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    Herbicidal activity and biochemical characteristics of the botanical drupacine against Amaranthus retroflexus L.

    YU Hua-long, TIAN Ci, SHEN Rong-yan, ZHAO Han, YANG Juan, DONG Jin-gao, ZHANG Li-hui, MA Shu-jie
    2023, 22 (5): 1434-1444.   DOI: 10.1016/j.jia.2022.08.120
    Abstract617)      PDF in ScienceDirect      

    Botanical herbicide has been a hot topic in the research and development of novel pesticides.  The herbicidal activity and biochemical characteristics of the botanical compound drupacine were studied by evaluating its effects on seed germination, seedling growth, morphological and physiological characteristics of Amaranthus retroflexus.  Drupacine inhibited seed germination and seedling growth, and had a median inhibition concentration (IC50) value of 38.99 mg L−1 against Aretroflexus root.  The α-amylase activity and soluble sugar content in treated plants were significantly lower than that of the control.  The expression of α-amylase gene was dosage-dependently inhibited compared to the untreated control.  This suggested that inhibition of α-amylase activity was a mode of action on seed germination.  The root hairs were significantly decreased and part of the root cap fell off after treatment with drupacine.  The ultrastructure observation showed that cell damage of root tips increased with the treatment time.  Drupacine also increased the relative conductivity and malondialdehyde (MDA) content.  Peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) activities were significantly enhanced in the treatment compared to the control.  These findings indicated that the physiological and biochemical reaction changes leading to morphological and membrane injuries were the main effects of drupacine on the inhibition of seedling growth.  Drupacine can be developed as a botanical herbicide. 

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    The miR164-TaNAC14 module regulates root development and abiotic-stress tolerance in wheat seedlings
    CHI Qing, DU Lin-ying, MA Wen, NIU Ruo-yu, WU Bao-wei, GUO Li-jian, MA Meng, LIU Xiang-li, ZHAO Hui-xian
    2023, 22 (4): 981-998.   DOI: 10.1016/j.jia.2022.08.016
    Abstract386)      PDF in ScienceDirect      

    Previous studies have revealed the miR164 family and the miR164-targeted NAC transcription factor genes in rice (Oryza sativa) and Arabidopsis that play versatile roles in developmental processes and stress responses.  In wheat (Triticum aestivum L.), we found nine genetic loci of tae-miR164 (tae-MIR164 a to i) producing two mature sequences that down-regulate the expression of three newly identified target genes of TaNACs (TaNAC1, TaNAC11, and TaNAC14) by the cleavage of the respective mRNAs.  Overexpression of tae-miR164 or one of its target genes (TaNAC14) demonstrated that the miR164-TaNAC14 module greatly affects root growth and development and stress (drought and salinity) tolerance in wheat seedlings, and TaNAC14 promotes root growth and development in wheat seedlings and enhances drought tolerance, while tae-miR164 inhibits root development and reduces drought and salinity tolerance by down-regulating the expression of TaNAC14.  These findings identify the miR164-TaNAC14 module as well as other tae-miR164-regulated genes which can serve as new genetic resources for stress-resistance wheat breeding.

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    Effect of high-molecular-weight glutenin subunit Dy10 on wheat dough properties and end-use quality
    WANG Yan, GUO Zhen-ru, CHEN Qing, LI Yang, ZHAO Kan, WAN Yong-fang, Malcolm J. HAWKESFORD, JIANG Yun-feng, KONG Li, PU Zhi-en, DENG Mei, JIANG Qian-tao, LAN Xiu-jin, WANG Ji-rui, CHEN Guo-yue, MA Jian, ZHENG You-liang, WEI Yu-ming, QI Peng-fei
    2023, 22 (6): 1609-1617.   DOI: 10.1016/j.jia.2022.08.041
    Abstract327)      PDF in ScienceDirect      
    High-molecular-weight glutenin subunits (HMW-GSs) are the most critical grain storage proteins that determine the unique processing qualities of wheat. Although it is a part of the superior HMW-GS pair (Dx5+Dy10), the contribution of the Dy10 subunit to wheat processing quality remains unclear. In this study, we elucidated the effect of Dy10 on wheat processing quality by generating and analyzing a deletion mutant (with the Dy10-null allele), and by elucidating the changes to wheat flour following the incorporation of purified Dy10. The Dy10-null allele was transcribed normally, but the Dy10 subunit was lacking. These findings implied that the Dy10-null allele reduced the glutenin:gliadin ratio and negatively affected dough strength (i.e., Zeleny sedimentation value, gluten index, and dough development and stability times) and the bread-making quality; however, it positively affected the biscuit-making quality. The incorporation of various amounts of purified Dy10 into wheat flour had a detrimental effect on biscuit-making quality. The results of this study demonstrate that the Dy10 subunit is essential for maintaining wheat dough strength. Furthermore, the Dy10-null allele may be exploited by soft wheat breeding programs.
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    Development and characterization of a novel common wheat–Mexico Rye T1DL·1RS translocation line with stripe rust and powdery mildew resistance
    LI Jiao-jiao, ZHAO Li, LÜ Bo-ya, FU Yu, ZHANG Shu-fa, LIU Shu-hui, YANG Qun-hui, WU Jun, LI Jia-chuang, CHEN Xin-hong
    2023, 22 (5): 1291-1307.   DOI: 10.1016/j.jia.2022.08.039
    Abstract316)      PDF in ScienceDirect      

    Rye (Secale cereale L., 2n=2x=14, RR) is a significant genetic resource for improving common wheat because of its resistance to multiple diseases and abiotic-stress tolerant traits.  The 1RS chromosome from the German cultivated rye variety Petkus is critical in wheat breeding.  However, its weakened disease resistance highlights the need to identify new resources.  In the present study, a novel derived line called D27 was developed from common wheat and Mexico Rye.  Cytological observations characterized the karyotype of D27 as 2n=42=21 II.  Genomic in situ hybridization indicated that a pair of whole-arm translocated Mexico Rye chromosomes were inherited typically in the mitotic and meiosis stages of D27.  Experiments using fluorescence in situ hybridization (FISH) and gliadin electrophoresis showed that D27 lacked wheat 1DS chromosomes.  They were replaced by 1RS chromosomes of Mexico Rye, supported by wheat simple-sequence repeat markers, rye sequence characterized amplified region markers, and wheat 40K SNP array analysis.  The wheat 1DS chromosomes could not be detected by molecular markers and wheat SNP array, but the presence of rye 1RS chromosomes was confirmed.  Agronomic trait assessments indicated that D27 had a higher tiller number and enhanced stripe rust and powdery mildew resistance.  In addition, dough properties analysis showed that replacing 1DS led to higher viscosity and lower dough elasticity in D27, which was beneficial for cake making.  In conclusion, the novel cytogenetically stable common wheat–Mexico Rye T1DL·1RS translocation line D27 offers excellent potential as outstanding germplasm in wheat breeding programs focusing on disease resistance and yield improvement.  Additionally, it can be valuable for researching the rye 1RS chromosome’s genetic diversity. 

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    Association mapping of lignin response to Verticillium wilt through an eight-way MAGIC population in Upland cotton
    TIAN Xiao-min, HAN Peng, WANG Jing, SHAO Pan-xia, AN Qiu-shuang, Nurimanguli AINI, YANG Qing-yong, YOU Chun-yuan, LIN Hai-rong, ZHU Long-fu, PAN Zhen-yuan, NIE Xin-hui
    2023, 22 (5): 1324-1337.   DOI: 10.1016/j.jia.2022.08.034
    Abstract305)      PDF in ScienceDirect      

    Lignin metabolism plays a pivotal role in plant defense against pathogens and is always positively correlated as a response to pathogen infection.  Thus, understanding resistance genes against pathogens in plants depends on a genetic analysis of lignin response.  In the study, eight upland cotton lines were used to construct a multi-parent advanced generation intercross (MAGIC) population (n=280), which exhibited peculiar characteristics from the convergence of various alleles coding for advantageous traits.  To measure the lignin response to Verticillium wilt (LRVW), artificial disease nursery (ADN) and rotation nursery (RN) were prepared for MAGIC population planting in four environments.  The stem lignin contents were collected, and the LRVW was measured with the lignin value of ADN/RN in each environment, which showed great variation.  A total of 9323 high-quality single-nucleotide polymorphism (SNP) markers obtained from the Cotton-SNP63K array were employed for genotyping the MAGIC population.  The SNPs were distributed through the whole genome with 4.78 SNP/Mb density, ranging from 1.14 (ChrA06) to 10.08 (ChrD08).  A genome-wide association study was performed using a mixed linear model (MLM) for LRVW, and three stable quantitative trait loci (QTLs), qLRVW-A04, qLRVW-A10 and qLRVW-D05, were identified in more than two environments.  Two key candidate genes, Ghi_D05G01046 and Ghi_D05G01221, were selected within the QTLs through the combination of variations in the coding sequence, induced expression patterns, and function annotations, both of which presented nonsynonymous mutations in coding regions and were strongly induced by Verticillium dahliae. Ghi_D05G01046 encodes a leucine-rich extensin (LRx) protein, which is involved in Arabidopsis cell wall biosynthesis and organization.  Ghi_D05G01221 encodes a transcriptional co-repressor novel interactor of jaz (NINJA), which functions in the jasmonic acid (JA) signaling pathway.  In summary, the study creates valuable genetic resources for breeding and QTL mapping and opens up a new perspective to uncover the genetic basis of VW resistance in upland cotton.

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    Identification and characterization of the chalkiness endosperm gene CHALK-H in rice (Oryza sativa L.)
    PIAO Ri-hua, CHEN Mo-jun, MENG Fan-mei, QI Chun-yan, KOH Hee-Jong, GAO Meng-meng, SONG An-qi, JIN Yong-mei, YAN Yong-feng
    2023, 22 (10): 2921-2933.   DOI: 10.1016/j.jia.2023.04.020
    Abstract303)      PDF in ScienceDirect      

    Chalkiness is one of the most important agronomic traits in rice breeding, which directly affects the quality of rice seed.  In this study, we identified a chalkiness endosperm mutant, chalk-h, from N-methyl-N-nitrosourea (MNU)-induced japonica rice cultivar Hwacheong (HC).  Compared with wild type (WT)-HC, chalk-h showed severe chalkiness in the endosperm, yellowish green leaves, as well as reduced plant height.  Scanning electron microscopy (SEM) analysis showed that starch grains in the chalk-h mutant were irregular in size and loosely arranged, with large gaps between granules, forming ovoid or orbicular shapes.  MutMap analysis revealed that the phenotype of chalk-h is controlled by a single recessive gene LOC_Os11g39670 encoding seryl-tRNA synthetase, which is renamed as CHALK-H.  A point mutation occurs in chalk-h on the sixth exon (at nucleotide 791) of CHALK-H, in which adenine (A) is replaced by thymidine (T), resulting in an amino acid codon change from glutamine (Glu) to valine (Val).  The chalk-h mutant exhibited a heat-sensitive phenotype from the 3-leaf stage, including yellow-green leaves and reduced pigment content.  The transcriptional expression of starch synthesis-related genes was down-regulated in the chalk-h mutants compared to WT-HC at different grain-filling stages.  With an increase in temperature, the expression of photosynthesis-related genes was down-regulated in the chalk-h mutant compared to WT-HC.  Overexpression of CHALK-H rescued the phenotype of chalk-h, with endosperm and leaf color similar to those of WT-HC.  Our findings reveal that CHALK-H is a causative gene controlling chalkiness and leaf color of the chalk-h mutant.  CHALK-H is the same gene locus as TSCD11, which was reported to be involved in chloroplast development under high temperature.  We suggest that CHALK-H/TSCD11 plays important roles not only in chloroplast development, but also in photosynthesis and starch synthesis during rice growth and development, so it has great application potential in rice breeding for high quality and yield.

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    OsDXR interacts with OsMORF1 to regulate chloroplast development and the RNA editing of chloroplast genes in rice
    CAO Peng-hui, WANG Di, GAO Su, LIU Xi, QIAO Zhong-ying, XIE Yu-lin, DONG Ming-hui, DU Tan-xiao, ZHANG Xian, ZHANG Rui, JI Jian-hui
    2023, 22 (3): 669-678.   DOI: 10.1016/j.jia.2022.08.005
    Abstract295)      PDF in ScienceDirect      

    Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors.  In this study, we identified OsDXR, a gene encoding a reductoisomerase that positively regulates chlorophyll biosynthesis and chloroplast development in rice.  OsDXR knock-out lines displayed the albino phenotype and could not complete the whole life cycle process.  OsDXR was highly expressed in rice leaves, and subcellular localization indicated that OsDXR is a chloroplast protein.  Many genes involved in chlorophyll biosynthesis and chloroplast development were differentially expressed in the OsDXR knock-out lines compared to the wild type.  Moreover, we found that the RNA editing efficiencies of ndhA-1019 and rpl2-1 were significantly reduced in the OsDXR knock-out lines.  Furthermore, OsDXR interacted with the RNA editing factor OsMORF1 in a yeast two-hybrid screen and bimolecular fluorescence complementation assay.  Finally, disruption of the plastidial 2-C-methyl-derythritol-4-phosphate pathway resulted in defects in chloroplast development and the RNA editing of chloroplast genes.

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    Raised bed planting promotes grain number per spike in wheat grown after rice by improving spike differentiation and enhancing photosynthetic capacity
    DU Xiang-bei, XI Min, WEI Zhi, CHEN Xiao-fei, WU Wen-ge, KONG Ling-cong
    2023, 22 (6): 1631-1644.   DOI: 10.1016/j.jia.2022.08.035
    Abstract280)      PDF in ScienceDirect      
    The yield of wheat in wheat–rice rotation cropping systems in the Yangtze River Plain, China, is adversely impacted by waterlogging. A raised bed planting (RBP) pattern may reduce waterlogging and increase the wheat yield after rice cultivation by improving the grain number per spike. However, the physiological basis for grain formation under RBP conditions remains poorly understood. The present study was performed over two growing seasons (2018/2019 and 2019/2020) to examine the effects of the planting pattern (i.e., RBP and flat planting (FP)) on the floret and grain formation features and leaf photosynthetic source characteristics of wheat. The results indicated that implementation of the RBP pattern improved the soil–plant nitrogen (N) supply during floret development, which facilitated balanced floret development, resulting in a 9.5% increase in the number of fertile florets per spike. Moreover, the RBP pattern delayed wheat leaf senescence and increased the photosynthetic source capacity by 13.9%, which produced more assimilates for grain filling. Delayed leaf senescence was attributed to the resultant high leaf N content and enhanced antioxidant metabolism. Correspondingly, under RBP conditions, 7.6–8.6% more grains per spike were recorded, and the grain yield was ultimately enhanced by 10.4–12.7%. These results demonstrate that the improvement of the spike differentiation process and the enhancement of the leaf photosynthetic capacity were the main reasons for the increased grain number per spike of wheat under the RBP pattern, and additional improvements in this technique should be achievable through further investigation.
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    Developing a duplex ARMS-qPCR method to differentiate genotype I and II African swine fever viruses based on their B646L genes
    DING Lei-lei, REN Tao, HUANG Lian-yu, Weldu TESFAGABER, ZHU Yuan-mao, LI Fang, SUN En-cheng, BU Zhi-gao, ZHAO Dong-ming
    2023, 22 (5): 1603-1607.   DOI: 10.1016/j.jia.2023.02.035
    Abstract276)      PDF in ScienceDirect      

    African swine fever (ASF), caused by the African swine fever virus (ASFV), is an acute, hemorrhagic, and contagious disease of domestic pigs and wild boars.  The disease is notifiable and listed by the World Organization for Animal Health (WOAH) (Wang N et al. 2019).  The outcomes of ASF infection can be peracute, acute, subacute, and chronic, depending on the virulence of ASFVs.  According to the report of WOAH (, from January 2020 to December 2022, ASF led to more than  2 million pig losses.  Currently, ASFV persists continuously in more than 23 countries and poses a serious threat to the global swine industry.  ASF invaded China on 3 August, 2018, caused by genotype II virulent Georgia-07-like ASFVs (Wen et al. 2019; Zhao et al. 2019; Wang et al. 2020; Wang L et al. 2022).  An experimental study showed that Georgia-07-like ASFV HLJ/18 isolated in China is highly lethal and efficiently transmissible in domestic pigs (Zhao et al. 2019; Jiang et al. 2021).  During the past four years, genotype II Georgia-07-like ASFVs dominantly spread in China.  However, the low virulent genotype II and I ASFVs have been successively reported in China in 2020 and 2021, respectively (Sun et al. 2021a, b; Shi et al. 2022).  Compared with the high virulent genotype II HLJ/18 strain, the low virulent genotype I and II ASFVs had lower virulence and high transmissibility in pigs and induced persistent and chronic infection showing irregular virus shedding at low levels (Sun et al. 2021a, b; Tsegay et al. 2022; Wang P et al. 2022).  Notably, when different genotype I and genotype II viruses infect the same pig in the field, a novel virus may be generated through viral genome recombination, which brings new problems and challenges for the prevention and control of ASF in China.  Thus, a diagnostic method that differentiates genotype I and II ASFVs with high sensitivity and stability is urgently needed and will be helpful for the prevention and control of ASF in China.  

    ASFVs have been divided into at least 24 genotypes based on the C-terminus of the B646L gene with 478 nt (Bastos et al. 2003).  B646L gene is one of the most used target genes for ASF diagnosis, which is also the target gene for the WOAH recommended PCR and fluorescent quantitative PCR assays (Agüero et al. 2003; King et al. 2003).  Sanger sequencing of targeted amplification of the B646L genes is the main genotyping approach for ASFVs.  Recently, Li et al. (2022) developed the duplex real-time PCR assay based on the ASFV E296R gene, and Cao et al. (2022) established the TaqMAN-MGB probe assay based on the N-terminal sequences of the B646L gene (Cao et al. 2022; Li et al. 2022), which could distinguish genotype I and II ASFVs with detection limits of 10 copies.  However, the target genes or regions in their methods were out of ASFV genotyping regions.  

    Single nucleotide polymorphism (SNP) is a single base change at a specific position in the genome of different individuals and can be used as a genotyping marker for the detection of different individual genotypes (Gut 2001).  The amplification refractory mutation system (ARMS), also named Allele-specific PCR (AS-PCR), relies on the extension of primer only when its 3´ end has a perfect complement to the template (Wang M et al. 2019).  ARMS-qPCR technology has been developed and widely used in SNP detection and genotyping (Ochsenreither et al. 2010; Shi et al. 2013; Wang M et al. 2019).  Compared with other assays for SNP detection and genotyping, ARMS-qPCR has the advantage of low-cost, simple operation, high sensitivity, and rapid and real-time detection.

    Here, 126 complete or partial B646L genes of ASFVs, including 78 genotype I and 48 genotype II viruses, were obtained from the GenBank database, and their information is shown in Appendix A.  After analyzing these genes by the MegAlign Software (DNAStar), there were 4 SNPs in the C-terminus of the B646L gene, differentiating genotype I viruses from genotype II viruses (Fig. 1-A).  Two SNPs at sites 1 656 and 1 710 were used to design primers and probes for differential detection of genotype I and II ASFVs (Fig. 1-A).  As previously described (Huang et al. 1992; Liu et al. 2012), primers (I F, II F and R) and probes (probe 1 and probe 2) were designed with the targeted gene sequences using Primer 5 Software (Fig. 1-B; Appendix B).  The duplex ARMS-qPCR reaction system volume was 25 μL: 12.5 μL of 2× HyperProbe Mixture (GENFINE), 0.5 μL of I F, II F and R primers (10 μmol L–1), 0.5 μL of probe 1 and probe 2 (10 μmol L–1), 5 μL of template DNA, and 5 μL of ddH2O.  The duplex ARMS-qPCR was performed by using the Bio-Rad CFX96 Touch Real-Time PCR Detection System with the following reaction conditions: 95°C for 30 s, followed by 40 cycles of 95°C for 10 s, and 60°C for 30 s.  Fluorescence signal was detected at the end of each cycle of extension step.  For the positive sample of genotype I ASFV, FAM and Cy5 fluorophores could be detected; however, for the positive sample of genotype II ASFV, only FAM fluorophore could be detected (Fig. 1-B).  

    The standard curve test revealed that for the standard plasmids of genotype I ASFV, the slopes were –3.3825 for Cy5 and –3.1906 for FAM; the correlation coefficient R2 was 0.999 for Cy5 and 0.998 for FAM; the amplification efficiency was 97.53% for Cy5 and 100.06% for FAM, respectively (Fig. 1-C); for the standard plasmids of genotype II ASFV, the slope was –3.2983 for FAM, the correlation coefficient R2 was 0.992 for FAM, the amplification efficiency was 100.01% for FAM, whereas Cy5 fluorophore could not be detected (Fig. 1-C).  In addition, the sensitivity of the duplex ARMS-qPCR was 10 copies per reaction for both genotype I and II ASFVs (Fig. 1-D).  Thus, these results indicated that the duplex ARMS-qPCR assay has high efficiency and sensitivity.  

    We then evaluated the specificity of the duplex ARMS-qPCR.  The nucleic acids of 7 other swine viruses, including PRRSV, CSFV, PRV, PCV2, PEDV, TGEV, and PoRV, were used as templates.  There were 3 amplification curves obtained for genotype I ASFV (FAM and Cy5 signals) and II ASFV (FAM signal), whereas no amplification curve was recorded for the nucleic acids of PRRSV, CSFV, PRV, PCV2, PEDV, TGEV, and PoRV, as well as genotype II ASFV (Cy5 signal) and ddH2O (Fig. 1-E).  The results demonstrated that the duplex ARMS-qPCR has a good specificity without cross-reactivity with other swine viruses.

    The results of the stable detection limit test showed that for the standard plasmids of genotype I ASFV, all 12 replicates were tested positive at the dilution of 10 copies, while 7/12 replicates were tested positive at the dilution of 5 copies (Fig. 1-F); for the standard plasmids of genotype II ASFV, all 12 replicates were tested positive at the dilution of 10 copies, while 6/12 replicates were tested positive at the dilution of 1 copy (Fig. 1-F).  Thus, the stable detection limit of the duplex ARMS-qPCR was 10 copies per reaction for both genotype I and II ASFVs (Fig. 1-F).

    We further assessed the repeatability and reproducibility of the duplex ARMS-qPCR.  The assay tested the standard plasmids of 3 concentrations (106, 104, and 102 copies).  For the standard plasmids of genotype I ASFV, the intra- and inter-assay variation of Ct value for the duplex ARMS-qPCR ranged from 0.07 to 0.93% and 1.2 to 2.17% in FAM fluorescence channel and from 0.38 to 1.02% and 0.85 to 1.27% in Cy5 fluorescence channel, respectively (Table 1).  For the standard plasmids of genotype II ASFV, the intra- and inter-assay variation of Ct value for the duplex ARMS-qPCR ranged from 0.27 to 0.61% and 0.77 to 1.07% in FAM fluorescence channel (Table 1).  These findings suggested that the duplex ARMS-qPCR assay has satisfactory repeatability and reproducibility.

    Finally, we evaluated the duplex ARMS-qPCR compared with WOAH-qPCR.  A total of 40 samples were detected using both assays, including blood, oral and rectal swabs, tissues, and cell cultures from pigs or PAMs infected by genotype I and II ASFVs.  Animal studies have evaluated the virulence and transmissibility of genotype I ASFV SD/DY-I/21 and genotype II virus HLJ/18 (Zhao et al. 2019; Sun et al. 2021a), respectively.  The results showed that 36 samples, including 18 of genotype I ASFV and 18 of genotype II ASFV were detected to be positive and differentiated by the duplex ARMS-qPCR, which were consistent with the results of the WOAH-qPCR (Appendix C).  

    In summary, we developed a duplex ARMS-qPCR assay based on ASFV genotyping region of B646L gene, which can effectively differentiate genotype I and II ASFVs.  The assay had high sensitivity and specificity and exhibited good results in detecting samples, including blood, oral and rectal swabs, tissues, and cell culture.  Whether our method could be used for differentiating other genotypes of ASFVs is needed for further evalution.  However, just genotype I and II ASFVs are spreading outside Africa.  Thus, our method will provide an additional epidemiological investigation tool to implement effective ASFV control and prevention.

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    A single nucleotide substitution in the MATE transporter gene regulates plastochron and many noded dwarf phenotype in barley (Hordeum vulgare L.)
    GUO Bao-jian, SUN Hong-wei, QI Jiang, HUANG Xin-yu, HONG Yi, HOU Jian, LÜ Chao, WANG Yu-lin, WANG Fei-fei, ZHU Juan, GUO Gang-gang, XU Ru-gen
    2023, 22 (8): 2295-2305.   DOI: 10.1016/j.jia.2023.02.006
    Abstract270)      PDF in ScienceDirect      
    In higher plants, the shoot apical meristem produces lateral organs in a regular spacing (phyllotaxy) and timing (plastochron).  The molecular analysis of mutants associated with phyllotaxy and plastochron would increase our understanding of the mechanism of shoot architecture formation.  In this study, we identified mutant mnd8ynp5 that shows an increased rate of leaf emergence and a larger number of nodes in combination with a dwarfed growth habit from an EMS-treated population of the elite barley cultivar Yangnongpi 5.  Using a map-based cloning strategy, the mnd8 gene was narrowed down to a 6.7-kb genomic interval on the long arm of chromosome 5H.  Sequence analysis revealed that a C to T single-nucleotide mutation occurred at the first exon (position 953) of HORVU5Hr1G118820, leading to an alanine (Ala) to valine (Val) substitution at the 318th amino acid site.  Next, HORVU5Hr1G118820 was defined as the candidate gene of MND8 encoding 514 amino acids and containing two multidrug and toxic compound extrusion (MATE) domains.  It is highly homologous to maize Bige1 and has a conserved function in the regulation of plant development by controlling the leaf initiation rate.  Examination of modern barely varieties showed that Hap-1 was the dominant haplotype and was selected in barley breeding around the world.  Collectively, our results indicated that mnd8ynp5 is a novel allele of the HORVU5Hr1G118820 gene that is possibly responsible for the shortened plastochron and many noded dwarf phenotype in barley.
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    Dek219 encodes the DICER-LIKE1 protein that affects chromatin accessibility and kernel development in maize
    XIE Si-di, TIAN Ran, ZHANG Jun-jie, LIU Han-mei, LI Yang-ping, HU Yu-feng, YU Guo-wu, HUANG Yu-bi, LIU Ying-hong
    2023, 22 (10): 2961-2980.   DOI: 10.1016/j.jia.2023.02.024
    Abstract263)      PDF in ScienceDirect      

    Chromatin accessibility plays a vital role in gene transcriptional regulation.  However, the regulatory mechanism of chromatin accessibility, as well as its role in regulating crucial gene expression and kernel development in maize (Zea mays) are poorly understood.  In this study, we isolated a maize kernel mutant designated as defective kernel219 (dek219), which displays opaque endosperm and embryo abortion.  Dek219 encodes the DICER-LIKE1 (DCL1) protein, an essential enzyme in miRNA biogenesis.  Loss of function of Dek219 results in significant reductions in the expression levels of most miRNAs and histone genes.  Further research showed that the Heat shock transcription factor17 (Hsf17)-Zm00001d016571 module may be one of the factors affecting the expression of histone genes.  Assay results for transposase-accessible chromatin sequencing (ATAC-seq) indicated that the chromatin accessibility of dek219 is altered compared with that of wild type (WT), which may regulate the expression of crucial genes in kernel development.  By analyzing differentially expressed genes (DEGs) and differentially accessible chromatin regions (ACRs) between WT and dek219, we identified 119 candidate genes that are regulated by chromatin accessibility, including some reported to be crucial genes for kernel development.  Taken together, these results suggest that Dek219 affects chromatin accessibility and the expression of crucial genes that are required for maize kernel development

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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 (02): 484-493.   DOI: 10.1016/j.jia.2023.05.039
    Abstract260)      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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    Multi-omics-driven development of alternative crops for natural rubber production
    YANG Ning, YANG Dan-dan, YU Xu-chen, XU Cao
    2023, 22 (4): 959-971.   DOI: 10.1016/j.jia.2023.03.007
    Abstract258)      PDF in ScienceDirect      

    Natural rubber (NR) is an irreplaceable biopolymer of economic and strategic importance owing to its unique physical and chemical properties.  The Pará rubber tree (Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg.) is currently the exclusive commercial source of NR, and it is primarily grown in plantations restricted to the tropical and subtropical areas of Southeast Asia.  However, current Pará rubber production barely meets the sharply increasing global industrial demand for rubber.  Petroleum-based synthetic rubber (SR) has been used to supplement the shortage of NR but its industrial performance is not comparable to that of NR.  Thus, there is an urgent need to develop new productive rubber crops with broader environmental adaptability.  This review summarizes the current research progress on alternative rubber-producing plants, including horticultural plants (Taraxacum kok-saghyz Rodin and Lactuca L. species), woody plants (Parthenium argentatum A. Gray and Eucommia ulmoides Oliv.), and other plant species with potential for NR production.  With an emphasis on the molecular basis of NR biosynthesis revealed by a multi-omics approach, we highlight new integrative strategies and biotechnologies for exploring the mechanism of NR biosynthesis with a broader scope, which may accelerate the breeding and improvement of new rubber crops. 

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    StOFP20 regulates tuber shape and interacts with TONNEAU1 Recruiting Motif proteins in potato
    AI Ju, WANG Ye, YAN Ya-wen, LI Chen-xiao, LUO Wei, MA Ling, SHANG Yi, GAO Dong-li
    2023, 22 (3): 752-761.   DOI: 10.1016/j.jia.2022.08.069
    Abstract256)      PDF in ScienceDirect      

    The OVATE family proteins (OFPs) are plant-specific proteins that modulate diverse aspects of plant growth and development.  In tomato, OFP20 has been shown to interact with TONNEAU1 Recruiting Motif (TRM) proteins to regulate fruit shape.  In this study, we demonstrated that the mutation of StOFP20 caused a shift from round to oval shaped tubers in a diploid accession C151, supporting the role of StOFP20 in controlling tuber shape.  Its expression reached a maximum in the tuber initiation stage and then decreased as the tuber develops.  To help elucidate the mechanism of tuber shape regulation by StOFP20, 27 TONNEAU1 Recruiting Motif (TRM) proteins were identified and 23 of them were successfully amplified in C151.  A yeast two-hybrid assay identified three TRM proteins that interacted with StOFP20, which was confirmed by firefly luciferase complementation in tobacco leaves.  The OVATE domain was indispensable for the interactions, while the necessity of the M10 motif in TRM proteins varied among the interactions between StOFP20 and the three TRMs.  In summary, both StOFP20 and SlOFP20 directed interactions with TRM proteins, but the corresponding interactants were not completely consistent, implying that they exert regulatory roles through mechanisms that are only partially overlapping.  

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    Review on the fully mulched ridge–furrow system for sustainable maize production on the semi-arid Loess Plateau
    WANG Jin-bin, XIE Jun-hong, LI Ling-ling, ADINGO Samuel
    2023, 22 (5): 1277-1290.   DOI: 10.1016/j.jia.2022.09.023
    Abstract244)      PDF in ScienceDirect      

    The fully mulched ridge–furrow (FMRF) system has been widely used on the semi-arid Loess Plateau of China due to its high maize (Zea mays L.) productivity and rainfall use efficiency.  However, high outputs under this system led to a depletion of soil moisture and soil nutrients, which reduces its sustainability in the long run.  Therefore, it is necessary to optimize the system for the sustainable development of agriculture.  The development, yield-increasing mechanisms, negative impacts, optimization, and their relations in the FMRF system are reviewed in this paper.  We suggest using grain and forage maize varieties instead of regular maize; mulching plastic film in autumn or leaving the mulch after maize harvesting until the next spring, and then removing the old film and mulching new film; combining reduced/no-tillage with straw return; utilizing crop rotation or intercropping with winter canola (Brassica campestris L.), millet (Setaria italica), or oilseed flax (Linum usitatissimum L.); reducing nitrogen fertilizer and partially replacing chemical fertilizer with organic fertilizer; using biodegradable or weather-resistant film; and implementing mechanized production.  These integrations help to establish an environmentally friendly, high quality, and sustainable agricultural system, promote high-quality development of dryland farming, and create new opportunities for agricultural development in the semi-arid Loess Plateau.

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    Estimation of the potential geographical distribution of a new potato pest (Schrankia costaestrigalis) in China under climate change
    XIAN Xiao-qing, ZHAO Hao-xiang, GUO Jian-yang, ZHANG Gui-fen, LIU Hui, LIU Wan-xue, WAN Fang-hao
    2023, 22 (8): 2441-2455.   DOI: 10.1016/j.jia.2022.08.023
    Abstract242)      PDF in ScienceDirect      

    Global food security is threatened by the impacts of the spread of crop pests and changes in the complex interactions between crops and pests under climate change.  Schrankia costaestrigalis is a newly-reported potato pest in southern China.  Early-warning monitoring of this insect pest could protect domestic agriculture as it has already caused regional yield reduction and/or quality decline in potato production.  Our research aimed to confirm the potential geographical distributions (PGDs) of Scostaestrigalis in China under different climate scenarios using an optimal MaxEnt model, and to provide baseline data for preventing agricultural damage by Scostaestrigalis.  Our findings indicated that the accuracy of the optimal MaxEnt model was better than the default-setting model, and the minimum temperature of the coldest month, precipitation of the driest month, precipitation of the coldest quarter, and the human influence index were the variables significantly affecting the PGDs of Scostaestrigalis.  The highly- and moderately-suitable habitats of Scostaestrigalis were mainly located in eastern and southern China.  The PGDs of Scostaestrigalis in China will decrease under climate change.  The conversion of the highly- to moderately-suitable habitat will also be significant under climate change.  The centroid of the suitable habitat area of Scostaestrigalis under the current climate showed a general tendency to move northeast and to the middle-high latitudes in the 2030s.  The agricultural practice of plastic film mulching in potato fields will provide a favorable microclimate for Scostaestrigalis in the suitable areas.  More attention should be paid to the early warning and monitoring of Scostaestrigalis in order to prevent its further spread in the main areas in China’s winter potato planting regions.

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    Effect of group size and regrouping on physiological stress and behavior of dairy calves
    LYU Jing, WANG Chao, ZHAO Xun-wu, MIAO Er-yu, WANG Zhi-peng, XU Yuan, BAI Xiu-juan, BAO Jun
    2023, 22 (3): 844-852.   DOI: 10.1016/j.jia.2022.08.073
    Abstract241)      PDF in ScienceDirect      

    Mixing or regrouping of calves from different pens is a common animal management practice on the farm, which frequently occurs after weaning and has a negative effect on calve welfare.  Social integration before regrouping may relieve stresses, but more evidences are needed to verify this hypothesis.  The present study aimed to investigate acute physiological and behavioral variations of individually- or group-housed calves after being introduced into a mixed group.  A total of 132 postnatal calves were randomly divided into groups of 1, 3, 6 and 12 animals (S, G3, G6, and G12; 6 replicates in each group) until 59 days of age.  At 60 days of age, every two replicates from different groups (S, G3, G6 and G12) were introduced in a larger pen which containing 44 of the aboved experimental calves.  Before and after regrouping, physiological parameters of stress, including heart rate (HR), saliva cortisol (S-CORT), saliva secretory immunoglobulin A (SIgA), interleukin-2 (IL-2), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) levels, and behavioral responses were recorded.  After regrouping, HR and S-CORT increased immediately (P<0.05), and higher (P<0.05) levels of such molecules were found in S calves compared to those in group-housed calves.  Levels of SIgA and IL-2 were decreased (P<0.05), and the lowest (P<0.05) IL-2 values were found in S calves compared to those in group-housed calves.  In addition, the introduced calves displayed a distinct behavior, including altered active and rest time, which was associated with negative emotions triggered by the novel surroundings.  Allogrooming, play, exploration behaviors and lying time were increased significantly (P<0.05) in group-housed calves than those in S calves.  Conversely, self-grooming, aggressive behaviors, standing and walking time were increased (P<0.05) in S calves than those in group-housed calves.  These findings suggest that individually-housed calves may be more susceptible to stressors arising from regrouping than group-housed calves, which consequently negatively affected behavioral and neuroendocrine responses.  Furthermore, moving calves with previous social experience may help mitigate regrouping stress.

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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
    Abstract236)      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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    OsPPR9 encodes a DYW-type PPR protein that affects editing efficiency of multiple RNA editing sites and is essential for chloroplast development
    CHEN Chang-zhao, WANG Ya-Liang, HE Meng-xing, LI Zhi-wen, SHEN Lan, LI Qing, RE De-yong, HU Jiang, ZHU Li, ZHANG Guang-heng, GAO Zhen-yu, ZENG Da-li, GUO Long-biao, QIAN Qian, ZHANG Qiang
    2023, 22 (4): 972-980.   DOI: 10.1016/j.jia.2022.08.026
    Abstract232)      PDF in ScienceDirect      

    Photosynthesis occurs mainly in chloroplasts, whose development is regulated by proteins encoded by nuclear genes.  Among them, pentapeptide repeat (PPR) proteins participate in organelle RNA editing.  Although there are more than 450 members of the PPR protein family in rice, only a few affect RNA editing in rice chloroplasts.  Gene editing technology has created new rice germplasm and mutants, which could be used for rice breeding and gene function study.  This study evaluated the functions of OsPPR9 in chloroplast RNA editing in rice.  The osppr9 mutants were obtained by CRISPR/Cas9, which showed yellowing leaves and a lethal phenotype, with suppressed expression of genes associated with chloroplast development and accumulation of photosynthetic-related proteins.  In addition, loss of OsPPR9 protein function reduces the editing efficiency of rps8-C182, rpoC2-C4106, rps14-C80, and ndhB-C611 RNA editing sites, which affects chloroplast growth and development in rice.  Our data showed that OsPPR9 is highly expressed in rice leaves and encodes a DYW-PPR protein localized in chloroplasts.  Besides, the OsPPR9 protein was shown to interact with OsMORF2 and OsMORF9.  Together, our findings provide insights into the role of the PPR protein in regulating chloroplast development in rice. 

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    Plastic-film-side seeding, as an alternative to traditional film mulching, improves yield stability and income in maize production in semi-arid regions
    ZHANG Bing-chao, HU Han, GUO Zheng-yu, GONG Shuai, SHEN Si, LIAO Shu-hua, WANG Xin, ZHOU Shun-li, ZHANG Zhong-dong
    2023, 22 (4): 1021-1034.   DOI: 10.1016/j.jia.2022.08.017
    Abstract231)      PDF in ScienceDirect      

    Planting under plastic-film mulches is widely used in spring maize production in arid-cold regions for water conservation and warming the soil.  To ameliorate the associated issues such as plastic-film residues and additional labor during the “seedling release” in spring maize production, we have developed a plastic-film-side seeding (PSS) technology with the supporting machinery.  In the semi-arid regions of Northwest China, a 7-year trial demonstrated that PSS increased plant number per hectare by 6 547 and maize yield by 1 686 kg ha–1 compared with the traditional method of seeding under plastic-film mulch (PM).  Two-year experiments were conducted in two semi-arid regions to further understand the effects of PSS on three important aspects of production: (i) the moisture and temperature of soil, (ii) maize development, yield output, and water use efficiency (WUE), and (iii) the revenue and plastic-film residuals in comparison with that of flat planting (CK) and PM.  Continuous monitoring of the soil status demonstrated that, compared with CK, the PSS treatment significantly increased the temperature and moisture of the 0–20 cm soil in the seeding row at the early stage of maize development, and it also promoted grain yield (at 884–1 089 kg ha–1) and WUE, achieving a similar effect as the PM treatment.  Economically, the labor inputs of PSS were equal to CK, whereas the PM cost an additional 960 CNY ha–1 in labor for releasing the seedlings from below the film.  Overall, the PSS system increased profits by 5.83% (547 CNY ha–1 yr–1) and 8.16% (748 CNY ha–1 yr–1) compared with CK and PM, respectively.  Environmentally, PSS achieved a residual film recovery rate of nearly 100% and eliminated 96 to 130 kg ha–1 of residual plastic-film in PM in 3–5 years of maize production.  Collectively, these results show that PSS is an eco-friendly technique for improving yield stability and incomes for the sustainable production of maize in semi-arid regions.

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