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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
    Abstract562)      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
    Abstract472)      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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    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
    Abstract383)      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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    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
    Abstract360)      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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    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
    Abstract309)      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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    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
    Abstract270)      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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    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
    Abstract270)      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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    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
    Abstract260)      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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    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
    Abstract257)      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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    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
    Abstract246)      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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    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
    Abstract242)      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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    Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding

    Shuliang Jiao, Qinyan Li, Fan Zhang, Yonghong Tao, Yingzhen Yu, Fan Yao, Qingmao Li, Fengyi Hu, Liyu Huang
    2024, 23 (3): 769-780.   DOI: 10.1016/j.jia.2023.05.010
    Abstract238)      PDF in ScienceDirect      

    Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution.  The Green Revolution gene Semidwarf 1 (SD1), which modulates gibberellic acid (GA) biosynthesis, plays a principal role in determining rice plant height.  Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production.  The plant height mediated by SD1 also favors grain yield under certain conditions.  However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production.  In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions.  In response to dryland environments, rice requires a reduction in plant height to cope with water deficits.  Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation.  Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem.  Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields.  In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height.  During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height.  Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production.  All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.

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    Genome-wide association study of grain micronutrient concentrations in bread wheat

    Yongchao Hao, Fanmei Kong, Lili Wang, Yu Zhao, Mengyao Li, Naixiu Che, Shuang Li, Min Wang, Ming Hao, Xiaocun Zhang, Yan Zhao
    2024, 23 (5): 1468-1480.   DOI: 10.1016/j.jia.2023.06.030
    Abstract231)      PDF in ScienceDirect      

    Bread wheat (Triticum aestivum) is a staple food crop worldwide.  The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world’s growing population.  Here, 45,298 single-nucleotide polymorphisms (SNPs) from 55K chip arrays were used to genotype a panel of 768 wheat cultivars, and a total of 154 quantitative trait loci (QTLs) were detected for eight traits under three environments by genome-wide association study (GWAS).  Three QTLs (qMn-3B.1, qFe-3B.4, and qSe-3B.1/qFe-3B.6) detected repeatedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant SNPs.  Significant SNPs in the three QTL regions formed six haplotypes for qMn-3B.1, three haplotypes for qFe-3B.4, and three haplotypes for qSe-3B.1/qFe-3B.6.  Phenotypic analysis revealed significant differences among haplotypes.  These results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern wheat.  Based on the QTL regions, we identified 15 high-confidence genes, eight of which were stably expressed in different tissues and/or developmental stages.  TraesCS3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology (GO) analysis.  TraesCS3B02G199000, which belongs to qSe-3B.1/qFe-3B.6, was determined to be a member of the WRKY gene family.  Overall, this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain, and this information will facilitate the breeding of wheat cultivars with improved grain properties.

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    Establishment of a transformation system in close relatives of wheat under the assistance of TaWOX5

    Yanan Chang, Junxian Liu, Chang Liu, Huiyun Liu, Huali Tang, Yuliang Qiu, Zhishan Lin, Ke Wang, Yueming Yan, Xingguo Ye
    2024, 23 (6): 1839-1849.   DOI: 10.1016/j.jia.2023.06.021
    Abstract228)      PDF in ScienceDirect      

    Species closely related to wheat are important genetic resources for agricultural production, functional genomics studies and wheat improvement.  In this study, a wheat gene related to regeneration, TaWOX5, was applied to establish the Agrobacterium-mediated transformation systems of Triticum monococcum, hexaploid triticale, and rye (Secale cereale L.) using their immature embryos.  Transgenic plants were efficiently generated.  During the transformation process, the Agrobacterium infection efficiency was assessed by histochemical staining for β-glucuronidase (GUS).  Finally, the transgenic nature of regenerated plants was verified by polymerase chain reaction (PCR)-based genotyping for the presence of the GUS and bialaphos resistance (bar) genes, histochemical staining for GUS protein, and the QuickStix strip assay for bar protein.  The transformation efficiency of Tmonococcum genotype PI428182 was 94.4%; the efficiencies of four hexaploid triticale genotypes Lin456, ZS3297, ZS1257, and ZS3224 were 52.1, 41.2, 19.4, and 16.0%, respectively; and the transformation efficiency of rye cultivar Lanzhou Heimai was 7.8%.  Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) analyses indicated that the GUS transgenes were integrated into the distal or near centromere (proximal) regions of the chromosomes in transgenic Tmonococcum and hexaploid triticale plants.  In the transgenic hexaploid triticale plants, the foreign DNA fragment was randomly integrated into the AABB and RR genomes.  Furthermore, the transgene was almost stably inherited in the next generation by Mendel’s law.  The findings in this study will promote the genetic improvement of the three plant species for grain or forage production and the improvement of cereal species including wheat for functional genomics studies.

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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
    Abstract224)      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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    Molecular mechanisms of stress resistance in sorghum: Implications for crop improvement strategies

    Hongxiang Zheng, Yingying Dang, Xianmin Diao, Na Sui
    2024, 23 (3): 741-768.   DOI: 10.1016/j.jia.2023.12.023
    Abstract224)      PDF in ScienceDirect      

    Abiotic stresses, such as drought, salt, extreme temperatures, and heavy metal pollution, are the main environmental factors that limit crop growth and yield.  Sorghum, a C4 grass plant with high photosynthetic efficiency, can grow in adverse environmental conditions due to its excellent stress resistance characteristics.  Therefore, unraveling the stress-resistance mechanism of sorghum could provide a theoretical basis for developing and cultivating various stress-resistant crops.  This understanding could also help to create a conducive environment for using marginal soil in agriculture and ensuring food security.  In this review, we discuss the adaptation mechanisms of sorghum under drought, salinity, temperature, and soil heavy metal stresses, the specific response to stress, the screening of sorghum-resistant germplasm, and the identification and functional analysis of the relevant genes and quantitative trait loci (QTL).  In addition, we discuss the application potential of different stress-tolerant sorghum germplasms reported to date and emphasize the feasibility and potential use in developing and promoting highly stress-tolerant sorghum in marginal soil.

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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
    Abstract223)      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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    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
    Abstract219)      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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    The underlying mechanism of variety–water–nitrogen–stubble damage interactions on yield formation in ratoon rice with low stubble height under mechanized harvesting

    Jingnan Zou, Ziqin Pang, Zhou Li, Chunlin Guo, Hongmei Lin, Zheng Li, Hongfei Chen, Jinwen Huang, Ting Chen, Hailong Xu, Bin Qin, Puleng Letuma, Weiwei Lin, Wenxiong Lin
    2024, 23 (3): 806-823.   DOI: 10.1016/j.jia.2023.05.038
    Abstract218)      PDF in ScienceDirect      

    Agronomic measures are the key to promote the sustainable development of ratoon rice by reducing the damage from mechanical crushing to the residual stubble of the main crop, thereby mitigating the impact on axillary bud sprouting and yield formation in ratoon rice.  This study used widely recommended conventional rice Jiafuzhan and hybrid rice Yongyou 2640 as the test materials to conduct a four-factor block design field experiment in a greenhouse of the experimental farm of Fujian Agricultural and Forestry University, China from 2018 to 2019.  The treatments included fertilization and no fertilization, alternate wetting and drying irrigation and continuous water flooding irrigation, and plots with and without artificial crushing damage on the rice stubble.  At the same time, a 13C stable isotope in-situ detection technology was used to fertilize the pot experiment.   The results showed significant interactions among varieties, water management, nitrogen application and stubble status.  Relative to the long-term water flooding treatment, the treatment with sequential application of nitrogen fertilizer coupled with moderate field drought for root-vigor and tiller promotion before and after harvesting of the main crop, significantly improved the effective tillers from low position nodes.  This in turn increased the effective panicles per plant and grains per panicle by reducing the influence of artificial crushing damage on rice stubble and achieving a high yield of the regenerated rice.  Furthermore, the partitioning of 13C assimilates to the residual stubble and its axillary buds were significantly improved at the mature stage of the main crop, while the translocation rate to roots and rhizosphere soil was reduced at the later growth stage of ratooning season rice.  This was triggered by the metabolism of hormones and polyamines at the stem base regulated by the interaction of water and fertilizer at this time.  We therefore suggest that to achieve a high yield of ratoon rice with low stubble height under mechanized harvesting, the timely application of nitrogen fertilizer is fundamental, coupled with moderate field drying for root-vigor preservation and tiller promotion before and after the mechanical harvesting of the main crop.

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    The auxin transporter OsAUX1 regulates tillering in rice (Oryza sativa)

    Luqi Jia, Yongdong Dai, Ziwei Peng, Zhibo Cui, Xuefei Zhang, Yangyang Li, Weijiang Tian, Guanghua He, Yun Li, Xianchun Sang
    2024, 23 (5): 1454-1467.   DOI: 10.1016/j.jia.2023.05.041
    Abstract217)      PDF in ScienceDirect      
    Tillering is an important agronomic trait of rice (Oryza sativa) that affects the number of effective panicles, thereby affecting yields.  The phytohormone auxin plays a key role in tillering.  Here we identified the high tillering and semi-dwarf 1 (htsd1) mutant with auxin-deficiency root characteristics, such as shortened lateral roots, reduced lateral root density, and enlarged root angles.  htsd1 showed reduced sensitivity to auxin, but the external application of indole-3-acetic acid (IAA) inhibited its tillering.  We identified the mutated gene in htsd1 as AUXIN1 (OsAUX1, LOC_Os01g63770), which encodes an auxin influx transporter.  The promoter sequence of OsAUX1 contains many SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) binding sites, and we demonstrated that SPL7 binds to the OsAUX1 promoter.  TEOSINTE BRANCHED1 (OsTB1), a key gene that negatively regulates tillering, was significantly downregulated in htsd1.  Tillering was enhanced in the OsTB1 knockout mutant, and the external application of IAA inhibited tiller elongation in this mutant.  Overexpressing OsTB1 restored the multi-tiller phenotype of htsd1.  These results suggest that SPL7 directly binds to the OsAUX1 promoter and regulates tillering in rice by altering OsTB1 expression to modulate auxin signaling.
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