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2022 Vol. 21 No. 9 Previous Issue    Next Issue

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Review
Crop Science
Horticulture
Plant Protection
Animal Science · Veterinary Medicine
Agro-ecosystem & Environment
Food Science


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Cassava (Manihot esculenta) is an important tropical crop for starch, biofuel production, and animal feed due to its starch-enriched root. Severe drought stresses affect cassava productivity and quality. In plants, it is known that long non-coding RNAs (lncRNAs) are involved in response to abiotic stresses by regulating gene expression. However, the function of cassava lncRNAs in drought response remains largely unknown. The present four-year study demonstrated that DROUGHT-INDUCED INTERGENIC lncRNA (DIR) play a pivotal role in regulating drought stress tolerance in cassava, which may be related to mRNA export and protein quality control pathways. Gain-of-function analysis revealed that DIR overexpression in transgenic cassava seedlings conferred tolerance to drought stress. RNA sequencing (RNA-seq) analysis indicated that a range of drought-responsive genes, such as TFs (NAC, WRKY and bHLH), were induced in DIR-overexpressing transgenic lines. Furthermore, we found that DIR interacted directly with proteins that regulate mRNAs or protein metabolisms in cassava cells to cope with drought stress. Taken together, this study greatly extends the repertoire of lncRNAs in plants, and may provide new insights into lncRNA functions conserved among tropical crops in response to drought stress. The cover photo shows the morphology of fieldgrown of cassava plant and the predicted secondary structure of DIR, which was provided by Prof. Ruan Mengbin and Prof. Li Shuxia from Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, China. See pages 2588–2602 for more details.


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Review

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Yield penalty of maize (Zea mays L.) under heat stress in different growth stages: A review LI Teng, ZHANG Xue-peng, LIU Qing, LIU Jin, CHEN Yuan-quan, SUI Peng 2022, 21(9): 2465-2476.  DOI: 10.1016/j.jia.2022.07.013 Abstract ( )   PDF in ScienceDirect   Maize (Zea mays L.) can exhibit yield penalties as a result of unfavorable changes to growing conditions.  The main threat to current and future global maize production is heat stress.  Maize may suffer from heat stress in all of the growth stages, either continuously or separately.  In order to manage the impact of climate driven heat stress on the different growth stages of maize, there is an urgent need to understand the similarities and differences in how heat stress affects maize growth and yield in the different growth stages.  For the purposes of this review, the maize growth cycle was divided into seven growth stages, namely the germination and seedling stage, early ear expansion stage, late vegetative growth stage before flowering, flowering stage, lag phase, effective grain-filling stage, and late grain-filling stage.  The main focus of this review is on the yield penalty and the potential physiological changes caused by heat stress in these seven different stages.  The commonalities and differences in heat stress related impacts on various physiological processes in the different growth stages are also compared and discussed.  Finally, a framework is proposed to describe the main influences on yield components in different stages, which can serve as a useful guide for identifying management interventions to mitigate heat stress related declines in maize yield.

Crop Science

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Heterosis and heterotic patterns of maize germplasm revealed by a multiple-hybrid population under well-watered and drought-stressed conditions SANG Zhi-qin, ZHANG Zhan-qin, YANG Yu-xin, LI Zhi-wei, LIU Xiao-gang, XU Yunbi, LI Wei-hua 2022, 21(9): 2477-2491.  DOI: 10.1016/j.jia.2022.07.006 Abstract ( )   PDF in ScienceDirect   Understanding the heterosis in multiple environments between different heterotic groups is of fundamental importance in successful maize breeding.  A total of 737 hybrids derived from 41 maize inbreds were evaluated over two years, with the aim of assessing the genetic diversity and their performance between heterotic groups under drought-stressed (DS) and well-watered (WW) treatments.  A total of 38 737 SNPs were employed to assess the genetic diversity.  The genetic distance (GD) between the parents ranged from 0.05 to 0.74, and the 41 inbreds were classified into five heterotic groups.  According to the hybrid performance (high yield and early maturity between heterotic groups), the heterosis and heterotic patterns of Iowa Stiff Stalk Synthetic (BSSS)×Non-Stiff Stalk (NSS), NSS×Sipingtou (SPT) and BSSS×SPT were identified to be useful options in China’s maize breeding.  The relative importance of general and specific combining abilities (GCA and SCA) suggests the importance of the additive genetic effects for grain yield traits under the WW treatment, but the non-additive effects under the DS treatment.  At least one of the parental lines with drought tolerance and a high GCA effect would be required to achieve the ideal hybrid performance under drought conditions.  GD showed a positive correlation with yield and yield heterosis in within-group hybrids over a certain range of GD.  The present investigation suggests that the heterosis is due to the combined accumulation of superior genes/alleles in parents and the optimal genetic distance between parents, and that yield heterosis under DS treatment was mainly determined by the non-additive effects.

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Genetic dissection of ear-related traits using immortalized F2 population in maize GAO Ri-xin, HU Ming-jian, ZHAO Hai-ming, LAI Jin-sheng, SONG Wei-bin 2022, 21(9): 2492-2507.  DOI: 10.1016/j.jia.2022.07.007 Abstract ( )   PDF in ScienceDirect   Ear-related traits are often selection targets for maize improvement.  This study used an immortalized F2 (IF2) population to elucidate the genetic basis of ear-related traits.  Twelve ear-related traits (namely, row number (RN), kernel number per row (KNPR), ear length (EL), ear diameter (ED), ten-kernel thickness (TKT), ear weight (EW), cob diameter (CD), kernel length (KL), kernel width (KW), grain weight per ear (GW), 100-kernel weight (HKW), and grain yield per plot (GY)), were collected from the IF2 population.  The ear-related traits were comprised of 265 crosses derived from 516 individuals of the recombinant inbred lines (RILs) under two separated environments in 2017 and 2018, respectively.  Quantitative trait loci (QTLs) analyses identified 165 ear traits related QTLs, which explained phenotypic variation ranging from 0.1 to 12.66%.  Among the 165 QTLs, 19 underlying nine ear-related traits (CD, ED, GY, RN, TKT, HKW, KL, GW, and KNPR) were identified across multiple environments and recognized as reliable QTLs.  Furthermore, 44.85% of the total QTLs showed an overdominance effect, and 12.72% showed a dominance effect. Additionally, we found 35 genomic regions exhibiting pleiotropic effects across the whole maize genome, and 17 heterotic loci (HLs) for RN, EL, ED and EW were identified.  The results provide insights into genetic components of ear-related traits and enhance the understanding of the genetic basis of heterosis in maize.

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Characterization of the petiole length in soybean compact architecture mutant M657 and the breeding of new lines GAO Hua-wei, SUN Ru-jian, YANG Meng-yuan, YAN Long, HU Xian-zhong, FU Guang-hui, HONG Hui-long, GUO Bing-fu, ZHANG Xiang, LIU Li-ke, ZHANG Shu-zhen, QIU Li-juan 2022, 21(9): 2508-2520.  DOI: 10.1016/j.jia.2022.07.004 Abstract ( )   PDF in ScienceDirect   Phenotypic screening of soybean germplasm suitable for high planting density is currently the most viable strategy to increase yield.  Previous studies have shown that soybean varieties with dwarf features and a short petiole often exhibit a compact plant architecture which could improve yield through increased planting density, although previously reported short petiole accessions were ultimately not usable for breeding in practice.  Here, we established a method to assess petiole length and identified an elite mutant line, M657, that exhibits high photosynthetic efficiency.  The agronomic traits of M657 were evaluated under field conditions, and appeared to be stable for short petiole across seven locations in northern, Huang–Huai, and southern China from 2017 to 2018.  Compared with the Jihuang 13 wild type, the mutant M657 was shorter in both petiole length and plant height, exhibited lower total area of leaf, seed weight per plant and 100-seed weight, but had an increased number of effective branches and the growth period was prolonged by 2–7 days.  Using M657 as a parental line for crosses with four other elite lines, we obtained four lines with desirable plant architecture and yield traits, thus demonstrating the feasibility of adopting M657 in breeding programs for soybean cultivars of high density and high yield.

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Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean ZHANG Hua, WU Hai-yan, TIAN Rui, KONG You-bin, CHU Jia-hao, XING Xin-zhu, DU Hui, JIN Yuan, LI Xi-huan, ZHANG Cai-ying 2022, 21(9): 2521-2537.  DOI: 10.1016/j.jia.2022.07.005 Abstract ( )   PDF in ScienceDirect   Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean.  The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem.  In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line (RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the T1 stage, and the six-leaf stage as the flowering critical stage was designated as the T2 stage.  In total, 200 single nucleotide polymorphism (SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the T1 stage, and 109 detected at the T2 stage.  Among these SNP loci, one SNP cluster (s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the T1 stage, and the elite haplotype showed significantly greater plant height than the others.  Meanwhile, one pleiotropic SNP cluster (ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the T2 stage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition.  Furthermore, four co-associated SNP loci (ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the T1 and T2 stages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population.  More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by qRT-PCR.  Thus, these genetic loci and candidate genes could be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.

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A geranylgeranyl pyrophosphate synthase gene, IbGGPS, increases carotenoid contents in transgenic sweetpotato LI Rui-jie, ZHAI Hong, HE Shao-zhen, ZHANG Huan, ZHAO Ning, LIU Qing-chang 2022, 21(9): 2538-2546.  DOI: 10.1016/j.jia.2022.07.029 Abstract ( )   PDF in ScienceDirect   Geranylgeranyl pyrophosphate synthase (GGPS) plays an important role in the biosynthesis of carotenoids.  In a previous study, the IbGGPS gene was isolated from a sweetpotato, Ipomoea batatas (L.) Lam., line Nongdafu 14 with high carotenoid contents, but its role and underlying mechanisms in carotenoid biosynthesis in sweetpotato were not investigated.  In the present study, the IbGGPS gene was introduced into a sweetpotato cv. Lizixiang and the contents of β-carotene, β-cryptoxanthin, zeaxanthin and lutein were significantly increased in the storage roots of the IbGGPS-overexpressing sweetpotato plants.  Further analysis showed that IbGGPS gene overexpression systematically up-regulated the genes involved in the glycolytic, 2-C-methyl-D-erythritol-4-phosphate (MEP) and carotenoid pathways, which increased the carotenoid contents in the transgenic plants.  These results indicate that the IbGGPS gene has the potential for use in improving the carotenoid contents in sweetpotato and other plants.

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Growth characteristics and grain yield of machine-transplanted medium indica hybrid rice with high daily yield DENG Fei, HE Lian-hua, CHEN Duo, ZHANG Chi, TIAN Qing-lan, WU Zhen-yuan, LI Qiu-ping, ZENG Yu-ling, ZHONG Xiao-yuan, CHEN Hong, WANG Li, REN Wan-jun 2022, 21(9): 2547-2558.  DOI: 10.1016/j.jia.2022.07.030 Abstract ( )   PDF in ScienceDirect   High-yield rice varieties with a suitable growth duration are required for mechanical transplanting in multiple cropping systems.  Daily yield is an appropriate criterion for the selection of machine-transplanted rice varieties.  The aim of this study was to investigate the growth characteristics and grain production in machine-transplanted medium indica hybrid rice with a high daily yield.  We conducted a field experiment on 20 medium indica hybrid rice varieties in 2017 and 2018.  Grain yield decreased significantly with growth duration between jointing and heading, but it increased with dry matter accumulation, growth rate between jointing and heading, dry matter partitioning to the stem plus sheath at heading, daily yield, and number of spikelets per panicle.  Compared with the medium and low daily yield variety types, the high daily yield variety type increased shoot biomass by improving crop growth rate and dry matter accumulation amount between jointing and heading and after heading.  The high daily yield variety type decreased the growth duration pre-heading and the proportions of dry matter partitioned to the leaf lamina at heading and maturity, but it also increased the post-heading accumulated dry matter in the grain and the remobilization of dry matter stored in the vegetative organs.  Furthermore, the high daily yield variety type significantly increased the occurrence rate of tillers, which is beneficial for the formation of a larger panicle size and an increase in the grain-filling rate.  These changes contributed to a 6.51–23.16% relative increase in grain yield of the high daily yield variety type.  In conclusion, the selection of high daily yield indica hybrid rice varieties with shorter pre-heading growth duration, greater tiller occurrence rate and spikelet numbers per panicle, higher post-jointing growth rates and stem plus sheath dry matter accumulation at heading is suitable for machine-transplanted rice.

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Strip deep rotary tillage combined with controlled-release urea improves the grain yield and nitrogen use efficiency of maize in the North China Plain HAN Yu-ling, GUO Dong, MA Wei, GE Jun-zhu, LI Xiang-ling, Ali Noor MEHMOOD, ZHAO Ming, ZHOU Bao-yuan 2022, 21(9): 2559-2576.  DOI: 10.1016/j.jia.2022.07.009 Abstract ( )   PDF in ScienceDirect   Inappropriate tillage practices and nitrogen (N) management have become seriously limitations for maize (Zea mays L.) yield and N use efficiency (NUE) in the North China Plain (NCP).  In the current study, we examined the effects of strip deep rotary tillage (ST) combined with controlled-release (CR) urea on maize yield and NUE, and determined the physiological factors involved in yield formation and N accumulation during a 2-year field experiment.  Compared with conventional rotary tillage (RT) and no-tillage (NT), ST increased the soil water content and soil mineral N content (Nmin) in the 20–40 cm soil layer due to reduction by 10.5 and 13.7% in the soil bulk density in the 0–40 cm soil layer, respectively.  Compared with the values obtained by common urea (CU) fertilization, CR increased the Nmin in the 0–40 cm soil layers by 12.4 and 10.3% at the silking and maturity stages, respectively.  As a result, root length and total N accumulation were enhanced under ST and CR urea, which promoted greater leaf area and dry matter (particularly at post-silking), eventually increasing the 1 000-kernel weight of maize.  Thus, ST increased the maize yield by 8.3 and 11.0% compared with RT and NT, respectively, whereas CR urea increased maize yield by 8.9% above the values obtained under CU.  Because of greater grain yield and N accumulation, ST combined with CR urea improved the NUE substantially.  These results show that ST coupled with CR urea is an effective practice to further increase maize yield and NUE by improving soil properties and N supply, so it should be considered for sustainable maize production in the NCP (and other similar areas worldwide).

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Cotton maturity and responses to harvest aids following chemical topping with mepiquat chloride during bloom period QI Hai-kun, DU Ming-wei, MENG Lu, XIE Liu-wei, A. Egrinya ENEJI, XU Dong-yong, TIAN Xiao-li, LI Zhao-hu 2022, 21(9): 2577-2587.  DOI: 10.1016/j.jia.2022.07.008 Abstract ( )   PDF in ScienceDirect   Early maturity, complete defoliation and boll opening are essential for the efficient machine harvesting of cotton.  Chemical topping, involving one extra application of mepiquat chloride (MC) in addition to its traditional multiple-application strategy, may be able to replace manual topping.  However, it is not known whether this chemical topping technique will influence maturity or cotton responses to harvest aids.  In this 2-yr field study, we determined the effects of the timing of chemical topping using various rates of MC on boll opening percentage (BOP) before application of harvest aids (50% thidiazuron·ethephon suspension concentrate, referred to as TE), and the defoliation percentage (DP) and BOP 14 days after TE application.  The results indicated that late chemical topping (near the physiological cutout, when the nodes above white flower is equal to 5.0) significantly decreased BOP before TE by 5.9–11.2% compared with early (at peak bloom) or middle (seven days after peak bloom) treatments in 2019, which was a relatively normal year based on crop condition.  Also, a high MC rate (270 g ha–1) showed a significantly lower (22.0%) BOP before TE than low (90 g ha–1) or medium (180 g ha–1) rates.  In 2020, which was characterized by stronger vegetative growth in the late season, the late chemical topping reduced the number of leaves before TE application relative to early or middle treatments, but had lower DP (23.2–27.2%) 14 days after TE application.  The high MC rate showed a leaf count before TE application that was similar to the low and medium rates, but it showed the most leaves after TE and much lower (15.0–21.7%) DP in 2020.  These results suggest that late timing of chemical topping and a high MC rate decreased the sensitivity of leaves to harvest aids.  Further analysis indicated that the late chemical topping mainly affected the leaf drop from the mainstem and fruiting branches where the late regrowth occurred, and the high MC rate reduced leaf shedding from these parts and also from the vegetative branches.  In conclusion, chemical topping with MC during the bloom period affected cotton maturity and responses to harvest aids in different ways according to the crop condition.  To avoid the risks of delayed maturity and poor defoliation after the application of harvest aids, chemical topping should not be performed too late (i.e., near the physiological cutout) by using MC at more than 180 g ha–1.  The optimum timing of chemical topping probably varies from peak bloom to around seven days later, and the safest MC rates for chemical topping should be less than 180 g ha–1.

Horticulture

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A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression DONG Shi-man, XIAO Liang, LI Zhi-bo, SHEN Jie, YAN Hua-bing, LI Shu-xia, LIAO Wen-bin, PENG Ming 2022, 21(9): 2588-2602.  DOI: 10.1016/j.jia.2022.07.022 Abstract ( )   PDF in ScienceDirect   Cassava is an important tropical cash crop.  Severe drought stresses affect cassava productivity and quality, and cause great economic losses in agricultural production.  Enhancing the drought tolerance of cassava can effectively improve its yield.  Long non-coding RNAs (lncRNAs) are present in a wide variety of eukaryotes.  Recently, increasing evidence has shown that lncRNAs play a critical role in the responses to abiotic stresses.  However, the function of cassava lncRNAs in the drought response remains largely unknown.  In this study, we identified a novel lncRNA, DROUGHT-INDUCED INTERGENIC lncRNA (DIR).  Gene expression analysis showed that DIR was significantly induced by drought stress treatment, but did not respond to abscisic acid (ABA) or jasmonic acid (JA) treatments.  In addition, overexpression of the DIR gene enhanced proline accumulation and drought tolerance in transgenic cassava.  RNA-seq analysis revealed that DIR preferentially affected drought-related genes that were linked to transcription and metabolism.  Moreover, RNA pull-down mass spectrometry analysis showed that DIR interacted with 325 proteins.  A protein–protein interaction (PPI) analysis found a marked enrichment in proteins associated with the mRNA export and protein quality control pathways.  Collectively, these results suggest that DIR and its interacting proteins that regulate mRNA or protein metabolism are involved in mediating the drought stress response.  Thus, regulating DIR expression has potential for improving cassava yield under drought conditions.

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Genome-scale mRNA and miRNA transcriptomic insights into the regulatory mechanism of cucumber corolla opening SONG Xiao-fei, GE Dan-feng, XIE Yang, LI Xiao-li, SUN Cheng-zhen, CUI Hao-nan, ZHU Xue-yun, LIU Ren-yi, YAN Li-ying 2022, 21(9): 2603-2614.  DOI: 10.1016/j.jia.2022.07.024 Abstract ( )   PDF in ScienceDirect   ‘Corollas and spines’ is an important trait for fresh market cucumber.  In a unique cucumber line, ‘6457’, the super ovary is much larger and corolla opening is delayed by 4–5 days, thus the resulting fruit has a flower that remains on the tip, which has a high commodity value.  In this study, to better understand the molecular basis of corolla opening, mRNA and miRNA transcriptome analyses were performed during corolla development of the super and normal ovaries.  A total of 234 differentially expressed miRNAs (DEMs) and 291 differentially expressed target genes (DE-target genes) were identified from four developmental stages, and the greatest number of DEMs was found at the yellow bud stage.  Thirty of the DE-target genes were regulated by more than five DEMs, among which, CsHD-Zip was regulated by 28 DEMs, followed by DD2X (18).  In addition, the expression patterns of miRNA_104, miRNA_157, miRNA_349, miRNA_242, and miRNA_98 were similar during corolla development, and they shared the same target gene, CsCuRX.  Moreover, several critical candidate DEMs and DE-target genes were characterized and profiled by a qRT-PCR experiment.  Three of the miRNAs, miRNA_157-CsCuRX, miRNA_411-CsGH3.6, and miRNA_161/297/257-CsHD-Zip, might be responsible for corolla opening in the cucumber super ovary.  This integrated study on the transcriptional and post-transcriptional profiles can provide insights into the molecular regulatory mechanism underlying corolla opening in the cucumber.

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Establishment of an efficient regeneration and genetic transformation system for Malus prunifolia Borkh. ‘Fupingqiuzi’ LIU Yu-song, WANG Hong-ying, ZHAO Yong-juan, JIN Yi-bo, LI Chao, MA Feng-wang 2022, 21(9): 2615-2627.  DOI: 10.1016/j.jia.2022.07.023 Abstract ( )   PDF in ScienceDirect   Malus prunifolia Borkh. ‘Fupingqiuzi’ has significant ecological and economic value and plays a key role in germplasm development and resistance research.  However, its long juvenile phase and high heterozygosity are barriers to the identification of ‘Fupingqiuzi’ progeny with excellent traits.  In-vitro regeneration techniques and Agrobacterium-mediated genetic transformation systems can efficiently produce complete plants and thus enable studies of gene function.  However, optimal regeneration and genetic transformation systems for ‘Fupingqiuzi’ have not yet been developed.  Here, we evaluated the factors that affect the in-vitro regeneration and transformation of ‘Fupingqiuzi’.  The best results were obtained when transverse leaf sections were used as explants, and they were grown in dark culture for three weeks with their adaxial sides contacting the culture medium (MS basal salts, 30 g L−1 sucrose, 8 g L−1 agar, 5 mg L−1  6-benzylaminopurine (6-BA), 2 mg L−1 thidiazuron (TDZ), and 1 mg L−1 1-naphthlcetic acid (NAA), pH 5.8).  A genetic transformation system based on this regeneration system was optimized: after inoculation with A. tumefaciens solution for 8 min, 4 days of co-culture, and 3 days of delayed culture, the cultures were screened with cefotaxime (150 mg L−1) and kanamycin (15 mg L−1).  We thus established an efficient regeneration and genetic transformation system for ‘Fupingqiuzi’, enabling the rapid production of transgenic material.  These findings make a significant contribution to apple biology research

Plant Protection

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BcSDR1 is involved in regulation of glucose transport and cAMP and MAPK signaling pathways in Botrytis cinerea SI He-long, ZHANG Kang, LI Bai, YUAN Xue-mei, ZANG Jin-ping, CAO Hong-zhe, XING Ji-hong, DONG Jin-gao 2022, 21(9): 2628-2640.  DOI: 10.1016/j.jia.2022.07.027 Abstract ( )   PDF in ScienceDirect   Botrytis cinerea is a typical necrotrophic pathogenic fungus that causes severe diseases in a wide range of plant species, leading to significant economic losses.  Our previous study showed that BcSDR1 positively regulates growth, development, and pathogenicity of B. cinerea.  However, the regulation mechanism of BcSDR1 and the relationship between BcSDR1 and cAMP and MAPK signaling pathways are not well understood.  In this study, transcriptome data showed that BcSDR1 is involved in glucose transmembrane transport, signal transduction, secondary metabolism, and other biological processes.  BcSDR1 mutant (BCt41) showed remarkably weak sensitivity to cAMP and MAPK signaling pathways specific inhibitors, SQ22536 and U0126, and significantly decreased cAMP content.  The key genes of cAMP and MAPK signaling pathways, BcGB1, BcBTP1, BcBOS1, BcRAS1, and BcBMP3 were significantly upregulated, whereas BcPLC1, BcBCG1, BcCDC4, BcSAK1, BcATF1, and BcBAP1 were significantly downregulated (P<0.05).   BcSDR1 was obviously upregulated in BcBCG2, BcBCG3, BcPKA1, and BcPKAR RNA interference (RNAi)  mutants, but significantly downregulated in BcPKA2, BcBMP1, and BcBMP3 RNAi mutants.  Thus, BcBCG2, BcBCG3, BcPKA1, and BcPKAR negatively regulate BcSDR1 expression, whereas BcPKA2, BcBMP1, and BcBMP3 positively regulate BcSDR1 expression.

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Tomato mottle mosaic virus: characterization, resistance gene effectiveness, and quintuplex RT-PCR detection system Carlos Kwesi TETTEY, YAN Zhi-yong, MA Hua-yu, ZHAO Mei-sheng, GENG Chao, TIAN Yan-ping, LI Xiang-dong 2022, 21(9): 2641-2651.  DOI: 10.1016/j.jia.2022.07.020 Abstract ( )   PDF in ScienceDirect   Tomato mottle mosaic virus (ToMMV), an economically important species of the genus Tobamovirus, causes significant loss in yield and quality of tomato fruits.  Here, we identified the Shandong isolate of ToMMV (ToMMV-SD) collected from symptomatic tomato fruits in Weifang, Shandong Province of China.  ToMMV-SD caused symptoms such as severe mosaic, mottling, and necrosis of tomato leaves, yellow spot and necrotic lesions on tomato fruits.  The obtained full genome of ToMMV-SD was 6 399 nucleotides (accession number MW373515) and had the highest identity of 99.5% with that of isolate SC13-051 from the United States of America at the genomic level.  The infectious clone of ToMMV-SD was constructed and induced clear mosaic and necrotic symptoms onto Nicotiana benthamiana leaves.  Several commercial tomato cultivars, harboring Tm-22 resistance gene, and pepper cultivars, containing L resistance gene, were susceptible to ToMMV-SD.  Plants of Solanum melongena (eggplant) and Brassica pekinensis (napa cabbage) showed mottling symptoms, while N. tabacum cv. Zhongyan 100 displayed latent infection.  ToMMV-SD did not infect plants of N. tabacum cv. Xanthi NN, Brassica rapa ssp. chinensis (bok choy), Raphanus sativus (radish), Vigna unguiculata cv. Yuanzhong 28-2 (cowpea), or Tm-22 transgenic N. benthamiana.  A quintuplex RT-PCR system differentiated ToMMV from tomato mosaic virus, tomato brown rugose fruit virus, tobacco mosaic virus, and tomato spotted wilt virus, with the threshold amount of 0.02 pg.  These results highlight the threat posed by ToMMV to tomato and pepper cultivation and offer an efficient detection system for the simultaneous detection of four tobamoviruses and tomato spotted wilt virus infecting tomato plants in the field.

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Study on burrowing nematode, Radopholus similis, pathogenicity test system in tobacco as host YANG Si-hua, ZHAO Li-rong, DING Sha, TANG Shi-qiao, CHEN Chun, ZHANG Huan-xin, XU Chun-ling, XIE Hui 2022, 21(9): 2652-2664.  DOI: 10.1016/j.jia.2022.07.021 Abstract ( )   PDF in ScienceDirect   Radopholus similis (Cobb 1893) Thorne (1949) is a destructive migratory endoparasitic plant nematode.  In this study, the pathogenic process of R. similis infection in Nicotiana benthamiana (tobacco) was studied using quartz sand culture in laboratory.  The results showed that R. similis mainly parasitised the root cortex, leading to cortical cell decomposition and tissue decay.  We optimised the inoculation conditions to establish a method for determining the pathogenicity of R. similis as follows: (1) a glass culture tube was filled with quartz sand (about 1/3 of the height) and sterilised twice; (2) 20-day-old N. benthamiana seedlings were transplanted into test tubes and cultivated for 10 days at (25±1)°C; (3) R. similis female nematodes were inoculated in the root rhizosphere at a rate of 150 nematodes per plant; (4) the number of nematodes, disease severity, and growth of the plant at 30 days post-inoculation (dpi) were determined.  The pathogenicity of eight R. similis populations from different hosts was determined, which proved the feasibility of this method.

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A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq LÜ Jing, Satyabrata NANDA, CHEN Shi-min, MEI Yang, HE Kang, QIU Bao-li, ZHANG You-jun, LI Fei, PAN Hui-peng 2022, 21(9): 2665-2674.  DOI: 10.1016/j.jia.2022.07.015 Abstract ( )   PDF in ScienceDirect   The specificity of the double-stranded RNA (dsRNA) used in the RNA interference (RNAi) technique is crucial for the success of sequence-specific gene silencing.  Currently, RNAi-mediated insect control is a trending research topic.  However, the off-target effects of the dsRNA in RNAi are a major concern.  In this study, the dsHvβ´COPI (coat protein complex I, β´ subunit)-treated and untreated transcriptomes of the 28-spotted potato lady beetle (Henosepilachna vigintioctopunctata) were compared to understand its off-target gene silencing effects.  The RNA-seq results revealed that 63 and 44 differentially expressed genes (DEGs) were upregulated and downregulated, respectively, in the dsHvβ´COPI treated group as compared with the control.  Validation of the differential expressions of some selected DEGs via reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed the reliability of the transcriptome analysis results.  Further downstream analysis revealed that there were no genes homologous with Hvβ´COPI in H. vigintioctopunctata.  Additionally, no genes with a >11 bp continuous match with dsHvβ´COPI were found in the H. vigintioctopunctata transcriptome.  Six genes (Hvcitron, Hvhelicase, Hvtransposase, Hvserine, Hvdynein, and HvE3 ubiquitin) were selected to examine the off-target activity of dsHvβ´COPI based on their potential involvement in various H. vigintioctopunctata metabolic pathways.  The severity of silencing these six off-target genes was evaluated by employing RNAi.  The RNAi results confirmed the downregulation of the expression of all six genes, although there was no significant lethality.  The findings of this study will be helpful in the risk analysis of future RNAi-mediated pest control experiments.

Animal Science · Veterinary Medicine

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Transcriptomic analysis elucidates the enhanced skeletal muscle mass, reduced fat accumulation, and metabolically benign liver in human follistatin-344 transgenic pigs LONG Ke-ren, LI Xiao-kai, ZHANG Ruo-wei, GU Yi-ren, DU Min-jie, XING Xiang-yang, DU Jia-xiang, MAI Miao-miao, WANG Jing, JIN Long, TANG Qian-zi, HU Si-lu, MA Ji-deng, WANG Xun, PAN Deng-ke, LI Ming-zhou 2022, 21(9): 2675-2690.  DOI: 10.1016/j.jia.2022.07.014 Abstract ( )   PDF in ScienceDirect   Follistatin (FST) is an important regulator of skeletal muscle growth and adipose deposition through its ability to bind to several members of the transforming growth factor-β (TGF-β) superfamily, and thus may be a good candidate for future animal breeding programs.  However, the molecular mechanisms underlying the phenotypic changes have yet to be clarified in pig.  We generated transgenic (TG) pigs that express human FST specifically in skeletal muscle tissues and characterized the phenotypic changes compared with the same tissues in wild-type pigs.  The TG pigs showed increased skeletal muscle growth, decreased adipose deposition, and improved metabolism status (P<0.05).  Transcriptome analysis detected important roles of the PIK3–AKT signaling pathway, calcium-mediated signaling pathway, and amino acid metabolism pathway in FST-induced skeletal muscle hypertrophy, and depot-specific oxidative metabolism changes in psoas major muscle.  Furthermore, the lipid metabolism-related process was changed in adipose tissue in the TG pigs.  Gene set enrichment analysis revealed that genes related to lipid synthesis, lipid catabolism, and lipid storage were down-regulated (P<0.01) in the TG pigs for subcutaneous fat, whereas genes related to lipid catabolism were significantly up-regulated (P<0.05) in the TG pigs for retroperitoneal fat compared with their expression levels in wild-type pigs.  In liver, genes related to the TGF-β signaling pathway were over-represented in the TG pigs, which is consistent with the inhibitory role of FST in regulating TGF-β signaling.  Together, these results provide new insights into the molecular mechanisms underlying the phenotypic changes in pig.

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Dietary threonine deficiency affects expression of genes involved in lipid metabolism in adipose tissues of Pekin ducks in a genotype-dependent manner JIANG Yong, MA Xin-yan, XIE Ming, ZHOU Zheng-kui, TANG Jing, CHANG Guo-bin, CHEN Guo-hong, HOU Shui-sheng 2022, 21(9): 2691-2699.  DOI: 10.1016/j.jia.2022.07.011 Abstract ( )   PDF in ScienceDirect   Dietary threonine (Thr) deficiency increases hepatic triglyceride content and reduces sebum and abdominal fat percentages in lean type (LT), but not in fatty type (FT) Pekin ducks.  However, the molecular changes regarding the role of Thr in lipid metabolism in LT and FT ducks induced by Thr deficiency remains unknown.  This study compared differential expression gene profiles related to lipid metabolism in FT and LT Pekin ducks affected by Thr deficiency.  We performed transcriptomic profiling and scanned the gene expression in the liver, sebum, and abdominal fat of Pekin ducks fed either Thr-deficient or Thr-adequate diet for 21 days from 14 to 35 days of age.  There were 187, 52, and 50 differentially expressed genes (DEGs) identified in the liver, sebum, and abdominal fat of LT ducks affected by Thr deficiency, of which 12, 9, and 5 genes were involved in lipid metabolism, respectively.  Thr deficiency altered the expression of 27, 6, and 3 genes in FT ducks’ liver, sebum, and abdominal fat, respectively.  None of the DEGs had a relationship with lipid metabolism in FT ducks.  KEGG analysis showed that the DEGs in the LT ducks’ livers were enriched in lipid metabolism pathways (linolenic acid metabolism, glycerophospholipid metabolism, and arachidonic acid metabolism) and amino acid metabolism pathways (biosynthesis of amino acids, phenylalanine metabolism, β-alanine metabolism, and glycine, serine and threonine metabolisms).  The DEGs in the sebum and abdominal fat of LT ducks were not enriched in lipid and amino acid metabolic pathways.  Additionally, DEGs involved in lipid metabolism were found to be upregulated by Thr deficiency in LT ducks, such as malic enzyme 3 (ME3), acyl-CoA synthetase short-chain family member 2 (ACSS2) in liver, and lipase member M (LIPM) in sebum.  In summary, dietary Thr deficiency regulated the gene expression involved in lipid metabolism in the liver, sebum, and abdominal fat of Pekin ducks in a genotype-dependent manner.

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Cold plasma promotes Sertoli cell proliferation via AMPK-mTOR signaling pathway ZHANG Jiao-jiao, LI Ya-qi, SHI Mei, WANG Yu-sha, TANG Yao, WANG Xian-zhong 2022, 21(9): 2700-2719.  DOI: 10.1016/j.jia.2022.07.010 Abstract ( )   PDF in ScienceDirect   This study investigated cold plasmas for multiple biological applications.  Our previous work has found dielectric barrier discharge plasma improves chicken sperm quality.  The number of Sertoli cells (SCs) decides spermatogenesis.  However, whether cold plasma can regulate SC proliferation remains unclear.  This study explored the effects of cold plasma on immature chicken SC proliferation and the regulation mechanism.  Results showed that cold plasma exposure at 2.4 W for 30 s twice with an interval of 6 h produced (P<0.05) the maximum SC viability, cell growth, and cell cycle progression.  SC proliferation-promoting effect of cold plasma treatment was regulated by increasing (P<0.05) the adenosine triphosphate production and the respiratory enzyme activity in the mitochondria.  This process was potentially mediated by the adenosine monophosphate-activated protein kinase (AMPK)–mammalian target of rapamycin (mTOR) signaling pathway, which was regulated by the microRNA (miRNA) targeting regulation directly and by the intracellular reactive oxygen species homeostasis indirectly.  The cold plasma treatment increased (P<0.01) the miR-7450-5p expression and led to a decreased (P<0.01) AMPKα1 level.  On the other hand, miR-100-5p expression was reduced (P<0.05) and led to an increased (P<0.05) mTOR level in SCs.  A single-stranded synthetic miR-7450-5p antagomir and a double-stranded synthetic miR-100-5p agomir reduced (P<0.05) the SC proliferation.  However, this could be ameliorated (P<0.05) by the cold plasma treatment.  Our findings suggest that appropriate cold plasma treatment provides a safe strategy to improve SC proliferation, which is beneficial to elevating male chicken reproductive capacity.

Agro-ecosystem & Environment

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Effect of long-term fertilization on phosphorus fractions in different soil layers and their quantitative relationships with soil properties WANG Qiong, QIN Zhen-han, ZHANG Wei-wei, CHEN Yan-hua, ZHU Ping, PENG Chang, WANG Le, ZHANG Shu-xiang, Gilles COLINET 2022, 21(9): 2720-2733.  DOI: 10.1016/j.jia.2022.07.018 Abstract ( )   PDF in ScienceDirect   Investigating the dynamics and distribution of soil phosphorus (P) fractions can provide a basis for enhancing P utilization by crops.  Four treatments from a 29-year long-term experiment in black soil with maize cropping were involved in this study: no fertilizer (CK), inorganic nitrogen and potassium (NK), inorganic nitrogen, phosphorus, and potassium (NPK), and NPK plus manure (NPKM).  We analyzed soil P fractions in different soil layers using a modified Hedley sequential method.  The long-term NPKM treatment significantly increased total P by 0.6–1.6 times in the different soil layers.  The Olsen-P concentration far exceeded the environmental threshold for soil Olsen-P (50.6 mg kg–1) in the NPKM treatment in the 0–60 cm soil profile.  Moreover, the concentrations and proportion of labile and partially labile inorganic P (Pi) fractions (i.e., NaHCO3-extracted Pi, NaOH-extracted Pi, and dilute HCl-extracted Pi) to the sum of all P fractions (Pt) in the 0–60 cm soil profile were higher in the NPKM treatment than in the NPK treatment, indicating that manure could promote the transformation of non-labile into more labile forms of P in soil, possibly by manure reducing P fixation by soil particles.  Soil organic matter, Mehlich-3 extractable iron (Fe), and organic-bound aluminum were increased by fertilization, and were the main factors influencing the differences in the P fractions in the 0–20 cm soil layer.  Soil mineral components, i.e., free Fe oxide and CaCO3, were the main factors influencing the P fractions in the subsoil.  The soil P transformation process varied with soil layer and fertilization.  Application of manure fertilizer can increase the labile (Olsen) P concentrations of the various soil layers, and thus should reduce the mineral P fertilizer requirement for crop growth and reduce potential environmental damage

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Long-term straw addition promotes moderately labile phosphorus formation, decreasing phosphorus downward migration and loss in greenhouse vegetable soil ZHANG Yin-Jie, GAO Wei, LUAN Hao-an, TANG Ji-wei, LI Ruo-nan, LI Ming-Yue, ZHANG Huai-zhi, HUANG Shao-wen 2022, 21(9): 2734-2749.  DOI: 10.1016/j.jia.2022.07.028 Abstract ( )   PDF in ScienceDirect   Phosphorus (P) leaching is a major problem in greenhouse vegetable production with excessive P fertilizer application.  Substitution of inorganic P fertilizer with organic fertilizer is considered a potential strategy to reduce leaching, but the effect of organic material addition on soil P transformation and leaching loss remains unclear.  The X-ray absorption near-edge structure (XANES) spectroscopy technique can determine P speciation at the molecular level.  Here, we integrated XANES and chemical methods to explore P speciation and transformation in a 10-year field experiment with four treatments: 100% chemical fertilizer (4CN), 50% chemical N and 50% manure N (2CN+2MN), 50% chemical N and 50% straw N (2CN+2SN), and 50% chemical N and 25% manure N plus 25% straw N (2CN+2MSN).  Compared with the 4CN treatment, the organic substitution treatments increased the content of labile P by 13.7–54.2% in the 0–40 cm soil layers, with newberyite and brushite being the main constituents of the labile P.  Organic substitution treatments decreased the stable P content; hydroxyapatite was the main species and showed an increasing trend with increasing soil depth.  Straw addition (2CN+2SN and 2CN+2MSN) resulted in a higher moderately labile P content and a lower labile P content in the subsoil (60–100 cm).  Moreover, straw addition significantly reduced the concentrations and amounts of total P, dissolved inorganic P (DIP), and particulate P in leachate.  DIP was the main form transferred by leaching and co-migrated with dissolved organic carbon.  Partial least squares path modeling revealed that straw addition decreased P leaching by decreasing labile P and increasing moderately labile P in the subsoil.  Overall, straw addition is beneficial for developing sustainable P management strategies due to increasing labile P in the upper soil layer for the utilization of plants, and decreasing P migration and leaching.

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Quantifying in situ N2 fluxes from an intensively managed calcareous soil using the 15N gas-flux method LIU Yan, WANG Rui, PAN Zhan-lei, ZHENG Xun-hua, WEI Huan-huan, ZHANG Hong-rui, MEI Bao-ling, QUAN Zhi, FANG Yun-ting, JU Xiao-tang 2022, 21(9): 2750-2766.  DOI: 10.1016/j.jia.2022.07.016 Abstract ( )   PDF in ScienceDirect   Denitrification-induced nitrogen (N) losses from croplands may be greatly increased by intensive fertilization.  However, the accurate quantification of these losses is still challenging due to insufficient available in situ measurements of soil dinitrogen (N2) emissions.  We carried out two one-week experiments in a maize–wheat cropping system with calcareous soil using the 15N gas-flux (15NGF) method to measure in situ N2 fluxes following urea application.  Applications of 15N-labeled urea (99 atom%, 130–150 kg N ha−1) were followed by irrigation on the 1st, 3rd, and 5th days after fertilization (DAF 1, 3, and 5, respectively).  The detection limits of the soil N2 fluxes were 163–1 565, 81–485, and 54–281 μg N m−2 h−1 for the two-, four-, and six-hour static chamber enclosures, respectively.  The N2 fluxes measured in 120 cases varied between 159 and 2 943 (811 on average) μg N m−2 h−1, which were higher than the detection limits, with the exception of only two cases.  The N2 fluxes at DAF 3 were significantly higher (by nearly 80% (P<0.01)) than those at DAF 1 and 5 in the maize experiment, while there were no significant differences among the irrigation times in the wheat experiment.  The N2 fluxes and the ratios of nitrous oxide (N2O) to the N2O plus N2 fluxes following urea application to maize were approximately 65% and 11 times larger, respectively (P<0.01), than those following urea application to wheat.  Such differences could be mainly attributed to the higher soil water contents, temperatures, and availability of soil N substrates in the maize experiment than in the wheat experiment.  This study suggests that the 15NGF method is sensitive enough to measure in situ N2 fluxes from intensively fertilized croplands with calcareous soils.

Food Science

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The metabolomics variations among rice, brown rice, wet germinated brown rice, and processed wet germinated brown rice REN Chuan-ying, LU Shu-wen, GUAN Li-jun, HONG Bin, ZHANG Ying-lei, HUANG Wen-gong, LI Bo, LIU Wei, LU Wei-hong 2022, 21(9): 2767-2776.  DOI: 10.1016/j.jia.2022.07.025 Abstract ( )   PDF in ScienceDirect   Germination and processing are always accompanied by significant changes in the metabolic compositions of rice.  In this study, polished rice (rice), brown rice, wet germinated brown rice (WGBR), high temperature and pressure-treated WGBR (WGBR-HTP), and low temperature-treated WGBR (WGBR-T18) were enrolled.  An untargeted metabolomics assay isolated 6 122 positive ions and 4 224 negative ions (multiple difference ≥1.2 or ≤0.8333, P<0.05, and VIP≥1) by liquid chromatography-mass spectrum.  These identified ions were mainly classified into three categories, including the compounds with biological roles, lipids, and phytochemical compounds.  In addition to WGBR-T18 vs. WGBR, massive differential positive and negative ions were revealed between rice of different forms.  Flavonoids, fatty acids, carboxylic acids, and organoxygen compounds were the dominant differential metabolites.  Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, there 7 metabolic pathways (phenylalanine/tyrosine/tryptophan biosynthesis, histidine metabolism, betalain biosynthesis, C5-branched dibasic acid metabolism, purine metabolism, zeatin biosynthesis, and carbon metabolism) were determined between brown rice and rice.  Germination changed the metabolic pathways of porphyrin and chlorophyll, pyrimidine, and purine metabolisms in brown rice.  In addition, phosphonate and phosphinate metabolism, and arachidonic acid metabolism were differential metabolic pathways between WGBR-HTP and WGBR-T18.  To sum up, there were obvious variations in metabolic compositions of rice, brown rice, WGBR, and WGBR-HTP.  The changes of specific metabolites, such as flavonoids contributed to the anti-oxidant, anti-inflammatory, anti-cancer, and immunomodulatory effects of GBR.  HTP may further improve the nutrition and storage of GBR through influencing specific metabolites, such as flavonoids and fatty acids.

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Identification of peanut oil origins based on Raman spectroscopy combined with multivariate data analysis methods ZHU Peng-fei, YANG Qing-li, ZHAO Hai-yan 2022, 21(9): 2777-2785.  DOI: 10.1016/j.jia.2022.07.026 Abstract ( )   PDF in ScienceDirect   This study aimed to use Raman spectroscopy to identify the producing areas of peanut oil and build a robust discriminant model to further screen out the characteristic spectra closely related to the origin.  Raman spectra of 159 peanut oil samples from different provinces and different cities of the same province were collected.  The obtained data were analyzed by stepwise linear discriminant analysis (SLDA), k-nearest neighbor analysis (k-NN), support vector machine (SVM) and multi-way analysis of variance.  The results showed that the overall recognition rate of samples based on full spectra was higher than 90%.  The producing origin, variety and their interaction influenced Raman spectra of peanut oil significantly, and 1 400–1 500 cm–1 and 1 600–1 700 cm–1 were selected as the characteristic spectra of origin and less affected by variety.  The best classification model established by SLDA combined with characteristic spectra could rapidly and accurately identify peanut oil’s origin.