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The development of a porcine 50K SNP panel using genotyping by target sequencing and its application Zipeng Zhang, Siyuan Xing, Ao Qiu, Ning Zhang, Wenwen Wang, Changsong Qian, Jia’nan Zhang, Chuduan Wang, Qin Zhang, Xiangdong Ding 2025, 24 (5): 1930-1943.   DOI: 10.1016/j.jia.2023.07.033 Abstract （413）      PDF in ScienceDirect       Genotyping by target sequencing (GBTS) integrates the advantages of silicon-based technology (high stability and reliability) and genotyping by sequencing (high flexibility and cost-effectiveness).  However, GBTS panels are not currently available in pigs.  In this study, based on GBTS technology, we first developed a 50K panel, including 52,000 single-nucleotide polymorphisms (SNPs), in pigs, designated GBTS50K.  A total of 6,032 individuals of Large White, Landrace, and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.  Our results showed that GBTS50K obtained a high genotyping ability, the SNP and individual call rates of GBTS50K were 0.997–0.998, and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993, respectively, in replicate samples.  We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis, selection signature detection, genome-wide association studies (GWAS), genotyped imputation, genetic selection (GS), etc.  The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.  For example, GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.  Particularly, due to the multiple SNPs (mSNPs), GBTS50K generated 100K qualified SNPs without increasing genotyping cost, and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.  Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs, and it is also helpful for developing SNP panels for other farm animals. Reference | Related Articles | Metrics

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Establishing an induced infertile chicken line for efficient germline transmission of exogenous PGCs Haimei Qin, Xiaoxuan Jia, Zhenwen Huang, Yifei Zhi, Na Ji, Meiyu Lan, Lang Zhang, Xingting Liu, Huiyan Xu, Yangqing Lu 2026, 25 (1): 227-234.   DOI: 10.1016/j.jia.2024.08.009 Abstract （413）      PDF in ScienceDirect       Primordial germ cells (PGCs) are the stem-cell population of adult animal gametes, which develop into sperm or eggs.  It can be propagated in vitro and injected into the host chicken for genome editing to obtain germline chimeric chicken.  However, it has the limitation that the host embryo contains endogenous PGCs, which raises complications, resultantly donor PGCs fail to compete, and transmission efficiency reduced.  Therefore, to increase the transmission efficiency, we generated a novel sterile chicken with the inducible elimination of endogenous PGCs in the host.  This is the first study that applied the herpes simplex virus thymidine kinase (HSV-TK) cell ablation system in avian.  CRISPR/Cas9-mediated homology-directed repair was performed to localize the HSV-TK suicide gene to the last exon of the deleted in azoospermia-like (DAZL) gene, and ganciclovir (GCV) was added to induce the apoptosis in the germ cells of the host embryo.  The sterilized host embryo introduced genome-edited PGCs to produce chimeric chicken carrying exogenous germ cells only.  It was observed that the germline transmission efficiency was 100% achieved, and the obtained chicks were purely from donor breeds.  The technologies established in the current study have important applications in germplasm conservation and gene editing in chicken. Reference | Related Articles | Metrics

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Activity of fungicide cyclobutrifluram against Fusarium fujikuroi and mechanism of the pathogen resistance associated with point mutations in FfSdhB, FfSdhC2 and FfSdhD Yang Sun, Yu Liu, Li Zhou, Xinyan Liu, Kun Wang, Xing Chen, Chuanqing Zhang, Yu Chen 2025, 24 (9): 3511-3528.   DOI: 10.1016/j.jia.2024.01.004 Abstract （400）      PDF in ScienceDirect       Rice bakanae disease (RBD) is a devastating plant disease caused by Fusarium fujikuroi. This study aimed to evaluate the potential of cyclobutrifluram, a novel succinate dehydrogenase inhibitor (SDHI), to control RBD, and determine the risk and mechanism of resistance to cyclobutrifluram in F. fujikuroi. In vitro experiments showed that cyclobutrifluram significantly inhibited mycelial growth and spore germination, and altered the morphology of mycelia and conidia. Treatment with cyclobutrifluram significantly decreased mycotoxin production and increased cell membrane permeability in F. fujikuroi. The baseline sensitivity of 72 F. fujikuroi isolates to cyclobutrifluram was determined using mycelial growth and spore germination inhibition assays, which revealed EC50 values of 0.0114 – 0.1304 μg mL-1 and 0.0012 – 0.016 μg mL-1, with mean EC50 values of 0.0410 ± 0.0470 μg mL-1 and 0.0038 ± 0.0015 μg mL-1, respectively. Pot experiments demonstrated that the protective effect of cyclobutrifluram against F. fujikuroi was more significant than that of phenamacril and azoxystrobin, indicating that cyclobutrifluram is a promising antifungal agent for the control of RBD. Six cyclobutrifluram-resistant mutants of F. fujikuroi were obtained via fungicide adaptation. Moreover, these mutants exhibited weaker fitness than their parental isolate and positive cross-resistance with other SDHI fungicides, including pydiflumetofen and penflufen; however, no cross-resistance was detected with other classes of fungicides, including phenamacril, fludioxonil, prochloraz, or azoxystrobin. These results indicated that the resistance risk of F. fujikuroi to cyclobutrifluram might be moderate. Sequencing analysis revealed that mutations, including H248D in FfSdhB, A83V in FfSdhC2, and S106F and E166K in FfSdhD, contributed to resistance, which was confirmed by molecular docking and homologous replacement experiments. The results suggest a high potential for cyclobutrifluram to control RBD and a moderate resistance risk of F. fujikuroi to cyclobutrifluram, which are meaningful findings for the scientific application of cyclobutrifluram. Reference | Related Articles | Metrics

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FGF7 secreted from dermal papillae cell regulates the proliferation and differentiation of hair follicle stem cell Niu Wang, Weidong Zhang, Zhenyu Zhong, Xiongbo Zhou, Xinran Shi, Xin Wang 2025, 24 (9): 3583-3597.   DOI: 10.1016/j.jia.2023.10.012 Abstract （378）      PDF in ScienceDirect       Hair follicle stem cell (HFSC), capable of self-renewal and differentiation in hair follicle, represents an emerging stem cell model for regenerative medicine.  The interaction between HFSC and dermal papilla cell (DPC) governs hair follicle development.  FGF7 functions as a paracrine protein regulating epithelial proliferation, differentiation and migration.  The single-cell transcriptome profiling and immunofluorescence analysis demonstrated that FGF7 localizes at DPC, while FGF7 receptor (FGFR2) expresses in both DPC and HFSC.  Through co-culture experiments of HFSC and DPC, the results indicated that FGF7 secreted from DPC promotes the proliferation of DPC and HFSC via Wnt signaling pathway and induces HFSC differentiation.  Furthermore, CUT&Tag assay revealed genomic colocalization between FGF7 and pluripotency-related genes and GSK3β.  Electrophoretic mobility shift assay (EMSA) demonstrated that FGF7 interacts with the promoter region of CISH and PRKX.  This research provides valuable insights into the molecular mechanisms underlying the hair cycle.  Understanding the interaction between HFSC and DPC, as well as the role of FGF7, may advance regenerative medicine and hair loss treatment. Reference | Related Articles | Metrics

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PDL1-dependent trans-acting siRNAs regulate lateral organ polarity development in rice Yi Zhang, Jing You, Jun Tang, Wenwen Xiao, Mi Wei, Ruhui Wu, Jinyan Liu, Hanying Zong, Shuoyu Zhang, Jie Qiu, Huan Chen, Yinghua Ling, Fangming Zhao, Yunfeng Li, Guanghua He, Ting Zhang 2025, 24 (9): 3297-3310.   DOI: 10.1016/j.jia.2024.01.025 Abstract （363）      PDF in ScienceDirect       Leaves and glumes act as lateral organs and have essential effects on photosynthesis and seed morphology, thus affecting yield.  However, the molecular mechanisms controlling their polarity development in rice still need further study.  Here, we isolated a polarity defect of lateral organs 1 (pdl1) mutant in rice, which exhibits twisted/filamentous-shaped leaves and cracked/filamentous-shaped lemmas caused by defects in polarity development.  PDL1 encodes a SUPPRESSOR OF GENE SILENCING 3 protein localized in the cytoplasmic granules.  PDL1 is expressed in the shoot apical meristem, inflorescence meristem, floral meristem, and lateral organs including leaves and floral organs.  PDL1 is involved in the synthesis of tasiR-ARF, which may subsequently modulate the expression of OsARFs.  Meanwhile, the expression levels of abaxial miR165/166 and the adaxial identity genes OSHBs were respectively increased and reduced significantly.  The results of this study clarify the molecular mechanism by which PDL1-mediated tasiR-ARF synthesis regulates the lateral organ polarity development in rice. Reference | Related Articles | Metrics

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Application of dsRNA of FgPMA1 for disease control on Fusarium graminearum Luoyu Wu, Furong Chen, Pengwei Wang, Chongjing Xu, Weidong Wen, Matthias Hahn, Mingguo Zhou, Yiping Hou 2025, 24 (6): 2285-2298.   DOI: 10.1016/j.jia.2023.11.046 Abstract （354）      PDF in ScienceDirect       Fusarium graminearum is a fungal plant pathogen which causes Fusarium head blight (FHB), a devastating disease on cereal crops.  Here we report that FgPMA1 could be a new target to control FHB by the application of double-stranded RNA (dsRNA) of FgPMA1.  FgPMA1 was divided into 6 segments to generated RNA interference (RNAi) constructs (FgPMA1RNAi-1, -2, -3, -4, -5, and -6), and these constructs were transformed in F. graminearum strain PH-1.  The expression of FgPMA1 reduced by 18.48, 33.48 and 56.93% in FgPMA1RNAi-1, FgPMA1RNAi-2 and FgPMA1RNAi-5, respectively.  FgPMA1RNAi-1, -2, and -5 mutants inhibited fungal development, including mycelium growth, mycelial morphology, asexual and sexual development, and toxin production.  The length of lesions on wheat leaves, wheat coleoptiles and wheat ears were shorter after infection with FgPMA1RNAi-1, -2, and -5 mutants than wild type PH-1.  These results showed that three segments (FgPMA1RNAi-1, -2, and -5) exhibited effective silencing effects.  After treatment with 25 ng µL–1 dsRNA of these segments in vitro, the growth rate of mycelium growth was significant decreased, mycelium became deformed with bulbous structure at the tip, and the mycelium lost the ability to produce conidia in F. graminearum strain PH-1, Fusarium asiacitum strain 2021 and phenamacril-resistant strain YP-1.  After application of FgPMA1RNAi-1-dsRNA and FgPMA1RNAi-2-dsRNA to wheat ears, pathogenicity reduced 34.21–35.40%. Reference | Related Articles | Metrics

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Mechanism of mitigating on Deoxynivalenol-induced intestinal toxicity in swine and its dietary regulation strategy Ting Pan, Ruiting Guo, Weiwei Wang, Xing Liu, Bing Xia, Linshu Jiang, Ming Liu 2025, 24 (7): 2449-2464.   DOI: 10.1016/j.jia.2024.07.037 Abstract （350）      PDF in ScienceDirect       Mycotoxins are the most widely existing pollutants in both dietary provisions and livestock feed, and they pose a series of hazards for humans and animals.  Deoxynivalenol (DON) is a prevalent mycotoxin that is primarily produced by Fusarium spp. and commonly found in various cereal products.  Feeding swine diets contaminated with trichothecene DON can lead to major adverse effects, including reduced feed intake, diminished weight gains, and compromised immune function.  Among all animal species, swine are the most sensitive to DON.  Here we explore the disruption of gut health by DON, considering aspects such as intestinal histomorphology, epithelial barrier functions,  immune system, microflora, and short-chain fatty acid production in the intestines.  Numerous additives have been documented for their potential in the detoxification of DON.  These additives can alleviate the toxic effects of DON on pigs by modulating the Nrf2-Keap1, mitogen-activated protein kinases (MAPKs) and Nuclear factor kappa-B (NF-κB) signaling pathways.  Additionally, there are additives capable of mitigating the toxicity of DON through adsorption or biotransformation.  This update has novel potential for advancing our comprehension of the mechanisms linked to DON intestinal toxicity and facilitating the formulation of innovative strategies to mitigate the impact of DON. Reference | Related Articles | Metrics

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Genome-wide association study identifies novel loci associated with feed efficiency traits in Hu lambs Deyin Zhang, Xiaolong Li, Fadi Li, Xiaoxue Zhang, Yuan Zhao, Yukun Zhang, Zongwu Ma, Huibin Tian, Xiuxiu Weng, Weimin Wang 2025, 24 (4): 1259-1269.   DOI: 10.1016/j.jia.2023.10.011 Abstract （347）      PDF in ScienceDirect       Feed efficiency (FE) is a crucial economic trait that significantly impacts profitability in intensive sheep production, and can be evaluated by the residual feed intake (RFI) and feed conversion ratio (FCR).  However, the underlying genetic mechanisms that underlie FE-related traits in sheep are not fully understood.  Herein, we measured the FE-related traits of 1,280 Hu sheep and conducted the phenotype statistics and correlation analysis, the result showcase that there was a large variation for FE-related traits, and RFI was significant positive correlation with average daily feed intake (ADFI) and FCR.  Moreover, a genome-wide association study (GWAS) was conducted using whole-genome resequencing data to investigate the genetic associations of ADFI, FCR and RFI.  For ADFI and FCR traits, 2 and one single nucleotide polymorphisms (SNPs) exceeded the genome-wide significance threshold, whereas ten and 5 SNPs exceeded the suggestive significance threshold.  For RFI traits, only 4 SNPs exceeded the suggestive significance threshold.  Finally, a total of 8 genes (LOC101121953, LOC101110202, CTNNA3, IZUMO3, PPM1E, YIPF7, ZSCAN12 and LOC105603808) were identified as potential candidate genes for FE-related traits.  Simultaneously, we further analyzed the effects of 2 candidate SNPs associated with RFI on growth and FE traits in enlarged experimental population, the results demonstrated that these 2 SNPs was not significantly associated with growth traits (P>0.05), but significantly related to RFI traits (P<0.05).  These findings will provide valuable reference data and key genetic variants that can be used to effectively select feed-efficient individual in sheep breeding programs. Reference | Related Articles | Metrics

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Transcriptome-wide N6-methyladenosine (m6A) profiling of compatible and incompatible responses reveals a nonhost resistance-specific m6A modification involved in soybean–soybean cyst nematode interaction Qianqian Shi, Xue Han, Xinhao Zhang, Jie Zhang, Qi Fu, Chen Liang, Fangmeng Duan, Honghai Zhao, Wenwen Song 2025, 24 (5): 1875-1891.   DOI: 10.1016/j.jia.2023.10.023 Abstract （337）      PDF in ScienceDirect       Soybean cyst nematode (SCN, Heterodera glycines) is a devastating pathogen that infects soybean (Glycine max L. Merrill) and disrupts soybean production worldwide.  SCN infection upregulates or downregulates the expression of multiple genes in soybean.  However, the regulatory mechanisms that underlie these changes in gene expression remain largely unexplored.  N6-methyladenosine (m6A) methylation, one of the most prevalent mRNA modifications, contributes to transcriptional reprogramming during plant responses to pathogen infection.  Nevertheless, the role of m6A methylation in establishing compatible and incompatible soybean responses to SCN has not previously been studied.  Here, we performed transcriptome-wide m6A profiling of soybean roots infected with virulent and avirulent populations of SCN.  Compared with the compatible response, the incompatible response was associated with higher global m6A methylation levels, as well as more differentially modified m6A peaks (DMPs) and differentially expressed genes (DEGs).  A total of 133 and 194 genes showed significant differences in both transcriptional expression and m6A methylation levels in compatible and incompatible interactions; the most significantly enriched gene ontology terms associated with these genes were plant–pathogen interaction (compatible) and folate biosynthesis (incompatible).  Our findings demonstrate that the m6A methylation profiles of compatible and incompatible soybean responses are distinct and provide new insights into the regulatory mechanism underlying soybean response to SCN at the post-transcriptional modification level, which will be valuable for improving the SCN-resistant breeding. Reference | Related Articles | Metrics

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Gas production characteristics of oats and tritical silages and techniques for reducing gas emissions Jing Tian, Rong Tian, Juanyan Wu, Liying Huang, Jianguo Zhang 2025, 24 (4): 1246-1258.   DOI: 10.1016/j.jia.2024.09.023 Abstract （336）      PDF in ScienceDirect       Greenhouse gas (GHG) production during ensiling not only causes the nutrient losses of silage but also promotes climate warming.  However, there is little information on the production of GHG and strategies for mitigating GHG emissions during ensiling.  This work aimed to study the gas production characteristics and techniques for reducing gas emissions during ensiling.  Oats and triticale, with Lactiplantibacillus plantarum (LP) or corn meal (CM) addition, were ensiled.  The cumulative gas volume rapidly increased and reached to the peak within the first 9 d of ensiling for both forage crops.  The highest cumulative gas volume of triticale silage was twice as much as that of oats silage.  Triticale silage produced lower carbon dioxide (CO2) concentration, higher methane (CH4) and nitrous oxide (N2O) concentrations than oats silage within the 28 d of ensiling.  Adding LP or CM significantly improved the fermentation quality and decreased the gas volume and GHG concentrations of 2 silages on d 56 (except CH4 of triticale).  At the early stage of ensiling, more Enterobacter, Lactococcus and Leuconostoc related to gas production were observed, and adding LP increased the abundance of Lactobacillus and decreased the abundance of bacteria like Kosakonia, Pantoea, Enterobacter and Lactococcus positively correlated with gas volume, CO2 and N2O concentrations.  These results suggest that gas formation during ensiling mainly occurs in the first 9 d.  Adding LP or CM can significantly improve the fermentation quality and decrease the gas volume.  This would benefit to reducing GHG emissions in silage production. Reference | Related Articles | Metrics

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OsEXO70L2 is required for large lateral root formation and arbuscular mycorrhiza establishment in rice Tongming Wang, Kai Zhou, Bingxian Yang, Benoit Lefebvre, Guanghua He 2025, 24 (6): 2035-2045.   DOI: 10.1016/j.jia.2024.04.007 Abstract （335）      PDF in ScienceDirect       As a major subunit of the exocyst complex, members of the EXO70 family have mainly been shown to play roles in cell polarity and morphogenesis in Arabidopsis, but their roles in plant endosymbiosis, such as with arbuscular mycorrhizal fungi (AMF), have rarely been reported.  Here, using knockout and overexpression lines, we show that OsEXO70L2, which encodes a divergent EXO70 protein in rice, controls the number of primary roots and is essential for large lateral root formation.  Furthermore, the OsEXO70L2 mutant sr1 displayed rare internal AMF hyphae and no arbuscules.  We also found that AMF sporulation can occur in roots despite low colonization and that AMF colonization and sporulation are modulated by photoperiod and co-culture with clover.  Finally, genes related to auxin homeostasis were found to be affected in the OsEXO70L2 knockout or overexpression lines, suggesting that auxin is at least partly responsible for the phenotypes.  This study provides new perspectives on the role of the exocyst complex during root development and AM in rice. Reference | Related Articles | Metrics

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Intramuscular fat deposition in pig: A key target for improving pork quality Qi Han, Xingguo Huang, Jun He, Yiming Zeng, Jie Yin, Yulong Yin 2025, 24 (12): 4461-4483.   DOI: 10.1016/j.jia.2024.03.005 Abstract （331）      PDF in ScienceDirect       Intramuscular fat (IMF) is an important economic trait for pork quality, affecting meat flavour, juiciness, and tenderness.  Hence, the improvement of IMF content is one of the hotspots of animal science to provide better meat product.  Here, we found that most IMF-related genes are enriched in lipid metabolism processes, including fatty acid transport and uptake, fatty acid beta oxidation, lipid synthesis, lipid storage, and lipolysis.  PPAR and AMPK signalling pathways are identified to be responsible for IMF deposition.  Genetics and nongenetic factors (i.e., diets, gut microbiota, age, sex and management) also positively or negatively regulate the IMF content in pigs.  Taken together, this review deepens our understanding of how these factors affect pig IMF deposition and provides valuable information for moderately increasing IMF content. Reference | Related Articles | Metrics

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A suitable organic fertilizer substitution ratio stabilizes rainfed maize yields and reduces gaseous nitrogen loss in the Loess Plateau, China Lihua Xie, Lingling Li, Junhong Xie, Jinbin Wang, Zechariah Effah, Setor Kwami Fudjoe, Muhammad Zahid Mumtaz 2025, 24 (6): 2138-2154.   DOI: 10.1016/j.jia.2024.03.021 Abstract （325）      PDF in ScienceDirect       The application of organic fertilizers has become an increasingly popular practice in maize production to reduce the gaseous nitrogen (N) loss and soil degradation caused by inorganic fertilizers.  Organic fertilizer plays a key role in improving soil quality and stabilizing maize yields, but few studies have compared different substitution rates.  A field study was carried out in 2021 and 2022, based on a long-term trial initiated in 2016, which included five organic fertilizer N substitution rates with equal inputs of 200 kg N ha–1: 0% organic fertilizer (T1, 100% inorganic fertilizer), 50.0% organic+50.0% inorganic fertilizer (T2), 37.5% organic+62.5% inorganic fertilizer (T3), 25.0% organic+75.0% inorganic fertilizer (T4), and 12.5% organic+87.5% inorganic fertilizer (T5), as well as a no fertilizer control (T6).  The results of the two years showed that T3 and T1 had the highest grain yield and biomass, respectively, and there was no significant difference between T1 and T3.  Compared with T1, the 12.5, 25.0, 37.5, and 50.0% substitution rates in T5, T4, T3, and T2 significantly reduced total nitrogen losses (NH3, N2O) by 8.3, 16.1, 18.7, and 27.0%, respectively.  Nitrogen use efficiency (NUE) was higher in T5, T3, and T1, and there were no significant differences among them.  Organic fertilizer substitution directly reduced NH3 volatilization and N2O emission from farmland by lowering the ammonium nitrogen and alkali-dissolved N contents and by increasing soil moisture.  These substitution treatments reduced N2O emissions indirectly by regulating the abundances of AOB and nirK-harboring genes by promoting soil moisture.  Specifically, the 37.5% organic fertilizer substitution reduces NH3 volatilization and N2O emission from farmland by reducing the ammonium nitrogen and alkali-dissolved N contents and increasing moisture, which negatively regulate the abundance of AOB and nirK-harboring genes to reduce N2O emissions indirectly in rainfed maize fields on the Loess Plateau of China. Reference | Related Articles | Metrics

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Rhizosphere flavonoids alleviate inhibition of soybean nodulation caused by shading under maize–soybean strip intercropping Ping Lin, Shanshan Liu, Zhidan Fu, Kai Luo, Yiling Li, Xinyue Peng, Xiaoting Yuan, Lida Yang, Tian Pu, Yuze Li, Taiwen Yong, Wenyu Yang 2026, 25 (3): 952-964.   DOI: 10.1016/j.jia.2024.09.030 Abstract （321）      PDF in ScienceDirect       Flavonoids produced by legume roots act as signaling molecules that induce the expression of nod genes in symbiotic rhizobia.  However, the role of flavonoids in root exudates under intercropping systems in promoting soybean nodulation remains unclear.  Two consecutive years of field experiments were conducted using maize–soybean strip intercropping with interspecific row spacings of 30 cm (MS30), 45 cm (MS45), and 60 cm (MS60), along with sole cropping of soybean (SS) and maize (MM).  Root interactions were manipulated using either no root barrier (NB) or a polyethylene plastic barrier (PB) to assess the relationship between flavonoids in root exudates and soybean nodulation.  We found that root–root interaction between soybean and maize increased nodule number and fresh weight in intercropped soybean, with enhancement gradually increasing as interspecific distance widened.  The proportion of nodules with diameters exceeding 0.4 cm was higher in intercropped soybean under NB compared to PB.  Additionally, the expression of nodule-related genes - GmENOD40, GmNIN2b, and GmEXPB2 - was up-regulated.  Furthermore, compared to monocropping, isoflavone secretion by soybean roots decreased, whereas flavonoid and flavonol secretion by both maize and soybean roots increased under intercropping.  The abundance of differentially secreted flavonoid metabolites in the rhizosphere of both species declined when root contact was prevented by the barrier.  In soybean roots, the expression of GmCHS8 and GmIFS1 was up-regulated, while GmICHG was down-regulated under root interaction.  Most flavonoid and flavonol compounds showed positive correlations with nodule diameter.  Nodule number, fresh weight, and the proportion of nodules larger than 0.2 cm increased in diverse soybean genotypes treated with maize root exudates, which contributed to enhanced nitrogen fixation capacity.  Therefore, maize–soybean strip intercropping, combined with optimal row spacing, enhances the positive effects of underground root interactions and improves nodulation and nitrogen fixation in intercropped soybean. Reference | Related Articles | Metrics

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Identification of QTLs for plant height and branching-related traits in cultivated peanut Shengzhong Zhang, Xiaohui Hu, Feifei Wang, Huarong Miao, Chu Ye, Weiqiang Yang, Wen Zhong, Jing Chen 2025, 24 (7): 2511-2524.   DOI: 10.1016/j.jia.2023.12.009 Abstract （317）      PDF in ScienceDirect       Plant height (PH), primary lateral branch length (PBL), and branch number (BN) are architectural components impacting peanut pod yield, biomass production, and adaptivity to mechanical harvesting.  In this study, a recombinant inbred population consisting of 181 individual lines was used to determine genetic controls of PH, PBL, and BN across three environments.  Phenotypic data collected from the population demonstrated continuous distributions and transgressive segregation patterns.  Broad-sense heritability of PH, PBL, and BN was found to be 0.87, 0.88, and 0.92, respectively.  Unconditional individual environmental analysis revealed 35 additive QTLs with phenotypic variation explained (PVE) ranging from 4.57 to 21.68%.  A two-round meta-analysis resulted in 24 consensus and 19 unique QTLs.  Five unique QTLs exhibited pleiotropic effects and their genetic bases (pleiotropy or tight linkage) were evaluated.  A joint analysis was performed to estimate the QTL by environment interaction (QEI) effects on PH, PBL, and BN, collectively explaining phenotypic variations of 10.80, 11.02, and 7.89%, respectively.  We identified 3 major and stable QTL regions (uq9-3, uq10-2, and uq16-1) on chromosomes 9, 10, and 16, spanning 1.43–1.53 Mb genomic regions.  Candidate genes involved in phytohormones biosynthesis, signaling, and cell wall development were proposed to regulate these morphological traits.  These results provide valuable information for further genetic studies and the development of molecular markers applicable to peanut architecture improvement. Reference | Related Articles | Metrics

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Abscisic acid reduces Cd accumulation by regulating Cd transport and cell wall sequestration in rice Zhijun Xu, Jiashi Peng, Yanlei Fu, Jing Zhao, Yan Peng, Bohan Liu, Xujun Hu, Yuchuan Liu, Meijuan Duan, Nenghui Ye, Zhenxie Yi, Shuan Meng 2025, 24 (10): 3703-3718.   DOI: 10.1016/j.jia.2025.02.010 Abstract （314）      PDF in ScienceDirect       Cadmium (Cd) uptake by rice plants and its subsequent movement through food chains pose a notable risk to the health of both plants and humans.  Therefore, understanding the fundamental mechanisms underlying the uptake and movement process is essential.  Through transcriptome analysis, we found that numerous abscisic acid (ABA)-related genes responded to Cd stress.  Exogenous application of ABA significantly reduced Cd accumulation in the shoots and roots of rice plants.  The increased ascorbate peroxidase (APX) enzyme activity, decreased H2O2 content, and elevated Cd tolerance index collectively suggest that ABA may mitigate the toxicity of Cd in rice plants.  Further study revealed that exogenous ABA reduced Cd accumulation by regulating Cd transport and cell wall sequestration.  Consistently, mutation of the ABA signaling factor OsABI5 resulted in a significant increase in Cd accumulation in shoots.  Moreover, foliar spraying of ABA during the grain-filling stage significantly reduced Cd accumulation in rice grains, which was attributed mainly to decreased Cd uptake and the inhibition of Cd transportation from roots to shoots and from leaves to grains.  These findings elucidate the underlying mechanisms of the ABA-mediated response to Cd stress in rice and provide a practical reference for coping with Cd pollution in farmlands Reference | Related Articles | Metrics

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Fine mapping and candidate gene analysis of a major QTL for grain length on chromosome 5BS in bread wheat Jianqi Zeng, Dehui Zhao, Li Yang, Yufeng Yang, Dan Liu, Yubing Tian, Fengju Wang, Shuanghe Cao, Xianchun Xia, Zhonghu He, Yong Zhang 2025, 24 (7): 2465-2474.   DOI: 10.1016/j.jia.2024.04.033 Abstract （312）      PDF in ScienceDirect       Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding.  The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895).  Here, a BC1F6 residual heterozygous line was selected from the cross of a ZM871/ZM895//ZM871 population, and six heterozygous recombinant plants were identified in the BC1F7 population from self-pollination of the heterozygous line.  QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2 (25.3–27.5 Mb) by phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants.  Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses.  Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS.  The gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed, and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population of 166 cultivars using this marker.  These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat. Reference | Related Articles | Metrics

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Soil nitrogen dynamics regulate differential nitrogen uptake between rice and upland crops Shending Chen, Ahmed S. Elrys, Siwen Du, Wenyan Yang, Zucong Cai, Jinbo Zhang, Lei Meng, Christoph Müller 2026, 25 (1): 302-312.   DOI: 10.1016/j.jia.2025.03.014 Abstract （312）      PDF in ScienceDirect       Nitrogen use efficiency in rice is lower than in upland crops, likely due to differences in soil nitrogen dynamics and crop nitrogen preferences.  However, the specific nitrogen dynamics in paddy and upland systems and their impact on crop nitrogen uptake remain poorly understood.  The N dynamics and impact on crop N uptake determine the downstream environmental pollution from nitrogen fertilizer.  To address this poor understanding, we analyzed 2,044 observations of gross nitrogen transformation rates in soils from 136 studies to examine nitrogen dynamics in both systems and their effects on nitrogen uptake in rice and upland crops.  Our findings revealed that nitrogen mineralization and autotrophic nitrification rates are lower in paddies than in upland soil, while dissimilatory nitrate reduction to ammonium is higher in paddies, these differences being driven by flooding and lower total nitrogen content in paddies.  Rice exhibited higher ammonium uptake, while upland crops had over twice the nitrate uptake.  Autotrophic nitrification stimulated by pH reduced rice nitrogen uptake, while heterotrophic nitrification enhanced nitrogen uptake of upland crops.  Autotrophic nitrification played a key role in regulating the ammonium-to-nitrate ratio in soils, which further affected the balance of plant nitrogen uptake.  These results highlight the need to align soil nitrogen dynamics with crop nitrogen preferences to maximize plant maximize productivity and reduce reactive nitrogen pollution. Reference | Related Articles | Metrics

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Protection of chickens from Mycoplasma gallisepticum through the MAPK/ERK/JNK pathway by a compound of ten Chinese medicine formulas Tengfei Wang, Changyong Fan, Yufei Xiao, Shan Lü, Guangyang Jiang, Mengyun Zou, Yingjie Wang, Qiao Guo, Zhenghao Che, Xiuli Peng 2025, 24 (6): 2356-2370.   DOI: 10.1016/j.jia.2023.11.043 Abstract （305）      PDF in ScienceDirect       Mycoplasma gallisepticum (MG) is a common avian pathogen that mainly infects poultry, causing significant reductions in body weight gain and egg production, along with damage to immune organs and immunosuppression.  MG is susceptible to co-infections with other pathogens, leading to increased mortality rates and significant economic losses in the global poultry industry.  While antibiotics have been extensively applied worldwide to treat MG infections in poultry production, concerns regarding antibiotic resistance and residue remain prevalent.  Traditional Chinese medicine (TCM), renowned for its natural, safe, and non-toxic properties, has shown significant anti-inflammatory and immune-enhancing effects.  This study aimed to investigate the protective effect of TCM on production performance and its impact on MG-induced immunosuppression through the MAPK/ERK/JNK signaling pathway in chickens.  Our results showed that TCM alleviated the negative effects of MG infection on production performance, as evidenced by improvements in body weight gain, feed conversion rate, survival rate, and immune organ index.  TCM exhibited direct inhibition of the MG proliferation in vitro and in vivo.  Furthermore, TCM treatment promoted the normalization of trachea and lung tissue structure in MG-infected chickens, leading to a significant reduction in inflammatory damage.  Moreover, following the treatment with the TCM, the production of pro-inflammatory cytokines interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) decreased significantly, accompanied by the downregulation of pro-apoptotic genes caspase3, caspase9, and BAX, both in vitro and in vivo.  A mechanism-based study showed that in vitro and in vivo treatment with the TCM significantly reduced the expression of key proteins, including early growth response gene 1 (EGR1), p-ERK, p-JNK, and p-JUN.  Altogether, TCM improved body weight gain, inhibited pro-inflammation responses, and alleviated tissue damage by inhibiting the MAPK/ERK/JNK signaling pathway to protect the performance and immune system of MG-infected chickens. Reference | Related Articles | Metrics

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Genome wide linkage mapping for black point resistance in a recombinant inbred line population of Zhongmai 578 and Jimai 22 Tiantian Chen, Lei Li, Dan Liu, Yubing Tian, Lingli Li, Jianqi Zeng, Awais Rasheed, Shuanghe Cao, Xianchun Xia, Zhonghu He, Jindong Liu, Yong Zhang 2025, 24 (9): 3311-3321.   DOI: 10.1016/j.jia.2023.12.039 Abstract （300）      PDF in ScienceDirect       Black point is a black discoloration of the grain embryo that reduces the grain quality and commodity grade.  Identifying the underlying genetic loci can facilitate the improvement of black point resistance in wheat.  Here, 262 recombinant inbred lines (RILs) from the cross of Zhongmai 578/Jimai 22 were evaluated for their black point reactions in five environments.  A high-density genetic linkage map of the RIL population was constructed with the wheat 50K single nucleotide polymorphism (SNP) array.  Six stable QTLs for black point resistance were detected, QBp.caas-2A, QBp.caas-2B1, QBp.caas-2B2, QBp.caas-2D, QBp.caas-3A, and QBp.caas-5B, which explained 2.1–28.8% of the phenotypic variances.  The resistance alleles of QBp.caas-2B1 and QBp.caas-2B2 were contributed by Zhongmai 578 while the others were from Jimai 22.  QBp.caas-2B2, QBp.caas-2D and QBp.caas-3A overlapped with previously reported loci, whereas QBp.caas-2A, QBp.caas-2B1 and QBp.caas-5B are likely to be new.  Five kompetitive allele-specific PCR (KASP) markers, Kasp_2A_BP, Kasp_2B1_BP, Kasp_2B2_BP, Kasp_3A_BP, and Kasp_5B_BP, were validated in a natural population of 165 cultivars.  The findings of this study provide useful QTLs and molecular markers for the improvement of black point resistance in wheat through marker-assisted breeding. Reference | Related Articles | Metrics