperus difformis.  To confirm the effect of mutations on AHAS function, six biotypes were collected, including Pro197Arg, Pro197Ser, Pro197Leu, Asp376Glu, Trp574Leu and wild type, from Hunan, Anhui, Jiangxi and Jiangsu provinces, China and the function of AHAS was characterized.  The AHAS in vitro inhibition assay results indicated that the mutations decreased the sensitivity of AHAS to pyrazosulfuron-ethyl, in which the I50 (the half maximal inhibitory concentration) of wild type AHAS was 0.04 μmol L–1 and Asp376Glu, Pro197Leu, Pro197Arg, Pro197Ser and Trp574Leu mutations were 3.98, 11.50, 40.38, 38.19 and 311.43 μmol L–1, respectively.  In the determination of enzyme kinetics parameters, the Km and the maximum reaction velocity (Vmax) of the wild type were 5.18 mmol L–1 and 0.12 nmol mg–1 min–1, respectively, and the Km values of AHAS with Asp376Glu, Trp574Leu, Pro197Leu and Pro197Ser mutations were 0.38–0.93 times of the wild type.  The Km value of the Pro197Arg mutation was 1.14 times of the wild type, and the Vmax values of the five mutations were 1.17–3.33-fold compared to the wild type.  It was found that the mutations increased the affinity of AHAS to the substrate, except for the Pro197Arg mutation.  At a concentration of 0.0032–100 mmol L–1 branched-chain amino acids (BCAAs), the sensitivity of the other four mutant AHAS biotypes to feedback inhibition decreased, except for the Pro197Arg mutation.  This study elucidated the effect of different mutations on AHAS function in Cyperus difformis and provided ideas for further study of resistance development.

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Host-induced silencing of MpPar6 confers Myzus persicae resistance in transgenic rape plants Qi Zhang, Wenqin Zhan, Chao Li, Ling Chang, Yi Dong, Jiang Zhang 2024, 23(1): 187-194.  DOI: 10.1016/j.jia.2023.05.027 Abstract ( )   PDF in ScienceDirect   Plant-mediated RNA interference (RNAi) has emerged as a promising technology for insect control.  The green peach aphid, Myzus persicae, feeds on over 400 species of host plants.  Brassica napus (rape) is the second most important oilseed crop worldwide.  Myzus persicae is highly reproductive and causes severe damage to the rape plants due to its quite flexible life cycle.  In this study, we tested the RNAi effects of transgenic rape plants on M. persicae.  By in vitro feeding M. persicae with artificial diets containing double-stranded RNAs (dsRNAs) targeting seven aphid genes, we identified a new gene encoding the partitioning-defective protein 6 (Par6) as the most potent RNAi target.  Tissue- and stage-expression analysis of Par6 suggested this gene is highly expressed in the embryo and adult stage of M. persicae.  We next generated transgenic rape plants expressing dsPar6 by Agrobacterium-mediated transformation and obtained nine independent transgenic lines.  Compared to wild-type control plants, transgenic rape lines expressing dsPar6 showed strong resistance to M. persicae.  Feeding assays revealed that feeding transgenic rape plants to M. persicae significantly decreased MpPar6 expression and survival rate and impaired fecundity.  Furthermore, we showed that the resistance levels to M. persicae are positively correlated with dsPar6 expression levels in transgenic rape plants.  Our study demonstrates that transgenic rape plants expressing dsPar6 are efficiently protected from M. persicae.  Interfering with the genes involved in embryo development could be the effective RNAi targets for controlling aphids and potentially other insect pests.

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Tissue distribution of cadmium and its effect on reproduction in Spodoptera exigua Honghua Su, Menglu Wu, Yong Yang, Yan Deng, Yizhong Yang, Qingming Sun 2024, 23(1): 195-204.  DOI: 10.1016/j.jia.2023.08.010 Abstract ( )   PDF in ScienceDirect   Vegetable fields are often contaminated by heavy metals, and Spodoptera exigua is a major vegetable pest which is stressed by heavy metals mainly by feeding.  In this study, cadmium accumulation in the tissues of S. exigua exposed to cadmium and its effects on the growth and development of the parents and the offspring were investigated.  Under the stress of different concentrations of cadmium (0.2, 3.2, and 51.2 mg kg–1), the cadmium content in each tissue of S. exigua increased in a dose-dependent manner.  At the larval stage, the highest cadmium accumulation was found in midgut in all three cadmium treatments, but at the adult stage, the highest cadmium content was found in fat body.  In addition, the cadmium content in ovaries was much higher than in testes.  When F1 S. exigua was stressed by cadmium and the F2 generation was not fed a cadmium-containing diet, the larval survival, pupation rate, emergence rate and fecundity of the F2 generation were significantly reduced in the 51.2 mg kg–1 treatment compared to the corresponding F1 generation.  Even in the F2 generation of the 3.2 mg kg–1 treatment, the fecundity was significantly lower than in the parental generation.  The fecundity of the only-female stressed treatment was significantly lower than that of the only-male stressed treatment at the 3.2 and 51.2 mg kg–1 cadmium exposure levels.  When only mothers were stressed at the larval stage, the fecundity of the F2 generation was significantly lower than that of the F1 generation in the 51.2 mg kg–1 treatment, and it was also significantly lower than in the 3.2 and 0.2 mg kg–1 treatments.  The results of our study can provide useful information for forecasting the population increase trends under different heavy metal stress conditions and for the reliable environmental risk assessment of heavy metal pollution.

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A mite parasitoid, Pyemotes zhonghuajia, negatively impacts the fitness traits and immune response of the fall armyworm, Spodoptera frugiperda Yanfei Song, Tai’an Tian, Yichai Chen, Keshi Zhang, Maofa Yang, Jianfeng Liu 2024, 23(1): 205-216.  DOI: 10.1016/j.jia.2023.05.022 Abstract ( )   PDF in ScienceDirect   Parasitoids are key regulators in ecological communities and widely used as agents in biocontrol programmes.  The fall armyworm, Spodoptera frugiperda, recently invaded multiple continents and caused substantial economic losses in agriculture.  Pyemotes zhonghuajia, a newly identified mite parasitoid, has shown potential for controlling various agricultural insect pests.  Therefore, this study tested the performance of P. zhonghuajia in parasitising S. frugiperda.  We also investigated the sublethal effects of parasitism by P. zhonghuajia on host fitness traits, transgenerational impacts, and cellular and humoral immunity.  Our result showed that the fifth-instar larvae of S. frugiperda parasitised by 40 P. zhonghuajia were all dead (i.e., a lethal effect), while parasitism by 5 or 10 P. zhonghuajia was considered sublethal since many S. frugiperda survived to adulthood and produced offspring after mating.  The sublethal influences from parasitism by P. zhonghuajia resulted in reduced pupal weight, adult emergence rate and fecundity, but increased developmental time and longevity.  Parasitism at both lethal (40 mites) and sublethal (10 mites) levels impaired the cellular and humoral immunity of S. frugiperda.  This study presents the first empirical evidence that mite parasitoids can negatively influence host immunity.  Moreover, it provides insights into the biocontrol potential of mite parasitoids and their interactions with hosts.

Animal Science · Veterinary Medicine

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Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs Mu Zeng, Binhu Wang, Lei Liu, Yalan Yang, Zhonglin Tang 2024, 23(1): 217-227.  DOI: 10.1016/j.jia.2023.02.040 Abstract ( )   PDF in ScienceDirect   Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.  As the major indicators of growth performance, the backfat thickness (BFT), loin eye area (LEA), and days to 100 kg (D100) traits are commonly used to the genetics improvement in pigs.  However, the available genetic markers for these traits are limited.  To uncover novel loci and candidate genes associated with growth performance, we collected the phenotypic information of BFT, LEA, and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.  We performed a genome-wide association study (GWAS) using 4 statistical models, including mixed linear models (MLM), fixed and random model circulating probability unification (FarmCPU), settlement of MLM under progressively exclusive relationships (SUPER), Bayesian-information and linkage-disequilibrium Iteratively nested keyway (Blink), and identified 5, 3, and 6 high-confidence single nucleotide polymorphisms (SNPs) associated with BFT, LEA, and D100, respectively.  Variant annotation and quantitative trait locus (QTL) mapping analysis suggested that 6 genes (SKAP2, SATB1, PDE7B, PPP1R16B, WNT3, and WNT9B) were potentially associated with growth performance in pigs.  Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2 (SKAP2) was higher in prenatal muscles than in postnatal muscles, and the expression of Phosphodiesterase 7B (PDE7B) continuously increased during the prenatal stages and gradually decreased after birth, implying their potential roles in prenatal skeletal muscle development.  Overall, this study provides new candidate loci and genes for the genetic improvement of pigs.

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Establishment of an indirect immunofluorescence assay for the detection of African swine fever virus antibodies Wan Wang, Zhenjiang Zhang, Weldu Tesfagaber, Jiwen Zhang, Fang Li, Encheng Sun, Lijie Tang, Zhigao Bu, Yuanmao Zhu, Dongming Zhao 2024, 23(1): 228-238.  DOI: 10.1016/j.jia.2023.05.021 Abstract ( )   PDF in ScienceDirect   African swine fever (ASF) continues to cause enormous economic loss to the global pig industry.  Since there is no safe and effective vaccine, accurate and timely diagnosis of ASF is essential to implement control measures.  Indirect immunofluorescence assay (IFA) is a gold standard serological method recommended by the World Organization for Animal Health (WOAH).  In this study, we used primary fetal kidney cells to establish a wild boar cell line (BK2258) that supported the efficient replication of ASF virus (ASFV) SD/DY-I/21 and showed visible cytopathic effect (CPE).  Moreover, using BK2258, we established a sensitive and specific IFA for ASFV antibody detection.  To standardize and evaluate the performance of this assay, we used serum samples from pigs infected with the low virulent genotype I SD/DY-I/21 and genotype II HLJ/HRB1/20, and immunized with the vaccine candidate HLJ/18-7GD, field samples, and negative serum samples.  The IFA reacted with the ASFV-positive sera and displayed bright fluorescence foci.  There was no non-specific green fluorescence due to cellular senescence or other cell damage-causing factors.  Compared to a commercial indirect enzyme-linked immunosorbent assay (iELISA), ASFV antibodies were detected 1–4 days earlier using our IFA.  The detection limits of the IFA and iELISA for the same ASFV-antibody positive serum samples were 1:25,600 and 1:6,400, respectively, indicating that the IFA is more sensitive than iELISA.  The newly established IFA was highly specific and did not cross-react with sera positive for six other important porcine pathogens (i.e., Classical swine fever virus (CSFV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcme circovirus type 2 (PCV2), Pseudorabies virus (PRV), Foot-and-Mouth disease virus type O (FMDV/O), and Porcine epidemic diarrhea virus (PEDV)).  This study thus provides a sensitive, specific, and reliable detection method that is suitable for the serological diagnosis of ASF.

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New insights into developmental biology of Eimeria tenella revealed by comparative analysis of mRNA N6-methyladenosine modification between unsporulated oocysts and sporulated oocysts Qing Liu, Bingjin M, Yijing Meng, Linmei Yu, Zirui Wang, Tao Jia, Wenbin Zheng, Wenwei Gao, Shichen Xie, Xingquan Zhu 2024, 23(1): 239-250.  DOI: 10.1016/j.jia.2023.07.011 Abstract ( )   PDF in ScienceDirect   Evidence showed that N6-methyladenosine (m6A) modification plays a pivotal role in influencing RNA fate and is strongly associated with cell growth and developmental processes in many species.  However, no information regarding m6A modification in Eimeria tenella is currently available.  In the present study, we surveyed the transcriptome-wide prevalence of m6A in sporulated oocysts and unsporulated oocysts of E. tenella.  Methylated RNA immunoprecipitation sequencing (MeRIP-seq) analysis showed that m6A modification was most abundant in the coding sequences, followed by stop codon.  There were 3,903 hypermethylated and 3,178 hypomethylated mRNAs in sporulated oocysts compared with unsporulated oocysts.  Further joint analysis suggested that m6A modification of the majority of genes was positively correlated with mRNA expression.  The mRNA relative expression and m6A level of the selected genes were confirmed by quantitative reverse transcription PCR (RT-qPCR) and MeRIP-qPCR.  GO and KEGG analysis indicated that differentially m6A methylated genes (DMMGs) with significant differences in mRNA expression were closely related to processes such as regulation of gene expression, epigenetic, microtubule, autophagy-other and TOR signaling.  Moreover, a total of 96 DMMGs without significant differences in mRNA expression showed significant differences at protein level.  GO and pathway enrichment analysis of the 96 genes showed that RNA methylation may be involved in cell biosynthesis and metabolism of E. tenella.  We firstly present a map of RNA m6A modification in E. tenella, which provides significant insights into developmental biology of E. tenella.

Agro-ecosystem & Environment

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Subsoil tillage enhances wheat productivity, soil organic carbon and available nutrient status in dryland fields Qiuyan Yan, Linjia Wu, Fei Dong, Shuangdui Yan, Feng Li, Yaqin Jia, Jiancheng Zhang, Ruifu Zhang, Xiao Huang 2024, 23(1): 251-266.  DOI: 10.1016/j.jia.2023.06.011 Abstract ( )   PDF in ScienceDirect   Tillage practices during the fallow period benefit water storage and yield in dryland wheat crops.  However, there is currently no clarity on the responses of soil organic carbon (SOC), total nitrogen (TN), and available nutrients to tillage practices within the growing season.  This study evaluated the effects of three tillage practices (NT, no tillage; SS, subsoil tillage; DT, deep tillage) over five years on soil physicochemical properties.  Soil samples at harvest stage from the fifth year were analyzed to determine the soil aggregate and aggregate-associated C and N fractions.  The results indicated that SS and DT improved grain yield, straw biomass and straw carbon return of wheat compared with NT.  In contrast to DT and NT, SS favored SOC and TN concentrations and stocks by increasing the soil organic carbon sequestration rate (SOCSR) and soil nitrogen sequestration rate (TNSR) in the 0–40 cm layer.  Higher SOC levels under SS and NT were associated with greater aggregate-associated C fractions, while TN was positively associated with soluble organic nitrogen (SON).  Compared with DT, the NT and SS treatments improved soil available nutrients in the 0–20 cm layer.  These findings suggest that SS is an excellent practice for increasing soil carbon, nitrogen and nutrient availability in dryland wheat fields in North China.

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The competition between Bidens pilosa and Setaria viridis alters soil microbial composition and soil ecological function Qiao Li, Jianying Guo, Han Zhang, Mengxin Zhao 2024, 23(1): 267-282.  DOI: 10.1016/j.jia.2023.07.025 Abstract ( )   PDF in ScienceDirect   Bidens pilosa is recognized as one of the major invasive plants in China.  Its invasion has been associated with significant losses in agriculture, forestry, husbandry, and biodiversity.  Soil ecosystems play an important role in alien plant invasion.  Microorganisms within the soil act as intermediaries between plants and soil ecological functions, playing a role in regulating soil enzyme activities and nutrient dynamics.  Understanding the interactions between invasive plants, soil microorganisms, and soil ecological processes is vital for managing and mitigating the impacts of invasive species on the environment.  In this study, we conducted a systematic analysis focusing on B. pilosa and Setaria viridis, a common native companion plant in the invaded area.  To simulate the invasion process of B. pilosa, we constructed homogeneous plots consisting of B. pilosa and S. viridis grown separately as monocultures, as well as in mixtures.  The rhizosphere and bulk soils were collected from the alien plant B. pilosa and the native plant S. viridis.  In order to focus on the soil ecological functional mechanisms that contribute to the successful invasion of B. pilosa, we analyzed the effects of B. pilosa on the composition of soil microbial communities and soil ecological functions.  The results showed that the biomass of B. pilosa increased by 27.51% and that of S. viridis was significantly reduced by 66.56%.  The organic matter contents in the bulk and rhizosphere soils of B. pilosa were approximately 1.30 times those in the native plant soils.  The TN and NO3– contents in the rhizosphere soil of B. pilosa were 1.30 to 2.71 times those in the native plant soils.  The activities of acid phosphatase, alkaline phosphatase, and urease in the rhizosphere soil of B. pilosa were 1.98–2.25 times higher than in the native plant soils.  Using high-throughput sequencing of the 16S rRNA gene, we found that B. pilosa altered the composition of the soil microbial community.  Specifically, many genera in Actinobacteria and Proteobacteria were enriched in B. pilosa soils.  Further correlation analyses verified that these genera had significantly positive relationships with soil nutrients and enzyme activities.  Plant biomass, soil pH, and the contents of organic matter, TN, NO3–, TP, AP, TK, and AK were the main factors affecting soil microbial communities.  This study showed that the invasion of B. pilosa led to significant alterations in the composition of the soil microbial communities.  These changes were closely linked to modifications in plant traits as well as soil physical and chemical properties.  Some microbial species related to C, N and P cycling were enriched in the soil invaded by B. pilosa.  These findings provide additional support for the hypothesis of soil-microbe feedback in the successful invasion of alien plants.  They also offer insights into the ecological mechanism by which soil microbes contribute to the successful invasion of B. pilosa.  Overall, our research contributes to a better understanding of the complex interactions between invasive plants, soil microbial communities, and ecosystem dynamics.

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Quantifying the agreement and accuracy characteristics of four satellite-based LULC products for cropland classification in China Jie Xue, Xianglin Zhang, Songchao Chen, Bifeng Hu, Nan Wang, Zhou Shi 2024, 23(1): 283-297.  DOI: 10.1016/j.jia.2023.06.005 Abstract ( )   PDF in ScienceDirect   Various land use and land cover (LULC) products have been produced over the past decade with the development of remote sensing technology.  Despite the differences in LULC classification schemes, there is a lack of research on assessing the accuracy of their application to croplands in a unified framework.  Thus, this study evaluated the spatial and area accuracies of cropland classification for four commonly used global LULC products (i.e., MCD12Q1 V6, GlobCover2009, FROM-GLC and GlobeLand30) based on the harmonised FAO criterion, and quantified the relationships between four factors (i.e., slope, elevation, field size and crop system) and cropland classification agreement.  The validation results indicated that MCD12Q1 and GlobeLand30 performed well in cropland classification regarding spatial consistency, with overall accuracies of 94.90 and 93.52%, respectively.  The FROM-GLC showed the worst performance, with an overall accuracy of 83.17%.  Overlaying the cropland generated by the four global LULC products, we found the proportions of complete agreement and disagreement were 15.51 and 44.72% for the cropland classification, respectively.  High consistency was mainly observed in the Northeast China Plain, the Huang-Huai-Hai Plain and the northern part of the Middle-lower Yangtze Plain, China.  In contrast, low consistency was detected primarily on the eastern edge of the northern and semiarid region, the Yunnan-Guizhou Plateau and southern China.  Field size was the most important factor for mapping cropland.  For area accuracy, compared with China Statistical Yearbook data at the provincial scale, the accuracies of different products in descending order were: GlobeLand30, FROM-GLC, MCD12Q1, and GlobCover2009.  The cropland classification schemes mainly caused large area deviations among the four products, and they also resulted in the different ranks of spatial accuracy and area accuracy among the four products.  Our results can provide valuable suggestions for selecting cropland products at the national or provincial scale and help cropland mapping and reconstruction, which is essential for food security and crop management, so they can also contribute to achieving the Sustainable Development Goals issued by the United Nations.

Food Science

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Quantification of the adulteration concentration of palm kernel oil in virgin coconut oil using near-infrared hyperspectral imaging Phiraiwan Jermwongruttanachai, Siwalak Pathaveerat, Sirinad Noypitak 2024, 23(1): 298-309.  DOI: 10.1016/j.jia.2023.08.002 Abstract ( )   PDF in ScienceDirect   The adulteration concentration of palm kernel oil (PKO) in virgin coconut oil (VCO) was quantified using near-infrared (NIR) hyperspectral imaging.  Nowadays, some VCO is adulterated with lower-priced PKO to reduce production costs, which diminishes the quality of the VCO.  This study used NIR hyperspectral imaging in the wavelength region 900–1,650 nm to create a quantitative model for the detection of PKO contaminants (0–100%) in VCO and to develop predictive mapping.  The prediction equation for the adulteration of VCO with PKO was constructed using the partial least squares regression method.  The best predictive model was pre-processed using the standard normal variate method, and the coefficient of determination of prediction was 0.991, the root mean square error of prediction was 2.93%, and the residual prediction deviation was 10.37.  The results showed that this model could be applied for quantifying the adulteration concentration of PKO in VCO.  The prediction adulteration concentration mapping of VCO with PKO was created from a calibration model that showed the color level according to the adulteration concentration in the range of 0–100%.  NIR hyperspectral imaging could be clearly used to quantify the adulteration of VCO with a color level map that provides a quick, accurate, and non-destructive detection method.

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The protective effect of cyclodextrin on the color quality and stability of Cabernet Sauvignon red wine Caiyun Liu, Lulu Wu, Shuyue Fan, Yongsheng Tao, Yunkui Li 2024, 23(1): 310-323.  DOI: 10.1016/j.jia.2023.10.034 Abstract ( )   PDF in ScienceDirect   The impact of cyclodextrins (CDs) on wine quality and stability remains largely unknown.  This study systematically assessed the protective effect of the post-fermentation addition of CDs on color stability of red wine from the viewpoints of color characteristics, copigmentation and phenolic profiles.  The grey relational analysis (GRA) and principal component analysis (PCA) methods were employed to dissect the key effective determinants related to color quality.  The addition of CDs induced a significant hyperchromic effect of 8.19–25.40%, a significant bathochromic effect and an enhancement of the color intensity.  Furthermore, the evolution of anthocyanin forms and the content of monomeric anthocyanins revealed that β-CD is a superior favorable cofactor during wine aging, but for long-term aging, 2-HP-β-CD and 2-HP-γ-CD are more beneficial in promoting the formation of polymerized anthocyanins and color stability.  This work provides an important reference for the use of CDs to enhance the color quality and stability of red wines.

Agricultural Economics and Management

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Promoting grain production through high-standard farmland construction: Evidence in China Shuai Hao, Guogang Wang, Yantao Yang, Sicheng Zhao, Shengnan Huang, Liping Liu, Huanhuan Zhang 2024, 23(1): 324-335.  DOI: 10.1016/j.jia.2023.11.021 Abstract ( )   PDF in ScienceDirect   Food security is a strategic priority for a country’s economic development.  In China, high-standard farmland construction (HSFC) is an important initiative to stabilize grain production and increase grain production capacity.  Based on panel data from 31 sample provinces, autonomous regions, and municipalities in China from 2005–2017, this study explored the impact of HSFC on grain yield using the difference-in-differences (DID) method.  The results showed that HSFC significantly increased total grain production, which is robust to various checks.  HSFC increased grain yield through three potential mechanisms.  First, it could increase the grain replanting index.  Second, it could effectively reduce yield loss due to droughts and floods.  Last, HSFC could strengthen the cultivated land by renovating the low- and medium-yielding fields.  Heterogeneity analysis found that the HSFC farmland showed a significant increase in grain yield only in the main grain-producing areas and balanced areas.  In addition, HSFC significantly increased the yields of rice, wheat, and maize while leading to a reduction in soybean yields.  The findings suggest the government should continue to promote HSFC, improve construction standards, and strictly control the “non-agriculturalization” and “non-coordination” of farmland to increase grain production further.  At the same time, market mechanisms should be used to incentivize soybean farming, improve returns and stabilize soybean yields.

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Can whole steps of grain production be outsourced?  Empirical analysis based on the three provinces of Jiangsu, Jilin, and Sichuan in China Jiacheng Liu, Shengzhi Mao, Qiufen Zheng, Zhigang Xu 2024, 23(1): 336-347.  DOI: 10.1016/j.jia.2023.09.034 Abstract ( )   PDF in ScienceDirect   Certain outsourcing services for agricultural management in China, such as pest control in grain production, have experienced prolonged sluggishness, contrasting with the relatively high level of outsourcing services observed in harvesting, land preparation, and sowing.  This study examines the feasibility of implementing whole-step outsourcing in grain production by conducting a case study of rice and maize production in Jiangsu, Jilin, and Sichuan provinces in China.  The provision of outsourcing services hinges on two essential conditions: technological advancements fostering specialized production and economies of scale, coupled with a market size sufficient to realize the aforementioned potential economies of scale.  The results showed that outsourcing pest control or harvesting services had varying economies of scale.  The outsourcing services in pest control were less common than in harvesting services, and their marginal growth space of the economies of scale with technological change was also smaller.  Determined by the operational characteristics of pest control itself, the market scale of its professional services is small.  Therefore, achieving the whole-step outsourcing of grain production necessitates not only technological innovation but also effective policy interventions to overcome the constraints of market scale.  Such interventions include (1) optimizing crop layouts between planning regions and reducing land fragmentation and (2) supplying timely and effective inter-regional agricultural information for service providers aided by information technology.

Letter

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Emergence of highly pathogenic avian influenza A (H5N8) clade 2.3.4.4b viruses in grebes in Inner Mongolia and Ningxia, China, in 2021 Qiuzi Xu, Xinru Lü, Yi Li, Hua Luo, Zhen Zhang, Xiang Li, Rongxiu Qin, Qing An, Fengyi Qu, Zhenliang Zhao, Chengbo Zhang, Weidong Wang, Yuecheng Li, Yajun Wang, Xiangwei Zeng, Zhijun Hou, Jingqiang Ren, Yulong Wang, Yanbing Li, Hongliang Chai 2024, 23(1): 348-353.  DOI: 10.1016/j.jia.2023.09.026 Abstract ( )   PDF in ScienceDirect