Scientia Agricultura Sinica

Progress in Transposable Element-Assisted Targeted Insertion of Large DNA Fragments

ZHAO ZiJie, SONG Hao, DONG XiaoOu, WAN JianMin

Scientia Agricultura Sinica. 2026, 59(6): 1141-1156. doi:10.3864/j.issn.0578-1752.2026.06.001

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The rapidly evolving genome editing technologies have demonstrated strong application potential in animal and plant breeding, microbial engineering, and basic scientific research. Current genome editing techniques allow for the insertion, deletion, and substitution of single or multiple nucleotides at specific genomic targets across a wide range of species. However, editing types involving large DNA fragment insertion or replacement still face technical bottlenecks, such as low efficiency and fidelity, as well as difficulties in donor delivery. These limitations restrict the application of gene editing in important scenarios, including multigene stacking with genetic linkage, precise replacement of favorable alleles, and targeted integration of DNA fragments at genomic safe harbors. Transposable elements, as mobile genetic elements widely present in biological genomes, offer a novel approach to overcoming these challenges due to their inherent mobility and large DNA cargo capacity. They hold promise for being engineered into key molecular tools for precise large DNA fragment editing. This review summarizes recent advances in targeted large DNA fragment insertion technologies based on transposable elements, focusing on the application status and prospects of prokaryotic-derived CRISPR-associated transposons (CAST) and certain DNA transposons and retrotransposons in eukaryotes. Prokaryotic-derived CAST systems have shown outstanding performance, enabling efficient large fragment integration in prokaryotes and, after optimization, also achieving large fragment insertion in eukaryotic cells. In eukaryotes, engineered DNA transposons such as mPing/Pong and retrotransposon-related tools like R2 and L1 have been utilized for large DNA fragment insertion in animals and plants. At the same time, the field of transposon-based large DNA fragment insertion faces challenges. On the one hand, the cross-species adaptability of transposable elements is limited, making it difficult for some elements to function when transferred to other species. On the other hand, the large size or multiplicity of protein components involved leads to low delivery efficiency in certain types of eukaryotic cells. Additionally, some systems carry safety risks, such as stimulating the mammalian immune system and triggering inflammatory responses. Future research may focus on the discovery of novel transposable elements, engineering of transposases, development of new delivery vectors, and in-depth elucidation of transposition mechanisms, in order to provide key technical support for establishing efficient and safe large fragment editing technologies. This will contribute to foundational innovations in crop genetic improvement, gene therapy, and microbial genome editing.

Genome-Wide Association Study-Based Identification of Loci Controlling Mature Embryo Size in Chinese Wheat Landraces and Their Genetic Effects Analysis

YE MeJin, WU Lei, MD NAHIBUZZAMAN Lohani, YIN Li, HU XinRong, LIU YaXi, JIANG YunFeng, CHEN GuoYue, PU ZhiEn, LI Yang, LI Ting, ZOU YaYa, WU JiaYi, MA Jian

Scientia Agricultura Sinica. 2026, 59(6): 1157-1171. doi:10.3864/j.issn.0578-1752.2026.06.002

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【Objective】As a critical component of wheat grains, the embryo is closely correlated to nutritional value, germination, and seedling establishment. Mining embryo size loci from genetically diverse Chinese wheat landraces and deciphering their genetic effects will enhance our understanding of the genetic basis of embryo size and provide molecular targets for future breeding programs. 【Method】We genotyped 240 Chinese wheat landraces using the 660K SNP array and performed genome-wide association studies (GWAS) via a mixed linear model, integrating embryo size phenotypic data across three environments. Significant loci were subjected to genetic effect analysis and candidate gene prediction. 【Result】Phenotypic variation ranges across environments and BLUP values were: embryo length (1.64-3.43 mm), width (0.93-2.58 mm), area (1.10-5.71 mm²), and length-to-width ratio (1.06-2.08), with broad-sense heritabilities of 0.76, 0.47, 0.54, and 0.60, respectively. Significant positive correlations (r=0.271-0.922) existed among embryo traits, and between major embryo traits (length, width, area) and grain length or thousand-kernel weight. A total of 18 stable SNP loci significantly associated with embryo length and area were identified across two environments and BLUP values, which were clustered into four quantitative trait locus (QTL) intervals. These included three QTLs for embryo length and one for embryo area, with colocalization observed between QEA.sicau.3B and QEL.sicau.3B.2. For the major QTL QEL.sicau.1B, we predicted nine candidate genes. Genetic effect analysis revealed that the increasing allele of QEL.sicau.1B significantly enhanced embryo length, grain length and width, thousand-kernel weight, and reduced flowering time, while demonstrating superior effects on seedling root dry weight and shoot biomass, albeit with minor negative impacts on tiller number and spikelet number. Comparative analysis suggested both QEL.sicau.1B and QEL.sicau.3B.2 represent novel loci. 【Conclusion】GWAS identified four stable loci significantly associated with embryo size, among which nine potential candidate genes were predicted for the major embryo-length QTL (QEL.sicau.1B). The study demonstrated significant positive correlations between embryo size and grain dimensions, and revealed a functional association with seedling root vigor.

Integrated Multi-Stage Evaluation of Salt Tolerance in Vicia faba L. and Itaconic Acid-Mediated Alleviation of Germination-Stage Salt Stress

ZHANG ZhiLin, LIU Rong, ZONG XuXiao, HAO XiaoPeng, YANG Tao

Scientia Agricultura Sinica. 2026, 59(6): 1172-1188. doi:10.3864/j.issn.0578-1752.2026.06.003

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【Objective】Salt stress limits the stable and increased yields of faba beans (Vicia faba L.) on saline-alkali soils. This study aims to improve the efficiency and accuracy of distinguishing salt tolerance differences among various materials at early stages by combining indoor germination assays with field observations. Additionally, it evaluates the potential of exogenous itaconic acid (IA) at different doses and acidic treatments to alleviate salt stress during the germination stage, providing complementary pathways for early prediction and exogenous regulation. 【Method】 Fifteen faba bean germplasm materials were selected for germination tests under 100 mmol·L^-1 NaCl conditions. Various indices, including relative germination rate (RGR), relative germination energy (RGE), relative root length (RRL), vigor index (VI), germination index (GI), and germination stress index (GSI), were measured. Comprehensive evaluation and classification were performed using the comprehensive membership value μ(X_i). Field trials were conducted on both saline-alkali and non-saline-alkali soils, tracking seedling emergence rate, Soil and Plant Analyzer Development (SPAD) values at the bud stage, flowering-stage salt injury index (SI), and 17 agronomic traits to form a field classification of salt tolerance. Stratified 5-fold cross-validation was employed to assess the performance of field-grade determination, using F1 metrics. For the IA treatment, three representative germplasms were selected, and a gradient of 0% to 1% IA was applied under 100 mmol·L^-1 NaCl. Acetic acid (CH₃COOH) and pH7.0 treatments served as controls to analyze the alleviating effects of IA on salt stress. 【Result】Significant differences were observed in all indices among the different classifications at the germination stage, showing strong discriminatory power across materials, with comprehensive scores showing a continuous gradient from salt-sensitive to salt-tolerant materials, allowing for classification. Field observations indicated that seedling emergence rates and SPAD values decreased in most materials under saline-alkali conditions, although some materials still performed well. Overall, germination-stage classification correlated well with field classification, with approximately 73% of materials showing consistency across both stages, suggesting that germination assessments are indicative of actual field salt tolerance. A supervised model built on key germination-stage traits (VI, RGE, RGR, and GSI) showed a moderate ability to predict field classification, achieving F1=0.50, Precision=0.46, and Recall=0.60 under stratified 5-fold cross-validation, providing quantitative support for early-stage screening of salt-tolerant germplasm. Low doses of IA (e.g., 0.01%) improved the germination vigor and root growth of the materials, but no similar effect was observed with equimolar acetic acid. When the external solution was adjusted to pH 7.0, the promoting effect of IA significantly weakened or disappeared, indicating that its alleviating effect is not only related to molecular structure but also closely associated with a weak acidic environment. Additionally, the effect exhibited variety-specific responses, with germplasm V434 showing higher responsiveness. 【Conclusion】 The combined evaluation of indoor germination assays and field observations effectively distinguishes salt tolerance differences among faba bean materials at early stages. Indices such as vigor index (VI), germination stress index (GSI), and relative germination rate (RGR) effectively reflect field-grade performance and improve initial screening efficiency. IA demonstrates a dose-dependent, pH-sensitive alleviating effect during germination; however, its stability and applicability need further validation under complex saline-alkali stress and field conditions.

Photo-Physiological Mechanism at Grain Filling Stage of No-Tillage with Plastic Re-Mulching to Increase Maize Yield in Oasis Irrigation Areas

WANG JiaNuo, CHEN GuiPing, LI Pan, WANG LiPing, NAN YunYou, HE Wei, FAN ZhiLong, HU FaLong, CHAI Qiang, YIN Wen, ZHAO LiaoHao

Scientia Agricultura Sinica. 2026, 59(6): 1189-1202. doi:10.3864/j.issn.0578-1752.2026.06.004

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【Objective】Aiming at the problems of low photosynthetic performance and yield decline of maize leaves caused by large amount of plastic input and extreme high temperature in traditional maize planting in oasis irrigation area, the photosynthetic physiological mechanism of maize during grain filling period under two years of plastic mulching was studied, so as to provide the theoretical basis for the construction of high grain yield technology of plastic reduction in oasis irrigation area. 【Method】In 2013, a randomized block experiment was conducted in the oasis irrigation area of the Hexi Corridor. According to the duration of plastic mulching, three treatments were formed: no-tillage with plastic re-mulching and using (NTP), no-tillage in autumn and plastic mulching in spring (RTP), and conventional tillage with annual new plastic mulching (CTP, as the control). The response of chlorophyll content, gas exchange parameters, key enzyme activities of photosynthetic physiology, relative gene expression and key protein content of maize leaves to different plastic utilization methods was explored. 【Result】Different plastic utilization methods promoted the increase and stability of maize yield by regulating the photosynthetic physiological characteristics of maize filling stage. Compared with CTP, chlorophyll a and b in NTP filling stage increased by 15.1% and 8.3% on average, respectively, indicating that NTP treatment was beneficial to maintain the chlorophyll content of maize, thus effectively delaying the degradation of chlorophyll and promoting the photosynthesis of maize. Compared with CTP treatment, the net photosynthetic rate and transpiration rate under NTP increased by 25.2% and 11.5%, 20.0% and 12.2%, respectively, in the middle and late stages of grain filling, indicating that NTP treatment was beneficial to regulate the gas exchange parameters of maize during grain filling stage and enhanced the photosynthesis of maize during grain filling stage. At the same time, NTP maintained higher photosynthetic physiological key enzyme activity, relative gene expression and key protein content during the filling stage, which provided a guarantee for the improvement of photosynthesis. Compared with CTP, the activities of PPDK, PEPC, and Rubisco in maize leaves treated with NTP increased by 18.9%, 20.0%, and 30.6% on average, respectively, the gene expression of pepc, ppdk, and rub in maize leaves increased by 22.1%, 75.8%, and 70.6%, respectively, and the protein content of D1 and D2 in photosynthetic reaction center increased by 12.6% and 13.2%, respectively. Compared with CTP treatment, the activities of PPDK, PEPC and Rubisco in maize leaves under RTP increased by 15.6%, 16.4%, and 19.2%, respectively. The expression levels of pepc, ppdk, and rub genes in maize leaves increased by 13.6%, 53.9%, and 57.7%, respectively. The content of D1 protein in photosynthetic reaction center increased by 10.1%. In addition, the grain yield of NTP was 5.2%, 6.0%, and 5.3% higher than that under CTP in 2021, 2022, and 2023, respectively. The grain yield of RTP was only 5.2% higher than that under CTP in 2022. 【Conclusion】No-tillage with plastic re-mulching and using was an effective cultivation and management measure to maintain high photosynthetic performance, reduce plastic input, and increase maize yield in the northwest oasis irrigation areas.

Effects of Calcium Peroxide on Root Morphology and Yield Formation of Summer Maize in Waterlogging Farmland

ZHOU XinJie, REN Hao, CHEN YingLong, ZHANG JiWang, ZHAO Bin, REN BaiZhao, LIU Peng, WANG HongZhang

Scientia Agricultura Sinica. 2026, 59(6): 1203-1216. doi:10.3864/j.issn.0578-1752.2026.06.005

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【Objective】In the context of global climate change, frequent extreme rainfall has exacerbated farmland waterlogging, which severely restricts high and stable yields of maize. This study aimed to elucidate the regulatory mechanisms of calcium peroxide (CaO₂) application on root morphology and yield formation in summer maize under waterlogged field conditions, for providing the theoretical support for stress-resistant and stable-yield cultivation of maize under waterlogging stress. 【Method】The experiment was conducted at the Huang-Huai-Hai Regional Maize Technology Innovation Center, Shandong Agricultural University during the 2023-2024 summer maize growing season. Using the maize variety Denghai 605 (DH605) and a randomized complete block design, treatments consisted of CaO₂ application and a non-amended control (CK). At the V3 stage of summer maize, artificial waterlogging was simulated. The effects of CaO₂ application were systematically investigated on: (1) soil oxygen concentration in the 0-40 cm profile; (2) maize root morphology parameters (total root length, total root surface area, total root volume, root dry weight); (3) leaf area index (LAI), SPAD value, photosynthetic parameters (net photosynthetic rate (P_n), stomatal conductance (G_s), intercellular CO₂ concentration (C_i), transpiration rate (T_r)) and aboveground dry matter accumulation; and (4) grain filling characteristics, yield formation. 【Result】Under waterlogging stress, two-year results indicate that CaO₂ application significantly improved the soil oxygen environment. During a total of 10 measurements from the start of the treatment to 10 days after the end of the treatment, the average oxygen content in the 0-20 cm and 20-40 cm soil layers increased by 7.38% and 7.44%, respectively, compared with the control (CK), averaged over two years. Root morphology was markedly altered: at the flowering stage, total root length, total root surface area, total root volume, and root dry weight increased by 51.63%, 44.10%, 39.81% and 51.98% versus CK, respectively; canopy photosynthetic performance was significantly enhanced: maximum LAI and SPAD value at the flowering stage increased by 11.28% and 11.61%, respectively. At the flowering stage, the P_n, G_s, and T_r of the ear leaf increased by 23.84%, 30.63%, and 85.99%, respectively, while dry matter accumulation at maturity increased by 31.51%. Grain filling parameters improved: maximum grain filling rate, mean grain filling rate, grain weight at maximum filling rate, and grain weight at maturity increased by 7.29%, 7.29%, 5.81%, and 6.24%, respectively, compared with CK. CaO₂ synergistically increased kernel number per ear and 1000-grain weight, with average two-year increases of 39.98% and 5.00%, respectively, ultimately increasing grain yield by 50.77% under CK. 【Conclusion】Calcium peroxide application mitigated waterlogging stress and enhanced grain yield in summer maize by optimizing soil oxygen environment, remodeling root morphology, improving canopy photosynthetic efficiency and increasing dry matter accumulation, thereby increasing the grain-filling rate. This measure significantly increased grain yield by simultaneously increasing kernel number per ear and 1000-grain weight. This study provided a novel agronomic approach for stabilizing and increasing maize yield under waterlogging stress at the seedling stage.

Evaluation of Nitrogen Efficiency of Different Stay-Green Maize Hybrids

HE JiHang, ZHANG Qing, LÜ XiangYue, XUE JiQuan, XU ShuTu, LIU JianChao

Scientia Agricultura Sinica. 2026, 59(6): 1217-1230. doi:10.3864/j.issn.0578-1752.2026.06.006

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【Objective】Stay-green trait is an important agronomic characteristic closely related to high yield, good quality, and stress resistance of maize. This study explored the differences in nitrogen uptake and translocation of different stay-green maize hybrids, aiming to provide a theoretical basis for the physiological mechanism of high nitrogen efficiency in maize. 【Method】The tested materials were the stay-green hybrid Shandan 650 and the non-stay-green hybrid Zhengdan 958. In 2023, 6 N treatments were applied: N1 (0 kg·hm^-2), N2 (60 kg·hm^-2), N3 (120 kg·hm^-2), N4 (180 kg·hm^-2), N5 (240 kg·hm^-2), and N6 (300 kg·hm^-2). In 2024, a nitrogen×density interaction experiment was conducted with three N levels—low N (LN, 0 kg·hm^-2), medium N (MN, 180 kg·hm^-2), and high N (HN, 240 kg·hm^-2)—and two planting densities—low density (LD, 60 000 plants·hm^-2) and high density (HD, 75 000 plants·hm^-2). After the silking stage of maize, indicators were determined for each treatment, such as SPAD value of ear leaves, total number of green leaves per plant, dry matter, and nitrogen accumulation in vegetative organs and grains. Meanwhile, nitrogen absorption and translocation rates as well as nitrogen use efficiency-related indicators were analyzed. 【Result】 Grain yield of both hybrids initially increased and then stabilized with rising N rates, with Shandan 650 consistently outperforming Zhengdan 958 across all N and density treatments. Post-silking, Shandan 650 exhibited faster chlorophyll degradation (SPAD decline: 65.1% vs. 49.9%) and greater green leaf loss than Zhengdan 958, particularly under low N. Shandan 650 demonstrated superior N remobilization efficiency, especially under low N and high density, with significantly higher N translocation from leaves to grains. Overall, Shandan 650 achieved significantly higher N remobilization efficiency, nitrogen use efficiency, nitrogen agronomic efficiency, and nitrogen harvest index than Zhengdan 958. Furthermore, under high-density planting conditions, reasonable nitrogen reduction further enhanced its nitrogen efficiency performance. 【Conclusion】 The functional stay-green maize variety Shandan 650 maintains consistent greenness and photosynthetic capacity until a certain period before physiological maturity, at which point a rapid decline occurs along with nitrogen remobilization. Its strong nitrogen translocation capacity in vegetative organs enhances nitrogen translocation rate and nitrogen use efficiency, and higher nitrogen efficiency could be achieved under reasonable nitrogen reduction and density increase.

Analysis of Population Dynamics and Migration Status of Harmonia axyridis Under Searchlight Trap and Ground Light Trap

DU MengYuan, HOU YanHong, LIU Di, CHEN Li, FAN ZhiYe, WANG WenHao, SHEN HaiLong, WANG CanGuan, LI ShiMin, HUANG JianRong, CHEN Qi

Scientia Agricultura Sinica. 2026, 59(6): 1231-1243. doi:10.3864/j.issn.0578-1752.2026.06.007

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【Objective】The objective of this study is to clarify the population dynamics and migration patterns of Harmonia axyridis under light traps in Luohe City, Henan Province, analyze their changing trends, and to provide data support for the effective protection and utilization of H. axyridis for biological control. 【Method】From 2015 to 2024, systematic monitoring of H. axyridis was conducted in Luohe City, Henan Province, using searchlight traps and ground light traps. From March 1 to November 30 each year, the number of H. axyridis under the two types of traps was sorted and counted daily. Based on the annual and monthly trapping amounts, as well as the first and last capture dates under the two traps, the patterns and trends of H. axyridis phototaxis were analyzed. The population dynamics of H. axyridis were examined based on the daily trapping percentage relative to the annual total and the distribution of peak occurrence days across different seasons. Additionally, the migration patterns of H. axyridis were analyzed using the optimized ratio of trapping amounts between searchlight traps and ground light traps. 【Result】Over the 10-year period, the searchlight traps accumulated a total of 19 771 H. axyridis individuals, while the ground light traps accumulated 11 061 individuals. The number of insects caught by the searchlight traps showed a significant decreasing trend, whereas the number caught by the ground light traps showed a significant increasing trend. The annual catches of the two types of traps exhibited a significant negative correlation (P<0.05). Except for the years 2021-2023, when the ground light traps captured more individuals than the searchlight traps, the searchlight traps captured more individuals in all other years. H. axyridis was detected over a longer period under the searchlight traps, with the first occurrence date approximately 20 days earlier and the last occurrence date about 19.5 days later compared to the ground light traps. There were exceptionally high peak capture days under the searchlight traps, while no such phenomenon was observed under the ground light traps. Under the searchlight traps, H. axyridis exhibited three peak periods: late May to mid-June, mid- to late July, and late September to mid-October, with the highest capture occurring from late May to mid-June. The peak capture days for the ground light traps were concentrated from early June to mid-August, with no distinct peak periods, though the highest capture occurred from late July to mid-August. The air-to-ground ratio indicated three migration peaks for H. axyridis: late May to early June, early to mid-July, and mid-September to late October, with the highest migration intensity observed in October. Over the past decade, the southward migration of H. axyridis has significantly decreased, and the annual migration days have shown a significant declining trend (P<0.01). 【Conclusion】There are notable differences in the annual capture numbers and population dynamics of H. axyridis between searchlight traps and ground light traps. The peak periods under searchlight traps are more distinct and exhibit sharper increases and decreases. The earlier first occurrence and later last occurrence dates under searchlight traps make them more advantageous for monitoring H. axyridis migration. Influenced by global warming, the occurrence of H. axyridis in Luohe is increasing, while its migration is decreasing. The combined use of searchlight traps and ground light traps allows for a more precise analysis of migration behavior and quantification of migration intensity.

Analysis of the Lethal Activity of Serine Carboxypeptidase DmSCBP1 from Dionaea muscipula Against Bactrocera dorsalis

LIU Jia, ZHOU ShiQi, ZHOU Yan, SHEN GuangMao

Scientia Agricultura Sinica. 2026, 59(6): 1244-1254. doi:10.3864/j.issn.0578-1752.2026.06.008

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【Background】The long-term use of chemical pesticides has led to a series of problems such as drug resistance and environmental residue. Therefore, the green control of pest requires safer and more efficient active substances. Plants are the largest source of active substances of natural products for pest control. Carnivorous plants have the ability to capture and digest insects, and the components of their secreted digestive fluids exhibit potential insecticidal activity. 【Objective】The purpose of this study is to identify the protein components in the digestive fluid of Dionaea muscipula, and to screen out the proteins with insecticidal activity by combining the transcriptome data of D. muscipula after being induced by prey. 【Method】The adults of Bactrocera dorsalis were put into the trap to observe and record the process of digestion, and confirm the digestive ability of the trap. By analyzing the transcriptome data of the traps and glands of D. muscipula, genes with stress expression in response to prey stimulation were identified. Combined with the proteomic sequencing of the digestive fluid within the traps, the proteases that play a crucial role in the digestion process were clarified. Recombinant proteins were expressed in Escherichia coli in vitro, and injected into or dripped onto B. dorsalis adult to test insecticidal activity of recombinant proteins. 【Result】By observing the process of D. muscipula digesting B. dorsalis, it was found that the D. muscipula has the ability to digest B. dorsalis. The secreted digestive fluid can damage the body wall of B. dorsalis, and it takes about 10 to 13 days to digest a B. dorsalis. Following enzymatic digestion, only the epidermal layer is left. After being stimulated by the prey, DNA-binding transcription factors, serine carboxypeptidase, calmodulin and K⁺ uptake protein were simultaneously identified in the differentially expressed genes of the transcriptome and proteome datasets, and they may play an important role in the process of digesting prey by D. muscipula. The expression levels of serine carboxypeptidase genes DmSCBP1, DmSCBP2, DmSCBP5, DmSCBP8 in the traps and glands significantly increased after being stimulated by the prey. Among them, the expression level of DmSCBP1 was the most significantly increased, and the protein sequence of this gene was also detected in the protein sequencing of the digestive fluid. The recombinant protein of DmSCBP1 was expressed through the prokaryotic expression system. The biological assay results showed that this protein had no contact toxicity on B. dorsalis, but the injection method could cause a high mortality, and the mortality increased with the increase of time and dose within a certain range. 【Conclusion】The recombinant DmSCBP1 has lethal activity against the B. dorsalis, but its effective usage methods need further improvement.

Characteristics of Organic Carbon Fractions and Carbon Dioxide Emissions of Different Size Aggregates in Rice Field Soils in Response to Long-Term Fertilization

LI XingYu, HUANG Rong, XIAN YiMing, TIAN JiaoJiao, MA XiaoJin, YANG QiaoXi, LI Bing, WANG ChangQuan

Scientia Agricultura Sinica. 2026, 59(6): 1255-1271. doi:10.3864/j.issn.0578-1752.2026.06.009

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【Objective】This study aimed to investigate the dynamic characteristics of organic carbon (OC) and its fractions, carbon dioxide (CO₂) emissions in different particle size aggregates under different fertilization regimes in paddy soil, and to analyze the influencing factors, so as to provide a scientific foundation for enhancing carbon sequestration and CO₂ emission reduction in paddy soils from an aggregate perspective. 【Method】Based on a soil incubation experiment, and using dichromate volumetric method, physical separation method and headspace periodic gas collection-gas chromatography, the OC and its fractions, CO₂ emission characteristics of different particle size aggregates (<0.25 mm, 0.25-1 mm, 1-2 mm) were comparatively analyzed under different fertilization treatments (no fertilization, CK; conventional fertilization, NPK; and 50% substitution for 50% nitrogen fertilizers, HOM). 【Result】 (1) The NPK treatment decreased OC content in 1-2 mm aggregates compared with the CK. In contrast, compared with NPK, the OC content of aggregates treated with HOM treatment increased by 5.8% to 29.4%, respectively. Both fertilization treatments (NPK and HOM) significantly enhanced the content of particulate organic carbon (POC) in 0.25-1 mm and 1-2 mm aggregates, with increases of 37.4%-79.6% and 4.3%-47.8% compared with CK, respectively, and HOM facilitated the turnover of mineral-associated organic carbon (MAOC) from 1-2 mm to <0.25 mm aggregates. (2) There were significant differences in the correlations between POC, MAOC, and OC across various aggregate particle sizes. For <0.25 mm aggregates, both POC and MAOC exhibited significantly positive correlations with OC content. For 0.25-1 mm aggregates, a significant positive correlation existed between MAOC and OC content. For 0.25-1 mm aggregates, a significant positive correlation existed between POC and OC content. (3) During the incubation experiment period, cumulative CO₂ emissions of <0.25 mm aggregates were the lowest, which significantly reduced by 51.0%-83.7% and 23.1%-89.9% compared with 0.25-1 mm and 1-2 mm aggregates, respectively. Compared with NPK, HOM treatment significantly reduced the cumulative CO₂ emissions in <0.25 mm and 0.25-1 mm aggregates by 146.27 and 364.27 g·kg^-1, respectively, which was related to the changes in organic carbon fractions and the increase of aggregate pH and C/N under HOM treatment. 【Conclusion】Different fertilization regimes have altered the OC and its fractions, CO₂ emissions in different particle size aggregates. In detail, organic substitution promoted the accumulation of OC in aggregates, significantly increasing the POC content in 0.25-1 mm and 1-2 mm aggregates. Concurrently, it promoted the transfer of MAOC from 1-2 mm to <0.25 mm aggregates, while significantly reducing the CO₂ emissions in <0.25 mm and 0.25-1 mm aggregated relative to conventional fertilization. Overall, organic substitution for 50% nitrogen fertilizers was beneficial for reducing the CO₂ emissions of <0.25 mm and 0.25-1 mm aggregates in paddy field and enhancing the stability of organic carbon.

Effects of Biochar Application on the Abundance and Community Composition of Nitrogen-Fixing Microbial nifH Gene in Soybean Rotation and Continuous Cropping Systems

LI YongJuan, ZHANG YueTong, WANG YiBo, ZHAO ChangJiang, SONG Jie, CHEN XueLi, YAO Qin

Scientia Agricultura Sinica. 2026, 59(6): 1272-1285. doi:10.3864/j.issn.0578-1752.2026.06.010

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【Objective】This study aimed to analyze the effects of biochar on the community structure and diversity of nitrogen-fixing microorganisms (nifH gene) in soil under continuous cropping and crop rotation, and would provide a theoretical basis for the sustainable improvement of degraded soils in the black soil of Northeast China and the precise application of biochar under different cropping systems. 【Method】 This study collected soil samples under continuous and rotational cropping conditions with biochar application rates of 0 (B0), 5 t·hm^-2 (B5), 15 t·hm^-2 (B15), and 25 t·hm^-2 (B25) at the soybean maturity stage based on a long-term biochar application field experiment. Real-time PCR and Illumina Miseq high-throughput sequencing were used to analyze the absolute abundance and community structure diversity of the nifH gene of nitrogen-fixing microorganisms. 【Result】Biochar application under both continuous cropping and crop rotation increased soil pH, total nitrogen (TN), total phosphorus (TP), alkaline hydrolyzable nitrogen (AN), available phosphorus (AP), and available potassium (AK), but decreased total potassium (TK) content. Biochar significantly affected the absolute abundance of the nifH gene. Under continuous cropping and crop rotation, the nifH gene abundance under the high-dose biochar treatment (B25) increased by 40.3% and 149.6%, respectively, compared with the control (B0). Moreover, the nifH gene abundance under crop rotation was significantly higher than under continuous cropping, regulated by the combined effects of total nutrients (TN, TP, and TK) and available nutrients (AN, AP, and AK). Additionally, moderate biochar application (B15) significantly enhanced the richness and diversity of the nifH gene community under both cropping systems. Redundancy analysis indicated that biochar indirectly drove changes in the nifH gene community structure by altering soil chemical properties. The dominant bacterial class in the nifH gene community composition of nitrogen-fixing microorganisms was Alphaproteobacteria, with Bradyrhizobium being the dominant genus, and its relative abundance increased with the increase of biochar application rates. Under continuous cropping conditions, the Bradyrhizobium genus showed the highest relative abundance under the B15 treatment, while in crop rotation condition, the highest relative abundance occurred under the B25 treatment. However, no significant correlation was found between its abundance and soil physicochemical properties. The second dominant genus, Skermanella, exhibited a highly significant positive correlation with AN and AP contents, and a significant positive correlation with TN content. 【Conclusion】 Biochar optimized the diversity of the nifH gene community in nitrogen-fixing microorganisms by regulating soil nutrient content, improved community structure and composition of the nifH gene, enhanced nutrient use efficiency under continuous cropping and rotation systems, and then finally promoted a virtuous cycle in the soil ecosystem.

Identification of Short Hypocotyl Cucumber Germplasm Under Low Light Stress and QTL Mapping of the Trait

CAO HaiShun, ZHOU DongYuan, WANG Rui, SHI ZhaoWan, WU TingQuan, ZHANG ChangYuan

Scientia Agricultura Sinica. 2026, 59(6): 1286-1301. doi:10.3864/j.issn.0578-1752.2026.06.011

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【Objective】Cucumber is the most widely cultivated greenhouse vegetable in China. However, low light stress frequently occurs during protected cultivation, which often induces excessive stem elongation and spindly growth of cucumber plants. Screening for cucumber germplasm with reduced susceptibility to spindly growth under low light stress and identifying the underlying genes can provide a theoretical basis for genetic improvement of low light tolerance in cucumber. 【Method】Using a low light stress screening system, cucumber germplasm was evaluated. Subsequently, a segregating population was constructed. The Bulked Segregant Analysis sequencing (BSA-seq) method was employed to identify significant loci associated with the target trait. Functional annotation and gene family analysis were then performed to elucidate candidate genes involved in low light stress response. 【Result】Two distinct cucumber materials, designated as long hypocotyl (CS ) and short hypocotyl (CR), were initially identified. Light quality treatment assays indicated that the differential response of hypocotyl between CS and CR was primarily associated with far-red light perception. Using CS and CR as parental lines, F₁ and F₂ populations were developed. Genetic analysis of hypocotyl length under low light stress revealed that the trait was predominantly governed by two novel QTL loci—LSH1 (Chr.4) and LSH2 (Chr.5). Through bulked segregant analysis (BSA), these loci were predicted to encompass 373 and 163 candidate genes, respectively. Subsequently, key components of the far-red light signaling pathway were systematically identified in cucumber, including Phytochrome A (PHYA), FAR-RED ELONGATED HYPOCOTYL 1 (FHY1)/FHY1-LIKE (FHL), and FAR1 RELATED SEQUENCE (FRS) transcription factors. The analysis yielded two PHYA genes (CsPHYA1 and CsPHYA2) on chromosome 6, one CsFHY1 gene on chromosome 3, and 22 CsFRS transcription factor genes distributed across all chromosomes except chromosome 2. Notably, CsFRS12 was physically located within the LSH1 interval on chromosome 4. Phylogenetic and motif analyses indicated that CsFRS12 contained three conserved domains: a FAR1 DNA-binding domain, a MULE transposase domain, and a SWIM Zinc finger domain. CsFRS12 clustered within subfamily Ⅰ and showed closest homology to Arabidopsis AtFRS2 (AT2G32250), AtFAR1 (AT4G15090), and AtFHY3 (AT3G22170), all key regulators of far-red light signaling. Cloning and sequence comparison revealed multiple SNPs between CsFRS12^CR and CsFRS12^CS alleles, which were significantly correlated with hypocotyl length under low light stress. Yeast transcriptional activity assays demonstrated that CsFRS12^C^R possessed significantly lower transcriptional activity than CsFRS12^CS. Expression profiling further indicated that CsFRS12 was highly expressed in the stem and hypocotyl tissues of cucumber. In summary, these findings highlight CsFRS12 as a promising candidate gene underlying low light-induced hypocotyl elongation in cucumber. 【Conclusion】Two cucumber materials with differential responses to low light stress were identified, and two significant loci (LSH1 and LSH2) associated with hypocotyl elongation under low light stress were mapped using BSA-seq. Furthermore, within the LSH1 interval, a key transcription factor CsFRS12, which participates in the far-red light signaling pathway, was found as a critical candidate gene for low light stress response in cucumber.

Evaluation of Curd Texture Quality in Loose-Curd Cauliflower Germplasm

CHEN MinDong, QIU BoYin, HUANG Hao, LI YongPing, WEN QingFang

Scientia Agricultura Sinica. 2026, 59(6): 1302-1316. doi:10.3864/j.issn.0578-1752.2026.06.012

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【Objective】By analyzing the curd texture trait data of loose-curd cauliflower germplasm resources, a unified and objective evaluation method for loose-curd cauliflower curd texture was established. The potential factors affecting curd texture were also studied to provide references for the evaluation of loose-curd cauliflower edible quality and quality breeding. 【Method】Texture Profile Analysis (TPA) and sensory evaluation method were used to evaluate 166 loose-curd cauliflower germplasm resources. Data of 5 TPA indicators (hardness, cohesiveness, springiness, chewiness, resilience) and 3 sensory evaluation indicators (sensory crispness, sensory hardness, sensory chewiness) were obtained. Correlation analysis and linear regression analysis were carried out to construct the relationship model between sensory evaluation indicators and texture parameters. Through principal component analysis, membership function analysis and cluster analysis, a mathematical model for loose-curd cauliflower curd texture evaluation was established, and the texture groups of loose-curd cauliflower germplasm resources were divided. Furthermore, the differences in cell microstructure and cell wall component contents of loose-curd cauliflower curds among different groups were analyzed to explore the potential factors affecting loose-curd cauliflower curd texture. 【Result】Significant differences were observed in eight curd texture indicators among different loose-curd cauliflower germplasms, with chewiness showing the greatest degree of dispersion. Sensory evaluation indicators were positively correlated with TPA indicators to varying extents. By establishing linear regression equations between them, it was found that hardness has important predictive value in sensory texture evaluation. Principal Component Analysis (PCA) extracted two principal components affecting loose-curd cauliflower curd texture, with a cumulative contribution rate of 90.22%. Among them, the first principal component mainly includes hardness, chewiness, and springiness, which are key parameters determining the palatability of loose-curd cauliflower. A mathematical model for evaluating loose-curd cauliflower curd texture was established: Comprehensive texture score C=-2.045+0.017×chewiness+3.108×resilience+0.555×springiness+0.010×hardness+1.950×cohesiveness. Based on the C values, 166 loose-curd cauliflower germplasms were classified into three groups. GroupⅠhad the lowest C values (0.01≤C≤0.35), characterized by low hardness and poor chewiness, and was classified as the soft type; GroupⅡ had moderate C values (0.37≤C≤0.62), with balanced texture and good palatability, and was classified as the crisp-tender type; GroupⅢhad the highest C values (0.65≤C≤1.00), exhibiting high hardness and chewiness, and was classified as the crisp-springy type. Significant differences in cell structure and cell wall components were detected among cauliflower florets of different textures. The crisp-springy type featured florets with high cell roundness, compact structure, and high contents of cellulose and hemicellulose; the crisp-tender type had florets with plump and uniformly structured cells, and an appropriate ratio of cellulose, hemicellulose, and soluble pectin contents; the soft type displayed florets with obvious cell gaps and loose structure, along with a higher soluble pectin content. 【Conclusion】A mathematical model for loose-curd cauliflower curd texture evaluation was established: C=-2.045+0.017×chewiness+3.108×resilience+0.555×springiness+0.010×hardness+1.950×cohesiveness. The C value ranges dividing different loose-curd cauliflower curd texture types can be used for the identification of loose-curd cauliflower germplasm resources. It was also found that cell structure and cell wall components have important effects on the texture quality of loose-curd cauliflower curds.

Extraction Optimization, Structural Characterization, and Anticoagulant Activity of Intestinal Polysaccharides from Yellow-Feathered Chickens

ZHAO QingYao, WANG XiaoMing, XING Tong, LI LingYun, XU XingLian, ZHAO Xue

Scientia Agricultura Sinica. 2026, 59(6): 1317-1332. doi:10.3864/j.issn.0578-1752.2026.06.013

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【Objective】 This study aimed to establish an efficient extraction process for polysaccharides from yellow-feathered chicken intestine (YFCI-P), to analyze the structural characteristics of its key components, and to evaluate their in vitro anticoagulant and antithrombotic activities, thereby providing a theoretical basis for the high-value utilization of chicken intestinal by-products. 【Method】Single-factor experiments combined with Response Surface Methodology (RSM) were used to optimize the enzymatic hydrolysis extraction conditions of YFCI-P; The anticoagulant potency of the enzymatic hydrolysate was determined by the sheep plasma method. The polysaccharide components YFCI-P1 and YFCI-P2 were obtained by separation and purification through gel filtration column chromatography. Activated partial thromboplastin time (APTT), thrombin time (TT), and prothrombin time (PT) levels were assessed to evaluate the anticoagulant activity of the polysaccharides, alongside an assessment of in vitro thrombolytic activity. The molecular weight of YFCI-P1 was determined by High-Performance Gel Permeation Chromatography (GPC/HPLC). Fourier Transform Infrared Spectroscopy (FT-IR) and Nuclear Magnetic Resonance (NMR) techniques were applied to analyze its functional group composition and glycosidic linkage patterns. 【Result】The optimum enzymatic hydrolysis conditions were determined as follows: temperature 55 ℃, enzyme-to-substrate ratio 0.9%, time 3 h, sodium chloride concentration 3%, solid-to-liquid ratio 1:1 (g·mL^-¹), and pH 8.5. Under these conditions, the anticoagulant potency of the enzymatic hydrolysate reached 5.13 U·mL^-1. The predicted value from the response surface model showed good agreement with the experimental value. Two polysaccharide fractions, including YFCI-P1 and YFCI-P2, were obtained through separation and purification by gel filtration chromatography. In vitro anticoagulant activity studies demonstrated that at a concentration of 1 000 μg·mL^-1, YFCI-P significantly prolonged APTT to 485.7 s; YFCI-P1 significantly prolonged PT to 600 s; and YFCI-P2 significantly prolonged TT to 367 s, suggesting their anticoagulant effects via the intrinsic and extrinsic pathways, extrinsic and common pathways, and intrinsic and common pathways, respectively. Molecular characterization revealed that YFCI-P1 had a weight-average molecular weight (Mw) of 10.2 kDa and contained uronic acid, acetyl amino, and sulfate groups. Its backbone consisted of repeating disaccharide units composed of glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc) linked alternately by β-1, 4 and β-1, 3 glycosidic bonds, exhibiting the characteristic features of glycosaminoglycans. Furthermore, YFCI-P, YFCI-P1, and YFCI-P2 promoted tissue plasminogen activator (tPA) generation and demonstrated in vitro thrombolytic activity, with clot dissolution rates of 42.38%, 36.91%, and 19.74% at 1 000 μg·mL^-1, respectively. 【Conclusion】An efficient and stable extraction process for YFCI-P was successfully established, and the optimized parameter combination demonstrated promising potential for industrial application. YFCI-P1 was identified as a polysaccharide exhibiting structural features characteristic of glycosaminoglycans. Moreover, YFCI-P, YFCI-P1, and YFCI-P2 all exhibited significant in vitro anticoagulant and thrombolytic activities.

Effects of Hypoxia on Proliferation of Bovine Renal Cells and Mitochondrial Autophagy

GERIQIMUGE, PUBUZHANDUI, XU Qing, HOU LingLing

Scientia Agricultura Sinica. 2026, 59(6): 1333-1347. doi:10.3864/j.issn.0578-1752.2026.06.014

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【Background】 Hypoxia is a unique environmental stressor that widely influences the physiological functions of multiple systems, including respiratory, circulatory, urinary, and digestive systems, exerting varying degrees of impact at the individual, organ, and cellular levels. Severe hypoxia can cause tissue and organ damage and disease, involving morphological structure, metabolism, proliferation, autophagy, and apoptosis at the cellular level. The kidney, a crucial component of the urinary system essential for maintaining homeostasis, regulating water-electrolyte and acid-base balance, and eliminating metabolic waste, is sensitive to hypoxia. Currently, the effects of hypoxia on bovine kidney cells and their underlying molecular mechanisms remain unclear. 【Objective】 This study employed the Madin-Darby Bovine Kidney (MDBK) cell line as a cellular model to investigate the effects of varying hypoxic concentrations (11% O₂, 5% O₂, and 1% O₂) and treatment durations (24, 48, and 72 h) on the proliferative capacity, ultrastructure, mitochondrial function, and hypoxic stress response of bovine kidney cells, in order to provide experimental evidence for further exploration of the hypoxic adaptation mechanisms in bovine kidney and a foundation for understanding cellular survival strategies and the regulatory mechanisms of mitophagy under hypoxic conditions. 【Method】 Different cells and organelles experience distinct oxygen partial pressures. Under normoxic conditions, atmospheric oxygen partial pressure was 159.22 mmHg (20.95%), arterial oxygen partial pressure was 100 mmHg (13%), venous oxygen partial pressure (PaO₂) was 40 mmHg (5.2%), and mitochondrial oxygen partial pressure ranges from 4-20 mmHg (0.52%-2.60%). Based on this, 11% O₂, 5% O₂, and 1% O₂ were selected as hypoxic treatment conditions. MDBK cells were seeded in DMEM complete medium supplemented with 10% fetal bovine serum and cultured at 37 ℃ with 5% CO₂ until reaching the logarithmic growth phase. Cells were then transferred to a tri-gas incubator and cultured under 11% O₂, 5% O₂, and 1% O₂ for 24, 48, and 72 h. The effects of hypoxia on bovine kidney cell proliferation were assessed by MTT assay. Ultrastructural changes in MDBK cells under hypoxic conditions were observed by transmission electron microscopy. Mitochondrial membrane potential was measured using the JC-1 fluorescent probe method. Reactive oxygen species (ROS) production was detected by the DCFH-DA fluorescent probe method. The expression of hypoxia-related and autophagy-related genes was analyzed by real-time quantitative PCR and Western blotting. 【Result】 Cell proliferation was significantly inhibited with decreasing oxygen concentration and prolonged treatment time, with more pronounced inhibition at lower oxygen concentrations and longer durations. Hypoxia caused mitochondrial structural damage and functional impairment, manifested as mitochondrial swelling, disorganized or absent cristae, a significant reduction in mitochondrial number, condensation of some mitochondria, and the presence of mitochondria enveloped by membranous structures indicative of mitophagy. Concurrently, mitochondrial membrane potential decreased significantly, but intracellular ROS levels increased markedly. The expression of hypoxia-related genes EPAS1 and PPARα was significantly upregulated, while the expression levels of mitophagy- related genes PINK1, PRKN, BNIP3, and BNIP3L (NIX) were significantly elevated. 【Conclusion】 This study demonstrated that treatment with 5% and 1% oxygen concentrations significantly inhibited the proliferative activity of bovine kidney cells, causing mitochondrial structural damage and dysfunction, decreased mitochondrial membrane potential, and increased ROS production. In response to hypoxic stress, bovine kidney cells activate mitophagy to eliminate dysfunctional mitochondria, thereby alleviating oxidative stress and maintaining intracellular homeostasis.

Whole-Genome Resequencing Reveals the Genetic Mechanisms Underlying Feather Coloration in Jingyuan Chicken

YANG LiJuan, CHEN SiYu, ZHAO Wei, ZHU Ling, GUO Lei, MA LiNa, MA RuiMin, ZHANG Juan

Scientia Agricultura Sinica. 2026, 59(6): 1348-1360. doi:10.3864/j.issn.0578-1752.2026.06.015

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【Background】Feather color is an important morphological and economic trait in poultry breeds, and understanding its genetic mechanisms is of great significance for the conservation and genetic improvement of local chicken genetic resources. The Jingyuan chicken, a distinctive local breed in China, exhibits rich diversity in feather color, providing an ideal model for studying the genetic basis of plumage coloration. Systematically exploring this genetic foundation is crucial for enhancing breeding competitiveness. 【Objective】This study aimed to utilize whole-genome resequencing to identify genetic markers and candidate genes associated with black, hemp, and white feather traits in Jingyuan chickens, thereby providing a theoretical basis for elucidating the molecular mechanisms underlying feather color formation and for molecular breeding. 【Method】A total of 150 healthy 126-day-old Jingyuan hens with different feather colors (black, hemp, and white) were selected from the Jingyuan Chicken National Conservation Farm. Blood samples were collected via wing vein puncture for high-quality genomic DNA extraction, followed by whole-genome resequencing. A multi-strategy cross-validation approach was employed: four independent methods, including genetic differentiation coefficient (Fst) calculation based on sliding windows, nucleotide diversity ratio (θπ ratio) analysis, cross-population composite likelihood ratio (XP-CLR) test, and genome-wide association study (GWAS), were used to systematically screen candidate genes associated with black, hemp, and white feather colors, respectively. Venn diagrams were used to identify key significant candidate genes specific to each feather color by taking the intersection of genes identified by these methods. Furthermore, cross-population comparative analysis was conducted using Fst analysis between different feather color populations to identify significant selection signal regions associated with feather color. Gene annotation and Venn diagram intersections were used to identify core candidate genes shared across feather colors. Finally, GO functional annotation and KEGG pathway enrichment analysis were performed to systematically analyze the biological functions and regulatory networks of the identified candidate genes. 【Result】The study systematically identified several key genes associated with feather color formation in Jingyuan chickens. Black feather traits were significantly associated with the LMO3, RERGL, and RTTN, and hemp feather traits were linked to the CDH19 and SLC25A1, while white feather traits were primarily governed by the IKZF1. Cross-feather color comparative analysis further identified 15 core candidate genes: NLRC5, POT1, IPP, DCUN1D4, XRCC4, PALM2AKAP2, UGCG, GNG10, PRIM2, SSBP2, ZBTB34, DHFR, SLC46A2, SLF1, and SHOC1. This indicated that feather color variation in Jingyuan chickens was regulated by multiple genes. Functional enrichment analysis revealed that these genes were significantly involved in important biological processes, such as the G protein-coupled receptor signaling pathway and transmembrane receptor signal transduction, forming a complex regulatory network for feather color. 【Conclusion】Through integrated multi-omics analysis, this study identified important candidate genes associated with feather color formation in Jingyuan chickens and preliminarily revealed their potential regulatory pathways. The findings not only provided novel molecular clues and technical support for the genetic dissection of feather color traits in Jingyuan chickens, filling some gaps in the research on feather color regulation mechanisms in local chicken breeds, but also offer scientific basis and practical guidance for the precise conservation, targeted breeding, and innovative utilization of genetic resources from local high-quality chicken breeds. Furthermore, this study accumulated key data for research in frontier areas, such as the molecular pathways and genetic regulatory networks of feather pigmentation in poultry, thereby enriching the theoretical system of genetic research on functional traits in livestock and poultry.

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