2022 Vol. 21 No. 4 Previous Issue    Next Issue

    Crop Science
    Plant Protection
    Animal Science · Veterinary Medicine
    Agro-ecosystem & Environment
    Agricultural Economics and Management

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    The roles of microRNAs in regulating root formation and growth in plants
    YAN Xiao-xiao, LIU Xiang-yang, CUI Hong, ZHAO Ming-qin
    2022, 21(4): 901-916.  DOI: 10.1016/S2095-3119(21)63818-2
    Abstract ( )   PDF in ScienceDirect  
    MicroRNAs (miRNAs) are small (ca. 20–24 nucleotides) non-coding RNAs that have recently been recognized as key post-transcriptional modulators of gene expression; and they are involved in many biological processes in plants, such as root growth and development.  The miRNAs regulate root elongation, lateral root (LR) formation and adventitious root (AR) development in response to hormone signaling, nutrient uptake and biotic/abiotic stress.  This review provides multiple perspectives on the involvement of miRNAs in regulating root growth and development in plants.  We also discuss several crucial mechanisms of miRNAs, their relationships with transcription factors and the target gene-mediated hormone signaling interactions in the regulation of root growth and development.
    Crop Science
    Identification of QTL and underlying genes for root system architecture associated with nitrate nutrition in hexaploid wheat
    Marcus GRIFFITHS, Jonathan A. ATKINSON, Laura-Jayne GARDINER, Ranjan SWARUP, Michael P. POUND, Michael H. WILSON, Malcolm J. BENNETT, Darren M. WELLS
    2022, 21(4): 917-932.  DOI: 10.1016/S2095-3119(21)63700-0
    Abstract ( )   PDF in ScienceDirect  
    The root system architecture (RSA) of a crop has a profound effect on the uptake of nutrients and consequently the potential yield.  However, little is known about the genetic basis of RSA and resource adaptive responses in wheat (Triticum aestivum L.).  Here, a high-throughput germination paper-based plant phenotyping system was used to identify seedling traits in a wheat doubled haploid mapping population, Savannah×Rialto.  Significant genotypic and nitrate-N treatment variation was found across the population for seedling traits with distinct trait grouping for root size-related traits and root distribution-related traits.  Quantitative trait locus (QTL) analysis identified a total of 59 seedling trait QTLs.  Across two nitrate treatments, 27 root QTLs were specific to the nitrate treatment.  Transcriptomic analyses for one of the QTLs on chromosome 2D, which was found under low nitrate conditions, revealed gene enrichment in N-related biological processes and 28 differentially expressed genes with possible involvement in a root angle response.  Together, these findings provide genetic insight into root system architecture and plant adaptive responses to nitrate, as well as targets that could help improve N capture in wheat.
    QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean
    TIAN Yu, YANG Lei, LU Hong-feng, ZHANG Bo, LI Yan-fei, LIU Chen, GE Tian-li, LIU Yu-lin, HAN Jia-nan, LI Ying-hui, QIU Li-juan
    2022, 21(4): 933-946.  DOI: 10.1016/S2095-3119(21)63693-6
    Abstract ( )   PDF in ScienceDirect  
    Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects.  Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height.  Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping.  This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines (RILs) and their bi-parents, Zhonghuang 13 (ZH) and Zhongpin 03-5373 (ZP).  The total genetic distance of this bin map was 3 139.15 cM, with an average interval of 0.78 cM between adjacent bin markers.  Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome.  Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci (qPH-b_11, qPH-b_17 and qPH-b_18).  Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56–32.7% of the phenotypic variance.  They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively.  Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.
    Deciphering the morpho–physiological traits for high yield potential in nitrogen efficient varieties (NEVs): A japonica rice case study
    ZHU Kuan-yu, YAN Jia-qian, SHEN Yong, ZHANG Wei-yang, XU Yun-ji, WANG Zhi-qin, YANG Jian-chang
    2022, 21(4): 947-963.  DOI: 10.1016/S2095-3119(20)63600-0
    Abstract ( )   PDF in ScienceDirect  
    The use of nitrogen (N)-efficient rice (Oryza sativa L.) varieties could reduce excessive N input without sacrificing yields. However, the plant traits associated with N-efficient rice varieties have not been fully defined or comprehensively explored.  Here, three japonica N-efficient varieties (NEVs) and three japonica N-inefficient varieties (NIVs) of rice were grown in a paddy field under N omission (0 N, 0 kg N ha–1) and normal N (NN, 180 or 200 kg N ha−1) treatments.  Results showed that NEVs exhibited higher grain yield and nitrogen use efficiency (NUE) than NIVs under both treatments, due to improved sink size and filled-grains percentage in the former which had higher root oxidation activity and greater root dry weight, root length and root diameter at panicle initiation (PI), as well as higher spikelet–leaf ratio and more productive tillers during the grain-filling stage.  Compared with NIVs, NEVs also exhibited enhanced N translocation and dry matter accumulation after heading and improved flag leaf morpho–physiological traits, including greater leaf thickness and specific leaf weight and higher contents of ribulose-1,5-bisphosphate carboxylase/oxygenase, chlorophyll, nitrogen, and soluble sugars, leading to better photosynthetic performance.  Additionally, NEVs had a better canopy structure, as reflected by a higher ratio of the extinction coefficient for effective leaf N to the light extinction coefficient, leading to enhanced canopy photosynthesis and dry matter accumulation.  These improved agronomic and physiological traits were positively and significantly correlated with grain yield and internal NUE, which could be used to select and breed N-efficient rice varieties.

    Grain dehydration rate is related to post-silking thermal time and ear characters in different maize hybrids
    SHI Wen-jun, SHAO Hui, SHA Ye, SHI Rong, SHI Dong-feng, CHEN Ya-chao, BAN Xiang-ben, MI Guo-hua
    2022, 21(4): 964-976.  DOI: 10.1016/S2095-3119(21)63641-9
    Abstract ( )   PDF in ScienceDirect  
    Mechanized grain harvest of maize becomes increasingly important with growing land plot size in Northeast China.  Grain moisture is an important factor affecting the performance of mechanized grain harvest.  However, it remains unclear what influences grain dehydration rate.  In this study, maize grain dehydrating process was investigated in a two-year field experiment with five hybrids under two planting densities in 2017 and 2018.  It was found that damaged-grain ratio was the main factor affecting mechanized harvest quality, and this ratio was positively correlated with grain moisture content at harvest (R2=0.6372, P<0.01).  To fulfill the national standard of <5% damaged-grain ratio for mechanized grain harvest, the optimal maize grain moisture content was 22.3%.  From silking to physiological maturity, grain dehydrating process was mostly dependent on the thermal time (growing degree days, GDDs) (r=–0.9412, P<0.01).  The average grain moisture content at physiological maturity was 29.4%.  Thereafter, the linear relationship between GDDs and grain moisture still existed, but the correlation coefficient became smaller (r=–0.8267, P<0.01).  At this stage, grain dehydrating process was greatly affected by genotypes.  Grain dehydrated faster when a hybrid has a smaller husk area (r=0.6591, P<0.05), larger ear angle (r=–0.7582, P<0.05), longer ear peduncle (r=–0.9356, P<0.01) and finer ear (r=0.9369, P<0.01).  These parameters can be used for breeders and farmers to select hybrids suitable for mechanized grain harvest.  
    Nitrogen application affects maize grain filling by regulating grain water relations
    WU Ya-wei, ZHAO Bo, LI Xiao-long, LIU Qin-lin, FENG Dong-ju, LAN Tian-qiong, KONG Fan-lei, LI Qiang, YUAN Ji-chao
    2022, 21(4): 977-994.  DOI: 10.1016/S2095-3119(20)63589-4
    Abstract ( )   PDF in ScienceDirect  
    Grain water relations play an important role in grain filling in maize.  The study aimed to gain a clear understanding of the changes in grain dry weight and water relations in maize grains by using hybrids with contrasting nitrogen efficiencies under differing nitrogen levels.  The objectives were: 1) to understand the changes in dry matter and percent moisture content (MC) during grain development in response to different nitrogen application rates and 2) to determine whether nitrogen application affects grain filling by regulating grain water relations.  Two maize hybrids, high N-efficient Zhenghong 311 (ZH311) and low N-efficient Xianyu 508 (XY508), were grown in the field under four levels of N fertilizer: 0, 150, 300, and 450 kg N ha–1 during three growing seasons.  Dry weight, percent MC and water content (WC) of basal–middle and apical grains were investigated.  The difference in the maximum WC and filling duration of basal–middle and apical grains in maize ears resulted in a significant difference in final grain weight.  Grain position markedly influenced grain drying down; specifically, the drying down rate of apical grains was faster than that of basal–middle grains.  Genotype and grain position both influenced the impact of nitrogen application rate on grain filling and drying down.  Nitrogen rate determined the maximum grain WC and percent MC loss rate in the middle and the late grain-filling stages, thus affecting final grain weight.  The use of high N-efficient hybrids, combined with the reduction of nitrogen application rate, can coordinate basal–middle and apical grain drying down to ensure yield.  This management strategy could lead to a win–win situation in which the maximum maize yield, efficient mechanical harvest and environmental safety are all achieved. 

    Systematical regulation involved in heterogeneous photosynthetic characteristics of individual leaf in pima cotton
    ZHANG Yu-jie, HAN Ji-mei, LEI Zhang-ying, MENG Hao-feng, ZHANG Wang-feng, ZHANG Ya-li
    2022, 21(4): 995-1003.  DOI: 10.1016/S2095-3119(20)63565-1
    Abstract ( )   PDF in ScienceDirect  
    Light heterogeneity leads to anatomically and physiologically heterogeneous features in leaves.  However, little attention has been paid to the effects of nonuniform illumination on the anatomical and photosynthetic performance on both sides along the leaf main vein.  This study explored such effects by combining in situ determination in the field with shading simulation in the phytotron, on pima cotton that has cupping leaves.  Photosynthetic characteristics and morphological structures were measured in the field on both sides along the main vein of eastward, westward, southward, and northward leaves.  The results showed that the difference in photosynthetic capacity between the two sides along the main vein in different directions was closely related to the daily photo irridiance (DPI).  This result indicates that the photosynthetic heterogeneity between the two sides is related to their intercepted light energy.  The conclusion was further verified by the shading simulation experiments.  Photosynthetic capacity and leaf thickness of the unshaded sides of leaves in the half-shaded treatment decreased, compared to those in the unshaded treatment.  Therefore, it is conjectured that the development of  photosynthetic characteristics on one side is systematically regulated by that on the other side.  The study provides theoretical guidance on accessing the feasibility of sampling and directional planting.   

    The impact of tandem duplication on gene evolution in Solanaceae species
    HUANG Yi-le, ZHANG Ling-kui, ZHANG Kang, CHEN Shu-min, HU Jian-bin, CHENG Feng
    2022, 21(4): 1004-1014.  DOI: 10.1016/S2095-3119(21)63698-5
    Abstract ( )   PDF in ScienceDirect  
    Whole genome duplication (WGD) and tandem duplication (TD) are important modes of gene amplification and functional innovation, and they are common in plant genome evolution.  We analyzed the genomes of three Solanaceae species (Solanum lycopersicum, Capsicum annuum, and Petunia inflata), which share a common distant ancestor with Vitis vinifera, Theobroma cacao, and Coffea canephora but have undergone an extra whole genome triplication (WGT) event.  The analysis was used to investigate the phenomenon of tandem gene evolution with (S. lycopersicum) or without WGT (V. vinifera).  Among the tandem gene arrays in these genomes, we found that V. vinifera, which has not experienced the WGT event, retained relatively more and larger tandem duplicated gene (TDG) clusters than the Solanaceae species that experienced the WGT event.  Larger TDG clusters tend to be derived from older TD events, so this indicates that continuous TDGs (absolute dosage) accumulated during long-term evolution.  In addition, WGD and TD show a significant bias in the functional categories of the genes retained.  WGD tends to retain dose-sensitive genes related to biological processes, including DNA-binding and transcription factor activity, while TD tends to retain genes involved in stress resistance.  WGD and TD also provide more possibilities for gene functional innovation through gene fusion and fission.  The TDG cluster containing the tomato fusarium wilt resistance gene I3 contains 15 genes, and one of these genes, Solyc07g055560, has undergone a fusion event after the duplication events.  These data provide evidence that helps explain the new functionalization of TDGs in adapting to environmental changes.  
    Transcriptome analysis reveals the differential regulatory effects of red and blue light on nitrate metabolism in pakchoi (Brassica campestris L.)
    FAN Xiao-xue, BIAN Zhong-hua, SONG Bo, XU Hai
    2022, 21(4): 1015-1027.  DOI: 10.1016/S2095-3119(21)63784-X
    Abstract ( )   PDF in ScienceDirect  
    Pakchoi (Brassica campestris L. ssp. chinensis) is an important leafy vegetable.  Various light spectra, especially red and blue light, play vital roles in the regulation of nitrate metabolism.  Information on the effects of red and blue light on nitrate metabolism at the transcriptome level in pakchoi is still limited, so this study used RNA sequencing technology to explore this molecular mechanism.  Through pairwise comparisons with white LED light, 3 939 and 5 534 differentially expressed genes (DEGs) were identified under red and blue light, respectively.  By Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses, these unigenes were found to be involved in nitrate assimilation, plant–pathogen interaction, biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis.  The differential effects of light spectra on the nitrate concentration and metabolism-related enzyme activities were also confirmed at the physiological level.  Several signal transduction modules, including Crys/Phys-COP1-HY5/HY5-like, were found to be involved in red and blue light-induced nitrate metabolism, and the transcript levels for this complex were consistent with the observed degree of nitrate assimilation.  The expression patterns of 15 randomly selected DEGs were further validated using qPCR.  Taken together, the results of this study could help improve our understanding of light spectrum-regulated nitrate metabolism in pakchoi at the transcriptome level.
    The use of widely targeted metabolite profiling to reveal the senescence changes in postharvest ‘Red Globe’ (Vitis vinifera) grape berries
    XU Teng-fei, YANG Xin, ZHANG Meng, GUO Shui-huan, FU Wen-jing, ZHOU Bi-jiang, LIU Yu-jia, MA Hai-jun, FANG Yu-lin, YANG Gang, MENG Jiang-fei
    2022, 21(4): 1028-1043.  DOI: 10.1016/S2095-3119(21)63725-5
    Abstract ( )   PDF in ScienceDirect  
    Changes in the metabolites of table grapes (Vitis vinifera) reportedly occur during postharvest senescence.  The aim of this study was to determine the metabolomic differences in postharvest table grapes (‘Red Globe’) after being subjected to different senescence periods.  To this end, we used widely targeted metabolomics based on ultra-performance liquid chromatography and tandem mass spectrometry.  A total of 135 differential metabolites were identified.  During postharvest senescence, the levels of most differential flavonoids (e.g., pelargonidin 3-O-glucoside, quercetin-3-O-glucoside, and cyanidin 3-O-glucoside) and L-aspartic acid decreased, while the levels of phenolic acids (e.g., trans-4-hydroxycinnamic acid methyl ester) and pantothenol increased.  During early and late senescence, the levels of most differential lipids, especially LysoPC, as well as those of nucleotides and their derivatives, such as uridine, decreased and increased, respectively.  Collectively, the findings of this study provide fundamental insights into the reasonable control of table grape fruit postharvest senescence and lay a solid foundation for further research.
    Establishment and application of an SNP molecular identification system for grape cultivars
    WANG Fu-qiang, FAN Xiu-cai, ZHANG Ying, SUN Lei, LIU Chong-huai, JIANG Jian-fu
    2022, 21(4): 1044-1057.  DOI: 10.1016/S2095-3119(21)63654-7
    Abstract ( )   PDF in ScienceDirect  
    We aimed to develop a set of single nucleotide polymorphism (SNP) markers that can be used to distinguish the main cultivated grape (Vitis L.) cultivars in China and provide technical support for domestic grape cultivar protection, cultivar registration, and market rights protection.  A total of 517 high-quality loci were screened from 4 241 729 SNPs obtained by sequencing 304 grape accessions using specific locus amplified fragment sequencing, of which 442 were successfully designed as Kompetitive Allele Specific PCR (KASP) markers.  A set of 27 markers that completely distinguishes 304 sequenced grape accessions was determined by using the program, and 26 effective markers were screened based on 23 representative grape cultivars.  Finally, a total of 46 out of 48 KASP markers, including 22 markers selected by the research group in the early stage, were re-screened based on 348 grape accessions.  Population structure, principal component, and cluster analyses all showed that the 348 grape accessions were best divided into two populations.  In addition, cluster analysis subdivided them into six subpopulations.  According to genetic distance, V. labrusca, V. davidii, V. heyneana, and V. amurensis were far from V. vinifera, while V. vinifera×V. labrusca and V. amurensis×V. vinifera were somewhere in between these two groups.  Furthermore, a core set of 25 KASP markers could distinguish 95.69% of the 348 grape accessions, and the other 21 markers were used as extended markers.  Therefore, SNP molecular markers based on KASP typing technology provide a new way for mapping DNA fingerprints in grape cultivars.  With high efficiency and accuracy and low cost, this technology is more competitive than other current identification methods.  It also has excellent application prospects in the grape distinctness, uniformity, and stability (DUS) test, as well as in promoting market rights protection in the near future.

    Kiwifruit (Actinidia chinensis ‘Hongyang’) cytosolic ascorbate peroxidases (AcAPX1 and AcAPX2) enhance salinity tolerance in Arabidopsis thaliana
    GUO Xiu-hong, HE Yan, ZHANG Yu, WANG Yi, HUANG Sheng-xiong, LIU Yong-sheng, LI Wei
    2022, 21(4): 1058-1070.  DOI: 10.1016/S2095-3119(21)63652-3
    Abstract ( )   PDF in ScienceDirect  
    Ascorbate peroxidase (APX) plays a key role in scavenging reactive oxygen species (ROS) in higher plants.  However, there is very little information available on the APXs in kiwifruit (Actinidia), which is an economically and nutritionally important horticultural crop with exceptionally high ascorbic acid (AsA) accumulation.  This study aims to identify and characterize two cytosolic APX genes (AcAPX1 and AcAPX2) derived from A. chinensis ‘Hongyang’.  The constitutive expression pattern was determined for both AcAPX1 and AcAPX2, and showed relatively higher expression abundances of AcAPX1 in leaf and AcAPX2 in root.  Transcript levels of AcAPX1 and AcAPX2 were increased in kiwifruit roots treated with NaCl.  Subcellular localization assays using GFP-fusion proteins in Arabidopsis protoplasts showed that both AcAPX1 and AcAPX2 are targeted to the cytosol.  Recombinant AcAPX1 or AcAPX2 proteins were successfully expressed in the prokaryotic expression system and their individual ascorbate peroxidase activities were determined.  Finally, constitutive over-expression of AcAPX1 or AcAPX2 could dramatically increase total AsA, glutathione level and salinity tolerance under NaCl stress in Arabidopsis thaliana.  Our findings revealed that cytosolic AcAPX1/2 may play an important protective role in the responses to unfavorable environmental stimuli in kiwifruit.
    Plant Protection
    P1 of strawberry vein banding virus, a multilocalized protein, functions as a movement protein and interacts with the coat protein
    RUI Peng-huan, WANG Zhan-qi, SHAN Wen-shu, XIA Wei-wei, ZHOU Xiu-hong, YANG Lian-lian, JIANG Lei, JIANG Tong
    2022, 21(4): 1071-1083.  DOI: 10.1016/S2095-3119(21)63711-5
    Abstract ( )   PDF in ScienceDirect  
    Although the complete nucleotide sequence of strawberry vein banding virus (SVBV) has been determined and bioinformatic analysis has revealed that the SVBV genome could encode seven proteins, the precise function of each protein is unclear.  This study provided evidence that the P1 protein of SVBV (SVBV-P1) possesses the following features.  Bioinformatic and subcellular localization analyses showed that SVBV-P1 is localized in the cytoplasm and cell walls of epidermal cells in Nicotiana benthamiana, and it forms inclusion bodies associated with microtubules and the endoplasmic reticulum.  Dilution experiments demonstrated that SVBV-P1 could move from the original agro-infiltrated cells to adjacent cells in N. benthamiana leaves.  Further trans-complementation experiments demonstrated that SVBV-P1 could facilitate the intercellular movement of a movement-deficient potato virus X mutant in N. benthamiana leaves.  Finally, yeast two-hybrid and bimolecular fluorescence complementation assays revealed that SVBV-P1 could interact with the SVBV coat protein, which is a major component of Caulimovirus virions.  Results of the electrophoretic mobility shift assay indicated that SVBV-P1 lacks DNA-binding capability.  In summary, the results suggest that SVBV-P1 is probably a movement protein of SVBV, providing new insights into the function of movement proteins of the Caulimovirus genus.
    The new effector AbSCP1 of foliar nematode (Aphelenchoides besseyi) is required for parasitism rice
    HUANG Xin, CHI Yuan-kai, Addisie Abate BIRHAN, ZHAO Wei, QI Ren-de, PENG De-liang
    2022, 21(4): 1084-1093.  DOI: 10.1016/S2095-3119(21)63706-1
    Abstract ( )   PDF in ScienceDirect  
    Plant parasitic nematodes secrete effector proteins to parasitize hosts successfully.  Of these proteins, serine carboxypeptidases have critical roles in pathogenicity.  This study investigated the role of new effector AbSCP1 in Aphelenchoides besseyi pathogenicity.  In situ hybridization and qRT-PCR analyses indicated that AbSCP1 was exclusively expressed in the esophageal glands and upregulated in juveniles.  Subcellular localization assays indicated that the protein was expressed in the nucleus.  The ability to hydrolyze C-terminal amino acid residues was proven for AbSCP1.  Moreover, RNAi significantly reduced the expression of AbSCP1 and RNAi-treated nematodes’ reproductive potential.  Pathogenicity assays on rice showed that RNAi-treated nematodes were less pathogenic than the untreated control groups.  These results suggest the important role of AbSCP1 in the A. besseyi infection process.
    Intelligent diagnosis of northern corn leaf blight with deep learning model
    PAN Shuai-qun, QIAO Jing-fen, WANG Rui, YU Hui-lin, WANG Cheng, Kerry TAYLOR, PAN Hong-yu
    2022, 21(4): 1094-1105.  DOI: 10.1016/S2095-3119(21)63707-3
    Abstract ( )   PDF in ScienceDirect  
    Maize (Zea mays L.), also known as corn, is the third most cultivated crop in the world.  Northern corn leaf blight (NCLB) is a globally devastating maize foliar disease caused by Setosphaeria turcica (Luttrell) Leonard and Suggs.  Early intelligent diagnosis and warning is an effective and economical strategy to control this disease.  Today, deep learning is beginning to play an essential role in agriculture.  Notably, deep convolutional neural networks (DCNN) are amongst the most successful machine learning techniques in plant disease detection and diagnosis.  Our study aims to identify NCLB in the maize-producing area in Jilin Province based on several DCNN models.  We established a database of 985 leaf images of healthy and infected maize and applied data augmentation techniques including image segmentation, image resizing, image cropping, and image transformation, to expand to 30 655 images.  Several proven convolutional neural networks, such as AlexNet, GoogleNet, VGG16, and VGG19, were then used to identify diseases.  Based on the best performance of the DCNN pre-trained model GoogleNet, some of the recent loss functions developed for deep facial recognition tasks such as ArcFace, CosFace, and A-Softmax were applied to detect NCLB.  We found that a pre-trained GoogleNet architecture with the Softmax loss function can achieve an excellent accuracy of 99.94% on NCLB diagnosis.  The analysis was implemented in Python with two deep learning frameworks, Pytorch and Keras.  The techniques, training, validation, and test results are presented in this paper.  Overall, our study explores intelligent identification technology for NCLB and effectively diagnoses NCLB from images of maize.
    Genome-wide characterization of miRNA and siRNA pathways in the parasitoid wasp Pteromalus puparum
    XIAO Shan, FANG Qi, LIU Ming-ming, ZHANG Jiao, WANG Bei-bei, YAN Zhi-chao, WANG Fang, David W. STANLEY, YE Gong-yin
    2022, 21(4): 1106-1115.  DOI: 10.1016/S2095-3119(20)63465-7
    Abstract ( )   PDF in ScienceDirect  
    microRNAs (miRNAs) and small interfering RNAs (siRNAs) are small non-coding RNAs (ncRNAs) that trigger RNA interference (RNAi) in eukaryotic organisms.  The biogenesis pathways for these ncRNAs are well established in Drosophila melanogaster, Aedes aegypti, Bombyx mori and other insects, but lacking in hymenopteran species, particularly in parasitoid wasps.  Pteromalus puparum is a parasitoid of pupal butterflies.  This study identified and analyzed two pathways by interrogating the P. puparum genome.  All core genes of the two pathways are present in the genome as a single copy, except for two genes in the siRNA pathway, R2D2 (two copies) and Argonaute-2 (three).  Conserved domain analyses showed the protein structures in P. puparum were similar to cognate proteins in other insect species.  Phylogenetic analyses of hymenopteran Dicer and Argonaute genes suggested that the siRNA pathway-related genes evolved faster than those in the miRNA pathway.  The study found a decelerated evolution rate of P. puparum Dicer-2 with respect to Dicer-1, which was contrary to other hymenopterans.  Expression analyses revealed high mRNA levels for all miRNA pathway genes in P. puparum adults and the siRNA related genes were expressed in different patterns.  The findings add valuable new knowledge of the miRNA and siRNA pathways and their regulatory actions in parasitoid wasps.
    Factors affecting the geographical distribution of invasive species in China
    CHEN Xiao-ling, NING Dong-dong, XIAO Qian, JIANG Qiu-ying, LU Yong-yue, XU Yi-juan
    2022, 21(4): 1116-1125.  DOI: 10.1016/S2095-3119(20)63497-9
    Abstract ( )   PDF in ScienceDirect  
    Frequent international trade has accelerated alien species invasion.  However, data on the distribution of invasive species after their introduction and research on the factors that determine their geographical distribution are lacking.  This study analyzed the distributional trends of invasive species in China and the drivers for such trends, by identifying the effect of international trade from a dynamic analysis of 13 main invasive insect pests in three time periods – before China’s reform and opening up in 1978, from 1979 to 2001, and after China’s accession to the World Trade Organization in 2001.  The results showed that the abundance of invasive species gradually decreased from south to north and from southeast coast to inland.  Guangdong (442 species) and Yunnan (404 species) provinces have the highest abundance of invasive species.  Among the 13 key invasive insects investigated, 3, 10 and 13 occurred chronologically in the three periods, and invaded 7, 28 and 34 provinces, respectively.  Alien pests are found to invade China through Xinjiang, the Bohai Rim and the southeast.  Value of imports was a strong predictor of the number of invasive species in China, and followed by temperature heterogeneity, in explaining the richness pattern of invasive animal, plants and insects, but not that of microorganisms.  This study provides a scientific basis for furthering international quarantine and effective invasive species control.

    Animal Science · Veterinary Medicine
    Incorporating genomic annotation into single-step genomic prediction with imputed whole-genome sequence data
    TENG Jin-yan, YE Shao-pan, GAO Ning, CHEN Zi-tao, DIAO Shu-qi, LI Xiu-jin, YUAN Xiao-long, ZHANG Hao, LI Jia-qi, ZHANG Xi-quan, ZHANG Zhe
    2022, 21(4): 1126-1136.  DOI: 10.1016/S2095-3119(21)63813-3
    Abstract ( )   PDF in ScienceDirect  
    Single-step genomic best linear unbiased prediction (ssGBLUP) is now intensively investigated and widely used in livestock breeding due to its beneficial feature of combining information from both genotyped and ungenotyped individuals in the single model.  With the increasing accessibility of whole-genome sequence (WGS) data at the population level, more attention is being paid to the usage of WGS data in ssGBLUP.  The predictive ability of ssGBLUP using WGS data might be improved by incorporating biological knowledge from public databases.  Thus, we extended ssGBLUP, incorporated genomic annotation information into the model, and evaluated them using a yellow-feathered chicken population as the examples.  The chicken population consisted of 1 338 birds with 23 traits, where imputed WGS data including 5 127 612 single nucleotide polymorphisms (SNPs) are available for 895 birds.  Considering different combinations of annotation information and models, original ssGBLUP, haplotype-based ssGHBLUP, and four extended ssGBLUP incorporating genomic annotation models were evaluated.  Based on the genomic annotation (GRCg6a) of chickens, 3 155 524 and 94 837 SNPs were mapped to genic and exonic regions, respectively.  Extended ssGBLUP using genic/exonic SNPs outperformed other models with respect to predictive ability in 15 out of 23 traits, and their advantages ranged from 2.5 to 6.1% compared with original ssGBLUP.  In addition, to further enhance the performance of genomic prediction with imputed WGS data, we investigated the genotyping strategies of reference population on ssGBLUP in the chicken population.  Comparing two strategies of individual selection for genotyping in the reference population, the strategy of evenly selection by family (SBF) performed slightly better than random selection in most situations.  Overall, we extended genomic prediction models that can comprehensively utilize WGS data and genomic annotation information in the framework of ssGBLUP, and validated the idea that properly handling the genomic annotation information and WGS data increased the predictive ability of ssGBLUP.  Moreover, while using WGS data, the genotyping strategy of maximizing the expected genetic relationship between the reference and candidate population could further improve the predictive ability of ssGBLUP.  The results from this study shed light on the comprehensive usage of genomic annotation information in WGS-based single-step genomic prediction.

    miR-99a-5p inhibits target gene FZD5 expression and steroid hormone secretion from goat ovarian granulosa cells
    ZHU Lu, JING Jing, QIN Shuai-qi, LU Jia-ni, ZHU Cui-yun, ZHENG Qi, LIU Ya, FANG Fu-gui, LI Yun-sheng, ZHANG Yun-hai, LING Ying-hui
    2022, 21(4): 1137-1145.  DOI: 10.1016/S2095-3119(21)63766-8
    Abstract ( )   PDF in ScienceDirect  
    MicroRNA (miRNA) has vital regulatory effects on the proliferation, differentiation and secretion of ovarian granulosa cells, but the role of miR-99a-5p in goat ovarian granulosa cells (GCs) is unclear.  Both miR-99a-5p and Frizzled-5 (FZD5) were found to be expressed in GCs in goat ovaries via fluorescence in situ hybridization and immunohistochemistry, respectively, and FZD5 was verified (P<0.001) as a target gene of miR-99a-5p by double luciferase reporter gene experiments.  Furthermore, FZD5 mRNA and protein expression were both found to be regulated (P<0.05) by miR-99a-5p in GCs.  Moreover, the overexpression of miR-99a-5p or knockdown of FZD5 suppressed (P<0.05) estradiol and progesterone secretion from the GCs, as determined by ELISA.  In summary, miR-99a-5p inhibits target gene FZD5 expression and estradiol and progesterone synthesis in GCs.  Our study thus provides seminal data and new insights into the regulatory mechanisms of follicular development in the goat and other animals.
    Long term effects of artificial rearing before weaning on the growth performance, ruminal microbiota and fermentation of fattening lambs
    HUANG Wen-qin, CUI Kai, HAN Yong, CHAI Jian-min, WANG Shi-qin, LÜ Xiao-kang, DIAO Qi-yu, ZHANG Nai-feng
    2022, 21(4): 1146-1160.  DOI: 10.1016/S2095-3119(21)63763-2
    Abstract ( )   PDF in ScienceDirect  
    Early life intervention is important to shape the gut microbiome profiles of adult animals due to the tremendous alteration of diet components.  Nevertheless, there is still no unified understanding about its long-term effects in lambs.  In this study, sixty 20-day-old lambs were assigned into ewe-rearing (ER) and artificial-rearing (AR) treatments to evaluate the effects of AR strategy on ruminal microbiota, fermentation, and morphology of pre-weaning lambs (from 20 to 60 days of age) and its long-term effects in the fattening stage (from 61 to 180 days of age).  During the pre-weaning stage, ER lambs were breastfed and supplemented starter, while AR lambs were artificially fed with milk replacer and starter.  During the fattening stage, all lambs in both treatments were fed with the same fattening diets.  At 60, 120 and 180 days of age, 6 lambs from each group were slaughtered to collect rumen content and tissue samples.  Compared with ER lambs, the dry matter feed intakes of AR lambs increased (P<0.05) from 20 to 180 days of age, companying an increased average daily gain (ADG) from 61 to 120 days of age (P<0.05) and from 121 to 180 days of age (0.05<P<0.1).  Although there was no difference in short-chain fatty acid (SCFA, including acetate, propionate, and butyrate) between treatments before weaning (P>0.05), it was higher (P<0.05) in AR lambs compared with ER lambs at the fattening stage.  The rumen keratin layer of AR lambs was thinner (P<0.05) than that of ER lambs.  Along with lamb growth from 60 to 180 days of age, the differences in rumen bacterial diversity between AR and ER treatments grew more distinct (P<0.05).  Compared with ER lambs, AR lambs increased (P<0.05) rumen bacteria abundance, such as phylum Spirochaetes and genus Treponema at 60 days of age, phylum Actinobacteria and genus Succiniclasticum at 120 days of age, and phylum Proteobacteria at 180 days of age, but decreased genus Selenomonas from 60 to 180 days of age, and Anaerovibrio at 180 days of age.  In summary, the early interventions before weaning could improve dry matter feed intake of lambs, which triggered robust rumen development and produced positive long-term effects on rumen fermentation and noticeable weight gain of fattening lambs.  It suggests that the artificial rearing strategy is effective in improving rumen fermentation and microbial maturity of intensive fattening lambs.
    NH4Cl promotes apoptosis and inflammation in bovine mammary epithelial cells via the circ02771/miR-194b/TGIF1 axis
    CHEN Zhi, LIANG Yu-sheng, ZONG Wei-cheng, GUO Jia-he, ZHOU Jing-peng, MAO Yong-jiang, JI De-jun, JIAO Pei-xin, Juan J LOOR, YANG Zhang-ping
    2022, 21(4): 1161-1176.  DOI: 10.1016/S2095-3119(21)63812-1
    Abstract ( )   PDF in ScienceDirect  
    Excess ammonia (NH3) in the circulation of dairy animals can reduce animal health and the quality of products for human consumption.  To develop effective prevention and treatment methods, it is essential to examine the molecular mechanisms through which excess NH3 may affect the mammary gland.  The present study used bovine mammary epithelial cells (BMECs) to evaluate the effects of exogenous NH4Cl on the abundance of circular RNAs (circRNAs) using high-throughput sequencing.  Among the identified circRNAs, circ02771 was the most significantly upregulated by exogenous NH4Cl (P<0.05), with a fold change of 4.12.  The results of the apoptosis and proliferation assays, transmission electron microscopy, H&E staining, and immunohistochemistry revealed that circ02771 increased apoptosis and inflammation.  A double luciferase reporter assay revealed that circ02771 targeted miR-194b, and the overexpression of circ02771 (pcDNA-circ02771) reduced (P<0.05) the expression of miR-194b and led to apoptosis and inflammation.  Circ02771 also enhanced the expression of transforming growth factor beta-induced factor homeobox 1 (TGIF1), which is a target gene of miR-194b.  Overall, this study suggests that the circ02771/miR-194b/TGIF1 axis plays a role in mediating the effects of NH4Cl on BMECs.  Therefore, this axis provides a novel target to help control hazards within the mammary gland from high circulating NH4Cl levels.
    Agro-ecosystem & Environment
    Transfer characteristics of nitrogen fixed by leguminous green manure crops when intercropped with maize in northwestern China
    LIU Rui, ZHOU Guo-peng, CHANG Dan-na, GAO Song-juan, HAN Mei, ZHANG Jiu-dong, SUN Xiao-feng, CAO Wei-dong
    2022, 21(4): 1177-1187.  DOI: 10.1016/S2095-3119(21)63674-2
    Abstract ( )   PDF in ScienceDirect  
    To ascertain the possibility of cultivating maize using biological nitrogen fixation (BNF) by leguminous green manure crops in maize/leguminous green manure intercropping systems, BNF and nitrogen (N) transfer were studied in Xining and Wuwei, two typical northwestern Chinese cities.  The experimental treatments included monocultured maize, monocultured green manures (hairy vetch and common vetch), and their intercropping systems.  The proportions of N derived from the atmosphere (%Ndfa) in intercropping systems were not significantly different from that in monocultured green manure systems at either experimental site, except for that in hairy vetch (HV) in Xining.  The amount of N derived from the atmosphere (Ndfa) of common vetch (CV) significantly decreased from 1.16 and 1.10 g/pot in monoculture to 0.77 and 0.55 g/pot when intercropped with maize, in Xining and Wuwei, respectively, and the Ndfa of HV when intercropped significantly decreased from 1.02 to 0.48 g/pot in Xining.  In the intercropping systems in Xining and Wuwei, the amounts of N transferred (Ntransfer) from CV to maize were 21.54 and 26.81 mg/pot, accounting for 32.9 and 5.9% respectively of the N accumulation in maize, and the values of Ntransfer from HV to maize were 39.61 and 46.22 mg/pot, accounting for 37.0 and 23.3%, respectively, of the N accumulation in maize.  Path analysis showed that soil nutrient and green manure biomass were mainly related to Ndfa, and that δ15N had a primary relationship with Ntransfer.  We found that 5.9–37.0% of N accumulation in maize was transferred from green manures, and that the N transfer ability to maize of HV was higher than that of CV.  In conclusion, intercropping with leguminous green manures provided a feasible way for maize to effectively utilize biologically fixed N.
    The rhizospheric microbiome becomes more diverse with maize domestication and genetic improvement
    HUANG Jun, LI Yun-feng, MA Yuan-ying, LI Yan-sheng, JIN Jian, LIAN Teng-xiang
    2022, 21(4): 1188-1202.  DOI: 10.1016/S2095-3119(21)63633-X
    Abstract ( )   PDF in ScienceDirect  
    Domestication and genetic improvement of maize improve yield and stress tolerance due to changes in morphological and physiological properties, which likely alter rhizosphere microbial diversity.  Understanding how the evolution of maize germplasm impacts its rhizobacterial traits during the growth stage is important for optimizing plant-microbe associations and obtaining yield gain in domesticated germplasms.  In this study, a total of nine accessions representing domestication and subsequent genetic improvement were selected.  We then sequenced the plant DNA and rhizobacterial DNA of teosinte, landraces and inbred lines at the seedling, flowering and maturity stages in a field trial.  Moreover, the soil chemical properties were determined at the respective stages to explore the associations of soil characteristics with bacterial community structures.  The results showed that domestication and genetic improvement increased the rhizobacterial diversity and substantially altered the rhizobacterial community composition.  The core microbiome in the rhizosphere differed among germplasm groups.  The co-occurrence network analysis demonstrated that the modularity in the bacterial network of the inbred lines was greater than those of teosinte and the landraces.  In conclusion, the increased diversity of the rhizobacterial community with domestication and genetic improvement may improve maize resilience to biotic stresses and soil nutrient availability to plants. 
    Agricultural Economics and Management
    Sustainability of the rice–crayfish farming model in waterlogged land: A case study in Qianjiang County, Hubei Province, China
    YUAN Peng-li, WANG Jin-ping, GUO Can, GUO Zi-yuan, GUO Yao, CAO Cou-gui
    2022, 21(4): 1203-1214.  DOI: 10.1016/S2095-3119(21)63787-5
    Abstract ( )   PDF in ScienceDirect  
    The rice–crayfish farming model has been rapidly developed and become an economically viable method to supply food in China in recent years.  However, its environmental and economic sustainability has not been thoroughly investigated.  This study uses a survey in 2016 and a field experiment in 2017 in Qianjiang, Hubei Province, China to assess the relative economics of concurrent rice–wheat (RW), rice–crayfish (RC), and crayfish monoculture (CM) models in waterlogged land areas.  The field survey indicated that the RC model had a higher benefit–cost ratio (3.5:1) than the RW (2.0:1) and CM (3.1:1) models and the RC model protected farmers’ enthusiasm for grain production facing unfavourable weather conditions.  The field experiment aimed to explore nitrogen management strategies in RC fields.  In the experiment, four levels of nitrogen concentration gradient - 0 kg N ha–1 (0 N), 75 kg N ha–1 (75 N), 150 kg N ha–1 (150 N) and 225 kg N ha–1 (225 N), were set in a 2-year-old rice–crayfish (RC2) field, an 8-year-old rice–crayfish (RC8) field, and a RW field as a control.  The field experiment results suggested that the peak  rice yield in RW, RC2, and RC8 occurred when 225 N, 150 N and 75 N were used, respectively.  In RC2 and RC8, however, residual feed-nitrogen that was not used by crayfish was utilized by rice plants.  Thus, an optimal amount of nitrogen in RC fields was proposed to improve the nitrogen use efficiency and reduce environmental pollution by nitrogen fertilizer.  Farmers use less nitrogen but have higher net income in RC than in RW and CM.  It is necessary to sustainably develop integrated farming technologies (i.e., proper field configurations for rice fields) to effectively sustain rice production.  The results also showed that the RC farming model was a viable diversification option for rice farmers in waterlogged land.  
    Wastewater irrigation and crop yield: A meta-analysis
    WANG Han-jie, Jingjing WANG, Xiaohua YU
    2022, 21(4): 1215-1224.  DOI: 10.1016/S2095-3119(21)63853-4
    Abstract ( )   PDF in ScienceDirect  
    Although wastewater irrigation in agriculture could be a potential adaptation to water scarcity, its effect on crop yield varies in the literature, making it difficult to evaluate its role in global food security comprehensively.  Using agronomic experiment data from 62 studies between 1987 and 2021, we employ a meta-analysis to analyze the factors contributing to the heterogeneous effects of wastewater irrigation on crop yield.  Our findings can be summarized as (1) the mean yield growth effect of wastewater irrigation is 19.7%; (2) domestic and breeding wastewater irrigation could significantly increase crop yield, while industrial wastewater has a negative effect although not significant; (3) high nutrients concentration of domestic wastewater is significantly positively correlated with crop yield; (4) agronomic experiment designs in terms of field experiment, experiment times, and fertilizer use could contribute to the divergent crop yield effects across the studies; (5) there is a publication bias of the research results between the English and Chinese literature; (6) the literature mainly sheds light on the short-run effect, and the long-run impact shall be an important research question in the future.