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    Creating large EMS populations for functional genomics and breeding in wheat

    Wenqiang Wang, Xizhen Guan, Yong Gan, Guojun Liu, Chunhao Zou, Weikang Wang, Jifa Zhang, Huifei Zhang, Qunqun Hao, Fei Ni, Jiajie Wu, Lynn Epstein, Daolin Fu
    2024, 23 (2): 484-493.   DOI: 10.1016/j.jia.2023.05.039
    Abstract519)      PDF in ScienceDirect      

    Wheat germplasm is a fundamental resource for basic research, applied studies, and wheat breeding, which can be enriched normally by several paths, such as collecting natural lines, accumulating breeding lines, and introducing mutagenesis materials.  Ethyl methane sulfonate (EMS) is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.  In this study, we created a million-scale EMS population (MEP) that started with the Chinese wheat cultivars ‘Luyan 128’, ‘Jimai 38’, ‘Jimai 44’, and ‘Shannong 30’.  In the M1 generation, the MEP had numerous phenotypical variations, such as >3,000 chlorophyll-deficient mutants, 2,519 compact spikes, and 1,692 male sterile spikes.  There were also rare mutations, including 30 independent tillers each with double heads.  Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable, appearing in the M2 or M3 generations.  To advance the entire MEP to higher generations, we adopted a single-seed descendent (SSD) approach.  All other seed composites of M2 were used to screen other agronomically important traits, such as the tolerance to herbicide quizalofop-P-methyl.  The MEP is available for collaborative projects, and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

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    OsNPF3.1, a nitrate, abscisic acid and gibberellin transporter gene, is essential for rice tillering and nitrogen utilization efficiency

    Junnan Hang, Bowen Wu, Diyang Qiu, Guo Yang, Zhongming Fang, Mingyong Zhang
    2024, 23 (4): 1087-1104.   DOI: 10.1016/j.jia.2023.04.024
    Abstract406)      PDF in ScienceDirect      

    Low-affinity nitrate transporter genes have been identified in subfamilies 4–8 of the rice nitrate transporter 1 (NRT1)/peptide transporter family (NPF), but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains unknown.  In this study, we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency (NUtE).  OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars, and its expression is positively associated with tiller number.  Its expression was higher in the basal part, culm, and leaf blade than in other parts of the plant, and was strongly induced by nitrate, abscisic acid (ABA) and gibberellin 3 (GA3) in the root and shoot of rice.  Electrophysiological experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter, with rice protoplast uptake assays showing it to be an ABA and GA3 transporter.  OsNPF3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering, especially at high nitrate concentrations.  The NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations, whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats (CRISPR) plants was increased under high nitrate concentrations.  The results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate concentrations.  The altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations, respectively.

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    FgGyp8 as a putative FgRab1 GAP is required for growth and pathogenesis by regulating FgSnc1-mediated secretory vesicles fusion in Fusarium graminearum
    ZHANG Xing-zhi, CHEN Shuang, Yakubu Saddeeq ABUBAKAR, MAO Xu-zhao, MIAO Peng-fei, WANG Zong-hua, ZHOU Jie, ZHENG Hua-wei
    2023, 22 (11): 3444-3457.   DOI: 10.1016/j.jia.2023.04.005
    Abstract369)      PDF in ScienceDirect      

    Fusarium graminearum is an important plant pathogenic fungus that causes disease and yield reduction in many cereal crops, such as wheat and barley.  Gyp8 stimulates GTP hydrolysis on Ypt1 in yeast.  However, the functions of Gyp8 in plant pathogenic fungi are still unknown.  In this study, we investigated the roles of FgGyp8 in Fgraminearum by genetic and pathological analyses.  Through gene knockout and phenotypic analyses, we found that FgGyp8 is required for vegetative growth in Fgraminearum.  The conidiation, conidial size and number of septa per conidium of ΔFggyp8 mutant are significantly reduced when compared to the wild type PH-1.  Furthermore, FgGyp8 is crucial for pathogenicity on wheat coleoptiles and wheat heads.  FgGyp8 contains a conserved TBC domain.  Domain deletion analysis showed that the TBC domain, C- and N-terminal regions of FgGyp8 are all important for its biological functions in Fgraminearum.  Moreover, we showed that FgGyp8 catalyzes the hydrolysis of the GTP on FgRab1 to GDP in vitro, indicating that FgGyp8 is a GTPase-activating protein (GAP) for FgRab1.  In addition, we demonstrated that FgGyp8 is required for FgSnc1-mediated fusion of secretory vesicles with the plasma membrane in Fgraminearum.  Finally, we showed that FgGyp8 has functional redundancy with another FgRab1 GAP, FgGyp1, in Fgraminearum.  Taken together, we conclude that FgGyp8 is required for vegetative growth, conidiogenesis, pathogenicity and acts as a GAP for FgRab1 in Fgraminearum.

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    Seedling Petri-dish inoculation method: A robust, easy-to-use and reliable assay for studying plant–Ralstonia solanacearum interactions
    CAO Peng, CHEN Jia-lan, LI Ning-ning, ZHANG Shuang-xi, WANG Rong-bo, LI Ben-jin, LIU Pei-qing, AN Yu-yan, ZHANG Mei-xiang
    2023, 22 (12): 3709-3719.   DOI: 10.1016/j.jia.2023.05.020
    Abstract354)      PDF in ScienceDirect      

    Ralstonia solanacearum causes a lethal bacterial wilt disease in many crops, leading to huge losses in crop production every year.  Understanding of plant–Rsolanacearum interactions will aid to develop efficient strategies to control the disease.  As a soilborne pathogen, Rsolanacearum naturally infects plants via roots.  A huge limitation in studying plant–Rsolanacearum interactions is the large variation of Rsolanacearum infection assay due to the variable soil conditions and uneven inoculum exposure.  Here, we developed a robust and reliable Petri-dish inoculation method which allows consistent and stable infection in young plant seedlings.  This method is easy to use, takes about only 10 days from seed germination to the completion of inoculation assay, and requires less inoculum of bacteria as well as growth chamber space.  We proved the efficacy of the seedling Petri-dish inoculation method by analyzing plant defense primed by molecular patterns, resistance of defense-related plant mutants, and virulence of Rsolanacearum mutants.  Furthermore, we demonstrated that the seedling Petri-dish inoculation method can be applied to other host plants such as tobacco and has great potential for high-throughput screening of resistant plant germplasms to bacterial wilt in the future.

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    Differential metabolites and their transcriptional regulation in seven major tea cultivars (Camellia sinensis) in China
    GAO Ting, HOU Bing-hao, SHAO Shu-xian, XU Meng-ting, ZHENG Yu-cheng, JIN Shan, WANG Peng-jie, YE Nai-xing
    2023, 22 (11): 3346-3363.   DOI: 10.1016/j.jia.2023.02.009
    Abstract349)      PDF in ScienceDirect      

    Various genetic and biochemical characteristics exist in tea plant cultivars, and they largely determine production suitability and tea quality.  Here, we performed transcriptomic and metabolomic analyses of young shoots of seven tea cultivars and identified major regulatory transcription factors (TFs) for the characteristic metabolites in different cultivars based on weighted gene co-expression network analysis (WGCNA).  Phenotypically, we found that ‘Tieguanyin’ (TGY) and ‘Fujian Shuixian’ (FJSX), which are suitable for oolong tea, had higher catechin contents.  The metabolites of ‘Jinxuan’ (JX) were more prominent, especially the contents of phenolic acids, flavonoids, terpenes, and tannins, which were higher than those of the other six cultivars.  Moreover, ‘Fudingdabai’ (FDDB), which is suitable for white tea, was rich in amino acids, linolenic acid, and saccharides.  At the molecular level, hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase (HCT) (CsTGY12G0001876, and CsTGY06G0003042) led to the accumulation of chlorogenic acid in TGY.  The main reason for the higher l-ascorbic acid content in FJSX was the high expression levels of L-galactono-1,4-lactone hydrogenase (GalLDH) (CsTGY13G0000389) and Myo-inositol oxygenase (MIOX) (CsTGY14G0001769, and CsTGY14G0001770), which were regulated by WRKY (CsTGY11G0001197).  Furthermore, FDDB, ‘Longjing 43’ (LJ43), ‘Shuchazao’ (SCZ)  and ‘Baihaozao’ (BHZ) had higher free fatty acid contents, among which MYB (CsTGY14G0002344) may be a hub gene for the regulation of palmitoleic acid accumulation.  More importantly, we found that the shoots of TGY were green with purple, mainly due to the accumulation of anthocyanins and the downregulation of the Mg-protoporphyrin IX nonomethyl ester cyclase (MPEC) (CsTGY10G0001989) gene that affects chlorophyll synthesis.  These results will provide a theoretical reference for tea cultivar breeding and suitability.

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    Establishment of a system for screening and identification of novel bactericide targets in the plant pathogenic bacterium Xanthomonas oryzae pv. oryzae using Tn-seq and SPR
    Chaoyue Pang, Ling Jin, Haoyu Zang, Damalk Saint-Claire S. Koklannou, Jiazhi Sun, Jiawei Yang, Yongxing Wang, Liang Xu, Chunyan Gu, Yang Sun, Xing Chen, Yu Chen
    2024, 23 (5): 1580-1592.   DOI: 10.1016/j.jia.2023.04.043
    Abstract346)      PDF in ScienceDirect      

    Xanthomonas spp. cause severe bacterial diseases.  However, effective strategies for prevention and management of these diseases are scarce.  Thus, it is necessary to improve the efficiency of control of diseases caused by Xanthomonas.  In this study, Xanthomonas oryzae pv. oryzae (Xoo), which causes rice bacterial leaf blight, has been studied as a representative.  A transposon insertion library of Xoo, comprising approximately 200,000 individual insertion mutants, was generated.  Transposon sequencing data indicated that the mariner C9 transposase mapped at 35.7–36.4% of all potential insertion sites, revealing 491 essential genes required for the growth of Xoo in rich media.  The results show that, compared to the functions of essential genes of other bacteria, the functions of some essential genes of Xoo are unknown, 25 genes might be dangerous for the Xanthomonas group, and 3 are specific to Xanthomonas.  High-priority candidates for developing broad-spectrum, Xanthomonas-specific, and environment-friendly bactericides were identified in this study.  In addition, this study revealed the possible targets of dioctyldiethylenetriamine using surface plasmon resonance (SPR) in combination with high performance liquid chromatography–mass spectrometry (HPLC–MS).  The study also provided references for the research of some certain bactericides with unknown anti-bacterial mode of action.  In conclusion, this study urged a better understanding of Xanthomonas, provided meaningful data for the management of bacterial leaf blight, and disclosed selected targets of a novel bactericide.

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    Identification, pathogenicity, and fungicide sensitivity of Eutiarosporella dactylidis associated with leaf blight on maize in China

    Cheng Guo, Xiaojie Zhang, Baobao Wang, Zhihuan Yang, Jiping Li, Shengjun Xu, Chunming Wang, Zhijie Guo, Tianwang Zhou, Liu Hong, Xiaoming Wang, Canxing Duan
    2024, 23 (3): 888-900.   DOI: 10.1016/j.jia.2023.09.032
    Abstract346)      PDF in ScienceDirect      

    Maize (Zea mays L.) is an economically vital grain crop that is cultivated worldwide.  In 2011, a maize foliar disease was detected in Lingtai and Lintao counties in Gansu Province, China.  The characteristic signs and symptoms of this disease include irregular chlorotic lesions on the tips and edges of infected leaves and black punctate fruiting bodies in dead leaf tissues.  Given favourable environmental conditions, this disease spread to areas surrounding Gansu.  In this study, infected leaves were collected from Gansu and Ningxia Hui Autonomous Region between 2018 and 2020 to identify the disease-causing pathogen.  Based on morphological features, pathogenicity tests, and multi-locus phylogenetic analysis involving internal transcribed spacer (ITS), 18S small subunit rDNA (SSU), 28S large subunit rDNA (LSU), translation elongation factor 1-alpha (TEF), and β-tubulin (TUB) sequences, Eutiarosporella dactylidis was identified as the causative pathogen of this newly discovered leaf blight.  Furthermore, an in vitro bioassay was conducted on representative strains using six fungicides, and both fludioxonil and carbendazim were found to significantly inhibit the mycelial growth of E. dactylidis.  The results of this study provide a reference for the detection and management of Eutiarosporella leaf blight.

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    Physiological and biochemical characteristics of boscalid resistant isolates of Sclerotinia sclerotiorum from asparagus lettuce
    SHI Dong-ya, LI Feng-jie, ZHANG Zhi-hui, XU Qiao-nan, CAO Ying-ying, Jane Ifunanya MBADIANYA, LI Xin, WANG Jin, CHEN Chang-jun
    2023, 22 (12): 3694-3708.   DOI: 10.1016/j.jia.2023.09.024
    Abstract297)      PDF in ScienceDirect      

    Laboratory mutants of Sclerotinia sclerotiorum (Lib) de Bary, resistant to boscalid, have been extensively characterized.  However, the resistance situation in the lettuce field remains largely elusive.  In this study, among the 172 Ssclerotiorum isolates collected from asparagus lettuce field in Jiangsu Province, China, 132 isolates (76.74%) exhibited low-level resistance to boscalid (BosLR), with a discriminatory dose of 5 μg mL–1.  In comparison to the boscalid-sensitive (BosS) isolates, most BosLR isolates demonstrated a slightly superior biological fitness, as evidenced by data on mycelial growth, sclerotium production and pathogenicity.  Moreover, most BosLR isolates showed comparable levels of oxalic acid (OA) accumulation, increased exopolysaccharide (EPS) content and reduced membrane permeability when compared to the BosS isolates.  Nevertheless, their responses to distinct stress factors diverged significantly.  Furthermore, the effectiveness of boscalid in controlling BosLR isolates on radish was diminished compared to its efficacy on BosS isolates.  Genetic mutations were identified in the SDH genes of BosLR isolates, revealing the existence of three resistant genotypes: I (A11V at SDHB, SDHBA11V), II (Q38R at SDHC, SDHCQ38R) and III (SDHBA11V+SDHCQ38R).  Importantly, no cross-resistance was observed between boscalid and other fungicides such as thifluzamide, pydiflumetofen, fluazinam, or tebuconazole.  Our molecular docking analysis indicated that the docking total score (DTS) of the type I resistant isolates (1.3993) was lower than that of the sensitive isolates (1.7499), implying a reduced affinity between SDHB and boscalid as a potential mechanism underlying the boscalid resistance in Ssclerotiorum.  These findings contribute to an enhanced comprehension of boscalid’s mode of action and furnish valuable insights into the management of boscalid resistance.

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    Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs
    Mu Zeng, Binhu Wang, Lei Liu, Yalan Yang, Zhonglin Tang
    2024, 23 (1): 217-227.   DOI: 10.1016/j.jia.2023.02.040
    Abstract256)      PDF in ScienceDirect      

    Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.  As the major indicators of growth performance, the backfat thickness (BFT), loin eye area (LEA), and days to 100 kg (D100) traits are commonly used to the genetics improvement in pigs.  However, the available genetic markers for these traits are limited.  To uncover novel loci and candidate genes associated with growth performance, we collected the phenotypic information of BFT, LEA, and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.  We performed a genome-wide association study (GWAS) using 4 statistical models, including mixed linear models (MLM), fixed and random model circulating probability unification (FarmCPU), settlement of MLM under progressively exclusive relationships (SUPER), Bayesian-information and linkage-disequilibrium Iteratively nested keyway (Blink), and identified 5, 3, and 6 high-confidence single nucleotide polymorphisms (SNPs) associated with BFT, LEA, and D100, respectively.  Variant annotation and quantitative trait locus (QTL) mapping analysis suggested that 6 genes (SKAP2, SATB1, PDE7B, PPP1R16B, WNT3, and WNT9B) were potentially associated with growth performance in pigs.  Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2 (SKAP2) was higher in prenatal muscles than in postnatal muscles, and the expression of Phosphodiesterase 7B (PDE7B) continuously increased during the prenatal stages and gradually decreased after birth, implying their potential roles in prenatal skeletal muscle development.  Overall, this study provides new candidate loci and genes for the genetic improvement of pigs.

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    A high-quality genome of Actinidia eriantha provides new insight into ascorbic acid regulation
    LIAO Guang-lian, HUANG Chun-hui, JIA Dong-feng, ZHONG Min, TAO Jun-jie, QU Xue-yan, XU Xiao-biao
    2023, 22 (11): 3244-3255.   DOI: 10.1016/j.jia.2023.07.018
    Abstract248)      PDF in ScienceDirect      

    Actinidia eriantha is one of the species of kiwifruit with a particularly high ascorbic acid (AsA) content.  However, the molecular mechanism driving AsA richness in fruit remains unclear.  In order to reveal the molecular mechanism of AsA richness in Aeriantha, this study constructed a regulatory network related to AsA metabolism by combining genomics, metabolomics and transcriptomics.  We assembled a high-quality genome of Aeriantha ‘Ganlv 1’ with only five remaining gaps.  The assembly is comprised of 29 pseudochromosomes with a total size of 615.95 Mb, and contig N50 of 20.35 Mb. Among them, 24 of the pseudochromosomes were obtained directly from telomere-to-telomere.  The LTR assembly index score and consensus quality value were 21.34 and 39.90%, respectively.  Subsequently, 61 metabolites and 2 092 genes were found to be differentially accumulated/expressed during fruit development by metabolome and transcriptome assays, respectively.  AsA metabolism and the cyclic regeneration pathway were found to have high expression levels throughout fruit growth and development, suggesting its crucial role in the regulation of AsA.  Furthermore, the AsA contents are highly associated with ascorbate peroxidase genes.  The genome obtained in this study provides genomic resources for the genetic and breeding research of Aeriantha, and the constructed regulatory network can provide a public data platform for future research on kiwifruit.

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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
    Abstract242)      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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    SUPER WOMAN 2 (SPW2) maintains organ identity in spikelets by inhibiting the expression of floral homeotic genes OsMADS3, OsMADS58, OsMADS13, and DROOPING LEAF
    ZHUANG Hui, LAN Jin-song, YANG Qiu-ni, ZHAO Xiao-yu, LI Yu-huan, ZHI Jing-ya, SHEN Ya-lin, HE Guang-hua, LI Yun-feng
    2024, 23 (1): 59-76.   DOI: 10.1016/j.jia.2023.07.010
    Abstract241)      PDF in ScienceDirect      

    Flower organ identity in rice is mainly determined by the A-, B-, C- and E-class genes, with the majority encoding MADS-box transcription factors.  However, few studies have investigated how the expression of these floral organ identity genes is regulated during flower development.  In this study, we identified a gene named SUPER WOMAN 2 (SPW2), which is necessary for spikelet/floret development in rice by participating in the regulation of the expression of pistil identity genes such as OsMADS3, OsMADS13, OsMADS58 and DL.  In the spw2 mutant, ectopic stigma/ovary-like tissues were observed in the non-pistil organs, including sterile lemma, lemma, palea, lodicule, and stamen, suggesting that the identities of these organs were severely affected by mutations in SPW2SPW2 was shown to encode a plant-specific EMF1-like protein that is involved in H3K27me3 modification as an important component of the PRC2 complex.  Expression analysis showed that the SPW2 mutation led to the ectopic expression of OsMADS3, OsMADS13, OsMADS58, and DL in non-pistil organs of the spikelet.  The ChIP-qPCR results showed significant reductions in the levels of H3K27me3 modification on the chromatin of these genes.  Thus, we demonstrated that SPW2 can mediate the process of H3K27me3 modification of pistil-related genes to regulate their expression in non-pistil organs of spikelets in rice.  The results of this study expand our understanding of the molecular mechanism by which SPW2 regulates floral organ identity genes through epigenetic regulation.

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    Transforming agri-food systems for multiple wins in nutrition, inclusion and environment
    Shenggen Fan, Qiran Zhao, Jingjing Wang
    2024, 23 (2): 355-358.   DOI: 10.1016/j.jia.2024.01.017
    Abstract233)      PDF in ScienceDirect      

    The call for agri-food system transformation is urgent in many global development agendas (UN 2023).  Food systems have contributed to economic prosperity and feeding the world, but they are also associated with numerous challenges, including climate change, continued hunger, poor diets and malnutrition, and increasing disparities (Webb et al. 2020; Fanzo et al. 2021).  The vulnerabilities of food systems have been further aggravated by the COVID-19 pandemic, geopolitical disruptions, extreme weather events, and economic uncertainties (IPCC 2023; FAO 2023).  The rapid population growth, urbanization and industrialization have also resulted in significant land and water resource pressures, as well as food safety and security in many developing countries.

    Thus, the agri-food systems transformation should shift from addressing singular dimension (e.g., grain supply or grain self-sufficiency) to achieving multiple goals simultaneously, including nutrition, health, inclusion, environmental sustainability and climate change (Fan et al. 2021). 

    There are several strategies that can be used for achieving these multiple goals including access to modern technologies such as internet, changing production structure, promoting more stable and resilient income for farmers, implementing social programs to protect vulnerable population, and of course continued technological and productivity improvement .

    Under this context, this special focus of the Journal of Integrative Agriculture is to provide empirical evidence on multiple win strategies to achieve agri-food systems transformation.  The issue comprises nine papers covering a wide array of topics aimed at improved nutrition, sustainability inclusion and continued efficiency or productivity improvement within the food systemWe trust that these papers will enhance readers’ comprehension of how food system transformation can contribute to multiple dimensions of the food system’s goals.

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    High serum reproductive hormone levels at mid-pregnancy support Meishan pig prolificacy
    ZHOU Rong, YANG Yalan, LIU Ying, CHEN Jie, YANG Bing, TANG Zhong-lin
    2023, 22 (11): 3489-3499.   DOI: 10.1016/j.jia.2023.05.014
    Abstract229)      PDF in ScienceDirect      
    Increasing prolificacy is an important aim in the pig industry.  Regions associated with litter size have been revealed, but detailed molecular mechanisms are unclear.  The Meishan pig is one of the most prolific breeds, with higher prolificacy than the Yorkshire pig, which exhibits high feeding efficiency and lean meat yield.  The ovary is the key organ determining reproductive traits during pregnancy by synthesizing and secreting reproductive hormones essential for conceptus maintenance.  In this comparative multi-omics study of the ovary transcriptome, proteome, and metabolome on day 49 of pregnancy, we aimed to identify genomic, proteomic, and metabolomic differences between the ovaries of Meishan and Yorkshire pigs to reveal potential molecular mechanisms conferring high prolificacy.  Meishan pigs demonstrated general downregulation of steroid biosynthesis and butanoate metabolism in the ovary during mid-pregnancy at both transcriptome and proteome levels but exhibited higher serum cholesterol, estradiol, and progesterone levels than Yorkshire pigs.  We also identified several single-nucleotide polymorphisms in the genes of the steroid hormone pathway associated with litter number, average birth weight, and total litter weight.  Lower biosynthesis rates but elevated serum levels of reproductive hormones during mid- and late pregnancy are essential for the greater prolificacy of Meishan pigs.
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    Effect of chemical regulators on the recovery of leaf physiology, dry matter accumulation and translocation, and yield-related characteristics in winter wheat following dry-hot wind
    Yanan Xu, Yue Wu, Yan Han, Jiqing Song, Wenying Zhang, Wei Han, Binhui Liu, Wenbo Bai
    2024, 23 (1): 108-121.   DOI: 10.1016/j.jia.2023.04.019
    Abstract217)      PDF in ScienceDirect      

    Dry-hot wind stress causes losses in wheat productivity in major growing regions worldwide, especially winter wheat in the Huang-Huai-Hai Plain of China, and both the occurrence and severity of such events are likely to increase with global climate change.  To investigate the recovery of physiological functions and yield formation using a new non-commercial chemical regulator (NCR) following dry-hot wind stress, we conducted a three-year field experiment (2018–2021) with sprayed treatments of tap water (control), monopotassium phosphate (CKP), NCR at both the jointing and flowering stages (CFS), and NCR only at the jointing stage (FSJ) or flowering stage (FSF).  The leaf physiology, biomass accumulation and translocation, grain-filling process, and yield components in winter wheat were assessed.  Among the single spraying treatments, the FSJ treatment was beneficial for the accumulation of dry matter before anthesis, as well as larger increases in the maximum grain-filling rate and mean grain-filling rate.  The FSF treatment performed better in maintaining a high relative chlorophyll content as indicated by the SPAD value, and a low rate of excised leaf water loss in flag leaves, promoting dry matter accumulation and the contribution to grain after anthesis, prolonging the duration of grain filling, and causing the period until the maximum grain-filling rate reached earlier.  The CFS treatment was better than any other treatments in relieving the effects of dry-hot wind.  The exogenous NCR treatments significantly increased grain yields by 12.45–18.20% in 2018–2019, 8.89–13.82% in 2019–2020, and 8.10–9.00% in 2020–2021.  The conventional measure of the CKP treatment only increased grain yield by 6.69% in 2020–2021.  The CFS treatment had the greatest mitigating effect on yield loss under dry-hot wind stress, followed by the FSF and FSJ treatments, and the CKP treatment only had a minimal effect.  In summary, the CFS treatment could be used as the main chemical control measure for wheat stress resistance and yield stability in areas with a high incidence of dry-hot wind.  This treatment can effectively regulate green retention and the water status of leaves, promote dry matter accumulation and efficient translocation, improve the grain-filling process, and ultimately reduce yield losses.

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    Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

    Wenting Li, Chaoqun Gao, Zhao Cai, Sensen Yan, Yanru Lei, Mengya Wei, Guirong Sun, Yadong Tian, Kejun Wang, Xiangtao Kang
    2024, 23 (3): 975-987.   DOI: 10.1016/j.jia.2023.10.009
    Abstract205)      PDF in ScienceDirect      
    Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations.  In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure.  The breeds were divided into five conservation populations (GS1, 2010, ex-situ; GS2, 2019, ex-situ; GS3, 2019, in-situ; XB1, 2010, in-situ; and XB2, 2019, in-situ) based on conservation methods and generations.  The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest.  The degree of inbreeding of GS2 was higher than that of GS1 and GS3.  Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2.  In terms of population structure, the GS3 population were stratified relative to GS1 and GS2.  According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar.   We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs (in-situ and ex-situ).  While XB1 and XB2 had similar levels of genetic diversity.  Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.
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    circRNA3669 promotes goat endometrial epithelial cells proliferation via miR-26a/RCN2 to activate PI3K/AKT-mTOR and MAPK pathways

    Xiaorui Liu, Jiuzeng Cui, Mengyao Wei, Xiaofei Wang, Yuexia Liu, Zhongshi Zhu, Min Zhou, Gui Ba, Langda Suo, Yuxuan Song, Lei Zhang
    2024, 23 (3): 960-974.   DOI: 10.1016/j.jia.2023.05.029
    Abstract203)      PDF in ScienceDirect      
    The development of receptive endometrium (RE) from pre-receptive endometrium (PE) for successful embryo implantation is a complex dynamic process in which the morphology and physiological states of the endometrial epithelium undergo a series of significant changes, including cell proliferation and apoptosis.  However, the molecular mechanisms are not yet fully understood.  In this study, a higher circRNA3669 level was observed in PE than in RE of goats.  Functional assays revealed that this overexpression promoted the proliferation of goat endometrial epithelial cells (GEECs) by activating the expression of genes related to the PI3K/AKT-mTOR and MAPK pathways, thereby inhibiting apoptosis in vitro.  Furthermore, circRNA3669 functioned as a competing endogenous RNA (ceRNA) to upregulate Reticulocalbin-2 (RCN2) expression at the post-transcriptional level by interacting with and downregulating miR-26a in GEECs.  In addition, RCN2, which is highly expressed in the PE of goats, was found to be regulated by β-estradiol (E2) and progesterone (P4).  Our results demonstrated that RCN2 also affected the key proteins PI3K, AKT, mTOR, JNK, and P38 in the PI3K/AKT-mTOR and MAPK pathways, thereby facilitating GEECs proliferation and suppressing their apoptosis in vitro.  Collectively, we constructed a new circRNA3669-miR-26a-RCN2 regulatory network in GEECs, which further provides strong evidence that circRNA could potentially play a crucial regulatory role in the development of RE in goats.
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    3D genome organization and its study in livestock breeding
    Jie Cheng, Xiukai Cao, Shengxuan Wang, Jiaqiang Zhang, Binglin Yue, Xiaoyan Zhang, Yongzhen Huang, Xianyong Lan, Gang Ren, Hong Chen
    2024, 23 (1): 39-58.   DOI: 10.1016/j.jia.2023.04.007
    Abstract199)      PDF in ScienceDirect      

    Eukaryotic genomes are hierarchically packaged into cell nucleus, affecting gene regulation.  The genome is organized into multiscale structural units, including chromosome territories, compartments, topologically associating domains (TADs), and DNA loops.  The identification of these hierarchical structures has benefited from the development of experimental approaches, such as 3C-based methods (Hi-C, ChIA-PET, etc.), imaging tools (2D-FISH, 3D-FISH, Cryo-FISH, etc.) and ligation-free methods (GAM, SPRITE, etc.).  In recent two decades, numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms, such as regulating enhancer activity and promoter-enhancer interactions.  However, there are relatively few studies about the 3D genome in livestock species.  Therefore, studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.  In this review, we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies, drawing inspiration to explore the 3D genomics of livestock species.  We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

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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
    Abstract199)      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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    Genetic dissection and validation of a major QTL for grain weight on chromosome 3B in bread wheat (Triticum aestivum L.)

    Simin Liao, Zhibin Xu, Xiaoli Fan, Qiang Zhou, Xiaofeng Liu, Cheng Jiang, Liangen Chen, Dian Lin, Bo Feng, Tao Wang
    2024, 23 (1): 77-92.   DOI: 10.1016/j.jia.2023.04.023
    Abstract198)      PDF in ScienceDirect      

    Grain weight is one of the key components of wheat (Triticum aestivum L.) yield.  Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.  A recombinant inbred line (RIL) population derived from a cross between W7268 and Chuanyu 12 (CY12) was employed to detect quantitative trait loci (QTLs) for thousand-grain weight (TGW), grain length (GL), grain width (GW), and the ratio of grain length to width (GLW) in six environments.  Seven major QTLs, QGl.cib-2D, QGw.cib-2D, QGw.cib-3B, QGw.cib-4B.1, QGlw.cib-2D.1, QTgw.cib-2D.1 and QTgw.cib-3B.1, were consistently identified in at least four environments and the best linear unbiased estimation (BLUE) datasets, and they explained 2.61 to 34.85% of the phenotypic variance.  Significant interactions were detected between the two major TGW QTLs and three major GW loci.  In addition, QTgw.cib-3B.1 and QGw.cib-3B were co-located, and the improved TGW at this locus was contributed by GW.  Unlike other loci, QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike (GNS).  They were further validated in advanced lines using Kompetitive Allele Specific PCR (KASP) markers, and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.  Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.  According to gene annotation, spatial expression patterns, ortholog analysis and sequence variation, the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.  Collectively, the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.

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