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    Trends in the global commercialization of genetically modified crops in 2023
    Xingru Cheng, Haohui Li, Qiaoling Tang, Haiwen Zhang, Tao Liu, Youhua Wang
    2024, 23 (12): 3943-3952.   DOI: 10.1016/j.jia.2024.09.012
    Abstract541)      PDF in ScienceDirect      

    The commercialization of genetically modified (GM) crops has increased food production, improved crop quality, reduced pesticide use, promoted changes in agricultural production methods, and become an important new production strategy for dealing with insect pests and weeds while reducing the cultivated land area.  This article provides a comprehensive examination of the global distribution of GM crops in 2023.  It discusses the internal factors that are driving their adoption, such as the increasing number of GM crops and the growing variety of commodities.  This article also provides information support and application guidance for the new developments in global agricultural science and technology.

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    Consensus linkage map construction and QTL mapping for eight yield-related traits in wheat using BAAFS 90K SNP array
    Lihua Liu, Pingping Qu, Yue Zhou, Hongbo Li, Yangna Liu, Mingming Zhang, Liping Zhang, Changping Zhao, Shengquan Zhang, Binshuang Pang
    2024, 23 (11): 3641-3656.   DOI: 10.1016/j.jia.2023.07.028
    Abstract322)      PDF in ScienceDirect      
    Identifying stable quantitative trait loci (QTLs) for yield-related traits across populations and environments is crucial for wheat breeding and genetic studies.  Consensus maps also play important roles in wheat genetic and genomic research.  In the present study, a wheat consensus map was constructed using a doubled haploid (DH) population derived from Jinghua 1×Xiaobaidongmai (JX), an F2 population derived from L43×Shanxibaimai (LS) and the BAAFS Wheat 90K SNP array single nucleotide polymorphism (SNP) array.  A total of 44,503 SNP markers were mapped on the constructed consensus map, and they covered 5,437.92 cM across 21 chromosomes.  The consensus map showed high collinearity with the individual maps and the wheat reference genome IWGSC RefSeq v2.1.  Phenotypic data on eight yield-related traits were collected in the JX population, as well as the F2:3 and F2:4 populations of LS, in six, two and two environments, respectively, and those data were used for QTL analysis.  Inclusive composite interval mapping (ICIM) identified 32 environmentally stable QTLs for the eight yield-related traits.  Among them, four QTLs (QPH.baafs-4B, QKNS.baafs-4B, QTGW.baafs-4B, and QSL.baafs-5A.3) were detected across mapping populations and environments, and nine stable QTLs (qKL.baafs-1D, QPH.baafs-2B, QKNS.baafs-3D, QSL.baafs-3D, QKW.baafs-4B, QPH.baafs-5D, QPH.baafs-6A.1, QSL.baafs-6A, and QSL.baafs-6D) are likely to be new.  The physical region of 17.25–44.91 Mb on chromosome 4B was associated with six yield-related traits, so it is an important region for wheat yield.  The physical region around the dwarfing gene Rht24 contained QTLs for kernel length (KL), kernel width (KW), spike length (SL), and thousand-grain weight (TGW), which are either from a pleiotropic effect of Rht24 or closely linked loci.  For the stable QTLs, 254 promising candidate genes were identified.  Among them, TraesCS5A03G1264300, TraesCS1B03G0624000 and TraesCS6A03G0697000 are particularly noteworthy since their homologous genes have similar functions for the corresponding traits.  The constructed consensus map and the identified QTLs along with their candidate genes will facilitate the genetic dissection of wheat yield-related traits and accelerate the development of wheat cultivars with desirable plant morphology and high yield.


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    Mapping and identification of QTLs for seed fatty acids in soybean (Glycine max L.)
    Yiwang Zhong, Xingang Li, Shasha Wang, Sansan Li, Yuhong Zeng, Yanbo Cheng, Qibin Ma, Yanyan Wang, Yuanting Pang, Hai Nian, Ke Wen
    2024, 23 (12): 3966-3982.   DOI: 10.1016/j.jia.2023.09.010
    Abstract308)      PDF in ScienceDirect      
    Soybean is one of the most important sources of vegetable oil.  The oil content and fatty acid ratio have attracted significant attention due to their impacts on the shelf-life of soybean oil products and consumer health.  In this study, a high-density genetic map derived from Guizao 1 and Brazil 13 was used to analyze the quantitative trait loci of palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), linolenic acid (LNA), and oil content (OC).  A total of 54 stable QTLs were detected in the genetic map linkage analysis, which shared six bin intervals.  Among them, the bin interval on chromosome 13 (bin106–bin118 and bin123–bin125) was found to include stable QTLs in multiple environments that were linked to OA, LA, and LNA.  Eight differentially expressed genes (DEGs) within these QTL intervals were determined as candidate genes according to the combination of parental resequencing, bioinformatics and RNA sequencing data.  All these results are conducive to breeding soybean with the ideal fatty acid ratio for food, and provide the genetic basis for mining genes related to the fatty acid and oil content traits in soybean.
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    Advances in the study of waterlogging tolerance in plants
    Zhengyuan Xu, Lingzhen Ye, Qiufang Shen, Guoping Zhang
    2024, 23 (9): 2877-2897.   DOI: 10.1016/j.jia.2023.12.028
    Abstract303)      PDF in ScienceDirect      
    Waterlogging is one of the major abiotic stresses threatening crop yields globally.  Under waterlogging stress, plants suffer from oxidative stress, heavy metal toxicity and energy deficiency, leading to metabolic disorders and growth inhibition.  On the other hand, plants have evolved waterlogging-tolerance or adaptive mechanisms, including morphological changes, alternation of respiratory pathways, antioxidant protection and endogenous hormonal regulation.  In this review, recent advances in studies on the effects of waterlogging stress and the mechanisms of waterlogging tolerance in plants are presented, and the genetic differences in waterlogging tolerance among plant species or genotypes within a species are illustrated.  We also summarize the identified QTLs and key genes associated with waterlogging tolerance.  
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    Genetic analysis and fine mapping of a grain size QTL in the small-grain sterile rice line Zhuo201S
    Bin Lei, Jiale Shao, Feng Zhang, Jian Wang, Yunhua Xiao, Zhijun Cheng, Wenbang Tang, Jianmin Wan
    2024, 23 (7): 2155-2163.   DOI: 10.1016/j.jia.2023.07.026
    Abstract300)      PDF in ScienceDirect      
    The development and application of the small-grain rice sterile line Zhuo201S (Z201S) has demonstrated its potential for mechanized hybrid rice seed production, leading to significant cost reductions.  However, the molecular mechanism responsible for the small-grain size characteristic of Z201S remains unclear.  In this study, we conducted a genetic analysis using near-isogenic lines constructed from Z210S, a small-grain rice sterile line, and R2115, a normal-grain variety.  The results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain number.  Through mapping, we localized the causal gene to the short arm of chromosome 2, within a 113 kb physical region delimited by the molecular markers S2-4-1 and LB63.  Transgenic analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene, suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.
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    Physiological and transcriptome analyses of Chinese cabbage in response to drought stress
    Lin Chen, Chao Li, Jiahao Zhang, Zongrui Li, Qi Zeng, Qingguo Sun, Xiaowu Wang, Limin Zhao, Lugang Zhang, Baohua Li
    2024, 23 (7): 2255-2269.   DOI: 10.1016/j.jia.2024.03.067
    Abstract293)      PDF in ScienceDirect      

    Chinese cabbage is an important leafy vegetable crop with high water demand and susceptibility to drought stress.  To explore the molecular mechanisms underlying the response to drought, we performed a transcriptome analysis of drought-tolerant and -sensitive Chinese cabbage genotypes under drought stress, and uncovered core drought-responsive genes and key signaling pathways.  A co-expression network was constructed by a weighted gene co-expression network analysis (WGCNA) and candidate hub genes involved in drought tolerance were identified.  Furthermore, abscisic acid (ABA) biosynthesis and signaling pathways and their drought responses in Chinese cabbage leaves were systemically explored.  We also found that drought treatment increased the antioxidant enzyme activities and glucosinolate contents significantly.  These results substantially enhance our understanding of the molecular mechanisms underlying drought responses in Chinese cabbage.


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    Karyotype establishment and development of specific molecular markers of Aegilops geniculata Roth based on SLAF-seq 
    Yongfu Wang, Jianzhong Fan, Hong Zhang, Pingchuan Deng, Tingdong Li, Chunhuan Chen, Wanquan Ji, Yajuan Wang
    2024, 23 (12): 3953-3965.   DOI: 10.1016/j.jia.2023.09.014
    Abstract285)      PDF in ScienceDirect      

    The constant evolution of pathogens poses a threat to wheat resistance against diseases, endangering food security.  Developing resistant wheat varieties is the most practical approach for circumventing this problem.  As a close relative of wheat, Aegilops geniculata, particularly accession SY159, has evolved numerous beneficial traits that could be applied to improve wheat.  In this study, we established the karyotype of SY159 by fluorescence in situ hybridization (FISH) using the oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat–Ae. geniculata accession TA2899 addition lines as a reference.  Using specific-locus amplified fragment sequencing (SLAF-seq) technology, 400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%.  The SY159-specific markers were used to classify the different homologous groups of SY159 against the wheat–Ae. geniculata addition lines.  We used these specific markers on the 7Mg chromosome after classification, and successfully confirmed their suitability for studying the different chromosomes of SY159.  This study provides a foundation for accelerating the application of SY159 in genetic breeding programs designed to improve wheat. 

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    The development of a porcine 50K SNP panel using genotyping by target sequencing and its application
    Zipeng Zhang, Siyuan Xing, Ao Qiu, Ning Zhang, Wenwen Wang, Changsong Qian, Jia’nan Zhang, Chuduan Wang, Qin Zhang, Xiangdong Ding
    2025, 24 (5): 1930-1943.   DOI: 10.1016/j.jia.2023.07.033
    Abstract263)      PDF in ScienceDirect      

    Genotyping by target sequencing (GBTS) integrates the advantages of silicon-based technology (high stability and reliability) and genotyping by sequencing (high flexibility and cost-effectiveness).  However, GBTS panels are not currently available in pigs.  In this study, based on GBTS technology, we first developed a 50K panel, including 52,000 single-nucleotide polymorphisms (SNPs), in pigs, designated GBTS50K.  A total of 6,032 individuals of Large White, Landrace, and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.  Our results showed that GBTS50K obtained a high genotyping ability, the SNP and individual call rates of GBTS50K were 0.997–0.998, and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993, respectively, in replicate samples.  We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis, selection signature detection, genome-wide association studies (GWAS), genotyped imputation, genetic selection (GS), etc.  The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.  For example, GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.  Particularly, due to the multiple SNPs (mSNPs), GBTS50K generated 100K qualified SNPs without increasing genotyping cost, and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.  Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs, and it is also helpful for developing SNP panels for other farm animals.

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    Optimizing nitrogen management can improve stem lodging resistance and stabilize the grain yield of japonica rice in rice–crayfish coculture systems
    Qiang Xu, Jingyong Li, Hui Gao, Xinyi Yang, Zhi Dou, Xiaochun Yuan, Weiyan Gao, Hongcheng Zhang
    2024, 23 (12): 3983-3997.   DOI: 10.1016/j.jia.2024.02.002
    Abstract250)      PDF in ScienceDirect      
    Nitrogen (N) significantly affects rice yield and lodging resistance.  Previous studies have primarily investigated the impact of N management on rice lodging in conventional rice monoculture (RM); however, few studies have performed such investigations in rice–crayfish coculture (RC).  We hypothesized that RC would increase rice lodging risk and that optimizing N application practices would improve rice lodging resistance without affecting food security.  We conducted a two-factor (rice farming mode and N management practice) field experiment from 2021 to 2022 to test our hypothesis.  The rice farming modes included RM and RC, and the N management practices included no nitrogen fertilizer, conventional N application, and optimized N treatment.  The rice yield and lodging resistance characteristics, such as morphology, mechanical and chemical characteristics, anatomic structure, and gene expression levels, were analyzed and compared among the treatments.  Under the same N application practice, RC decreased the rice yield by 11.1–24.4% and increased the lodging index by 19.6–45.6% compared with the values yielded in RM.  In RC, optimized N application decreased the plant height, panicle neck node height, center of gravity height, bending stress, and lodging index by 4.0–4.8%, 5.2–7.8%, 0.5–4.5%, 5.5–10.5%, and 1.8–19.5%, respectively, compared with those in the conventional N application practice.  Furthermore, it increased the culm diameter, culm wall thickness, breaking strength, and non-structural and structural carbohydrate content by 0.8–4.9%, 2.2–53.1%, 13.5–19.2%, 2.2–24.7%, and 31.3–87.2%, respectively.  Optimized N application increased sclerenchymal and parenchymal tissue areas of the vascular bundle at the culm wall of the base second internode.  Furthermore, optimized N application upregulated genes involved in lignin and cellulose synthesis, thereby promoting lower internodes on the rice stem and enhancing lodging resistance.  Optimized N application in RC significantly reduced the lodging index by 1.8–19.5% and stabilized the rice yield (>8,570 kg ha–1 on average).  This study systematically analyzed and compared the differences in lodging characteristics between RM and RC.  The findings will aid in the development of more efficient practices for RC that will reduce N fertilizer application.

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    Genetic analysis and candidate gene identification of salt tolerancerelated traits in maize
    Hui Fang, Xiuyi Fu, Hanqiu Ge, Mengxue Jia, Jie Ji, Yizhou Zhao, Zijian Qu, Ziqian Cui, Aixia Zhang, Yuandong Wang, Ping Li, Baohua Wang
    2024, 23 (7): 2196-2210.   DOI: 10.1016/j.jia.2024.02.009
    Abstract242)      PDF in ScienceDirect      
    Soil salinization poses a threat to maize production worldwide, but the genetic mechanism of salt tolerance in maize is not well understood.  Therefore, identifying the genetic components underlying salt tolerance in maize is of great importance.  In the current study, a teosinte-maize BC2F7 population was used to investigate the genetic basis of 21 salt tolerance-related traits.  In total, 125 QTLs were detected using a high-density genetic bin map, with one to five QTLs explaining 6.05–32.02% of the phenotypic variation for each trait.  The total phenotypic variation explained (PVE) by all detected QTLs ranged from 6.84 to 63.88% for each trait.  Of all 125 QTLs, only three were major QTLs distributed in two genomic regions on chromosome 6, which were involved in three salt tolerance-related traits.  In addition, 10 pairs of epistatic QTLs with additive effects were detected for eight traits, explaining 0.9 to 4.44% of the phenotypic variation.  Furthermore, 18 QTL hotspots affecting 3–7 traits were identified.  In one hotspot (L5), a gene cluster consisting of four genes (ZmNSA1, SAG6, ZmCLCg, and ZmHKT1;2) was found, suggesting the involvement of multiple pleiotropic genes.  Finally, two important candidate genes, Zm00001d002090 and Zm00001d002391, were found to be associated with salt tolerance-related traits by a combination of linkage and marker-trait association analyses.  Zm00001d002090 encodes a calcium-dependent lipid-binding (CaLB domain) family protein, which may function as a Ca2+ sensor for transmitting the salt stress signal downstream, while Zm00001d002391 encodes a ubiquitin-specific protease belonging to the C19-related subfamily.  Our findings provide valuable insights into the genetic basis of salt tolerance-related traits in maize and a theoretical foundation for breeders to develop enhanced salt-tolerant maize varieties.


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    Heterogeneous population distribution enhances resistance to wheat lodging by optimizing the light environment
    Yibo Hu, Feng Qin, Zhen Wu, Xiaoqin Wang, Xiaolong Ren, Zhikuan Jia, Zhenlin Wang, Xiaoguang Chen, Tie Cai
    2024, 23 (7): 2211-2226.   DOI: 10.1016/j.jia.2023.07.006
    Abstract242)      PDF in ScienceDirect      

    Lodging is still the key factor that limits continuous increases in wheat yields today, because the mechanical strength of culms is reduced due to low-light stress in populations under high-yield cultivation.  The mechanical properties of the culm are mainly determined by lignin, which is affected by the light environment.  However, little is known about whether the light environment can be sufficiently improved by changing the population distribution to inhibit culm lodging.  Therefore, in this study, we used the wheat cultivar “Xinong 979” to establish a low-density homogeneous distribution treatment (LD), high-density homogeneous distribution treatment (HD), and high-density heterogeneous distribution treatment (HD-h) to study the regulatory effects and mechanism responsible for differences in the lodging resistance of wheat culms under different population distributions.  Compared with LD, HD significantly reduced the light transmittance in the middle and basal layers of the canopy, the net photosynthetic rate in the middle and lower leaves of plants, the accumulation of lignin in the culm, and the breaking resistance of the culm, and thus the lodging index values increased significantly, with lodging rates of 67.5% in 2020–2021 and 59.3% in 2021–2022.  Under HD-h, the light transmittance and other indicators in the middle and basal canopy layers were significantly higher than those under HD, and the lodging index decreased to the point that no lodging occurred.  Compared with LD, the activities of phenylalanine ammonia-Lyase (PAL), 4-coumarate: coenzyme A ligase (4CL), catechol-O-methyltransferase (COMT), and cinnamyl-alcohol dehydrogenase (CAD) in the lignin synthesis pathway were significantly reduced in the culms under HD during the critical period for culm formation, and the relative expression levels of TaPAL, Ta4CL, TaCOMT, and TaCAD were significantly downregulated.  However, the activities of lignin synthesis-related enzymes and their gene expression levels were significantly increased under HD-h compared with HD.  A partial least squares path modeling analysis found significant positive effects between the canopy light environment, the photosynthetic capacity of the middle and lower leaves of plants, lignin synthesis and accumulation, and lodging resistance in the culms.  Thus, under conventional high-density planting, the risk of wheat lodging was significantly higher.  Accordingly, the canopy light environment can be optimized by changing the heterogeneity of the population distribution to improve the photosynthetic capacity of the middle and lower leaves of plants, promote lignin accumulation in the culm, and enhance lodging resistance in wheat.  These findings provide a basis for understanding the mechanism responsible for the lower mechanical strength of the culm under high-yield wheat cultivation, and a theoretical basis and for developing technical measures to enhance lodging resistance.


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    A novel secreted protein FgHrip1 from Fusarium graminearum triggers immune responses in plants
    Zhenchao Fu, Huiqian Zhuang, Vincent Ninkuu, Jianpei Yan, Guangyue Li, Xiufen Yang, Hongmei Zeng
    2024, 23 (11): 3774-3787.   DOI: 10.1016/j.jia.2023.08.009
    Abstract240)      PDF in ScienceDirect      

    Fusarium graminearum, the primary pathogenic fungus responsible for Fusarium head blight (FHB) in wheat, secretes abundant chemical compounds that interact with host plants.  In this study, a secreted protein FgHrip1, isolated from the culture filtrate of Fgraminearum, was found to induce typical cell death in tobacco.  The FgHrip1 gene was then cloned and expressed in Escherichia coli.  Further bioassay analysis showed that the recombinant FgHrip1 induced early defense induction events, such as reactive oxygen species (ROS) production, callose deposition, and up-regulation of defense-related genes in tobacco.  Furthermore, FgHrip1 significantly enhanced immunity in tobacco seedlings against Pseudomonas syringae pv. tabaci 6605 (Pst. 6605) and tobacco mosaic virus (TMV).  FgHrip1-treated wheat spikes also exhibited defense-related transcript accumulation and developed immunity against FHB infection.  Whereas the expression of FgHrip1 was induced during the infection process, the deletion of the gene impaired the virulence of F. graminearum.  Our results suggest that FgHrip1 triggers immunity and induces disease resistance in tobacco and wheat, thereby providing new insight into strategy for biocontrol of FHB.

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    Dynamic transcriptome profiles and novel markers in bovine spermatogenesis revealed by single-cell sequencing
    Yuan Gao, Fuxia Bai, Qi Zhang, Xiaoya An, Zhaofei Wang, Chuzhao Lei, Ruihua Dang
    2024, 23 (7): 2362-2378.   DOI: 10.1016/j.jia.2023.04.036
    Abstract236)      PDF in ScienceDirect      
    Testicular development is an important biological process in male and requires interaction between the male germ cells and somatic cells. However, the mechanisms of testicular development in livestock, particularly in cattle, are poorly understood. Furthermore, cellular heterogeneity hinders the profiling of different cell types at different developmental stages. In this study, we first performed a single-cell transcriptomic study of the bovine testis development during puberty by using 10× genomics single-cell RNA sequencing (scRNA-seq). By collecting the scRNA-seq data from 11,083 cells from prepubertal and pubertal bovine testes, a high-resolution scRNA-seq atlas was described, identifying 9 somatic and 13 spermatogenic clusters. We also distinguished several stage-specific marker genes for bovine germ cells and somatic cells, such as GRAF2 and MORC1 for SSC (spermatogonial stem cells), HJURP and TCF19 for differentiating spermatogonia, ARSE for immature Sertoli, CLEC12B for mature Sertoli, LOC112441470 for Leydig. In conclusion, we have examined the transcription levels and constructed the single-cell developmental maps of germ cells and somatic cells during testicular development in Angus cattle. The datasets provided new insights into spermatogenesis and testicular somatic cell development in cattle.
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    Effects of water and nitrogen rate on grain-filling characteristics under high-low seedbed cultivation in winter wheat
    Junming Liu, Zhuanyun Si, Shuang Li, Lifeng Wu, Yingying Zhang, Xiaolei Wu, Hui Cao, Yang Gao, Aiwang Duan
    2024, 23 (12): 4018-4031.   DOI: 10.1016/j.jia.2023.12.002
    Abstract236)      PDF in ScienceDirect      
    A high-efficiency mode of high-low seedbed cultivation (HLSC) has been listed as the main agricultural technology to increase land utilization ratio and grain yield in Shandong Province, China.  However, limited information is available on the optimized water and nitrogen management for yield formation, especially the grain-filling process, under HLSC mode.  A three-year field experiment with four nitrogen rates and three irrigation rates of HLSC was conducted to reveal the response of grain-filling parameters, grain weight percentage of spike weight (GPS), spike moisture content (SMC), and winter wheat yield to water and nitrogen rates.  The four nitrogen rates were N1 (360 kg ha–1 pure N), N2 (300 kg ha–1 pure N), N3 (240 kg ha–1 pure N), and N4 (180 kg ha–1 pure N), respectively, and the three irrigation quotas were W1 (120 mm), W2 (90 mm), and W3 (60 mm), respectively.  Results showed that the determinate growth function generally performed well in simulating the temporal dynamics of grain weight (0.989<R2<0.999, where R2 is the determination coefficient).  The occurrence time of maximum filling rate (Tmax) and active grain-filling period (AGP) increased with the increase in the water or nitrogen rate, whereas the average grain-filling rate (Gmean) had a decreasing trend.  The final 1,000-grain weight (FTGW) increased and then decreased with the increase in the nitrogen rates and increased with the increase in the irrigation rates.  The GPS and SMC had a highly significant quadratic polynomial relationship with grain weight and days after anthesis.  Nitrogen, irrigation, and year significantly affected the Tmax, AGP, Gmean, and FTGW.  Particularly, the AGP and FTGW were insignificantly different between high seedbed (HLSC-H) and low seedbed (HLSC-L) across the water and nitrogen levels.  Moreover, the moderate water and nitrogen supply was more beneficial for grain yield, as well as for spike number and grain number per hectare.  The principal component analysis indicated that combining 240–300 kg N ha–1 and 90–120 mm irrigation quota could improve grain-filling efficiency and yield for the HLSC-cultivated winter wheat.  


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    Dietary manganese supplementation inhibits abdominal fat deposition possibly by regulating gene expression and enzyme activity involved in lipid metabolism in the abdominal fat of broilers
    Xiaoyan Cui, Ke Yang, Weiyun Zhang, Liyang Zhang, Ding Li, Wei Wu, Yun Hu, Tingting Li, Xugang Luo
    2024, 23 (12): 4161-4171.   DOI: 10.1016/j.jia.2023.08.004
    Abstract229)      PDF in ScienceDirect      
    Excessive abdominal fat deposition seriously restricts the production efficiency of broilers.  Several studies found that dietary supplemental manganese (Mn) could effectively reduce the abdominal fat deposition of broilers, but the underlying mechanisms remain unclear.  The present study aimed to investigate the effect of dietary supplementation with the inorganic or organic Mn on abdominal fat deposition, and enzyme activity and gene expression involved in lipid metabolism in the abdominal fat of male or female broilers.  A total of 420 1-d-old AA broilers (half males and half females) were randomly allotted by body weight and gender to 1 of 6 treatments with 10 replicates cages of 7 chicks per cage in a completely randomized design involving a 3 (dietary Mn addition)×2 (gender) factorial arrangement.  Male or female broilers were fed with the Mn-unsupplemented basal diets containing 17.52 mg Mn kg–1 (d 1–21) and 15.62 mg Mn kg–1 (d 22–42) by analysis or the basal diets supplemented with 110 mg Mn kg–1 (d 1–21) and 80 mg Mn kg–1 (d 22–42) as either the Mn sulfate or the Mn proteinate with moderate chelation strength (Mn-Prot M) for 42 d.  The results showed that the interaction between dietary Mn addition and gender had no impact (P>0.05) on any of the measured parameters; abdominal fat percentage of broilers was decreased (P<0.003) by Mn addition; Mn addition increased (P<0.004) adipose triglyceride lipase (ATGL) activity, while Mn-Prot M decreased (P<0.002) the fatty acid synthase (FAS) activity in the abdominal fat of broilers compared to the control; Mn addition decreased (P<0.009) diacylglycerol acyltransferase 2 (DGAT2) mRNA expression level and peroxisome proliferator-activated receptor γ (PPARγ) mRNA and protein expression levels, but up-regulated (P<0.05) the ATGL mRNA and protein expression levels in the abdominal fat of broilers.  It was concluded that dietary supplementation with Mn inhibited the abdominal fat deposition of broilers possibly via decreasing the expression of PPARγ and DGAT2 as well as increasing the expression and activity of ATGL in the abdominal fat of broilers, and Mn-Prot M was more effective in inhibiting the FAS acitivity.
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    A novel chorismate mutase effector secreted from root-knot nematode Meloidogyne enterolobii manipulates plant immunity to promote parasitism
    Tuizi Feng, Yuan Chen, Zhourong Li, Ji Pei, Deliang Peng, Huan Peng, Haibo Long
    2024, 23 (12): 4107-4119.   DOI: 10.1016/j.jia.2023.11.039
    Abstract226)      PDF in ScienceDirect      
    Meloidogyne spp. is an economically important plant-parasitic nematode distributed worldwide.  To fight with host immune system for successful parasitism, plant parasitic nematodes secrete effectors to promote infection.  In this study, we identified one chorismate mutase (CM) effector from Menterolobii, named Me-CM.  Spatial and temporal expression assays exhibited Me-cm is expressed in esophageal glands and up-regulated at parasitic-stage juveniles.  Me-CM affects the pathogenicity of Menterolobii based on the reduced infection rate, number of galls, egg masses, eggs per mass and multiplication rate collected from RNA silencing experiments.  We showed that Me-CM localized in the cytoplasm and nucleus of plant cells and decreased the expression level of the marker gene PR1 of salicylic acid (SA) pathway.  Besides, constitutive expression of Me-cm in Arabidopsis thaliana significantly reduced salicylic acid concentration.  These results suggested that Menterolobii may secrete effector Me-CM to fight with plant immune systems via regulating SA signaling pathway when interacting with host plants, ultimately facilitating parasitism.
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    Natural variation in the cytochrome c oxidase subunit 5B OsCOX5B regulates seed vigor by altering energy production in rice
    Chengwei Huang, Zhijuan Ji, Qianqian Huang, Liling Peng, Wenwen Li, Dandan Wang, Zepeng Wu, Jia Zhao, Yongqi He, Zhoufei Wang
    2024, 23 (9): 2898-2910.   DOI: 10.1016/j.jia.2023.06.018
    Abstract225)      PDF in ScienceDirect      
    Seed vigor is a crucial trait for the direct seeding of rice.  Here we examined the genetic regulation of seed vigor traits in rice, including germination index (GI) and germination potential (GP), using a genome-wide association study approach.  One major quantitative trait locus, qGI6/qGP6, was identified simultaneously for both GI and GP.  The candidate gene encoding the cytochrome c oxidase subunit 5B (OsCOX5B) was validated for qGI6/qGP6.  The disruption of OsCOX5B caused the vigor traits to be significantly lower in Oscox5b mutants than in the japonica Nipponbare wild type (WT).  Gene co-expression analysis revealed that OsCOX5B influences seed vigor mainly by modulating the tricarboxylic acid cycle process.  The glucose levels were significantly higher while the pyruvic acid and adenosine triphosphate levels were significantly lower in Oscox5b mutants than in WT during seed germination.  The elite haplotype of OsCOX5B facilitates seed vigor by increasing its expression during seed germination.  Thus, we propose that OsCOX5B is a potential target for the breeding of rice varieties with enhanced seed vigor for direct seeding.


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    Genome-wide identification, molecular evolution, and functional characterization of fructokinase gene family in apple reveal its role in improving salinity tolerance
    Jing Su, Lingcheng Zhu, Pingxing Ao, Jianhui Shao, Chunhua Ma
    2024, 23 (11): 3723-3736.   DOI: 10.1016/j.jia.2024.09.001
    Abstract215)      PDF in ScienceDirect      
    Fructokinase (FRK) is a regulator of fructose signaling in plants and gateway proteins that catalyze the initial step in fructose metabolism through phosphorylation.  Our previous study demonstrated that MdFRK2 protein exhibit not only high affinity for fructose, but also high enzymatic activity due to sorbitol.  However, genome-wide identification of the MdFRK gene family and their evolutionary dynamics in apple are yet to be reported.  A systematic genome-wide analysis in this study identified a total of nine MdFRK gene members, which could phylogenetically be clustered into seven groups.  Chromosomal location and synteny analysis of MdFRKs revealed that their expansion in the apple genome is primarily driven by tandem and segmental duplication events.  Divergent expression patterns of MdFRKs were observed in four source-sink tissues and at five different apple fruit developmental stages, which suggested their potential crucial roles in the apple fruit development and sugar accumulation.  Reverse transcription-quantitative PCR (RT-qPCR) identified candidate NaCl or drought stress responsive MdFRKs, and transgenic apple plants overexpressing MdFRK2 exhibited considerably enhanced salinity tolerance.  Our results will be useful for understanding the functions of MdFRKs in the regulation of apple fruit development and salt stress response.


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    A potential hyphal fusion protein complex with an important role in development and virulence interacts with autophagy-related proteins in Fusarium pseudograminearum
    Linlin Chen, Yixuan Shan, Zaifang Dong, Yake Zhang, Mengya Peng, Hongxia Yuan, Yan Shi, Honglian Li, Xiaoping Xing
    2024, 23 (12): 4093-4106.   DOI: 10.1016/j.jia.2023.09.005
    Abstract211)      PDF in ScienceDirect      

    Hyphal fusion (anastomosis) is a common process serving many important functions at various developmental stages in the life cycle of ascomycetous fungi.  However, the biological roles and molecular mechanisms in plant pathogenic fungi were widely unknown.  In this study, a hyphal fusion protein FpHam-2 was screened from a T-DNA insertion mutant library of Fusarium pseudograminearum, and FpHam-2 interacts with another 2 hyphal fusion protein homologues FpHam-3 and FpHam-4.  Each of these 3 genes deletion mutant revealed in similar defective phenotypes compared with the WT and complemented strains, including reduction in growth rate, defects in hyphal fusion and conidiation, more sensitive for cell membrane, cell wall and oxidative stress responses, and decreased in virulence.  The yeast two-hybrid assay was used to identify that FpHam-2 interacts with 3 autophagy-related proteins, including FpAtg3, FpAtg28 and FpAtg33.  Furthermore, FpHam-2-deletion mutant showed decreased accumulation of autophagic bodies in hypha.  In conclusion, FpHam-2, FpHam-3 and FpHam-4 have an essential role for hyphal fusion and regulating the growth, conidiation and virulence in Fpseudograminearum.


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    Knock-out of GhPDCT with the CRISPR/Cas9 system increases the oleic acid content in cottonseed oil
    Tingwan Li, Lu Long, Yingchao Tang, Zhongping Xu, Guanying Wang, Man Jiang, Shuangxia Jin, Wei Gao
    2024, 23 (10): 3468-3471.   DOI: 10.1016/j.jia.2024.07.030
    Abstract210)      PDF in ScienceDirect      

    Cotton is a pivotal economic crop for natural textile fibers that also serves as an important source of edible oil (Long et al. 2023). Cottonseed oil contains approximately 14% oleic acid and 59% linoleic acid. An increase in monounsaturated fatty acids, particularly oleic acid, enhances the oxidative stability and nutritional value of edible oil (Chen et al. 2021). Currently, the demand for edible oil in China is increasing in terms of both production and nutrition. Improving cottonseed oil’s storability and nutritional value is crucial for the comprehensive utilization of cotton. However, cottonseed has long been regarded as a by-product in the cotton industry, so research on improving the content and quality of cottonseed oil has lagged compared to other crop attributes.

    Phosphatidylcholine: diacylglycerol cholinephospho-transferase (PDCT) is the gate-keeping enzyme for the conversion between phosphatidylcholine and diacylglycerol (Lu et al. 2009). Studies in multiple plants have revealed increases in monounsaturated fatty acids in seeds with PDCT knock-out. To clone the PDCTs of upland cotton (Gossypium hirsutum), the protein sequences of PDCT from Arabidopsis (Lu et al. 2009), oilseed rape (Brassica napus; Bai et al. 2020), soybean (Glycine max; Li et al. 2023), peanut (Arachis hypogaea), and sesame (Sesamum indicum) were used as references for BLAST searches in CottonMD (https://yanglab.hzau.edu.cn/CottonMD; Yang et al. 2023). Four PDCT homologs in cotton were obtained and named GhPDCT1 (Gh_D06G1990), GhPDCT2 (Gh_A06G1621), GhPDCT3 (Gh_A05G3864), and GhPDCT4 (Gh_D05G1178) (Fig. 1-A). The sequence similarities between the four GhPDCTs and AtPDCT are 58.47, 60.13, 45.18, and 58.61%, respectively. Further, the phylogenetic analysis revealed that the GhPDCTs are clustered with the PDCTs of Brassica napus (Fig. 1-A).

    The heatmap of GhPDCTs in cotton tissues was built using released transcriptome data. The results showed that GhPDCT3 and GhPDCT4 had very little expression in all tissues (Fig. 1-B). GhPDCT2 was expressed in roots, stems, leaves and ovules at different developmental stages, but at relatively low levels. GhPDCT1 shared similar basal expression with GhPDCT2, but the transcript level of GhPDCT1 in ovules was significantly higher than that of GhPDCT2. Notably, the expression of GhPDCT1 was sharply up-regulated in ovules at 20 and 25 days post anthesis (DPA). The expression pattern of GhPDCT1 was further verified by RT-qPCR, which indicated that GhPDCT1 was up-regulated in the late stage of ovule development and peaked around 25 DPA. Previous reports highlighted the rapid accumulation of oil content in cotton seeds at 20–30 DPA (Zhao et al. 2018). Therefore, GhPDCT1 is considered the key candidate for regulating the seed oil content of cotton (Fig. 1-B).

    Sequence analysis showed that GhPDCT1/2 and GmPDCT1/2 contain similar conserved motifs, as well as a C-terminal PAP2_3 domain (Fig. 1-C). The GmPDCT1 and GmPDCT2 in soybean were both found to be located in the cytosol (Li et al. 2023). To study the subcellular localization of GhPDCT, a GFP-PDCT1 fusion protein was expressed in the protoplasts of cotton cotyledons (Hu et al. 2022), and the RFP-labeled transcription factor GoPGF (Zhang et al. 2024) was co-expressed to mark the nucleus. Observations with a laser scanning confocal microscope showed the green fluorescence of GFP-PDCT1 expressed in the cytoplasm (Fig. 1-D).

    Knock-out of GhPDCT was achieved with the optimized CRISPR/Cas9 system of cotton (Wang et al. 2018). Due to the high similarity (94.2%) of the coding sequences of GhPDCT1 and GhPDCT2, two sgRNAs respectively targeting two different sites of the 1st exon were designed for the simultaneous mutagenesis of GhPDCT1 and GhPDCT2 (Fig. 1-E). The Ghirsutum L. line ‘Jin668’ was used to produce the GhPDCT1/2 mutant of cotton (ghpdct) with Agrobacterium-mediated transformation (Zhu et al. 2023). The DNA of the ghpdct mutant was extracted for Hi-TOM sequencing, and the offspring of ghpdct-5 with the full mutation were planted for further studies. As shown in Fig. 1-F, ghpdct-5 has a 1 nt deletion at target 2 of GhPDCT2 (A subgenome). In addition, two types of mutations were found in GhPDCT1 (D subgenome), one with a 1 nt insertion at target 1, and the other with a 1 nt insertion and a 2 nt deletion at target 1. The wild type (WT) and ghpdct were planted in the field and a phenotypic study was conducted during the whole growing period. No obvious differences in plant growth were observed between WT and ghpdct. For example, the plant height, fiber length, seed weight of WT and ghpdct showed no statistically significant differences (Fig. 1-G–I).

    The fatty acids in seeds of WT and ghpdct were measured by gas chromatography-mass spectrometry (GC-MS) (Fig. 1-J). Oleic acid (OA, C18:1) accounted for an average of 14.46% of the total fatty acids in seeds of WT, and 16.49% in seeds of ghpdct, which indicates the up-regulation of oleic acid in the ghpdct mutant. Conversely, linoleic acid (LA, C18:2) was reduced in seeds of ghpdct (52.83%) compared to seeds of WT (59.98%). In addition, knockout of GhPDCT increased the seed content of palmitic acid (PA, C16:0) from 21.24% in WT to 25.85% in ghpdct, and the content of stearic acid (SA, C18:0) increased from 1.70% in WT seeds to 2.39% in ghpdct seeds. These results indicated that the GhPDCT mutation alters the balance of monounsaturated and polyunsaturated fatty acids in cotton seeds, with minimal impacts on growth and development beyond seed oil metabolism.

    In conclusion, we have produced the ghpdct mutant of cotton using the CRISPR/Cas9 system. Knock-out of GhPDCT1/2 affects the conversion between phosphatidylcholine and diacylglycerol in cottonseeds, and changes the contents of oleic acid, linoleic acid, palmitic acid, and stearic acid. We obtained a new germplasm with a higher oleic acid content in cottonseed oil, which can be applied to enhance the economic and nutritional value of cotton as an oil crop, thereby contributing to the industrial upgrading of cotton.

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