2022 Vol. 21 No. 11 Previous Issue    Next Issue

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

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    Crop Science
    Characterization and fine mapping of a semi-rolled leaf mutant srl3 in rice
    YU Xiao-qi, XIE Wei, LIU He, LIU Wei, ZENG Da-li, QIAN Qian, REN De-yong
    2022, 21(11): 3103-3113.  DOI: 10.1016/j.jia.2022.07.059
    Abstract ( )   PDF in ScienceDirect  

    Moderate leaf rolling can maintain leaf erectness, improve light transmittance in the population, and improve light energy utilization, thereby increasing rice yield.  This study used ethyl methanesulfonate (EMS) to treat Yunjing 17 (YJ17) and obtained a semi-rolled leaf mutant that was named semi-rolled leaf 3 (srl3).  We found that the rolled-leaf phenotype was due to the aberrant development of bulliform cells and the loss of sclerenchymatous cells.  In addition, the shoot and root length of srl3 seedlings differed from the wild type.  The srl3 mutant had significantly lower plant height and seed-setting rate but notably greater tiller number, panicle length, and primary branch number per panicle than the wild type.   Genetic analysis showed that a single recessive nuclear gene defined the srl3 mutant, and it was precisely located in a 144-kb region between two insertion-deletion (InDel) markers, M8 and M19, on chromosome 2.  In this region, no leaf-rolling-related genes have been reported previously.  Thus, the study indicated that SRL3 is a novel leaf-rolling-related gene, and the results laid the foundation for the cloning and functional analysis of the SRL3 gene.

    TaNF-YB11, a gene of NF-Y transcription factor family in Triticum aestivum, confers drought tolerance on plants via modulating osmolyte accumulation and reactive oxygen species homeostasis
    ZHAO Ying-jia, ZHANG Yan-yang, BAI Xin-yang, LIN Rui-ze, SHI Gui-qing, DU Ping-ping, XIAO Kai
    2022, 21(11): 3114-3130.  DOI: 10.1016/j.jia.2022.07.058
    Abstract ( )   PDF in ScienceDirect  

    Transcription factors (TFs) regulate diverse stress defensive-associated physiological processes and plant stress responses.  We characterized TaNF-YB11, a gene of the NF-YB TF family in Triticum aestivum, in mediating plant drought tolerance.  TaNF-YB11 harbors the conserved domains specified by its NF-YB partners and targets the nucleus after the endoplasmic reticulum (ER) assortment.  Yeast two-hybrid assay indicated the interactions of TaNF-YB11 with TaNF-YA2 and TaNF-YC3, two proteins encoded by genes in the NF-YA and NF-YC families, respectively.  These results suggested that the heterotrimer established among them further regulated downstream genes at the transcriptional level.  The transcripts of TaNF-YB11 were promoted in roots and leaves under a 27-h drought regime.  Moreover, its upregulated expression levels under drought were gradually restored following a recovery treatment, suggesting its involvement in plant drought response.  TaNF-YB11 conferred improved drought tolerance on plants; the lines overexpressing target gene displayed improved phenotype and biomass compared with wild type (WT) under drought treatments due to enhancement of stomata closing, osmolyte accumulation, and cellular reactive oxygen species (ROS) homeostasis.  Knockdown expression of TaP5CS2, a P5CS family gene modulating proline biosynthesis that showed upregulated expression in drought-challenged TaNF-YB11 lines, alleviated proline accumulation of plants treated by drought.  Likewise, TaSOD2 and TaCAT3, two genes encoding superoxide dismutase (SOD) and catalase (CAT) that were upregulated underlying TaNF-YB11 regulation, played critical roles in ROS homeostasis via regulating SOD and CAT activities.  RNA-seq analysis revealed that numerous genes associated with processes of ‘cellular processes’, ‘environmental information processing’, ‘genetic information processing’, ‘metabolism’, and ‘organismal systems’ modified transcription under drought underlying control of TaNF-YB11.  These results suggested that the TaNF-YB11-mediated drought response is possibly accomplished through the target gene in modifying gene transcription at the global level, which modulates complicated biological processes related to drought response.  TaNF-YB11 is essential in plant drought adaptation and a valuable target for molecular breeding of drought-tolerant cultivars in Taestivum.

    Identification and validation of novel loci associated with wheat quality through a genome-wide association study
    PU Zhi-en, YE Xue-ling, LI Yang, SHI Bing-xin, GUO Zhu, DAI Shou-fen, MA Jian, LIU Ze-hou, JIANG Yun-feng, LI Wei, JIANG Qian-tao, CHEN Guo-yue, WEI Yu-ming, ZHENG You-liang
    2022, 21(11): 3131-3147.  DOI: 10.1016/j.jia.2022.08.085
    Abstract ( )   PDF in ScienceDirect  
    Understanding the genetic basis of quality-related traits contributes to the improvement of grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) in wheat, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed on the 236 wheat accessions including 160 cultivars and 76 landraces using 55K single nucleotide polymorphism (SNP) array in multiple environments. A total of twelve stable QTL/SNPs were identified to control different quality traits in this populations at least two environments under stripe rust stress; three, seven and two QTLs associated with GPC, GSC, and WGC were characterized respectively and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D with the range of phenotypic variation explained (PVE) from 4.2 to 10.7%. Compared with the previously reported QTLs/genes, five QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. KASP markers for SNPs AX-108770574 and AX-108791420 on chromosome on 5D associated with wet gluten concentration were successfully developed. Phenotype of the cultivars containing the A-allele in AX-108770574 and T-allele in AX-108791420 were extremely significantly (P<0.01) higher than that of the landraces containing the G-allele or C-allele of wet gluten concentration in each of the environments. The developed and validated KASP markers could be utilized in molecular breeding aiming to improve the quality in wheat.
    Evidence of silk growth hampering in maize at high planting density using phenotypic and transcriptional analysis
    ZHANG Min, XING Li-juan, REN Xiao-tian, ZOU Jun-jie, SONG Fu-peng, WANG Lei, XU Miao-yun
    2022, 21(11): 3148-3157.  DOI: 10.1016/j.jia.2022.08.083
    Abstract ( )   PDF in ScienceDirect  
    Increasing the planting density is an effective way to increase the yield of maize (Zea mays L.), although it can also aggravate ovary apical abortion-induced bald tips of the ears, which might, in turn, reduce the yield.  While the mechanism underlying the regulation of drought-related abortion in maize is well established, high planting density-related abortion in maize remains poorly understood.  Therefore, the present study was designed to investigate the mechanism underlying the ovary apical abortion response to high density.  This was achieved by evaluating the effects of four different plant densities (60 000 plants ha–1 (60 k), 90 k, 120 k, and 150 k) on plant traits related to plant architecture, the plant ear, flowering time, and silk development in two inbred lines (Zheng58 and PH4CV) and two hybrid lines (Zhengdan958 and Xianyu335).  The phenotypes of both inbred and hybrid plants were observed under different planting density treatments, and the high planting density was found to increase the phenotypic performance values of the evaluated traits.  The anthesis–silking interval (ASI) was extended, and the amount of the silk extruded from husks was reduced upon increasing the planting density.  Delayed silk emergence resulted in asynchronous flowering and ear bald tips.  Observations of the silk cells revealed that the silk cells became smaller as planting density increased.  The changes in transcript abundances in the silks involved the genes associated with expansive growth rather than carbon metabolism.  These findings further our understanding of silk growth regulation under high planting density and provide a theoretical basis for further research on improving high planting density breeding in maize.  
    Cytological study on haploid male fertility in maize
    YANG Ji-wei, LIU Zong-hua, QU Yan-zhi, ZHANG Ya-zhou, LI Hao-chuan
    2022, 21(11): 3158-3168.  DOI: 10.1016/j.jia.2022.07.055
    Abstract ( )   PDF in ScienceDirect  
    Doubled haploid (DH) breeding technology, which relies on haploid genome doubling, is widely used in commercial maize breeding.  Spontaneous haploid genome doubling (SHGD), a more simplified and straightforward method, is gaining popularity among maize breeders.  However, the cytological mechanism of SHGD remains unclear.  This study crossed inbred lines RL36 and RL7, which have differing SHGD abilities, with inducer line YHI-1 to obtain haploid kernels.  The meiotic processes of pollen mother cells (PMCs) in the haploid plants were compared with diploid controls.  The results suggested that three main pathways, the early doubling of haploid PMCs, the first meiotic metaphase chromosomal segregation distortion, and anomaly of the second meiosis, are responsible for SHGD.  Furthermore, flow cytometry analysis of ploidy levels in leaves and PMCs from haploids and diploid controls revealed that somatic cell chromosome doubling and germ cell chromosome doubling are independent processes.  These findings provide a foundation for further studies on the underlying mechanism of SHGD, aiding the application of DH technology in maize breeding practices.  
    Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean [Glycine max (L.) Merr.]
    JIA Jia, WANG Huan, CAI Zhan-dong, WEI Ru-qian, HUANG Jing-hua, XIA Qiu-ju, XIAO Xiao-hui, MA Qi-bin, NIAN Hai, CHENG Yan-bo
    2022, 21(11): 3169-3184.  DOI: 10.1016/j.jia.2022.08.082
    Abstract ( )   PDF in ScienceDirect  

    Pod shattering is an important domesticated trait which can cause great economic loss of crop yield in cultivated soybean.  In this study, we utilized two recombinant inbred line populations (RILs, CY, Huachun 2×Wayao; GB, Guizao 1×B13) to identify quantitative trait loci (QTLs) associated with pod shattering in soybean across multiple environments.  A total of 14 QTLs for pod shattering were identified in the two RIL populations, which had LOD scores ranging from 2.64 to 44.33 with phenotypic variance explanation (PVE) ranging from 1.33 to 50.85%.  One QTL qPS16-1, located on chromosome 16, included a well-known functional gene Pod dehiscence 1 (Pdh1) that was reported previously.  Ten new putative QTLs were validated in two RIL populations, and their LOD scores were between 2.55 and 4.24, explaining 1.33 to 2.60% of the phenotypic variation.  Of which four novel QTLs (qPS01-1, qPS03-2, qPS05-1, and qPS07-1) could be detected in two environments where nine genes had specific changes in gene expression.  Although the nine genes may have significant effects on pod shattering of soybean, their detailed functions still need to be further explored in the future.  The results of this study will facilitate a better understanding of the genetic basis of the pod shattering-resistant trait and benefit soybean molecular breeding for improving pod shattering resistance

    dep1 improves rice grain yield and nitrogen use efficiency simultaneously by enhancing nitrogen and dry matter translocation
    HUANG Li-ying, Li Xiao-xiao, ZHANG Yun-bo, Shah FAHAD, WANG Fei
    2022, 21(11): 3185-3198.  DOI: 10.1016/j.jia.2022.07.057
    Abstract ( )   PDF in ScienceDirect  

    The rice cultivars carrying dep1 (dense and erect panicle 1) have the potential to achieve both high grain yield and high nitrogen use efficiency (NUE).  However, few studies have focused on the agronomic and physiological performance of those cultivars associated with high yield and high NUE under field conditions.  Therefore, we evaluated the yield performance and NUE of two near-isogenic lines (NILs) carrying DEP1 (NIL-DEP1) and dep1-1 (NIL-dep1) genes under the Nanjing 6 background at 0 and 120 kg N ha–1.  Grain yield and NUE for grain production (NUEg) were 25.5 and 21.9% higher in NIL-dep1 compared to NIL-DEP1 averaged across N treatments and planting years, respectively.  The yield advantage of NIL-dep1 over NIL-DEP1 was mainly due to larger sink size (i.e., higher total spikelet number), grain-filling percentage, total dry matter production, and harvest index.  N utilization rather than N uptake contributed to the high yield of NIL-dep1.  Significantly higher NUEg in NIL-dep1 was associated with higher N and dry matter translocation efficiency, lower leaf and stem N concentration at maturity, and higher glutamine synthetase (GS) activity in leaves.  In conclusion, dep1 improved grain yield and NUE by increasing N and dry matter transport due to higher leaf GS activity under field conditions during the grain-filling period.

    Genotype×tillage interaction and the performance of winter bread wheat genotypes in temperate and cold dryland conditions
    Ebrahim ROOHI, Reza MOHAMMADI, Abdoul Aziz NIANE, Javad VAFABAKHSH, Mozaffar ROUSTAEE, Mohammad Reza JALAL KAMALI, Shahriar SOHRABI, Shahriar FATEHI, Hossain TARIMORADI
    2022, 21(11): 3199-3215.  DOI: 10.1016/j.jia.2022.08.096
    Abstract ( )   PDF in ScienceDirect  

    Growing concerns for food security and the alleviation of hunger necessitate knowledge-based crop management technologies for sustainable crop production.  In this study, 13 winter bread wheat genotypes (old, relatively old, modern, and breeding lines) were evaluated under three different tillage systems, i.e., conventional tillage (CT, full tillage with residue removed), reduced tillage (RT, chisel tillage with residue retained) and no-tillage (NT, no-tillage with residue retained on the soil surface) in farmer’s fields under rainfed conditions using strip-plot arrangements in a randomized complete block design with three replications in the west of Iran (Kamyaran and Hosseinabad locations) over two cropping seasons (2018–2019 and 2019–2020).  The main objectives were to investigate the effects of tillage systems and growing conditions on the agronomic characteristics, grain yield and stability performance of rainfed winter bread wheat genotypes.  Significant (P<0.01) genotype×tillage system interaction effects on grain yield and agronomic traits suggested that the genotypes responded differently to the different tillage systems.  The number of grains per spike and plant height were positively (P<0.0) associated with grain yield under the NT system, so they may be considered as targeted traits for future wheat breeding.  Using statistical models, the modern cultivars (“Sadra” and “Baran”) were identified as high yielding and showed yield stability across the different tillage systems.  As per each tillage system, genotype “Sadra” followed by “Zargana-6//Dari 1-7 Sabalan” exhibited higher adaption to CT; while cultivars “Jam” and “Azar2” showed better performance under the RT system; and cultivars “Varan” and “Baran” tended to have better performance expression in the NT condition.  The increased grain yields achieved in combination with lower costs and greater profits from conservation agriculture suggest that adapted cultivar and NT systems should be evaluated and promoted more widely to farmers in the west of Iran as an attractive package of crop management technologies.  In conclusion, variations in the performance of genotypes and the significant genotype×tillage system interaction effects on grain yield and some agronomic traits assessed in this study suggest that the development and selection of cultivars adapted to the NT system should be considered and included in the strategies and objectives of winter wheat breeding programs for the temperate and cold dryland conditions of Iran.

    Transcriptional search to identify and assess reference genes for expression analysis in Solanum lycopersicum under stress and hormone treatment conditions
    DUAN Yao-ke, HAN Rong, SU Yan, WANG Ai-ying, LI Shuang, SUN Hao, GONG Hai-jun
    2022, 21(11): 3216-3229.  DOI: 10.1016/j.jia.2022.07.051
    Abstract ( )   PDF in ScienceDirect  

    Tomato (Solanum lycopersicum) is a model plant for research on fruit development and stress response, in which gene expression analysis is frequently conducted.  Quantitative PCR (qPCR) is a widely used technique for gene expression analysis, and the selection of reference genes may affect the accuracy of results and even conclusions.  Although there have been some frequently used reference genes in tomato, it has been shown that the expressions of some of these genes are not constant in different tissues and environmental conditions.  Moreover, little information on genomic identification of reference genes is available in tomato.  Here, we mined the publicly available transcriptional sequencing data and screened out fifteen candidate reference genes, and the expression stability of these candidate genes and seven traditionally used ones were evaluated under stress and hormone treatment.  The results showed that over half of the selected candidate references were housekeeping genes in tomato cells.  Among the candidate reference genes and the traditionally used ones, the most stably expressed genes varied under different treatments, and most of these genes were recommended as preferred reference genes at least once except Solyc04g009030 and Solyc07g066610, two traditionally used reference genes.  This study provides some novel reference genes in tomato, and the preferred reference genes under different environmental stimuli, which may be useful for future research.  Our study suggests that excavating stably expressed genes from transcriptome sequencing data is a reliable approach to screening reference genes for qPCR analysis.  

    Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum
    LIU Lei, WANG Heng-bo, LI Yi-han, CHEN Shu-qi, WU Ming-xing, DOU Mei-jie, QI Yi-yin, FANG Jing-ping, ZHANG Ji-sen
    2022, 21(11): 3230-3244.  DOI: 10.1016/j.jia.2022.08.129
    Abstract ( )   PDF in ScienceDirect  

    Sugarcane has a large, complex, polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection.  The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes.  However, these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes.  In this present study, 744 305 and 361 638 candidate SSRs were identified from the genomes of Sofficinarum and Sspontaneum, respectively.  We verified the reliability of the predicted SSRs by using 1 200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum, including Sspontaneum, Sofficinarum, Srobustum, and modern sugarcane hybrid.  The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions.  Furthermore, 100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions.  A total of 320 alleles were generated using 100 polymorphic primers, with each marker ranging from two to seven alleles.  The genetic diversity analysis revealed that these accessions were distributed in four main groups, including group I (14 Sspontaneum accessions), group II (two Sofficinarum accessions), group III (18 modern sugarcane hybrid accessions), and group IV (five Srobustum accessions).  Experimental verification supported the reliability of the SSR markers based on genome-wide predictions.  The development of a large number of SSR markers based on wet experiments is valuable for genetic studies, including genetic linkage maps, comparative genome analysis, genome-wide association studies, and marker-assisted selection in Saccharum.

    Plant Protection
    Nonphytotoxic copper oxide nanoparticles are powerful “nanoweapons” that trigger resistance in tobacco against the soil-borne fungal pathogen Phytophthora nicotianae
    CHEN Juan-ni, WU Lin-tong, SONG Kun, ZHU Yun-song, DING Wei
    2022, 21(11): 3245-3262.  DOI: 10.1016/j.jia.2022.08.086
    Abstract ( )   PDF in ScienceDirect  

    Investigations into the potential application of nanoparticles acting as nanofungicides in sustainable agriculture are rapidly expanding due to the high antimicrobial properties of these compounds, which do not risk inducing pathogen resistance to fungicides.  A detailed understanding of the impact of copper oxide nanoparticles (CuO NPs) on soil-borne phytopathogenic fungi is yet to be obtained.  This study aimed to explore the in vitro antifungal activity and control efficacy of CuO NPs applied via irrigation with respect to tobacco black shank (TBS) disease caused by Phytophthora nicotianae.  The results revealed that CuO NPs greatly interfered with the reproductive growth process of this fungus, repressing hyphal growth, spore germination and sporangium production.  Additionally, morphological damage, intracellular ROS accumulation and increased SOD enzyme activity in hyphae were the antifungicidal mechanisms of these NPs.  In pot experiments, treatment with CuO NPs at 100 mg L–1 significantly suppressed TBS development, compared with the effect on control plants, and the control efficacy reached 33.69% without inducing phytotoxicity.  Exposure to CuO NPs significantly activated a series of defense enzymes, and resistance genes in tobacco can further explain the mechanisms by which CuO NPs suppressed fungal infection.  The Cu content in both the leaves and roots of Pnicotianae-infested plants increased by 50.03 and 27.25%, respectively, after treatment with 100 mg L–1 CuO NPs, compared with that of healthy plants.  In particular, a higher Cu content was observed in infected roots than in leaves.  Therefore, this study showed the potential of CuO NPs applied as nanofungicides and as nanoinducers of fungus resistance genes for the management of TBS through inhibition of pathogen infection and stimulation of plant defenses.

    Potassium sulphate induces resistance of rice against the root-knot nematode Meloidogyne graminicola
    LIU Mao-Yan, PENG De-liang, SU Wen, XIANG Chao, JIAN Jin-zhuo, ZHAO Jie, PENG Huan, LIU Shi-ming, KONG Ling-an, DAI Liang-ying, HUANG Wen-kun, LIU Jing
    2022, 21(11): 3263-3277.  DOI: 10.1016/j.jia.2022.08.002
    Abstract ( )   PDF in ScienceDirect  

    Potassium (K), an important nutrient element, can improve the stress resistance/tolerance of crops.  The application of K in resisting plant-parasitic nematodes shows that the K treatment can reduce the occurrence of nematode diseases and increase crop yield.  However, data on K2SO4 induced rice resistance against the root-knot nematode Meloidogyne graminicola are still lacking.  In this work, K2SO4 treatment reduced galls and nematodes in rice plants and delayed the development of nematodes.  Rather than affecting the attractiveness of roots to nematodes and the morphological phenotype of giant cells at feeding sites, such an effect is achieved by rapidly priming hydrogen peroxide (H2O2) accumulation and increasing callose deposition.  Meanwhile, galls and nematodes in rice roots were more in the potassium channel OsAKT1 and transporter OsHAK5 gene-deficient plants than in wild-type, while the K2SO4-induced resistance showed weaker in the defective plants.  In addition, during the process of nematode infection, the expression of jasmonic acid (JA)/ethylene (ET)/brassinolide (BR) signaling pathway-related genes and pathogenesis-related (PR) genes OsPR1a/OsPR1b was up-regulated in rice after K2SO4 treatment.  In conclusion, K2SO4 induced rice resistance against M. graminicola.  The mechanism of inducing resistance was to prime the basal defense and required the participation of the K+ channel and transporter in rice.  These laid a foundation for further study on the mechanism of rice defense against nematodes and the rational use of potassium fertilizer on improving rice resistance against nematodes in the field.

    Identification of chorion genes and RNA interference-mediated functional characterization of chorion-1 in Plutella xylostella
    DONG Shi-jie, LIU Bo, ZOU Ming-min, LIU Li-li, CAO Min-hui, HUANG Meng-qi, LIU Yan, Liette VASSEUR, YOU Min-sheng, PENG Lu
    2022, 21(11): 3278-3292.  DOI: 10.1016/j.jia.2022.08.079
    Abstract ( )   PDF in ScienceDirect  

    Choriogenesis is the last step of insect oogenesis, a process by which the chorion polypeptides are produced by the follicular cells and deposited on the surface of oocytes in order to provide a highly specialized protective barrier to the embryo.  The essential features of chorion genes have yet to be clearly understood in the diamondback moth, Plutella xylostella, a worldwide Lepidoptera pest attacking cruciferous crops and wild plants.  In this study, complete sequences for 15 putative chorion genes were identified, and grouped into A and B classes.  Phylogenetic analysis revealed that both classes were highly conserved and within each, branches are also species-specific.  Chorion genes from each class were located in pairs on scaffolds of the Pxylostella genome, some of which shared the common promoter regulatory region.  All chorion genes were highly specifically expressed in the Pxylostella adult females, mostly in the ovary with full yolk, which is a crucial period to build the shells of the eggs.  RNAi-based knockdown of chorion-1, which is located on the Px_scaffold 6 alone, although had no effect on yolk deposition, resulted in smaller eggs and sharply reduced hatchability.  Additionally, inhibition of PxCho-1 expression caused a less dense arrangement of the columnar layers, reduced exochorion roughness and shorter microvilli.  Our study provides the foundation for exploring molecular mechanisms of female reproduction in Pxylostella, and for making use of chorion genes as the potential genetic-based molecular target to better control this economically important pest.

    Animal Science · Veterinary Medicine

    Genome-wide detection for runs of homozygosity analysis in three pig breeds from Chinese Taihu Basin and Landrace pigs by SLAF-seq data

    TONG Shi-feng, ZHU Mo , XIE Rui , LI Dong-feng , ZHANG Li-fan , LIU Yang
    2022, 21(11): 3293-3301.  DOI: 10.1016/j.jia.2022.08.061
    Abstract ( )   PDF in ScienceDirect  

    Erhualian (E), Meishan (MS) and Mi (MI) pigs are excellent indigenous pig breeds in Chinese Taihu Basin, which have made great contributions to the genetic improvement of commercial pigs.  Investigation of the genetic structure and inbreeding level of the 3 pig breeds is of great significance for the sustainable breeding of commercial pigs.  The length and number of runs of homozygosity (ROH) as well as the frequency of genomes covered by ROH can be used as indicators to evaluate the level of inbreeding and the origin of the population.  In this study, the ROH characteristics of E, MS, MI and Landrace (L) pigs were analyzed by SLAF-seq data, and the inbreeding coefficient based on ROH (FROH) was calculated.  In addition, we have identified candidate genes in the genomic regions associated with ROH.  A total of 10 568 ROH were detected in 116 individuals of 4 pig breeds.  The analysis showed that there were significant differences in genetic structure between 3 Taihu Basin pig breeds and L, and the genetic structure of E and MI was similar.  The results of FROH showed that the inbreeding level of MS was the highest (0.25±0.07), while E and MI were lower than L.  Compared with the other 3 pig populations, MS showed a higher frequency of long ROH (>5 Mb), indicating higher inbreeding in MS in recent generations.  A large number of candidate genes related to reproductive traits are located in the genomic regions with a high frequency of ROH, and these genes are expected to be used as candidate genes in marker-assisted selection (MAS) breeding programs.  Our findings can provide theoretical support for genetic conservation and genetic improvement of 3 pig breeds in Chinese Taihu Basin.

    Long-term effect of subacute ruminal acidosis on the morphology and function of rumen epithelial barrier in lactating goats
    HU Hong-lian, YANG Shu-qing, CHENG Meng, SONG Li-wen, XU Ming, GAO Min, YU Zhong-tang
    2022, 21(11): 3302-3313.  DOI: 10.1016/j.jia.2022.08.087
    Abstract ( )   PDF in ScienceDirect  

    Grain-induced subacute ruminal acidosis (SARA) impairs rumen epithelial barrier function, but it is yet to be determined if SARA can cause persistent damage to the morphology and function of the rumen epithelial barrier.  The objective of the present study was to investigate if SARA has persistent effects on the morphological structure and permeability of ruminal epithelium and the expression of the genes involved in epithelial barrier function using a lactating goat model.  Twelve mid-lactating Saanen goats with rumen cannulas were randomly assigned to 1 of 2 groups: control group (Ctrl, n=4) fed a basal diet with a non-fiber carbohydrate (NFC) to neutral detergent fiber (NDF) ratio of 1.40, and SARA group (SARA, n=8) fed the same basal diet but with increasing NFC to NDF ratio from 1.4 to 1.79, 2.31, and 3.23 overtime to induce SARA.  At the end of the SARA challenge (post-SARA), 4 goats were randomly selected from the SARA group and fed only hay mixture ad libitum for another 4 weeks to allow for restitution (post-SARA).  Ruminal pH was continuously recorded to monitor the severity of SARA.  Samples of the ventral ruminal epithelium were collected after slaughter to examine the structural and functional changes of the ruminal epithelium using transmission electron microscopy (TEM), Ussing chambers, qRT-PCR, and Western bolt analyses.  Compared with the Ctrl group, ruminal papilla length, width, surface area and thickness of stratum corneum increased (P<0.05), while stratum spinosum and basale thickness, and total depth of the epithelium decreased (P<0.05) in the SARA group.  These changes diminished or tended to return to the levels of the Ctrl group in the post-SARA group (P>0.05).  The SARA challenge also decreased cellular junction and widened the intercellular space between epithelial cells.  Rumen transepithelial short-circuit current (Isc), tissue conductance (Gt), and mucosa-to-serosa flux of paracellular horseradish peroxidase (HRP) all increased (P<0.05) both in the SARA and post-SARA groups, which indicates that SARA can induce a sustained increase in epithelial permeability and barrier dysfunction.  Moreover, the mRNA and protein expressions of CLDN1, OCLN and ZO-1 were down-regulated (P<0.01) in both the SARA and post-SARA groups.  The results of this study showed that SARA could result in sustained epithelial barrier dysfunction, at both structural and functional levels, which is associated with decreased expression of rumen epithelial tight junction proteins, and the restitution of rumen epithelial barrier function is slower than that of its morphology.

    Dynamic change of fungal community in the gastrointestinal tract of growing lambs
    YIN Xue-jiao, JI Shou-kun, DUAN Chun-hui, TIAN Pei-zhi, JU Si-si, YAN Hui, ZHANG Ying-jie, LIU Yue-qin
    2022, 21(11): 3314-3328.  DOI: 10.1016/j.jia.2022.08.092
    Abstract ( )   PDF in ScienceDirect  

    Although fungal communities in the gastrointestinal tract have a significant role in animal health and performance, their dynamics within the tract are not well known.  Thus, this study investigated fungal community dynamics in the rumen and rectum of lambs from birth to 4 mon of age by using IT1S rDNA sequencing technology together with the RandomForest approach to determine age-related changes in the fungal ecology.  The results indicated that gastrointestinal fungal community composition, diversity, and abundance altered (P<0.05) with the increasing age of the lambs.  Two phyla, Ascomycota and Basidiomycota, dominated the samples.  Similarity within age groups of the rumen fungi increased sharply after 45 days of age, while the similarity increased (P<0.05) significantly after 60 days of age in the rectum.  The age-related genera, Acremonium, Microascus, Valsonectria, Myrmecridium, Scopulariopsis, Myrothecium, Saccharomyces, and Stephanonectria, were presented in both ruminal and rectal communities, and their changes in relative abundance were consistent at both sites.  The principal coordinates analysis showed significant differences (P<0.05) between the fungal communities in the rumen and rectum.  Our findings demonstrate that both the age of lambs and the gastrointestinal tract region can affect the composition of these fungal communities, and this provides new insight and directions for future studies in this research area.

    Influence of preceding crop and tillage system on forage yield and quality of selected summer grass and legume forage crops under arid conditions
    Hend H. M. HASSAN, El-Sayed E. A. EL-SOBKY, Elsayed MANSOUR, Ahmed S. M. El-KHOLY, Mohamed F. AWAD, Hayat ULLAH, Avishek DATTA
    2022, 21(11): 3329-3344.  DOI: 10.1016/j.jia.2022.08.088
    Abstract ( )   PDF in ScienceDirect  

    Among the crop production factors, preceding crop and tillage management affect the sustainable use of soil resources and ultimately crop growth and productivity.  This study aimed at investigating the impact of preceding winter crops (grass or legume) and different tillage systems on forage yield, quality and nutritive values of three summer grass (Sudan grass, pearl millet and teosinte) and two legume forage crops (cowpea and guar) under arid conditions.  The results exhibited that growing forage crops after legumes (as berseem clover) produced the highest fresh and dry forage yields and quality attributes compared with grasses (as wheat) with the exception of crude fiber content, which was decreased.  Moreover, tillage practices showed positive impact on forage yields and quality attributes.  The maximum forage yields and quality parameters were recorded under conventional tillage (CT) practice compared with reduced tillage (RT) and no-tillage (NT) systems.  Among the evaluated crops, the highest yields of fresh forage, dry forage, crude fiber, crude protein and total digestible nutrient were exhibited by grass forage crops (Sudan grass, pearl millet and teosinte), whereas the highest crude protein content and the digestible energy values were produced by legume forage crops (cowpea and guar).  The maximum fresh forage, dry forage, crude fiber, crude protein, total digestible nutrient and digestible crude protein yields were produced by pearl millet followed by Sudan grass under CT and RT after berseem clover.  The highest net return was recorded by sowing pearl millet after berseem clover and applying CT followed by RT practices, which could be recommended for the commercial production.  Moreover, it could be assumed that the combination of growing grass forage crops after legume crops under CT or RT systems could enhance forage crop yield and quality with an improvement in soil properties for sustainable agriculture with low cost and the highest net income.

    Agro-ecosystem & Environment
    Substituting nitrogen and phosphorus fertilizer with optimal amount of crop straw improved rice grain yield, nutrient use efficiency and soil carbon sequestration
    XIE Jun, Blagodatskaya EVGENIA, ZHANG Yu, WAN Yu, HU Qi-juan, ZHANG Cheng-ming, WANG Jie, ZHANG Yue-qiang, SHI Xiao-jun
    2022, 21(11): 3345-3355.  DOI: 10.1016/j.jia.2022.08.059
    Abstract ( )   PDF in ScienceDirect  

    Crop straw return after harvest is considered an important way to achieve both agronomic and environmental benefits.  However, the appropriate amount of straw to substitute for fertilizer remains unclear.  A field experiment was performed from 2016 to 2018 to explore the effect of different amounts of straw to substitute for fertilizer on soil properties, soil organic carbon (SOC) storage, grain yield, yield components, nitrogen (N) use efficiency, phosphorus (P) use efficiency, N surplus, and P surplus after rice harvesting.  Relative to mineral fertilization alone, straw substitution at 5 t ha–1 improved the number of spikelets per panicle, effective panicle, seed setting rate, 1 000-grain weight, and grain yield, and also increased the aboveground N and P uptake in rice.  Straw substitution exceeding 2.5 t ha–1 increased the soil available N, P, and K concentrations as compared with mineral fertilization, and different amounts of straw substitution improved SOC storage compared with mineral fertilization.  Furthermore, straw substitution at 5 t ha–1 decreased the N surplus and P surplus by up to 68.3 and 28.9%, respectively, compared to mineral fertilization.  Rice aboveground N and P uptake and soil properties together contributed 19.3% to the variation in rice grain yield and yield components.  Straw substitution at 5 t ha–1, an optimal fertilization regime, improved soil properties, SOC storage, grain yield, yield components, N use efficiency (NUE), and P use efficiency (PUE) while simultaneously decreasing the risk of environmental contamination.

    Apparent variations in nitrogen runoff and its uptake in paddy rice under straw incorporation
    Muhammad Amjad BASHIR, ZHAI Li-mei, WANG Hong-yuan, LIU Jian, Qurat-Ul-Ain RAZA, GENG Yu-cong, Abdur REHIM, LIU Hong-bin
    2022, 21(11): 3356-3367.  DOI: 10.1016/j.jia.2022.08.062
    Abstract ( )   PDF in ScienceDirect  

    Straw incorporation is a widespread practice to promote agricultural sustainability.  However, the potential effects of straw incorporation with the prolonged time on nitrogen (N) runoff loss from paddy fields are not well studied.  The current study addresses the knowledge gap by assessing the effects of straw incorporation on the processes influencing N runoff patterns and its impacts on crop yield, N uptake, total N (TN), and soil organic matter (SOM).  We conducted field experiments with rice (Oryza sativa L.)–wheat (Triticum aestivum L.) rotation, rice–tobacco (Nicotiana tabacum L.) rotation, and double-rice cropping in subtropical China from 2008 to 2012.  Each rotation had three N treatments: zero N fertilization (CK), chemical N fertilization (CF), and chemical N fertilization combined with straw incorporation (CFS).  The treatment effects were assessed on TN runoff loss, crop yield, N uptake, soil TN stock, and SOM.  Results showed that TN runoff was reduced by substituting part of the chemical N fertilizer with straw N in the double rice rotation, while crop N uptake was significantly (P<0.05) decreased due to the lower bioavailability of straw N.  In contrast, in both rice–wheat and rice–tobacco rotations, TN runoff in CFS was increased by 0.9–20.2% in the short term when straw N was applied in addition to chemical N, compared to CF.  However, TN runoff was reduced by 2.3–19.3% after three years of straw incorporation, suggesting the long-term benefits of straw incorporation on TN loss reduction.  Meanwhile, crop N uptake was increased by 0.8–37.3% in the CFS of both rotations.  This study demonstrates the challenges in reducing N runoff loss while improving soil fertility by straw incorporation over the short term but highlights the potential of long-term straw incorporation to reduce N loss and improve soil productivity.

    Effects of super-absorbent polymers on the soil structure and hydro-physical properties following continuous wetting and drying cycles
    JI Bing-yi, ZHAO Chi-peng, WU Yue, HAN Wei, SONG Ji-qing, BAI Wen-bo
    2022, 21(11): 3368-3381.  DOI: 10.1016/j.jia.2022.08.065
    Abstract ( )   PDF in ScienceDirect  

    Super-absorbent polymers (SAPs) are widely used chemical water-saving materials, which play an active role in the accumulation of soil water and the improvement of soil structure.  Little is known about their performance with repeated usage or about factors influencing their efficiency under alternate wetting and drying cycles.  In this study, various concentrations of SAP (0, 0.1, 0.2 and 0.3%) in soil following three continuous wetting and drying cycles (T1, T2 and T3), were studied to determine effects on soil structure stability and hydro-physical properties.  The results indicated that the SAP improved soil water supply capacity under conditions of mild drought (T2) and sufficient irrigation (T3) at concentrations of 0.2 and 0.3%, but a reduction was observed under severe drought conditions (T1), which was negatively correlated with the SAP concentration.  The physical adsorption of the SAP by soil and the chemical connection between the SAP and soil mineral colloids as Si-O-Si bonds, -OH bonds and different crystalline silica were the important factors that directly lead to the reduction of water retention capacities of the SAP with alternating wet and dry conditions.  Compared with the control, the soil liquid phase ratios of the SAP treatments were increased by 8.8–202.7% in the T1 and T2 cycles, which would have led to a decrease in the soil air phase ratios.  After repeated wetting and drying cycles, the SAP treatments increased the amount of >0.25 mm soil aggregates and the contents of water-stable macro-aggregate (R0.25), and decreased the amount of <0.053 mm soil aggregates, especially with higher concentrations of the SAP.  Increases in mean weight diameter (MWD) and geometric mean diameter (GMD), and declines in fractal dimension (D) and unstable aggregates index (ELT) were all observed with the SAP treatments, which indicated an improvement in soil stability and structure.  It was concluded that the distribution and stability of soil aggregates and soil water supply capacity was closely related to SAP concentration, soil moisture condition and the interaction between the SAP and soil particles

    Agricultural Economics and Management
    Explaining farmers’ reluctance to adopt green manure cover crops planting for sustainable agriculture in Northwest China
    Sheng-Han-Erin CHANG, YI Xiao-yan, Johannes SAUER, YIN Chang-bin, LI Fu-duo
    2022, 21(11): 3382-3394.  DOI: 10.1016/j.jia.2022.09.005
    Abstract ( )   PDF in ScienceDirect  
    Green manure cover crops (GMCCs) planting has a potential for mitigating greenhouse gas emissions (GHG) in agroecosystems and provides important ecosystem services, thereby achieving the Sustainable Development Goals (SDGs) stipulated by the United Nations.  However, the advantages of cultivating GMCCs on arable land are not widely recognized.  For example, in the whole of China, the GMCCs planting area is less than 3.5% of total arable land.  The aim of this study is to explore reasons for the low adoption rate of GMCCs planting.  Using best–worst scaling (BWS) approach, farmers ranked their preferred conservation practices including three types of GMCC cropping systems.  Taking Gansu Province in Northwest China as a case study, a survey with 276 farmers was conducted.  The findings indicated that three factors are related to the low adoption rate of GMCCs: 1) farmers preferred improving farmland irrigation facilities and substituting chemical fertilizers with organic rather than planting GMCCs; 2) lack of awareness and understanding of government policy on GMCCs and limited access to training courses; 3) financial support and subsidies from the government are insufficient.  This study provides insights and strategic implications for policymakers on how to further promote GMCCs in the future.

    Commercial cash crop production and households’ economic welfare: Evidence from the pulse farmers in rural China
    MA Ji-liang, LI Fan, ZHANG Hui-jie, Khan NAWAB
    2022, 21(11): 3395-3407.  DOI: 10.1016/j.jia.2022.09.006
    Abstract ( )   PDF in ScienceDirect  

    Whether promoting cash crop production can increase household welfare has long been the focus of the food policy debate.  This study first investigated the determinants of household behavior in commercial pulse farming.  It then examined how households’ commercial pulse production improves their economic welfare.  We used a dataset of 848 households collected from 2018 to 2019 to estimate the determinants of household behavior in commercial pulse farming by the Heckman two-step model.  The endogenous treatment regression (ETR) method was employed to examine the impact of commercial pulse farming on household economic welfare.  The results showed that factors such as market purchase prices, agricultural technology services, farmers’ access to loans, and government subsidies promoted smallholders’ commercial pulse farming; production costs and perceptions of climate change risks constrained smallholders’ commercial pulse production.  Overall, commercial pulse production has increased household farm income but there was a limited impact on household off-farm income.  Our findings suggest that policies aiming to increase households’ cash crop production and market access could significantly improve the economic welfare of pulse farmers.Whether promoting cash crop production can increase household welfare has long been the focus of the food policy debate.  This study first investigated the determinants of household behavior in commercial pulse farming.  It then examined how households’ commercial pulse production improves their economic welfare.  We used a dataset of 848 households collected from 2018 to 2019 to estimate the determinants of household behavior in commercial pulse farming by the Heckman two-step model.  The endogenous treatment regression (ETR) method was employed to examine the impact of commercial pulse farming on household economic welfare.  The results showed that factors such as market purchase prices, agricultural technology services, farmers’ access to loans, and government subsidies promoted smallholders’ commercial pulse farming; production costs and perceptions of climate change risks constrained smallholders’ commercial pulse production.  Overall, commercial pulse production has increased household farm income but there was a limited impact on household off-farm income.  Our findings suggest that policies aiming to increase households’ cash crop production and market access could significantly improve the economic welfare of pulse farmers.

    Short Communication
    Study on PCR rapid molecular detection technique of Meloidogyne vitis
    YANG Yan-mei, LIU Pei, LI Hong-mei, PENG Huan, DU Xia, DONG Ye, HU Xian-qi
    2022, 21(11): 3408-3416.  DOI: 10.1016/j.jia.2022.08.100
    Abstract ( )   PDF in ScienceDirect  
    Meloidogyne vitis is a new root-knot nematode parasitic on grape root in Yunnan Province, China.  In order to establish a rapid, reliable and specific molecular detection method for Mvitis, the species-specific primers were designed with rDNA-ITS (ribosomal DNA internal transcribed spacer) gene fragment as the target.  The reaction system was optimized and the reliability, specificity and sensitivity of primer were testified, therefore, a rapid PCR detection method for Mvitis was established.  The result showed that the optimal annealing temperature of the primers was 53°C, which was suitable for the detection of different life stages of Mvitis.  Specificity test showed that the specific fragment size of 174 bp was obtained from Mvitis, but other five non-target nematodes did not have any amplification bands, thus effectively distinguish Mvitis and the other five species, and could specifically detect the Mvitis from mixed populations.  Sensitivity test showed that this PCR technique could detect the DNA of a single second-stage juvenile (J2) and 10–4 female.  Futhermore, this PCR technique could be used to detect directly M. vitis from soil samples.  The rapid, sensitive and specific PCR molecular detection technique could be used for the direct identification of a single J2 of Mvitis and the detection of Mvitis in mixed nematode populations and the detection of two J2s or one male in 0.5 g soil samples, which will provide technical support for the investigation of the occurrence and damage of Mvitis and the formulation of efficient green control strategies.