Scientia Agricultura Sinica

Analysis of Genetic and Breeding Selection Effects of A Major QTL-qSl-2D for Wheat Spike Length

DONG JiZi, CHEN LinQu, GUO HaoRu, ZHANG MengYu, LIU ZhiXiao, HAN Lei, TIAN ZhaoSaShuang, XU NingHao, GUO QingJie, HUANG ZhenJie, YANG AoYu, ZHAO ChunHua, WU YongZhen, SUN Han, QIN Ran, CUI Fa

Scientia Agricultura Sinica. 2023, 56(20): 3917-3930. doi:10.3864/j.issn.0578-1752.2023.20.001

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【Objective】By analyzing the genetic and breeding selection effects of the stable major QTL for spike length in wheat, its genetic effects on yield-related traits were clarified, and the future breeding application potential was evaluated. The results could provide a basis for subsequent gene mining and molecular breeding of wheat. 【Method】A major QTL for spike length, named qSl-2D, was detected in multiple environments using a recombinant inbred lines population derived from the cross of Kenong9204 and Jing411, denoted as KJ-RIL; Two molecular markers closely linked to qSl-2D were developed by using the InDel sites in target interval. The genetic effects of yield-related traits based on KJ-RIL, MY-F₂, NILs and natural mapping populations, were analyzed by combining genotype data of molecular markers or wheat 55K array, respectively. By genotyping the natural mapping population, the breeding selection effect of qSl-2D haplotype was parsed across different wheat regions and different ages. 【Result】QTL mapping results showed that qSl-2D could be detected in 7/10 sets of environmental data, and could explain 4.02%-10.10% of the phenotypic variation. The peak LOD of 5/10 sets of environmental data was positioned at 608.75 Mb. The results of genetic effect analysis showed that the enhancing allele of qSl-2D could significantly increase spike length in the four populations with different genetic backgrounds. In addition, it has positive effects on kernel number per spike and plant height, but has negative effects on thousand kernel weight, kernel weight per spike and yield per plant in most population backgrounds. Further analysis of plant height in KJ-RIL population showed that the enhancing allele had rod lowering effect on all internode lengths except the internode length below spike, which resulted in the insignificant increase in plant height. The results of qSl-2D haplotype analysis showed that the utilization rates of the long-spike haplotype Hap-AA-GG varied greatly in different wheat regions, with the highest utilization rate in the northern winter wheat region, accounting for 24%; while the short-spike haplotype Hap-CC-CC accounted for more than 30% in most wheat regions. Moreover, the utilization rate of qSl-2D long-spike haplotype showed a gradual decrease over time, while that of short-spike haplotype consistently maintained a higher selection trend. 【Conclusion】A stable major QTL-qSl-2D for spike length was identified, the enhancing allele of qSl-2D could significantly increase spike length under different genetic backgrounds, and had certain genetic effects on yield-related traits. The closely linked molecular markers developed in the target region can be used for the genetic improvement of wheat spike length and yield-related traits in wheat.

QTL Analysis for Seeding Traits Related to Low Nitrogen Tolerance in Foxtail Millet

QIN Na, FU SenJie, ZHU CanCan, DAI ShuTao, SONG YingHui, WEI Xin, WANG ChunYi, YE ZhenYan, LI JunXia

Scientia Agricultura Sinica. 2023, 56(20): 3931-3945. doi:10.3864/j.issn.0578-1752.2023.20.002

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【Objective】The analysis of quantitative trait loci (QTL) related to low nitrogen tolerance traits of millet (Setaria italica L.) laid a foundation for fine mapping, cloning and functional research of low nitrogen tolerance genes. At the same time, it also provided technical support for revealing the genetic mechanism of low nitrogen tolerance of millet and breeding low nitrogen tolerance varieties. 【Method】The recombinant inbred line (RIL) population consisting of 120 family lines was used as experimental materials, that was constructed from parents Yugu 28, a low nitrogen tolerant variety, and Qiyehuang, a low nitrogen sensitive variety. The RIL populations were treated with low nitrogen and normal nitrogen at seedling stage, and seven traits were analyzed of hydroponic for 21 days, which inculding seedling length, maximum root length, root dry weight, seedling dry weight, plant dry weight, relative chlorophyll content and plant nitrogen content. At the same time, we used composite interval mapping (CIM) to locate and analyze QTLs for traits related to low nitrogen tolerance, and predicted the candidate genes in the confidence intervals of QTL_S. 【Result】The traits associated with low nitrogen tolerance of RIL populations exhibited continuous distribution with apparent transgressive segregation both under low nitrogen and normal nitrogen levels, which conformed to the typical genetic characteristics of quantitative traits and were suitable for QTL genetic analysis. Correlation analysis showed that seeding length was positively correlated with maximum root length, root dry weight, seeding dry weight, plant dry weight and relative chlorophyll content, and maximum root length was negatively correlated with plant nitrogen content. A total of thirty-four QTLs related to seeding length, maximum root length, root dry weight, seeding dry weight, plant dry weight, relative chlorophyll content and plant nitrogen content were located under low nitrogen and normal nitrogen levels, which distributed on chromosomes from 1 to 9. They explained individually 5.15%-52.42% phenotypic variation. Ten QTLs were simultaneously detected under both two nitrogen levels, eleven and thirteen QTLs were only identified under single low nitrogen and normal nitrogen conditions, respectively. A total of fifteen QTLs were major QTL, and five major QTLs were repeatedly detected under both two nitrogen levels, which including qRDW3, qMRL1.1, qMRL1.2, qSL5 and qSPAD1. Five QTL overlaps were detected with gathering multiple QTLs under two nitrogen levels. Six candidate genes related to nitrogen metabolism were identified from the confidence interval of the five QTL overlaps, suggesting that genes related to nitrogen assimilation, absorption and utilization probably control the expression of these genes. 【Conclusion】Thirty-four QTLs were scattered on sixteen clusters of nine chromosomes. Based on gene annotation, a total of 6 candidate genes related to nitrogen metabolism were screened in foxtail millet, indicating the different traits involved in common genetic mechanisms, and the favorable alleles for low nitrogen tolerance can be polymerized by marker-assisted selection.

Genome-Wide Association Study of Nitrogen Efficiency Related Traits at Seedling Stage in Brassica juncea

ZENG Jian, WANG RuMeng, GONG Pan, YANG Xiao, YIN XiaoQi, LI JiangHe, CHEN ShiLong, YAO Lei, SONG HaiXing, KANG Lei, ZHANG ZhenHua

Scientia Agricultura Sinica. 2023, 56(20): 3946-3959. doi:10.3864/j.issn.0578-1752.2023.20.003

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【Objective】The genome-wide association analysis was performed to identify SNP loci significantly associated with nitrogen use efficiency (NUE) traits in Brassica juncea at seedling stage and to predict the relevant candidate genes, providing a theoretical basis for revealing the molecular mechanism of nitrogen use efficiency in rapeseed and creating nitrogen-efficient germplasm. 【Method】The population of 153 Brassica juncea resources was used as the analysis population. Two treatments, low N and normal N, were established using three replicates for each treatment, and two replicated nutrient culture trials were conducted over a two-year period (2021 and 2022). The relative values of root-shoot ratio and shoot nitrogen concentration (low/normal N) were calculated and utilized as NUE traits for a genome-wide association study (GWAS) aimed at exploring candidate genes for NUE. 【Result】NUE traits of Brassica juncea resources exhibited abundant variation, ranging from 0.21-2.44 with coefficients of variation of 22.92%-26.19%. The GWAS identified 45 significant SNP loci, among which 16 overlapped between the first relative root-shoot ratio (RRSR1) and the second relative root-shoot ratio (RRSR2), accounting for a phenotype variance range of 10.69%-15.39%. Additionally, 29 significant SNP loci were shared between the first relative shoot nitrogen concentration (RSNC1) and the second relative shoot nitrogen concentration (RSNC2), explaining a phenotype variance range of 13.22%-23.96%. 15 candidate genes for NUE were identified within 200 kb upstream and downstream regions of significant SNP loci, including 5 genes related to nitrate transport (BjuNPF5.8, BjuNRT2.7, BjuNPF2.3, BjuCLCb and BjuNRT1.3), 3 genes associated with nitrogen metabolism (BjuASN3, BjuGLU2 and BjuADCS), 4 genes involved in plant growth and development (BjuCOBL8, BjuPYL6, BjuSAUR72 and BjuUP3) and 3 genes participated in stress response (BjuNTP7, BjuJUB1 and BjuPYL6). 【Conclusion】45 SNP loci were detected significantly associated with NUE traits and 15 candidate genes for NUE were identified in this study.

Investigation on Outcrossing Seed-Setting Characteristics of Machine- Transplanted Hybrid Rice Seed Production

HUANG BangChao, TAO YouFeng, QIN Qin, LI Hui, ZHOU ZhongLin, GUO JinYue, DENG TianTian, LEI XiaoLong, SUN BoTeng, ZHOU GaoZi, JIA YuanLi, REN WanJun

Scientia Agricultura Sinica. 2023, 56(20): 3960-3974. doi:10.3864/j.issn.0578-1752.2023.20.004

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【Objective】The objective of this research is to clarify the panicle seeding characteristics of sterile lines in machine- transplanted seed production and explore the reasons for the lower seed yield of hybrid rice in mechanized seed production mode. 【Method】Two combinations of Chenghui 727×Shu 21A and Yahui 2115×Yixiang 1A were selected as the materials, and the field experiment was conducted in Chongzhou from 2020 to 2021. Two methods of machine and hand-transplanted were utilized. During the heading to flowering stage, the state of flower synchronization was judged by the heading condition of restorer line and sterile line, and panicle seeding condition of sterile line was investigated at maturity stage. Statistical analysis of seeding characteristics of sterile line in different rows, panicle positions and different branches under two transplanting methods. 【Result】 (1) Under the condition of flower synchronization, the hand-transplanted restorer line and sterile line had a complete coincidence of flowering period with a flower synchronization index of 100%. On the other hand, the machine-transplanted restorer lines and sterile line had a flowering deviation of 3-4 days and 6-8 days, respectively, resulting in poor flower synchronization with a flower synchronization index of 33.33%-55.56%. (2) The overall setting rate was lower in the machine-transplanted group compared to the hand-transplanted group, with a 33.45% reduction in the setting rate of machine-transplanted. (3) The setting rate of panicles in rows 1-6 of sterile line showed a gradual decrease trend, and a higher setting rate was observed in the flower synchronization treatment in the same line. (4) The upper part panicles of the sterile line had a good pollination posture with a small shielding effect on the pollen. Under normal pollination conditions, the panicle setting rate of sterile line was significantly shown as upper> middle > lower part, while the empty grain rate was lower> middle > upper part. (5) The setting rate of primary branches of sterile line was significantly higher than that of secondary branches under different transplanting methods. The machine-transplanted treatment further reduced the setting rate of primary and secondary branches of sterile line. The primary and secondary branch ustilagomaydis grains of sterile line showed no significant difference under the machine-transplanted treatment, whereas the secondary branch ustilagomaydis grains were significantly higher than the primary branches under the hand-transplanted treatment. (6) The flower synchronization of the restorer line and sterile line was poor under the machine-transplanted treatment, resulting in lower actual seed production yield than the hand-transplanted group. The seed production yield decreased by 39.34% and 41.48% in two years. 【Conclusion】The flowering deviation of the sterile line was found to be 3-4 days longer than that of the restorer line, which resulted in poor flower synchronization. This is the primary reason for the lower setting rate of machine-transplanted compared to hand-transplanted. Additionally, the low setting rate of sterile line in the middle and lower parts of the panicle, as well as those further away from the restorer line, further contributes to the low overall setting rate in machine-transplanted. However, the effects of blighted and infected grains on the setting rate and yield were found to be relatively small. To improve the setting rate of hybrid rice in machine-transplanted seed production mode, we suggest the following measures. Arrange the sowing of machine-transplanted parents at different intervals during the full flowering stage to improve the degree of flower synchronization. Standardize the pollination operation to improve the effectiveness of pollination. Strengthen field management to reduce the occurrence of blighted and infected grains. By implementing these measures, we can improve the yield of hybrid rice in machine-transplanted seed production mode.

Effects of Nitrogen Application on Delayed Harvest Summer Maize Grain Yield, Superior and Inferior Grains Morphology and Weight Under Different Rainfall Years

LIU Meng, ZHANG Yao, GE JunZhu, YANG YongAn, WU XiDong, HOU HaiPeng

Scientia Agricultura Sinica. 2023, 56(20): 3975-3995. doi:10.3864/j.issn.0578-1752.2023.20.005

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【Objective】The North China Plain is the thermal resource limited area, summer maize grain mechanical harvesting technology were astricted by higher grain moisture content at harvest stage, which affects the quality of mechanical grain harvest. Under delayed harvest conditions, nitrogen application rate affect summer maize grain yield, and superior and inferior grains morphology and weight are not clear. Through the systematic observation of summer maize superior and inferior grains morphology, filling and dehydration process under different nitrogen application levels, clarified the regulation effect of nitrogen, and which provided support for summer maize grain mechanical harvesting technology cultivation to obtain stabilize yield, reduce nitrogen application and improve efficiency in the of region. 【Method】Summer maize grain mechanical harvesting hybrid Jingnongke 728 was used as the research materials, the field experiment were conducted in 2020-2021 by a harvest time and nitrogen application rate two-factor randomized block design, harvest time were normal harvest time (NH) and delayed harvest (DH), and six nitrogen application rate were 0 (N₀), 120 (N₁₂₀, 2021), 180 (N₁₈₀), 240 (N₂₄₀), 300 (N₃₀₀), 360 (N₃₆₀) and 450 kg hm^-2 (N₄₅₀, 2020). Summer maize grain yield (GY), superior and inferior grains fresh volume (GFV), fresh weight (GFW), dry weight (GDW), and moisture content (GMC) and their change rates were measured. 【Result】Compared to the dry year (2020), the inferior grains maximum grain filling rate (G_max), the increment at G_max (W_max) and initial potential (R₀) of GFV, GFW and GDW were significantly reduced in the rainy year (2021), and the days reached G_max (T_max) were delayed, and the active duration (P) were prolonged, which resulted in GFV, GFW and GDW reduced significantly by 15.4%-50.6%, 25.4%-62.0% and 31.2%-57.3%, respectively, however, there were no significant change in superior grains, and so led GY declined significantly by 3.03×10³-5.44×10³ kg·hm^-2. The inferior grains GDW_Gmax, GDW_Wmax and GDW_R0 in the rainy year were significantly decreased by 55.1%-258.1%, 13.4%-143.0% and 12.0%-126.6%, respectively, and GDW_Tmax were delayed by 4.2-20.7 d compared to superior grains. The superior grains GFV, GFW and GDW were significantly increased by 56.8%-69.6%, 67.0%-80.4% and 54.1%-92.1%, respectively, than inferior grains. Compared with NH, the grains G_max and R₀ at DH treatments were increased, and the P for superior and inferior grains were significantly prolonged, which led the GFV, GFW decreased significantly by 2.1%-8.1% and 12.2%-17.1%, 4.0%-5.2% and 15.7%-19.5, respectively, under the dry year and rainy year, meanwhile GDW increased from 25.1-28.2 g/100 grains to 28.0-34.4 g/100 grains, the GMC decreased from 22.6%-26.0% to 22.6%-26.0% as well, which were declined by 31.3%-40.4% than NH. The GY for DH were increased 0.02×10³-1.67×10³ kg·hm^-2 than NH. There was no significant difference in GFV, GFW and GDW between nitrogen application levels in dry year. While in the rainy year, the GDW_Gmax and GDW_Wmax for N₂₄₀-N₃₆₀ treatment were significantly higher than N₁₈₀, GDW_Tmax were delayed, and GDW_P was prolonged (P<0.05), and the effects were more intense on inferior grains than on superior grains. Under DH treatment, the GFV, GFW and GDW of inferior grains for N₂₄₀-N₃₆₀ were significantly increased by 25.7%-85.3%, 59.4%-83.6% and 17.9%-43.9% than N₁₈₀, respectively. The nitrogen yield increasing effect in rainy year were significantly intense than dry year, as 74.4%-169.5% vs. 51.5%-99.1%. GY of N₂₄₀ was significantly rised by 12.6%-54.5% than N₁₂₀-N₁₈₀. 【Conclusion】In the thermal resource limited area of the North China Plain, changed winter wheat into spring wheat in the wheat-maize cropping system, with summer maize delayed harvest for 23-33 days, the inferior grains capacity and weight were significantly increased, and so the grain moisture content were reduced to the grain mechanical harvesting technology standard to realized the annual grain mechanical harvesting. And by optimized nitrogen application rate at 247.2-248.6 kg·hm^-2, the production strategy of stable yield at 7.0×10³-12.0×10³ kg·hm^-2, nitrogen reduction and improve efficiency under different rainfall years were achieved in the region.

Spatial Differences and Driving Factors of Aboveground Nitrogen Uptake in Per Hundred Kilograms Grain of Maize in China

WANG DanDan, CHEN HuanXuan, ZHANG Chong, JU XiaoTang

Scientia Agricultura Sinica. 2023, 56(20): 3996-4009. doi:10.3864/j.issn.0578-1752.2023.20.006

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【Objective】 We aim to quantify aboveground nitrogen (N) uptake in per hundred kilograms grain (N₁₀₀) of maize in different agro-ecological zones at different yield levels in China, and analyze the effects of climate, soil, variety and N fertilization on N₁₀₀ of maize, thus to provide a scientific basis for determining rational N fertilizer rate. 【Method】 We divided Chinese cropland into six major regions, i.e., northeast, northwest, North China Plain, middle and lower Yangtze River, southwest, and southeast, and collected 349 peer-reviewed papers published during 1980-2022 to analyze the spatial variation of N₁₀₀ and its changes at different yield levels, and compared the differences in calculated theoretical N rate between constant and region-specific N₁₀₀. The effects of climate, soil and fertilization on N₁₀₀ were analyzed using Pearson correlation coefficient, Random forest model and Meta-analysis, to reveal the causes of spatial variation in N₁₀₀. 【Result】 Under the optimized N management, N₁₀₀ of spring maize was significantly lower than that of summer maize which were 2.21 and 2.46, respectively; and there were significant differences in N₁₀₀ of maize among different agro-ecological zones, which were 2.19 (Northeast spring maize), 2.12 (Northwest spring maize), 2.54 (Northwest summer maize), 2.45 (North China Plain summer maize), 2.77 (Middle and Lower Yangtze River spring maize), 2.38 (Middle and Lower Yangtze River summer maize), and 2.39 (Southwestern maize zone), respectively. The difference between calculated the theoretical N rate based on the national average N₁₀₀ (2.34) and that based on regional-specific N₁₀₀ was -22-31 kg N·hm^-2. Aboveground N uptake, yield, and mean annual temperature were the most important factors affecting N₁₀₀. The N₁₀₀ showed a significant quadratic decrease with increasing yield (P<0.01), and grain yield was a good predictor of N₁₀₀. Varieties significantly affected maize N₁₀₀, the N₁₀₀ of common Chinese maize varieties Zhengdan 958, Xianyu 335, and Denghai 605 are 2.42, 2.12, and 2.39, respectively. New varieties had a significant lower N₁₀₀ than old varieties. The application of N fertilizer significantly increased the N₁₀₀ of maize, and the greatest increase effect of N₁₀₀ caused by N fertilizer application was observed at 200-300 kg N·hm^-2. Once application of slow and controlled release fertilizer, deep placement, reduction of the ratio of basal N fertilization and increasing the frequency of N fertilizer application all significantly increased N₁₀₀. 【Conclusion】 When calculate the rational N fertilization, we need to considerate the regional differences of N₁₀₀, thus to obtain accurate fertilizer N rate, and the N₁₀₀ of maize is mainly driven by variation in aboveground N uptake, yield and mean annual temperature.

Complete Genomic Sequence Characteristics and Establishment of qPCR Detection Technique of Sweet Potato Virus E in China

TANG Wei, ZHANG ChengLing, YANG DongJing, MA JuKui, CHEN JingWei, GAO FangYuan, XIE YiPing, SUN HouJun

Scientia Agricultura Sinica. 2023, 56(20): 4010-4020. doi:10.3864/j.issn.0578-1752.2023.20.007

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【Objective】Sweet potato virus E (SPVE) is a novel virus infecting Ipomoea batatas. The objectives of this study are to determine the complete genomic sequence of SPVE Xuzhou isolate (SPVE-XZ) in China, analyze the genomic sequence characteristics of SPVE-XZ, and develop the quantitative PCR (qPCR) assay for the specific detection of SPVE. This study will provide theoretical basis and technical support for the detection, monitoring and controlling SPVE in China. 【Method】The complete genomic sequence of SPVE-XZ was obtained by using small RNA deep sequencing, combined with RT-PCR and RACE technologies. The sequence alignment and phylogenetic relationship analysis of SPVE-XZ were performed by using software MegAlign and MEGA11. The primers of qPCR for rapid detection of SPVE were designed, and the qPCR detection method for SPVE was established by optimizing the annealing temperature and primer concentration. The specificity and sensitivity of the qPCR were determined. The developed qPCR technology was used to detect sweet potato samples collected from Jiangsu Province and Shandong Province. 【Result】The complete genomic sequence of SPVE-XZ was 10 919 nt, excluding the 3′-terminal poly (A) tail, containing the typical open reading frame of 10 560 nt in length and encoding a putative large polyprotein of 3 519 amino acids. The 5′UTR and 3′UTR of SPVE-XZ were 129 and 230 nt, respectively. PISPO and PIPO were produced with the frameshift in P1 and P3, respectively. Genomic sequence analysis showed that the genomic nucleotide sequence identity between SPVE-XZ and Korean SPVE-GS isolate was 98.6%, and the amino acid sequence identity of polyprotein between them was 98.5%. Phylogenetic trees were constructed based on the coat protein gene sequences and polyprotein amino acid sequence using the neighbor-joining method. The result showed that SPVE-XZ was clustered with SPVE-GS in these phylogenetic analyses. The established qPCR method could detect SPVE specifically, however sweet potato virus 2 (SPV2), sweet potato virus C (SPVC), sweet potato virus G (SPVG), sweet potato feathery mottle virus (SPFMV), sweet potato chlorotic stunt virus (SPCSV), sweet potato latent virus (SPLV), sweet potato chlorotic fleck virus (SPCFV), cucumber mosaic virus (CMV) could not be detected in this qPCR system. The lowest sensitivity of the qPCR was 3.12×10²copies/μL and it was 100 times that of conventional RT-PCR. SPVE was detected in 1 sample of 6 samples collected from Shandong Province and 13 samples of 52 samples collected from Jiangsu Province by using the established qPCR detection method. 【Conclusion】The complete genome sequence of SPVE-XZ is 10 919 nt. The genome structure of SPVE-XZ is consistent with SPVE-GS reported in Korean. The established qPCR detection system for SPVE is specific and highly sensitive, which can be used for the rapid detection of SPVE.

Genome-Wide Identification of AP2/ERF Gene Family in Alternanthera philoxeroides and Its Expression Patterns Under Herbicide Stresses

HAN XiaoWen, HAN Shuo, HU YiFeng, WANG MengRu, CHEN ZhongYi, ZHU YongXing, YIN JunLiang

Scientia Agricultura Sinica. 2023, 56(20): 4021-4034. doi:10.3864/j.issn.0578-1752.2023.20.008

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【Background】Alternanthera philoxeroides is a malignant invasive weed that is extremely difficult to control, causing serious harm to ecology and environment in China. The AP2/ERF (APETALA2/ethylene responsive factor) family is one of the largest transcription factor families in plants, which not only participates in the regulation of various signal networks in plants, but also plays an important role in plant response to herbicides. 【Objective】The objective of this study is to systematically analyze the basic characteristics of ApAP2/ERF, reveal its expression patterns under herbicide stress, decipher the biological functions of ApAP2/ERF in response to herbicide stress, identify potential target genes for herbicide resistance, and to provide a theoretical basis for accurate and reasonable selection of herbicides. 【Method】The AP2/ERF family members were identified from A. philoxeroides genome database using local BLASTp. MEME, ExPASyServer10, Plant-mPLoc, SWISS-MODEL, NCBI SRA database, and psRNA Target online website were used to obtain conserved motif, protein physicochemical property, subcellular localization, tertiary structure, transcriptome, and targeted miRNA information. Gene structure information was obtained from the GFF3 genome annotation file. Phylogenetic tree, expression pattern heatmap, and miRNA target relationship network were constructed using MEGA 11, TBtools, and R software. The expression patterns of AP2/ERF family members in response to five herbicides and at different time points (0-7 d) were analyzed using RT-qPCR. 【Result】A total of 96 ApERF, 9 ApAP2, and 4 ApRAV genes were identified from A. philoxeroides, and they were named ApERF1 to ApERF96, ApAP2-1 to ApAP2-9, and ApRAV1 to ApRAV4, respectively. The identified ApAP2/ERF proteins are hydrophilic. Subcellular localization prediction revealed that the ApAP2/ERFs are located in the nucleus and cytoplasm. The expression patterns of ApAP2/ERFs were regulated by geographical condition, water condition, and low potassium stress. Under 41% glyphosate treatment, ApERF7/74/94 were highly induced within 3-7 days; under 50% isoproturon treatment, all six ApERFs were highly induced at a specific time; under 10% fluoroglycofen treatment, the expression levels of ApERF7/13/49/94 showed a trend of first increasing, then decreasing, and then increasing; under 20% fluroxypyr treatment, ApERF7/13/49/54/94 were highly induced at 0.5 d; under 13% oxadiazon treatment, ApERF13/49/54/74 were significantly downregulated in expression in a short period of time. 【Conclusion】109 ApAP2/ERF family members were identified, and members located in the same group have similar motifs. The expression of ApAP2/ERFs is regulated by geographical condition, water condition, and low potassium stress, and is also induced by herbicides, suggesting that it responds to herbicide stress by influencing the ethylene signaling pathway.

Effects of Long-Term Straw Return and Nitrogen Application Rate on Organic Carbon Storage, Components and Aggregates in Cultivated Layers

GUO RongBo, LI GuoDong, PAN MengYu, ZHENG XianFeng, WANG ZhaoHui, HE Gang

Scientia Agricultura Sinica. 2023, 56(20): 4035-4048. doi:10.3864/j.issn.0578-1752.2023.20.009

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【Objective】The results of carbon sequestration studies on combining straw returning with nitrogen fertilizer are controversial. Aimed at such problem, this experiment was carried out to reveal the effects of combining straw returning with nitrogen fertilizer on Carbon sequestration capacity and mechanism of farmland, so as to provide a reference for the future research. 【Method】Based on 11 years of long-term positioning experiments, this paper adopted split-zone design, the main treatment included straw returning to soil and removal straw from field, and the subplots included three N application rate, which were no nitrogen (N0), 168 kg·hm^-2 (N168, nitrogen), and 336 kg·hm^-2 (N336, excessive nitrogen application). 【Result】Compared with wheat without nitrogen fertilizer, wheat yield increased by 14.4%-19.5% with nitrogen fertilizer. The effect of straw returning to the field on yield was not significant. Straw returning significantly increased the cumulative input of soil carbon by 70.8% (P<0.05), but had no significant effect on soil organic carbon storage. Compared N0, the nitrogen application significantly increased soil carbon accumulation input and soil organic carbon storage by 7.7%-8.5% (P<0.05) and 4.7%-8.1% (P<0.05), respectively. The application of nitrogen fertilizer significantly increased the carbon fixation rate by 32.7%-56.1% (P<0.05), and N336 significantly increased the soil carbon fixation efficiency by 51.8% (P<0.05); straw returning to the field did not significantly improve the soil carbon fixation rate, but significantly reduced the carbon fixation efficiency by 30.9% (P<0.05). Both nitrogen application and straw returning could improve soil carbon pool capacity, and N0 and N168 have reached carbon saturation. The content of soluble organic carbon (DOC), microbial biomass carbon (MBC) and easily oxidized organic carbon (EO) in the soil increased by 4.6%, 11.2% and 4.5% respectively after returning straw to the field. Compared N0, DOC under N168 and N336 increased by 14.12% and 29.54% respectively; MBC decreased by 14.0% and 28.0% on average, respectively; EO increased by 8.2% and 11.5%, respectively. Straw returning to the field was beneficial to the improvement of soil DOC/SOC and microbial entropy. Applying nitrogen fertilizer was beneficial to the increase of DOC/SOC, but reduced the microbial entropy. Both straw returning and nitrogen fertilizer application had no effect on soil EO/SOC. Both straw returning and nitrogen application were beneficial to the improvement of macroaggregates (>0.25 mm), and straw returning significantly increased the organic carbon content of macroaggregates by 5.2%. The average weight diameter (MWD) and geometric average diameter (GMD) of aggregates under non-return showed a trend of first increasing and then decreasing with the increase of nitrogen level, while under straw returning, it showed an increase with the increase of nitrogen level. Straw returning increased the MWD and GMD of aggregates by 8.8% and 7.5% respectively, and the application of nitrogen fertilizer increased the MWD and GMD by 14.1%-22.7% and 16.8%-23.4% respectively, compared with CK. Both straw returning and nitrogen application could improve the distribution of organic carbon in large aggregates. 【Conclusion】Straw returning with nitrogen fertilizer could increase carbon input, increase activated organic carbon content, reduce microbial activity, and improve the protection of organic carbon by aggregates.

Spatial-Temporal Evolution, Decoupling Effect and Performance Evaluation of China’s Agricultural Carbon Emissions

MENG QingLei, YIN YuXiang, WANG YuHao

Scientia Agricultura Sinica. 2023, 56(20): 4049-4066. doi:10.3864/j.issn.0578-1752.2023.20.010

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【Objective】The temporal characteristics, spatial pattern, evolution mode, decoupling relationship and performance evaluation of China’s agricultural carbon emissions were analyzed scientifically, so as to provide a basis for helping China achieve the goal of “carbon peaking and carbon neutrality” and strengthen the construction of an agricultural power. 【Method】This study constructed an index system for assessing agricultural carbon emissions and agricultural carbon emission performance in China, and measured the systematic measurement index of agricultural carbon emissions in Chinese provinces from 2007 to 2020. The Kernel density estimation and standardized ellipsoidal visualization analysis were used to analyze the regional distribution characteristics and spatial-temporal evolution trends of agricultural carbon emissions, Tapio model was used to examine the decoupling relationship between examining agricultural carbon emissions and economic growth, and the super-efficient SBM model with non-expected output was constructed to report the agricultural carbon emission performance and decomposition efficiency of China and the seven economic regions. 【Result】 From 2007 to 2020, the overall agricultural carbon emissions in China showed an “inverted U-shaped” curve of rising and then declining, with obvious regional differences and stable distribution of ranks. The eastern region had the best emission reduction effect, the central region had a “bipolar” distribution, and the western region had a higher pressure of emission reduction, with the overall spatial pattern dominated by the northeast-southwest direction, and tended to be decentralized to the northeast and northwest. China’s agricultural carbon emissions and agricultural economic development have been maintained at a weakly decoupled level and have made a breakthrough to a strongly decoupled level, which could be divided into two stages: a stable period (2007-2016) and a breakthrough period (2017-2020). The assessment of agricultural carbon emission performance showed a trend of “rapid rise - slow decline - steady improvement”, with the Great Northwest Economic Zone and the Northern Coastal Economic Zone in the first and last positions, respectively, and the contribution of technological change in agricultural production (TC) was more prominent than that of technical efficiency change (EC). 【Conclusion】With 2017 as the inflection point, China’s agricultural carbon emissions as a whole showed a decreasing trend, and the agricultural economic development as a whole was gradually getting rid of the dependence on agricultural carbon emissions, with different agricultural bases and different emission reduction targets in each region and province. It was necessary to reasonably plan the scale and internal structure of agricultural comparative advantage industries according to local conditions, reasonably select the resource endowment production characteristics of industries in the region. At the same time, we should pay attention to technology iteration and updating in the agricultural economic development and energy conservation and emission reduction in the role of promoting, taking into account the regional ecological benefits and economic benefits.

The Conception of Eco-Circular Agriculture of "Rice-Potato-Pig"

FAN ZiYao, LI Kui, LI JiaYang, HUANG SanWen

Scientia Agricultura Sinica. 2023, 56(20): 4067-4071. doi:10.3864/j.issn.0578-1752.2023.20.011

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Empowered by breakthroughs in hybrid potato breeding technology and the well-established molecular design breeding in rice cultivation, we propose a new eco-circular agricultural model, referred to as "rice-potato-pig (RPP)". This model involves planting rice in spring and summer, growing potatoes in winter, and using potatoes and bran as feed for pigs, while simultaneously utilizing pig manure and urine to fertilize the fields. RPP has the potential to alleviate the pressure of China's feed imports and address issues such as low efficiency, resource wastage, and environmental harm caused by the gap between planting and feeding. In this paper, we analyze the feasibility of the RPP model, which utilizes winter fields for potato cultivation to produce animal protein. We also discuss the operational characteristics and implementation of this model. Based on the design principles of agricultural system engineering, the entire RPP system is divided into four sub-systems, including field planting management, potato storage, pig feeding with potatoes, and manure and urine treatment followed by returning nutrients to the fields. Through stepwise optimization, integration, and modeling of these sub-systems, we explore the practical implementation of the eco-circular agricultural model of RPP according to local conditions and moderate scale in southern China.

Functional Identification of Peach Gene PpSAUR73

YANG Li, CAO HongBo, ZHANG XueYing, ZHAI HanHan, LI XinMiao, PENG JiaWei, TIAN Yi, CHEN HaiJiang

Scientia Agricultura Sinica. 2023, 56(20): 4072-4086. doi:10.3864/j.issn.0578-1752.2023.20.012

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【Objective】 The object of this study was to isolate a peach potential-related gene PpSAUR73, to analyze its expression response to hormones, and to identify its role in regulating seedling growth in transgenic Arabidopsis, so as to provide the molecular basis for the regulation of tree potential. 【Method】 Using Zhongyou Pan 9 as the material for hormone treatment, the real-time fluorescence quantitative analysis was used to analyze the dynamic response of PpSAUR73 within 24 hours. PpSAUR73 was cloned from the peach variety Jiuyan. PpSAUR73 overexpression vector was constructed and transformed into Arabidopsis. Phenotypic observation of genetical modified Arabidopsis was carried out, and the germination rate statistics of both genetically modified and wild-type Arabidopsis sown simultaneously were performed too. The root length and hypocotyl of 7-day growing Arabidopsis with consistent germination were measured, and Arabidopsis with consistent germination was treated with different concentration hormone. Transcriptome sequencing was performed using 7-day-old seedlings, and the differentially expressed genes were analyzed by functional analysis, KEGG pathway enrichment analysis, and regulatory genes analysis, respectively. 【Result】 PpSAUR73 could respond quickly to hormone treatments. The overexpression of PpSAUR73 could affect the germination of Arabidopsis seeds. The hypocotyl and root length of seedlings were longer than those of wild type. In addition, the rosette of transgenic Arabidopsis was larger, and the overall growth potential was larger than wild type. The transgenic Arabidopsis showed decreased sensitivity to auxin. The transcriptome analysis of overexpressing PpSAUR73 showed that there were 128 differentially expressed genes in both control groups, including 84 up-regulated genes and 44 down-regulated genes, and 20 differentially expressed genes were described. The GO function significant enrichment analysis of the differentially expressed genes generated by overexpression of PpSAUR73 showed that the differentially expressed genes were the most abundant in cell components, located in cytoplasm, cell membrane, organelle and extracellular regions. KEGG pathway enrichment analysis on differentially expressed genes were conducted, and the results showed that the differentially expressed genes in pairwise comparisons CK vs SAUR73-1 and CK vs SAUR73-14 were mainly enriched in phenylalanine biosynthesis pathway, plant hormone signal transduction pathway, starch sucrose metabolic pathway and other metabolic pathways. In the phenylalanine biosynthesis pathway, PpSAUR73 could regulate the upregulation of peroxidase encoding genes AT1G05260, AT3G01190, AT3G32980 and AT5G15180. Peroxidases were associated with lignin synthesis, and lignin content was significantly correlated with plant growth, suggesting that overexpression of PpSAUR73 might be involved in regulating lignin synthesis in Arabidopsis and thus growth. In plant hormone signal transduction pathway, the expression of some auxin responsive genes of AtSAUR41, AtSAUR71, AtSAUR51, AtSAUR72 and AtSAUR1 in auxin signal transduction pathway was down-regulated, the expression of phosphatase protein AtPP2CA in abscisic acid signal transduction pathway was up-regulated, and the expression of abscisic acid signal pathway gene AtPYL5 was down-regulated. PpSAUR73 could regulate the growth of Arabidopsis and participate in multiple hormone signal transduction pathways. 【Conclusion】 This study found that PpSAUR73 could quickly respond to hormones and regulate the growth in transgenic Arabidopsis. The differentially expressed genes caused by overexpressed genes caused by overexpression of PpSAUR73 were mainly enriched in metabolic pathways, such as phenylalanine biosynthesis pathway, plant hormone signaling pathway, and starch sucrose metabolism pathway. PpSAUR73 also played an important role in IAA and ABA signal transduction pathways, it was speculated that it played an important role in the growth and development of peach trees.

A Transcriptome Analysis Identifies Candidate Genes Related to Fruit Cracking in Pomelo Fruits

LU YanQing, LIN YanJin, WANG XianDa, LU XinKun

Scientia Agricultura Sinica. 2023, 56(20): 4087-4101. doi:10.3864/j.issn.0578-1752.2023.20.013

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【Objective】Fruit cracking is a universal physiological disorder that occurs during growth in citrus fruits. However, the molecular mechanisms that regulate cracking in citrus fruits remain unclear. The aim of this study was to screen genes that were related to resistance to fruit cracking. 【Method】 Normal fruits from a pomelo (Citrus grandis (L). Osbeck) cultivar (Duxin 1) resistant to cracking, as well as normal and cracked fruits from Duwei, a cultivar sensitive to cracking, were collected on August 3, 2021 and August 20, 2021, respectively. The pericarp surrounding blossom ends of the fruits (the blossom end was considered the center, approximate 30 millimeters radius) were sampled for RNA-seq. 【Result】 The differentially expressed genes (DEGs) in each stage were screened based on the comparisons of a transcriptome between cracked fruits from the cracking-sensitive cultivar and normal fruits from both cultivars. In the stage A, 1 660 DEGs were obtained, and 104 DEGs were common between the comparison. A total of 1 972 DEGs were screened in stage B, and 82 were common in the comparison. All the DEGs screened at both stages were used for a Gene Ontology enrichment analysis. In the classification of biological process, the major common sub-classifications, including ‘metabolic process’, ‘cellular process’, ‘single-organism process’, ‘biological regulation’, ‘response to stimulus’, and ‘signaling’ were identified in both stages. All the screened DEGs were also analyzed using Kyoto Encyclopedia of Genes and Genomes enrichment. Many genes were enriched in several metabolic pathways, including ‘carbon metabolism’, ‘MAPK signaling pathway-plant’, ‘plant hormone signal transduction’ and ‘protein processing in endoplasmic reticulum’. In addition, these pathways were identified in both stages. Several genes related to resistance to fruit cracking were identified in this study. The levels of transcription of Expansin-A1 were significantly higher in the pericarp of normal fruits from the two cultivars than that in the pericarp of cracked fruits from the sensitive cultivar. Calcineurin B-like protein gene was highly expressed in the pericarp of normal fruits from both cultivars when compared with the pericarp of cracked fruits from the sensitive cultivar. However, this difference disappeared at the stage B. The genes for heat stress transcription factor, serine/threonine-protein kinase, auxin-responsive protein, and dehydration-responsive element-binding protein were upregulated in the pericarp of cracked fruits from the sensitive cultivar compared with the pericarp of normal fruits from the two cultivars in both stages. 【Conclusion】These findings suggested that the genes related to strength of pericarp, water movement, and responsing to high temperature and water deficiency stresses were critical to regulating resistance to fruit cracking.

Effects of Oat Bran Flour and Tartary Buckwheat Bran Flour on Structure, Cooking Quality and Digestive Characteristics of Wheat Noodles

PENG Pai, WANG XiaoLong, MA Lan, ZOU XiaoYang, MA QianYing, ZHANG XinYu, LI XiaoPing, HU XinZhong

Scientia Agricultura Sinica. 2023, 56(20): 4102-4114. doi:10.3864/j.issn.0578-1752.2023.20.014

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【Objective】 This study aimed to explore the effects of oat bran flour and Tartary buckwheat bran flour addition on the structure, quality and digestive characteristics of wheat noodles, so as to confirm their application values in the production of wheat-based food products. 【Method】 Three types of noodles were prepared with three recombinant flours containing 30% oat bran flour + 70% wheat flour, 30% Tartary buckwheat bran flour + 70% wheat flour, and 15% oat bran flour + 15% Tartary buckwheat bran flour + 70% wheat flour, respectively, with pure wheat noodle as control. The cooking quality, sensory quality and digestive characteristics of different noodles were determined and compared firstly. Then the structural characteristics of protein and starch in noodles were analyzed and compared by Fourier infrared spectrometer, X-ray diffractometer, Size-exclusion high performance liquid chromatography, Scanning electron microscope and Laser confocal scanning microscope, respectively. 【Result】 The introduction of oat bran flour and Tartary buckwheat bran flour weakened the cooking and sensory quality of noodles, but improved the starch digestion resistance of noodles. The noodle containing 30% oat bran flour showed the lowest glycemic index (GI) of 47.9 among all the noodles. Protein denaturation and reconstruction during noodle cooking facilitated the binding between protein and other molecules higher proportion α-helix and lower proportion β-sheets was found in the protein of cooked oat bran noodles, which led to the transformation of protein aggregates into a loose and extended protein network that enforced the wrapping effect of protein to starch. After cooking, the starch crystal in noodles was destroyed, leading to the reduced orderliness. The addition of oat bran flour and buckwheat bran flour promoted the starch-lipid interactions in noodles, which contributed to the formation of resistant starch. Compared with buckwheat bran four, oat bran flour was more beneficial to maintaining the short-range order of starch and promoting the formation of more V-type crystals in noodle. In addition, the high content of β-glucan in oat bran flour further contributed to the interactions between starch and other molecules. 【Conclusion】 The addition of oat bran flour and Tartary buckwheat bran flour decreased the cooking and sensory quality of wheat noodle, but reduced the GI value of the noodle. The noodles containing 30% oat bran flour was a low GI food. The addition of oat bran flour and buckwheat bran flour in noodles contributed to the formation of resistant starch deriving from complex starch-protein and starch-lipid interactions during starch gelatinization. Oat bran flour was conductive to maintaining the thermal stability of protein network and improving the digestion resistance of starch in noodle by enhancing the interactions between starch and other molecules.

Fatty Liver Model Construction and Its Effectiveness Evaluation Induced by Dexamethasone in Broilers

WANG ChaoHui, SUN Xi, WANG QiangGang, LIU RuiBing, LI Ni, YANG XiaoJun, LIU YanLi

Scientia Agricultura Sinica. 2023, 56(20): 4115-4124. doi:10.3864/j.issn.0578-1752.2023.20.015

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【Background】Excessive abdominal fat deposition and fatty liver syndrome are important industrial problems of lipid metabolism disorder in poultry breeding. The liver is the main site of de novo fatty acid synthesis in poultry, which plays a vital function in nutrients metabolism, formation of bile acids and detoxication. Therefore, the mechanism analysis of lipid metabolism disorder will provide reference for the healthy development of poultry industry, but the disease model is necessary for pathogenesis research. 【Objective】This experiment was conducted to evaluate the effect of dexamethasone-induced fatty liver in broilers, aiming to provide the reference for the construction of lipid metabolism disorder model in poultry. 【Method】Sixteen 35-day-old AA broilers with similar body weight were randomly divided into control group and dexamethasone group (DXM), with 8 replicates in each group. The birds in the DXM were injected subcutaneously with dexamethasone sodium phosphate (4.5 mg·kg^-1) for 7 days, and the birds in the control group were given the administration of normal saline injection. After 7 days, oil red O staining was used to analyze the histopathological changes of the liver, and serum biochemical and antioxidant indexes were detected. RT-PCR was applied to detect genes expression related to lipid metabolism and inflammatory response in the liver. 【Result】Compared with the control group, the liver index of broilers in the DXM was significantly increased (P<0.05). Oil red O sections showed a large number of red lipid droplets, and the contents of TG and TC in the liver were higher than those in the control group (P<0.05). Serum biochemical results showed that aspartate amino transferase (AST), total bilirubin (TBIL), uric acid (UA), total protein (TP), high density lipoprotein cholesterol (HDL-c), low density lipoprotein cholesterol (LDL-c), total cholesterol (TC) and triglyceride (TG) levels in the DXM were significantly higher than those in the control group (P<0.05), but there was no significant difference about alanine aminotransferase (ALT) and glucose (GLU) (P>0.05). Dexamethasone injection significantly increased genes expression about lipid synthesis, such as ACC, FAS, SCD1, PPARγ, ChREBP, SREBP-1c, IGF2 and GR in the liver (P<0.05), but ELOVL6 expression was not affected (P>0.05). In addition, genes expression about lipid catabolism such as CPT1, LPL and PPARα were deceased in DXM group (P<0.05). However, the expression of ATGL gene related to lipid hydrolysis, CETP and MTTP gene related to lipid transport were significantly higher in DXM group (P<0.05). On the other hand, DXM injection significantly increased the genes expression of MyD88, NFκB, IL-6, TNF-α in the liver of broilers (P<0.05). Antioxidant analysis showed that there was no significant change in the total antioxidant capacity of liver and serum (P>0.05), but the content of malondialdehyde in serum was significantly higher in DXM group (P<0.05). 【Conclusion】Neck subcutaneous injection of DXM could cause lipid metabolism disorders in broilers, and lead to oxidative stress and liver inflammation, which was similar to the characteristics of fatty liver disease, indicating that this method could be used to establish the fatty liver model in broilers quickly.

Establishment of Real-Time PCR Method for Detection of Extraneous Marek’s Disease Virus

SU Jia, ZHAO Wei, LIU Dan, WANG Jia, BAI HongXu, WU HuaWei, XUE QingHong, CHEN XiaoChun

Scientia Agricultura Sinica. 2023, 56(20): 4125-4136. doi:10.3864/j.issn.0578-1752.2023.20.016

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【Objective】 In order to solve the problems of low sensitivity, long detection time, and poor discrimination of existing exogenous Marek’s disease virus (MDV) testing methods, this study was designed to establish two real-time PCR detection methods for the identification of MDV serotype 1 (MDV 1) and MDV serotype 3 (MDV 3) strains, which could be used for purity control of poultry-derived biological products. 【Method】 The UL19 sequences of MDV 1, MDV serotype 2 (MDV 2) and MDV 3 strains were downloaded from the NCBI database and were used for nucleotide and amino acid homology comparison. A pair of specific primers and corresponding Taqman probe was designed from the known sequence of conserved UL19 of MDV 1 CVI988 strain and MDV 3 FC126 strain, respectively, and two real-time PCR detection methods were established. The corresponding recombinant plasmids were constructed and used as positive standards to make standard curves, and the sensitivity of gene copy number of the methods were evaluated. Other avian virus-associated biological products, virus, the full-length plasmid of UL19 of MDV 2 SB-1 strain and the raw materials for production (SPF chicken embryo allantoic fluid, embryonic body, allantoic membrane, chicken embryo fibroblasts) were detected to evaluate the specificity of the established methods. 600, 60, 6, 0.6, 0.06, 0.006 and 0.0006 PFU of CVI988 or FC126 strains were detected, respectively, and the sensitivity of the established two methods for detecting live virions was evaluated. Three repeatability tests were performed using corresponding recombinant plasmids of different dilutions, and the correlation coefficient were calculated to analyze the reproducibility of the two established detection methods. 【Result】 The nucleotide and the derived amino acid homology of MDV UL19 in the same serotype was highly conserved with 99.99%, and the nucleotide homology between different serotypes was only about 75%, while the derived amino acid homology was only about 85%. MDV 1 and MDV 3 real-time PCR detection methods were established, respectively. About the MDV 1 real-time PCR detection method, the amplification efficiency was 98.8%, the correlation coefficient was 0.992, with the standard curve : Y=-3.351X+38.828 (Y = Ct, X = lg ( copy number)). About the MDV 3 real-time PCR detection method, the amplification efficiency was 95%, the correlation coefficient was 0.998, and the standard curve: Y=-3.447X+36.496 (Y = Ct, X = lg ( copy number)). The established detection methods could specially detect MDV 1 or MDV 3 without detecting any other avian virus-associated biological products, virus, the full-length plasmid of UL19 of MDV 2 SB-1 strain, along with production materials for poultry. The sensitivity of MDV 1 real-time PCR detection method was high, with the gene copy number detection limit of 32.8 copies/μL, which could detect at least 0.006 PFU of CVI988 strain. The sensitivity of MDV 3 real-time PCR detection method was high, with the gene copy number detection limit of 10 copies/μL, which could detect at least 0.006 PFU of FC126 strain. The coefficient of variation of the repeatability test was less than 1% in MDV 1 real-time PCR detection method, and less than 1.5% in MDV 3 real-time PCR detection method, respectively. 【Conclusion】 The established real-time PCR detection methods would be beneficial for detecting exogenous MDV 1 and MDV 3 strains in poultry-derived biological products.

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