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2023 Vol. 22 No. 7 Previous Issue   

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Review
Crop Science
Horticulture
Plant Protection
Animal Science · Veterinary Medicine
Agro-ecosystem & Environment
Food Science


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Porcine reproductive and respiratory syndrome (PRRS) is a highly pathogenic infectious disease caused by PRRS virus (PRRSV). In our study, we reported the use of two precise CRISPR/Cas9 editing systems to identify important CD163 residues involved in PRRSV infection. From a dual-sgRNA editing system, we obtained the immortalized porcine alveolar macrophage (IPAM) cell lines with 40-residue (residues 523–562) deletion in CD163. From a CRISPR/Cas9-mediated HDR-based biallelic editing system, we generated precisely-edited cloned pigs with a single arginine (R) to alanine (A) substitution at position 561 of CD163 (CD163^R561A), and PAMs were isolated from these CD163^R561A pigs. PRRSV infection experiments showed that the IPAM cell line with the 40-residue deletion in CD163 were completely resistant to PRRSV-WUH3 (genotype 2 PRRSV) infection, and that CD163-R561A PAMs showed significantly lower susceptibility to PRRSV-WUH3 infection. Through this study, we believe that CD163 residues 523–562 are essential residues that mediate PRRSV infection, and that R561 is an important residue involved in PRRSV infection. Our study offers a valuable reference for exploring the mechanism of CD163-mediated PRRSV infection and provides other potential target sites for the generation of PRRSV-resistant CD163 gene-edited pigs. The cover photo depicts the CD163 specific edited pigs are resistant to PRRSV, which is provided by Dr. Xu Kui from Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing. See pages 2188–2199 for details.


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Review

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Advancing approach and toolbox in optimization of chloroplast genetic transformation technology LIU Yu-xin, LI Fan, GAO Liang, TU Zhang-li, ZHOU Fei, LIN Yong-jun 2023, 22(7): 1951-1966.  DOI: 10.1016/j.jia.2023.02.031 Abstract ( )   PDF in ScienceDirect   Chloroplast is a discrete, highly structured, and semi-autonomous cellular organelle. The small genome of chloroplast makes it an up-and-coming platform for synthetic biology. As a special means of synthetic biology, chloroplast genetic engineering shows excellent potential in reconstructing various sophisticated metabolic pathways within the plants for specific purposes, such as improving crop photosynthetic capacity, enhancing plant stress resistance, and synthesizing new drugs and vaccines. However, many plant species exhibit limited efficiency or inability in chloroplast genetic transformation. Hence, new transformation technologies and tools are being constantly developed. In order to further expand and facilitate the application of chloroplast genetic engineering, this review summarizes the new technologies in chloroplast genetic transformation in recent years and discusses the choice of appropriate synthetic biological elements  for the construction of efficient chloroplast transformation vectors.

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Signatures of positive selection for local adaptation of African native cattle populations: A review Wondossen AYALEW, WU Xiao-yun, Getinet Mekuriaw TAREKEGN, CHU Min, LIANG Chun-nian, Tesfaye SISAY TESSEMA, YAN Ping 2023, 22(7): 1967-1984.  DOI: 10.1016/j.jia.2023.01.004 Abstract ( )   PDF in ScienceDirect   Cattle are central to the lives and diverse cultures of African people. It has played a crucial role in providing valuable protein for billions of households and sources of income and employment for producers and other actors in the livestock value chains. The long-term natural selection of African cattle typically signals signatures in the genome, contributes to high genetic differentiations across breeds. This has enabled them to develop unique adaptive traits to cope with inadequate feed supply, high temperatures, high internal and external parasites, and diseases. However, these unique cattle genetic resources are threatened by indiscriminate cross-breeding, breed replacements with exotic cosmopolitan breeds, and climate change pressures. Although there are no functional genomics studies, recent advancements in genotyping and sequencing technologies have identified and annotated limited functional genes and causal variants associated with unique adaptive and economical traits of African cattle populations. These genome-wide variants serve as candidates for breed improvement and support conservation efforts for endangered cattle breeds against future climate changes. Therefore, this review plans to collate comprehensive information on the identified selection footprints to support genomic studies in African cattle to confirm the validity of the results and provide a framework for further genetic association and QTL fine mapping studies.

Crop Science

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Identification of genetic loci for grain yield‑related traits in the wheat population Zhongmai 578/Jimai 22 LIU Dan, ZHAO De-hui, ZENG Jian-qi, Rabiu Sani SHAWAI, TONG Jing-yang, LI Ming, LI Fa-ji, ZHOU Shuo, HU Wen-li, XIA Xian-chun, TIAN Yu-bing, ZHU Qian, WANG Chun-ping, WANG De-sen, HE Zhong-hu, LIU Jin-dong, ZHANG Yong 2023, 22(7): 1985-1999.  DOI: 10.1016/j.jia.2022.12.002 Abstract ( )   PDF in ScienceDirect   The identification of stable quantitative trait locus (QTL) for yield-related traits and tightly linked molecular markers is important for improving wheat grain yield. In the present study, six yield-related traits in a recombinant inbred line (RIL) population derived from the Zhongmai 578/Jimai 22 cross were phenotyped in five environments. The parents and 262 RILs were genotyped using the wheat 50K single nucleotide polymorphism (SNP) array. A high-density genetic map was constructed with 1 501 non-redundant bin markers, spanning 2 384.95 cM. Fifty-three QTLs for six yield-related traits were mapped on chromosomes 1D (2), 2A (9), 2B (6), 2D, 3A (2), 3B (2), 4A (5), 4D, 5B (8), 5D (2), 7A (7), 7B (3) and 7D (5), which explained 2.7–25.5% of the phenotypic variances. Among the 53 QTLs, 23 were detected in at least three environments, including seven for thousand-kernel weight (TKW), four for kernel length (KL), four for kernel width (KW), three for average grain filling rate (GFR), one for kernel number per spike (KNS) and four for plant height (PH). The stable QTLs QKl.caas-2A.1, QKl.caas-7D, QKw.caas-7D, QGfr.caas-2B.1, QGfr.caas-4A, QGfr.caas-7A and QPh. caas-2A.1 are likely to be new loci. Six QTL-rich regions on 2A, 2B, 4A, 5B, 7A and 7D, showed pleiotropic effects on various yield traits. TaSus2-2B and WAPO-A1 are potential candidate genes for the pleiotropic regions on 2B and 7A, respectively. The pleiotropic QTL on 7D for TKW, KL, KW and PH was verified in a natural population. The results of this study enrich our knowledge of the genetic basis underlying yield-related traits and provide molecular markers for high-yield wheat breeding.

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A 2-bp frameshift deletion at GhDR, which encodes a B-BOX protein that co-segregates with the dwarf-red phenotype in Gossypium hirsutum L. WANG Xue-feng, SHAO Dong-nan, LIANG Qian, FENG Xiao-kang, ZHU Qian-hao, YANG Yong-lin, LIU Feng, ZHANG Xin-yu, LI Yan-jun, SUN Jie, XUE Fei 2023, 22(7): 2000-2014.  DOI: 10.1016/j.jia.2022.10.007 Abstract ( )   PDF in ScienceDirect   Plant architecture and leaf color are important factors influencing cotton fiber yield. In this study, based on genetic analysis, stem paraffin sectioning, and phytohormone treatments, we showed that the dwarf-red (DR) cotton mutant is a gibberellin-sensitive mutant caused by a mutation in a single dominant locus, designated GhDR. Using bulked segregant analysis (BSA) and genotyping by target sequencing (GBTS) approaches, we located the causative mutation to a ~197-kb genetic interval on chromosome A09 containing 25 annotated genes. Based on gene annotation and expression changes between the mutant and normal plants, GH_A09G2280 was considered to be the best candidate gene responsible for the dwarf and red mutant phenotypes. A 2-nucleotide deletion was found in the coding region of GhDR/GH_A09G2280 in the DR mutant, which caused a frameshift and truncation of GhDR. GhDR is a homolog of Arabidopsis AtBBX24, and encodes a B-box zinc finger protein. The frameshift deletion eliminated the C-terminal nuclear localization domain and the VP domain of GhDR, and altered its subcellular localization. A comparative transcriptome analysis demonstrated downregulation of the key genes involved in gibberellin biosynthesis and the signaling transduction network, as well as upregulation of the genes related to gibberellin degradation and the anthocyanin biosynthetic pathway in the DR mutant. The results of this study revealed the potential molecular basis by which plant architecture and anthocyanin accumulation are regulated in cotton.

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The HD-Zip transcription factor GhHB12 represses plant height by regulating the auxin signaling in cotton LIU Yan, WANG Wei-ping, ZHANG Lin, ZHU Long-fu, ZHANG Xian-long, HE Xin 2023, 22(7): 2015-2024.  DOI: 10.1016/j.jia.2022.09.022 Abstract ( )   PDF in ScienceDirect   Upland cotton (Gossypium hirsutum L.) is the most important natural textile fiber crop worldwide. Plant height (PH) is a significant component of plant architecture, strongly influencing crop cultivation patterns, overall yield, and economic coefficient. However, cotton genes regulating plant height have not been fully identified. Previously, an HD-Zip gene (GhHB12) was isolated and characterized in cotton, which regulates the abiotic and biotic stress responses and the growth and development processes. In this study, we showed that GhHB12 was induced by auxin. Moreover, overexpression of GhHB12 induces the expression of HY5, ATH1, and HAT4, represses the spatial-temporal distribution, polar transport, and signaling of auxin, alters the expression of genes involved in cell wall expansion, and restrains the plant height in cotton. These results suggest a role of GhHB12 in regulating cotton plant height, which could be achieved by affecting the auxin signaling and cell wall expansion.

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Effects of the potassium application rate on lipid synthesis and eating quality of two rice cultivars CHEN Guang-yi, PENG Li-gong, LI Cong-mei, TU Yun-biao, LAN Yan, WU Chao-yue, DUAN Qiang, ZHANG Qiu-qiu, YANG Hong, LI Tian 2023, 22(7): 2025-2040.  DOI: 10.1016/j.jia.2022.09.020 Abstract ( )   PDF in ScienceDirect   Lipid content has an important effect on rice eating quality, but the effects of fertilizer application rate on the lipid synthesis and eating quality of rice are not well understood. Potassium (K) has a strong influence on rice quality and the requirement for K fertilizer in rice is greater than for nitrogen (N) and phosphorus (P) fertilizers. To investigate the effects of K fertilizer on the lipid synthesis and eating quality of rice, we used Nanjing 9108 (NJ9108, japonica) and IR72 (indica) rice as experimental materials and four K levels: K0 (0 kg ha–1), K1 (90 kg ha–1), K2 (135 kg ha–1) and K3 (180 kg ha–1). The results showed that the lipid content, free fatty acid (FFA) content, unsaturated fatty acid (UFA) content, malonyl-CoA (MCA) content, phosphatidic acid (PA) content, lipid synthesis-related enzyme activities and eating quality first increased and then decreased with increasing K in both cultivars. The maximum values were obtained under K2. However, the saturated fatty acid (SFA) content showed the opposite trend. No significant differences were found in pyruvate (PYR) content among the K treatments. The protein and oxaloacetic acid (OAA) contents and phosphoenolpyruvate carboxylase (PEPCase) activity of NJ9108 first decreased and then increased with increasing K, and the minimum values were obtained under K2; while IR72 showed the opposite trend and the maximum values were obtained under K1. Overall, increasing K optimized the fatty acid components and increased the lipid content and eating quality of rice by enhancing lipid synthesis-related enzyme activities and regulating substrate competition for lipid and protein synthesis. The optimal K application rate for lipid synthesis, eating quality and grain yield was 135 kg ha–1 for both cultivars.

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Decreased panicle N application alleviates the negative effects of shading on rice grain yield and grain quality WEI Huan-he, GE Jia-lin, ZHANG Xu-bin, ZHU Wang, DENG Fei, REN Wan-jun, CHEN Ying-long, MENG Tian-yao, DAI Qi-gen 2023, 22(7): 2041-2053.  DOI: 10.1016/j.jia.2022.08.045 Abstract ( )   PDF in ScienceDirect   Light deficiency is a growing abiotic stress in rice production. However, few studies focus on shading effects on grain yield and quality of rice in East China. It is also essential to investigate proper nitrogen (N) application strategies that can effectively alleviate the negative impacts of light deficiency on grain yield and quality in rice. A two-year field experiment was conducted to explore the effects of shading (non-shading and shading from heading to maturity) and panicle N application (NDP, decreased panicle N rate; NMP, medium panicle N rate; NIP, increased panicle N rate) treatments on rice yield- and quality-related characteristics. Compared with non-shading, shading resulted in a 9.5–14.8% yield loss (P<0.05), mainly due to lower filled-grain percentage and grain weight. NMP and NIP had higher (P<0.05) grain yield than NDP under non-shading, and no significant difference was observed in rice grain yield among NDP, NMP, and NIP under shading. Compared with NMP and NIP, NDP achieved less yield loss under shading because of the increased filled-grain percentage and grain weight. Shading reduced leaf photosynthetic rate after heading, as well as shoot biomass weight at maturity, shoot biomass accumulation from heading to maturity, and nonstructural carbohydrate (NSC) content in the stem at maturity (P<0.05). The harvest index and NSC remobilization reserve of NDP were increased under shading. Shading decreased (P<0.05) percentages of brown rice, milled rice, head rice, and amylose content while increasing (P<0.05) chalky rice percentage, chalky area, chalky degree, and grain protein. NMP demonstrated a better milling quality under non-shading, while NDP demonstrated under shading. NDP exhibited both lower chalky rice percentage, chalky area, and chalky degree under non-shading and shading, compared with NMP and NIP. NDP under shading decreased amylose content and breakdown but increased grain protein content and setback, contributing to similar overall palatability to nonshading. Our results suggested severe grain yield and quality penalty of rice when subjected to shading after heading. NDP improved NSC remobilization, harvest index, and sink-filling efficiency and alleviated yield loss under shading. Besides, NDP would maintain rice’s milling, appearance, and cooking and eating qualities under shading. Proper N management with a decreased panicle N rate could be adopted to mitigate the negative effects of shading on rice grain yield and quality.

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Tiller fertility is critical for improving grain yield, photosynthesis and nitrogen efficiency in wheat DING Yong-gang, ZHANG Xin-bo, MA Quan, LI Fu-jian, TAO Rong-rong, ZHU Min, Li Chun-yan, ZHU Xin-kai, GUO Wen-shan, DING Jin-feng 2023, 22(7): 2054-2066.  DOI: 10.1016/j.jia.2022.10.005 Abstract ( )   PDF in ScienceDirect   Genetic improvement has promoted wheat’s grain yield and nitrogen use efficiency (NUE) during the past decades. Therefore, the current wheat cultivars exhibit higher grain yield and NUE than previous cultivars in the Yangtze River Basin, China since the 2000s. However, the critical traits and mechanisms of the increased grain yield and NUE remain unknown. This study explores the mechanisms underlying these new cultivars’ increased grain yield and NUE by studying 21 local cultivars cultivated for three growing seasons from 2016 to 2019. Significantly positive correlations were observed between grain yield and NUE in the three years. The cultivars were grouped into high (HH), medium (MM), and low (LL) grain yield and NUE groups. The HH group exhibited significantly high grain yield and NUE. High grain yield was attributed to more effective ears by high tiller fertility and greater single-spike yield by increasing postanthesis single-stem biomass. Compared to other groups, the HH group demonstrated a longer leaf stay-green ability and a greater flag leaf photosynthetic rate after anthesis. It also showed higher N accumulation at pre-anthesis, which contributed to increasing N accumulation per stem, including stem and leaf sheath, leaf blade, and unit leaf area at preanthesis, and promoting N uptake efficiency, the main contribution of high NUE. Moreover, tiller fertility was positively related to N accumulation per stem, N accumulation per unit leaf area, leaf stay-green ability, and flag leaf photosynthetic rate, which indicates that improving tiller fertility promoted N uptake, leaf N accumulation, and photosynthetic ability, thereby achieving synchronous improvements in grain yield and NUE. Therefore, tiller fertility is proposed as an important kernel indicator that can be used in the breeding and management of cultivars to improve agricultural efficiency and sustainability.

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Response of dryland crops to climate change and drought-resistant and water-suitable planting technology: A case of spring maize FAN Ting-lu, LI Shang-zhong, ZHAO Gang, WANG Shu-ying, ZHANG Jian-jun, WANG Lei, DANG Yi, CHENG Wan-li 2023, 22(7): 2067-2079.  DOI: 10.1016/j.jia.2022.08.044 Abstract ( )   PDF in ScienceDirect   Climate change has a significant impact on agriculture. However, the impact investigation is currently limited to the analysis of meteorological data, and there is a dearth of long-term monitoring of crop phenology and soil moisture associated with climate change. In this study, temperature and precipitation (1957–2020) were recorded, crop growth (1981–2019) data were collected, and field experiments were conducted at central and eastern Gansu and southern Ningxia, China. The mean temperature increased by 0.36°C, and precipitation decreased by 11.17 mm per decade. The average evapotranspiration (ET) of winter wheat in 39 years from 1981 to 2019 was 362.1 mm, demonstrating a 22.1-mm decrease every 10 years. However, the ET of spring maize was 405.5 mm over 35 years (1985–2019), which did not show a downward trend. Every 10 years, growth periods were shortened by 5.19 and 6.47 d, sowing dates were delayed by 3.56 and 1.68 d, and maturity dates advanced by 1.76 and 5.51 d, respectively, for wheat and maize. A film fully-mulched ridge–furrow (FMRF) system with a rain-harvesting efficiency of 65.7‒92.7% promotes deep rainwater infiltration into the soil. This leads to double the soil moisture in-furrow, increasing the water satisfaction rate by 110‒160%. A 15-year grain yield of maize increased by 19.87% with the FMRF compared with that of half-mulched flat planting. Grain yield and water use efficiency of maize increased by 20.6 and 17.4% when the density grew from 4.5×104 to 6.75×104 plants ha–1 and improved by 12.0 and 12.7% when the density increased from 6.75×104 to 9.0×104 plants ha–1, respectively. Moreover, responses of maize yield to density and the corresponding density of the maximum yield varied highly in different rainfall areas. The density parameter suitable for water planting was 174 maize plants ha–1 with 10 mm rainfall. Therefore, management strategies should focus on adjusting crop planting structure, FMRF water harvesting system, and water-suitable planting to mitigate the adverse effects of climate change and enhance sustainable production of maize in the drylands.

Horticulture

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Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple ZHANG Li-hua, ZHU Ling-cheng, XU Yu, LÜ Long, LI Xing-guo, LI Wen-hui, LIU Wan-da, MA Feng-wang, LI Ming-jun, HAN De-guo 2023, 22(7): 2080-2093.  DOI: 10.1016/j.jia.2023.05.024 Abstract ( )   PDF in ScienceDirect   Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality.  However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking.  In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1.  The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological functions and biochemical properties were analyzed.  A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion.  The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication.  Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies.  In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development.  Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit.  The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.

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A cyclic effect of cAMP and calcium signaling contributes to jujube growth and development WANG Li-xin, WANG Lin-xia, ZHANG Meng-ling, QU Ying-yue, YUAN Ye, Ehsan SADEGHNEZHAD, GAO Meng-jiao, ZHAO Ruo-yu, QI Chao-feng, GUO Xiao-xue, ZHU Wen-hui, LI Rui-mei, DAI Li, LIU Meng-jun, LIU Zhi-guo 2023, 22(7): 2094-2110.  DOI: 10.1016/j.jia.2023.04.039 Abstract ( )   PDF in ScienceDirect   3´,5´-Cyclic adenosine monophosphate (cAMP) is an important metabolite that is specifically enriched in jujube. However, the effect of cAMP on jujube cellular responses has not been comprehensively studied. Here, we established jujube cell suspension cultures and investigated the calcium influx in response to cAMP treatment through protoplast isolation and fluorescence intensity. Firstly, cAMP treatment could promote jujube growth and increase the content of endogenous cAMP. Using transcriptome analysis with transgenic Arabidopsis plants overexpressing adenylate cyclase (ZjAC) as a positive control, we identified 60 calcium-related differential expressed genes (DEGs) that contributed to the calcium signaling and inter- or intra-cellular responses. Pharmacological treatments such as cAMP and the calcium ionophore A23187 could induce ZjAC expression, the accumulation of cAMP and calcium influx in jujube cells, while ethylene glycol tetraacetic acid (EGTA) or bithionol treatment inhibited these changes. Moreover, the calcium channels and transporters in calcium influx, such as the ZjCNGC2 channel and the mitogen activated protein (MAP) kinase pathway, could be activated by cAMP treatment. In summary, our findings demonstrated that cAMP biosynthesis is dependent on calcium influx and the amplifying effect between calcium and cAMP may be involved in intracellular signal induction, which might contribute to the growth and development of jujube.

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Volatile metabolome and transcriptome reveal fragrance release rhythm and molecular mechanisms of Rosa yangii ZHOU Li-jun, HUANG Run-huan, LIU Ting-han, LIU Wei-chao, CHEN Yun-yi, LU Pei-feng, LUO Le, PAN Hui-tang, YU Chao, ZHANG Qi-xiang 2023, 22(7): 2111-2125.  DOI: 10.1016/j.jia.2023.06.015 Abstract ( )   PDF in ScienceDirect   Rose is a highly significant ornamental plant with substantial edible and medicinal value, cultivated worldwide primarily for perfume production. Recently, Rosa yangii, a new species found in northwestern Yunnan, China, has drawn attention due to its strong sweet scented flowers. In this study, the floral components of R. yangii were extracted at different flowering stages using solid phase micro extraction (SPME) and analyzed through gas chromatography–mass spectrometry (GC–MS). A total of 131 volatile organic compounds (VOCs) were detected from R. yangii, including 69 odor compounds. The production and release of floral VOCs were the highest during the initial-open stage, making it the most suitable time for harvesting as a significant number of floral components were synthesized and preserved. The analysis of the odor activity values (OAV) highlighted several key aromatic ingredients of R. yangii, such as eugenol, methyleugenol, benzeneacetaldehyde and phenylethylalcohol, heptanal, decanal, (E)-2-hexen-1-yl acetate, caryophyllene, and others. Metabolome and time-order gene co-expression networks (TO-GCN) revealed that VOCs and benzenoids/phenylpropanoids, along with associated genes, played a pivotal role in the overall floral regulatory network of R. yangii. MYB and bHLH were identified as the essential regulatory factors governing the regulation of eugenol synthase (EGS) and isoeugenol synthase (IGS), consequently influencing the sweet scent of R. yangii. The findings of this study provide a scientific foundation for enhancing fragrance through molecular breeding of ornamental plants. Furthermore, the study facilitated the development and utilization of this new plant’s essential oil material in various industries, including food storage, aromatherapy, cosmetic, and perfumery.

Plant Protection

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SsRSS1 mediates salicylic acid tolerance and contributes to virulence in sugarcane smut fungus ZHANG Hao-yang, YANG Yan-fang, GUO Feng, SHEN Xiao-rui, LU Shan, CHEN Bao-sha 2023, 22(7): 2126-2137.  DOI: 10.1016/j.jia.2022.10.006 Abstract ( )   PDF in ScienceDirect   Sugarcane smut caused by Sporisorium scitamineum is a destructive disease responsible for significant losses in sugarcane production worldwide. However, the mechanisms underlying the pathogenicity of this fungus remain largely unknown. In this study, we found that the disruption of the SsRSS1 gene, which encodes a salicylic acid (SA) sensing regulator, does not affect phenotypic traits such as the morphology, growth rate, and sexual mating ability of haploid basidiospores, but rather reduces the tolerance of basidiospores to SA stress by blocking the induction of SsSRG1, a gene encoding a SA response protein in S. scitamineum. SsRSS1 deletion resulted in the attenuation of the virulence of the fungus. In addition to a significant reduction in whip formation, a portion of plantlets (18.3%) inoculated with the ΔSsRSS1 strains were found to be infected but failed to produce whips for up to 90 days post-inoculation. However, the development of hyphae and teliospore from the ΔSsRSS1-infected plants that formed whips seemed indistinguishable from that in the wild-type-infected plants. Combined, our findings suggested that SsRss1 is required for maintaining fungal fitness in planta by counteracting SA stress.

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Potential global distribution of the guava root-knot nematode Meloidogyne enterolobii under different climate change scenarios using MaxEnt ecological niche modeling PAN Song, PENG De-liang, LI Ying-mei, CHEN Zhi-jie, ZHAI Ying-yan, LIU Chen, HONG Bo 2023, 22(7): 2138-2150.  DOI: 10.1016/j.jia.2023.06.022 Abstract ( )   PDF in ScienceDirect   In recent years, Meloidogyne enterolobii has emerged as a major parasitic nematode infesting many plants in tropical or subtropical areas. However, the regions of potential distribution and the main contributing environmental variables for this nematode are unclear. Under the current climate scenario, we predicted the potential geographic distributions of M. enterolobii worldwide and in China using a Maximum Entropy (MaxEnt) model with the occurrence data of this species. Furthermore, the potential distributions of M. enterolobii were projected under three future climate scenarios (BCC-CSM2-MR, CanESM5 and CNRM-CM6-1) for the periods 2050s and 2090s. Changes in the potential distribution were also predicted under different climate conditions. The results showed that highly suitable regions for M. enterolobii were concentrated in Africa, South America, Asia, and North America between latitudes 30° S to 30° N. Bio16 (precipitation of the wettest quarter), bio10 (mean temperature of the warmest quarter), and bio11 (mean temperature of the coldest quarter) were the variables contributing most in predicting potential distributions of M. enterolobii. In addition, the potential suitable areas for M. enterolobii will shift toward higher latitudes under future climate scenarios. This study provides a theoretical basis for controlling and managing this nematode.

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Selection, effective dominance, and completeness of Cry1A.105/Cry2Ab2 dual-protein resistance in Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) Tiago SILVA, Ying NIU, Tyler TOWLES, Sebe BROWN, Graham P. HEAD, Wade WALKER, Fangneng HUANG 2023, 22(7): 2151-2161.  DOI: 10.1016/j.jia.2022.09.024 Abstract ( )   PDF in ScienceDirect   In the U.S., Helicoverpa zea (Boddie) is a major pest targeted by both transgenic maize and cotton expressing Bacillus thuringiensis (Bt) proteins. Resistance of insect to Bt maize and cotton containing cry1A and cry2A genes has widely occurred in the U.S. In this study, two trials were performed to investigate larval survival and development of a Cry1A.105/Cry2Ab2 dual-protein resistant (VT2P-RR), a susceptible, and an F1 heterozygous (VT2P-RS) populations of H. zea on ears of nine Bt and three non-Bt maize hybrids. The Bt maize hybrids evaluated represent five common pyramided traits expressing two or three of the Cry1A.105, Cry1Ab, Cry1F, Cry2Ab2, and Vip3Aa20 proteins. In the laboratory, neonates of the three H. zea populations were inoculated on silks of ears collected from maize at R1-R2 plant stages; and larval survivorship was checked 10 d after neonate release. All three insect populations survived normally on non-Bt maize ears. Varied numbers of VT2P-RR and VT2P-RS survived on ears of Cry1A.105/Cry2Ab2 maize, while all larvae of the three populations died or could not develop on ears of Vip3Aa20-expressing maize. The results demonstrated that the dual-protein resistant H. zea was not cross-resistant to Vip3Aa20-expressing maize, and thus traits with vip3Aa20 gene should be effective to manage Cry1A.105/Cry2Ab2-resistant H. zea. The resistance in VT2P-RR was determined to be incomplete on Cry1A.105/Cry2Ab2 maize. The effective dominance levels varied greatly, from recessive to incompletely dominant, depending on maize hybrids and trials, suggesting that proper selection of maize hybrids could be important for mitigating the Cry1A.105/Cry2Ab2 resistance. The data generated should aid in modeling multiple-protein Bt resistance in H. zea.

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Mutagenesis of odorant coreceptor Orco reveals the distinct role of olfaction between sexes in Spodoptera frugiperda CAO Song, SUN Dong-dong, LIU Yang, YANG Qing, WANG Gui-rong 2023, 22(7): 2162-2172.  DOI: 10.1016/j.jia.2022.11.004 Abstract ( )   PDF in ScienceDirect   Odorant receptor (OR) is crucial for insects to detect and recognize external chemical cues closely related to their survival.  The insect OR forms a heteromeric complex composed of a ligand-specific receptor and a ubiquitously odorant receptor coreceptor (Orco).  This study used the CRISPR/Cas9 technique to knock out (KO) Orco and reveal its essential role in acting on OR-meditated olfactory behavior in a critical invasive agricultural pest, the fall armyworm (FAW), Spodoptera frugiperda.  Electroantennogram (EAG) results suggested that the Orco mutants of both male and female moths severely reduced their electrophysiological responses to the eight tested plant volatiles and two sex pheromones.  However, the Orco gene played distinct roles in mating behavior between sexes: the mating behavior was fully disrupted in mutated males but not in mutated females.  The oviposition result indicated that the Orco KO females displayed reduced egg laying by 24.1% compared with the mated wild type (WT) females.  Overall, these results strongly suggest that Orco is an excellent target for disrupting FAW’s normal behavior and provides a feasible pest control approach.

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Accurate recognition of the reproductive development status and prediction of oviposition fecundity in Spodoptera frugiperda (Lepidoptera: Noctuidae) based on computer vision LÜ Chun-yang, GE Shi-shuai, HE Wei, ZHANG Hao-wen, YANG Xian-ming, CHU Bo, WU Kong-ming 2023, 22(7): 2173-2187.  DOI: 10.1016/j.jia.2022.12.003 Abstract ( )   PDF in ScienceDirect   Spodoptera frugiperda (Lepidoptera: Noctuidae) is an important migratory agricultural pest worldwide, which has invaded many countries in the Old World since 2016 and now poses a serious threat to world food security. The present monitoring and early warning strategies for the fall army worm (FAW) mainly focus on adult population density, but lack an information technology platform for precisely forecasting the reproductive dynamics of the adults. In this study, to identify the developmental status of the adults, we first utilized female ovarian images to extract and screen five features combined with the support vector machine (SVM) classifier and employed male testes images to obtain the testis circular features. Then, we established models for the relationship between oviposition dynamics and the developmental time of adult reproductive organs using laboratory tests. The results show that the accuracy of female ovary development stage determination reached 91%. The mean standard error (MSE) between the actual and predicted values of the ovarian developmental time was 0.2431, and the mean error rate between the actual and predicted values of the daily oviposition quantity was 12.38%. The error rate for the recognition of testis diameter was 3.25%, and the predicted and actual values of the testis developmental time in males had an MSE of 0.7734. A WeChat applet for identifying the reproductive developmental state and predicting reproduction of S. frugiperda was developed by integrating the above research results, and it is now available for use by anyone involved in plant protection. This study developed an automated method for accurately forecasting the reproductive dynamics of S. frugiperda populations, which can be helpful for the construction of a population monitoring and early warning system for use by both professional experts and local people at the county level.

Animal Science · Veterinary Medicine

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Pig macrophages with site-specific edited CD163 decrease the susceptibility to infection with porcine reproductive and respiratory syndrome virus XU Kui, ZHOU Yan-rong, SHANG Hai-tao, XU Chang-jiang, TAO Ran, HAO Wan-jun, LIU Sha-sha, MU Yu-lian, XIAO Shao-bo, LI Kui 2023, 22(7): 2188-2199.  DOI: 10.1016/j.jia.2022.11.010 Abstract ( )   PDF in ScienceDirect   Porcine reproductive and respiratory syndrome (PRRS) is recognized as one of the most infectious viral diseases of swine. Although Cluster of differentiation 163 (CD163) is identified as an essential receptor for mediating PRRS virus (PRRSV) infection, the important residues involved in infection on CD163 are still unclear. Therefore, it is very important to identify these key residues to study the mechanism of PRRSV infection and to generate anti-PRRSV pigs. In this study, we first generated immortalized porcine alveolar macrophage (IPAM) cell lines harboring 40-residues (residues 523–562, including R561 (arginine (R) at position 561)) deletion of CD163. PRRSV infection experiments showed that these IPAM cell lines were completely resistant to PRRSV infection. We then generated cloned pigs carrying CD163- R561A (an arginine (R) to alanine (A) substitution at position 561 of CD163). PRRSV challenge experiments in porcine alveolar macrophages (PAMs) isolated from the CD163-R561A pigs showed significantly lower susceptibility to PRRSV than that of CD163-R561 PAMs. Through this study, we show that CD163 523–562 contains essential residues for mediating PRRSV infection, and that CD163 R561 significantly contributes to PRRSV infection but is not essential for infection. These functional sites can therefore serve as new targets for understanding the mechanism of PRRSV infection. Furthermore, CD163-R561A pigs can be used as an important model for improving pig germplasm with resistance against PRRSV.

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Whole genome SNPs among 8 chicken breeds enable identification of genetic signatures that underlie breed features WANG Jie, LEI Qiu-xia, CAO Ding-guo, ZHOU Yan, HAN Hai-xia, LIU Wei, LI Da-peng, LI Fu-wei, LIU Jie 2023, 22(7): 2200-2212.  DOI: 10.1016/j.jia.2022.11.007 Abstract ( )   PDF in ScienceDirect   Many different chicken breeds are found around the world, their features vary among them, and they are valuable resources.  Currently, there is a huge lack of knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these breeds of chickens.  Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved chicken breeds.  The whole-genomes of 140 chickens from 7 Shandong native breeds and 20 introduced recessive white chickens from China were re-sequenced.  Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed geographically based clusters among the chickens.  Through genome-wide scans for selective sweeps, we identified thyroid stimulating hormone receptor (TSHR, reproductive traits, circadian rhythm), erythrocyte membrane protein band 4.1 like 1 (EPB41L1, body size), and alkylglycerol monooxygenase (AGMO, aggressive behavior), as major candidate breed-specific determining genes in chickens.  In addition, we used a machine learning classification model to predict chicken breeds based on the SNPs significantly associated with recourse characteristics, and the prediction accuracy was 92%, which can effectively achieve the breed identification of Laiwu Black chickens.  We provide the first comprehensive genomic data of the Shandong indigenous chickens.  Our analyses revealed phylogeographic patterns among the Shandong indigenous chickens and candidate genes that potentially contribute to breed-specific traits of the chickens.  In addition, we developed a machine learning-based prediction model using SNP data to identify chicken breeds.  The genetic basis of indigenous chicken breeds revealed in this study is useful to better understand the mechanisms underlying the resource characteristics of chicken.

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A novel short transcript isoform of chicken IRF7 negatively regulates interferon-β production MA Yu-chen, CHEN Hua-yuan, GAO Shen-yan, ZHANG Xiao-zhan, LI Yong-tao, YANG Xia, ZHAO Jun, WANG Zeng 2023, 22(7): 2213-2220.  DOI: 10.1016/j.jia.2022.12.015 Abstract ( )   PDF in ScienceDirect   Type I interferon (IFN-I) provides an important first line to protect avian species against pathogens invasion. IFN regulatory factor 7 (IRF7) has been identified as the most important regulator for both DNA and RNA virus-induced IFN-I production in chickens. Although four splicing variants of IRF7 have been identified in mammals, it is still unclear whether alternative splicing patterns and the function of IRF7 isoform(s) exist in chickens. In this study, we reported a novel short transcript isoform of chicken IRF7 (chIRF7), termed chIRF7-iso, which contained an intact N-terminal DNAbinding domain (DBD) and 14 amino acids different from chIRF7 in the C-terminal. Overexpression of chIRF7 in chicken leghorn male hepatocellular (LMH) cells activated the IFN-β promoter and significantly inhibited Newcastle disease virus (NDV) and fowl adenovirus serotype 4 (FAdV-4) replication. Conversely, overexpression of chIRF7-iso blocked the IFN-β promoter activity and was favorable for NDV and FAdV-4 replication in vitro. Collectively, our results confirm that a novel chIRF7 isoform-mediated negative regulates IFN-β production, which will contribute to understanding the role of chIRF7 in innate antiviral response in chicken.

Agro-ecosystem & Environment

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Improvement of soil fertility and rice yield after long-term application of cow manure combined with inorganic fertilizers GAO Peng, ZHANG Tuo, LEI Xing-yu, CUI Xin-wei, LU Yao-xiong, FAN Peng-fei, LONG Shi-ping, HUANG Jing, GAO Ju-sheng, ZHANG Zhen-hua, ZHANG Hui-min 2023, 22(7): 2221-2232.  DOI: 10.1016/j.jia.2023.02.037 Abstract ( )   PDF in ScienceDirect   Fertilization is an effective technique to improve soil fertility and increase crop yield. The long-term effects of different fertilizers on soil considerably vary. Over 38 consecutive years of different fertilization positioning experiments in a double cropping rice field of Qiyang Red Soil Experimental Station, seven different fertilization treatments including CK (no fertilization), NPK (nitrogen, phosphorus, and potassium fertilizer), M (cow manure), NPKM (nitrogen, phosphorus, and potassium with cow manure), NPM (nitrogen and phosphorus with cow manure), NKM (nitrogen and potassium with cow manure), and PKM (phosphorus and potassium with cow manure) were applied to study the effects on rice yield, soil fertility, and nutrient apparent balance in a paddy field. The results showed that the annual average yields of rice in NPKM, NPM, NKM, PKM, M, NPK and CK treatments ranged from 6 214 to 11 562 kg ha–1. Yields under longterm organic and inorganic treatments (NPKM, NPM, NKM and PKM) were 22.58, 15.35, 10.53 and 4.41%, respectively, greater than under the NPK treatment. Soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN) and available potassium (AK) concentration with long-term organic and inorganic treatment (NPKM, NPM, NKM and PKM) were significantly higher than in inorganic fertilizer (NPK) treatments. Soil total phosphorus (TP) and available phosphorus (AP) contentration with organic fertilizer combined with inorganic N and P fertilizer treatment (NPKM, NPM and PKM) were significantly higher than with inorganic fertilizer alone (NPK treatments). The average annual rice yield (11 562 kg ha–1), SOC (20.88 g kg–1), TN (2.30 g kg–1), TP (0.95 g kg–1), TK (22.50 g kg–1) and AP (38.94 mg kg–1) concentrations were the highest in the NPKM treatment. The soil AN concentration (152.40 mg kg–1) and AK contentration (151.00 mg kg–1) were the highest in the NKM treatment. N and P application led to a surplus of nitrogen and phosphorus in the soil, but NPKM treatment effectively reduced the surplus compared with other treatments. Soils under all treatments were deficient in potassium. Correlation analysis showed that SOC, TN, AN, TP, and AP contentration was significantly correlated with rice yield; the correlation coefficients were 0.428, 0.496, 0.518, 0.501, and 0.438, respectively. This study showed that the combined application of N, P, and K with cow manure had important effects on rice yield and soil fertility, but balanced application of N, P, and K with cow manure was required.

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The potential of green manure to increase soil carbon sequestration and reduce the yield-scaled carbon footprint of rice production in southern China GAO Song-juan, LI Shun, ZHOU Guo-peng, CAO Wei-dong 2023, 22(7): 2233-2247.  DOI: 10.1016/j.jia.2022.12.005 Abstract ( )   PDF in ScienceDirect   Green manure (GM) has been used to support rice production in southern China for thousands of years. However, the effects of GM on soil carbon sequestration (CS) and the carbon footprint (CF) at a regional scale remain unclear. Therefore, we combined the datasets from long-term multisite experiments with a meta-analysis approach to quantify the potential of GM to increase the CS and reduce the CF of paddy soils in southern China. Compared with the fallow– rice practice, the GM–rice practice increased the soil C stock at a rate of 1.62 Mg CO2-eq ha–1 yr–1 and reduced chemical N application by 40% with no loss in the rice yield. The total CF varied from 7.51 to 13.66 Mg CO2-eq ha–1 yr–1 and was dominated by CH4 emissions (60.7–81.3%). GM decreased the indirect CF by 31.4% but increased the direct CH4 emissions by 19.6%. In the low and high CH4 emission scenarios, the CH4 emission factors of GM (EFgc) were 5.58 and 21.31%, respectively. The greater soil CS offset the increase in GM-derived CF in the low CH4 scenario, but it could not offset the CF increase in the high CH4 scenario. A trade-off analysis also showed that GM can simultaneously increase the CS and reduce the total CF of the rice production system when the EFgc was less than 9.20%. The variation in EFgc was mainly regulated by the GM application rates and water management patterns. Determining the appropriate GM application rate and drainage pattern warrant further investigation to optimize the potential of the GM–rice system to increase the CS and reduce the total CF in China.

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A double-layer model for improving the estimation of wheat canopy nitrogen content from unmanned aerial vehicle multispectral imagery LIAO Zhen-qi, DAI Yu-long, WANG Han, Quirine M. KETTERINGS, LU Jun-sheng, ZHANG Fu-cang, LI Zhi-jun, FAN Jun-liang 2023, 22(7): 2248-2270.  DOI: 10.1016/j.jia.2023.02.022 Abstract ( )   PDF in ScienceDirect   The accurate and rapid estimation of canopy nitrogen content (CNC) in crops is the key to optimizing in-season nitrogen fertilizer application in precision agriculture. However, the determination of CNC from field sampling data for leaf area index (LAI), canopy photosynthetic pigments (CPP; including chlorophyll a, chlorophyll b and carotenoids) and leaf nitrogen concentration (LNC) can be time-consuming and costly. Here we evaluated the use of high-precision unmanned aerial vehicle (UAV) multispectral imagery for estimating the LAI, CPP and CNC of winter wheat over the whole growth period. A total of 23 spectral features (SFs; five original spectrum bands, 17 vegetation indices and the gray scale of the RGB image) and eight texture features (TFs; contrast, entropy, variance, mean, homogeneity, dissimilarity, second moment, and correlation) were selected as inputs for the models. Six machine learning methods, i.e., multiple stepwise regression (MSR), support vector regression (SVR), gradient boosting decision tree (GBDT), Gaussian process regression (GPR), back propagation neural network (BPNN) and radial basis function neural network (RBFNN), were compared for the retrieval of winter wheat LAI, CPP and CNC values, and a double-layer model was proposed for estimating CNC based on LAI and CPP. The results showed that the inversion of winter wheat LAI, CPP and CNC by the combination of SFs+TFs greatly improved the estimation accuracy compared with that by using only the SFs. The RBFNN and BPNN models outperformed the other machine learning models in estimating winter wheat LAI, CPP and CNC. The proposed double-layer models (R2=0.67–0.89, RMSE=13.63–23.71 mg g–1, MAE=10.75–17.59 mg g–1) performed better than the direct inversion models (R2=0.61– 0.80, RMSE=18.01–25.12 mg g–1, MAE=12.96–18.88 mg g–1) in estimating winter wheat CNC. The best winter wheat CNC accuracy was obtained by the double-layer RBFNN model with SFs+TFs as inputs (R2=0.89, RMSE=13.63 mg g–1, MAE=10.75 mg g–1). The results of this study can provide guidance for the accurate and rapid determination of winter wheat canopy nitrogen content in the field.

Food Science

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Untargeted UHPLC–Q-Exactive-MS-based metabolomics reveals associations between pre- and post-cooked metabolites and the taste quality of geographical indication rice and regular rice SHI Shi-jie, ZHANG Gao-yu, CAO Cou-gui, JIANG Yang 2023, 22(7): 2271-2281.  DOI: 10.1016/j.jia.2023.06.003 Abstract ( )   PDF in ScienceDirect   Geographical indication (GI) rice refers to the rice of specific geographical origin, which tends to have a good taste quality and a high commodity price.  Rice is favored for its soft texture and chewiness after cooking.  However, GI rice is also plagued by rice fraud.  Understanding the reasons for the excellent taste quality of GI rice and identifying its geographical origin can help maintain the stability of the rice market and promote the development of the rice industry.  In this study, we determined the taste quality of rice.  Untargeted metabolomics based on UHPLC–Q-Exactive-MS was used to identify metabolites in GI and regular rice before and after cooking.  Our findings suggested that GI rice showed lower protein and amylose content, resulting in higher starch gelatinization properties and taste quality.  This study identified 520 metabolites, among which 142 and 175 were significantly different between GI and regular rice, before and after cooking, respectively.  The increased variety of metabolites after cooking was significantly negatively correlated with the taste quality of rice.  GI rice was lower in amino acids and lipid metabolite content before and after cooking, which may be the reason for the excellent taste quality.  Through linear discriminant analysis, we found that the differential metabolites of rice after cooking were more accurate in discriminating rice from different geographic origins, up to 100%.  This work gained new insights into the metabolites of GI rice, which explains its excellent taste quality.  The rice metabolites after cooking could be used for more accurate geographical identification of rice.

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Understanding changes in volatile compounds and fatty acids of Jincheng orange peel oil at different growth stages using GC–MS XIE Jiao, CAO Qi, WANG Wen-jun, ZHANG Hong-yan, DENG Bing 2023, 22(7): 2282-2294.  DOI: 10.1016/j.jia.2023.05.015 Abstract ( )   PDF in ScienceDirect   Jincheng orange (Citrus sinensis Osbeck) is widely grown in Chongqing, China, and is commonly consumed because of its characteristic aroma contributed by the presence of diverse volatile compounds.  The changes in aroma during the development and maturation of fruit are indicators for ripening and harvest time.  However, the influence of growth stages on the volatile compounds in Jincheng orange remains unclear.  In addition, volatiles originate from fatty acids, most of which are the precursors of volatile substances.  On this basis, gas chromatography–mass spectrometry (GC–MS) was performed to elaborate the changes in volatile constituents and fatty acids as precursors.  This study tested proximately 60 volatiles and 8 fatty acids at 9 growth and development stages (AF1–AF9).  Of those compounds, more than 92.00% of total volatiles and 87.50% of fatty acids were terpenoid and saturated fatty acids, respectively.  As shown in the PCA plot, the AF5, AF6, and AF9 stages were confirmed as completely segregated and appeared different.  In addition, most of the volatiles and fatty acids first increased at the beginning of the development stage, then decreased from the AF6 development stage, and finally increased at the AF9 maturity stage.  Moreover, the highest contents of terpenoid, alcohols, aldehydes, ketones, and saturated fatty acids in Jincheng orange peel oil were d-limonene, linalool, octanal, cyclohexanone, and stearic acid during development stages, respectively.  Our results found that the growth stages significantly affected the volatile constituents and precursors in Jincheng orange peel oil.