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Identification of novel antisense long non-coding RNA APMAP-AS that modulates porcine adipogenic differentiation and inflammatory responses

ZHANG Lin-zhen, HE Li, WANG Ning, AN Jia-hua, ZHANG Gen, CHAI Jin, WU Yu-jie, DAI Chang-jiu, LI Xiao-han, LIAN Ting, LI Ming-zhou, JIN Long

2023, 22 (8): 2483-2499. DOI: 10.1016/j.jia.2022.11.005

Abstract （208） PDF in ScienceDirect

Long non-coding RNAs (lncRNAs) are emerging as powerful regulators of adipocyte differentiation, fat metabolism and gene expression. However, the functional roles and mechanisms of lncRNAs in these processes remain unclear. Here, we identified a novel antisense transcript, named APMAP-AS, transcribed from adipocyte membrane-associated protein (APMAP) in the pig genome. APMAP-AS and APMAP were highly expressed in retroperitoneal adipose of obese pigs, compared with that in control pigs. Using a bone mesenchymal stem cells (BMSCs) adipogenic differentiation model, we found that APMAP-AS positively regulated adipogenic differentiation. APMAP-AS had the potential to form an RNA–RNA duplex with APMAP, and increased the stability of APMAP mRNA. Additionally, APMAP-AS promoted lipid metabolism and inhibited the expression of inflammatory factors. These findings of a natural antisense transcript for a regulatory gene associated with lipid synthesis might further our understanding of lncRNAs in driving adaptive adipose tissue remodeling and preserving metabolic health.

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Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple

ZHANG Li-hua, ZHU Ling-cheng, XU Yu, LÜ Long, LI Xing-guo, LI Wen-hui, LIU Wan-da, MA Feng-wang, LI Ming-jun, HAN De-guo

2023, 22 (7): 2080-2093. DOI: 10.1016/j.jia.2023.05.024

Abstract （241） PDF in ScienceDirect

Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality. However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking. In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1. The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological functions and biochemical properties were analyzed. A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion. The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication. Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies. In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development. Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit. The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.

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Identification of genetic loci for grain yield‑related traits in the wheat population Zhongmai 578/Jimai 22

LIU Dan, ZHAO De-hui, ZENG Jian-qi, Rabiu Sani SHAWAI, TONG Jing-yang, LI Ming, LI Fa-ji, ZHOU Shuo, HU Wen-li, XIA Xian-chun, TIAN Yu-bing, ZHU Qian, WANG Chun-ping, WANG De-sen, HE Zhong-hu, LIU Jin-dong, ZHANG Yong

2023, 22 (7): 1985-1999. DOI: 10.1016/j.jia.2022.12.002

Abstract （301） PDF in ScienceDirect

The identification of stable quantitative trait locus (QTL) for yield-related traits and tightly linked molecular markers is important for improving wheat grain yield. In the present study, six yield-related traits in a recombinant inbred line (RIL) population derived from the Zhongmai 578/Jimai 22 cross were phenotyped in five environments. The parents and 262 RILs were genotyped using the wheat 50K single nucleotide polymorphism (SNP) array. A high-density genetic map was constructed with 1 501 non-redundant bin markers, spanning 2 384.95 cM. Fifty-three QTLs for six yield-related traits were mapped on chromosomes 1D (2), 2A (9), 2B (6), 2D, 3A (2), 3B (2), 4A (5), 4D, 5B (8), 5D (2), 7A (7), 7B (3) and 7D (5), which explained 2.7–25.5% of the phenotypic variances. Among the 53 QTLs, 23 were detected in at least three environments, including seven for thousand-kernel weight (TKW), four for kernel length (KL), four for kernel width (KW), three for average grain filling rate (GFR), one for kernel number per spike (KNS) and four for plant height (PH). The stable QTLs QKl.caas-2A.1, QKl.caas-7D, QKw.caas-7D, QGfr.caas-2B.1, QGfr.caas-4A, QGfr.caas-7A and QPh. caas-2A.1 are likely to be new loci. Six QTL-rich regions on 2A, 2B, 4A, 5B, 7A and 7D, showed pleiotropic effects on various yield traits. TaSus2-2B and WAPO-A1 are potential candidate genes for the pleiotropic regions on 2B and 7A, respectively. The pleiotropic QTL on 7D for TKW, KL, KW and PH was verified in a natural population. The results of this study enrich our knowledge of the genetic basis underlying yield-related traits and provide molecular markers for high-yield wheat breeding.

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Dry matter production and panicle characteristics of high yield and good taste indica hybrid rice varieties

LI Min, ZHU Da-wei, JIANG Ming-jin, LUO De-qiang, JIANG Xue-hai, JI Guang-mei, LI Li-jiang, ZHOU Wei-jia

2023, 22 (5): 1338-1350. DOI: 10.1016/j.jia.2022.08.033

Abstract （210） PDF in ScienceDirect

Indica hybrid rice (Oryza sativa) production aims to achieve two crucial targets: high yield and good taste. This study selected three types of indica hybrid rice according to grain yield and taste value, including high yield and good taste (HYGT), low yield and good taste (LYGT), and high yield and poor taste (HYPT), to analyze yield components, corresponding growth characteristics, and rice taste quality. When values were averaged across varieties and years, there were almost no differences in taste value between HYGT and LYGT; HYGT showed a significant increase in yield, owing to a higher number of panicles and spikelets per panicle, with a respective increment of 16.2 and 20.6%. The higher grain yield of HYGT compared with LYGT was attributed to three key factors: a higher leaf area index (LAI) during heading, a higher ratio of grain to leaf, and a higher biomass accumulation at maturity. HYGT and HYPT achieved similar high yields; however, HYGT had more panicle numbers and lower grain weight. In addition, HYGT showed a significantly higher taste value than HYPT, attributed to its significantly lower protein and amylose contents, with reductions of 8.8 and 15.7%, respectively. Lower protein and amylose contents might be caused by a proper matter translocation from vegetative organs to panicle. This study suggested that reasonable panicle characteristics and translocation efficiency from vegetative organs to panicle during heading to maturity are the key factors in balancing yield and rice taste quality. These results will provide valuable insights for rice breeders to improve the grain yield and quality of indica hybrid rice.

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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 （213） 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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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 （325） 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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Growth and yield responses to simulated hail damage in drip-irrigated cotton

WANG Le, LIU Yang, WEN Ming, LI Ming-hua, DONG Zhi-qiang, CUI Jing, MA Fu-yu

2022, 21 (8): 2241-2252. DOI: 10.1016/S2095-3119(21)63672-9

Abstract （220） PDF in ScienceDirect

The frequent occurrence of hailstorm in Xinjiang affects cotton (Gossypium hirsutum L.) production and causes enormous economic loss. The indeterminate growth habit of cotton allows for varying degrees of recovery and yield when different hail damage levels occur at different stages, which brings inconvenience to agricultural insurance claims and post-damage management. Therefore, this study aimed to elucidate cotton recovery and yield responses to different levels of simulated hail damage at different growth stages. Four levels of hail damage (0, 30, 60, and 90%) were simulated every 15 d from the five-leaf stage to the boll opening stage in 2018 and 2019, for a total of six times (I, II, III, IV, V, and VI). The results showed that seed cotton yield decreased as the damage level increased and yield reduction increased when the damage was applied to older plants (for 30, 60 and 90% damage levels, yield reduction was 9–17%, 22–37% and 48–71%, respectively). One possible reason was that the leaf area index and leaf area duration of plant canopy decreased after hail damage, resulting in a reduction in the accumulation of above-ground biomass. However, when hail damage occurred before bloom, due to the indeterminate growth habit of cotton, the vegetative organs produced a strong compensation ability that promoted the bud development. The compensation ability of vegetative organs decreased when hail damage occurred after bloom and the recovery time was too short to promote new boll maturity. As the first study to understand the recovery of cotton after hail damage, it analyzed the leaf area index, leaf area duration, above-ground biomass accumulation and yield, rather than the yield alone. The findings are of great importance for cotton production as they inform decisions about post-damage management practices, yield forecasts and insurance compensation.

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Effects of a decade of organic fertilizer substitution on vegetable yield and soil phosphorus pools, phosphatase activities, and the microbial community in a greenhouse vegetable production system

ZHANG Yin-Jie, GAO Wei, LUAN Hao-an, TAND Ji-wei, LI Ruo-nan, LI Ming-Yue, ZHANG Huai-zhi, HUANG Shao-wen

2022, 21 (7): 2119-2133. DOI: 10.1016/S2095-3119(21)63715-2

Abstract （224） PDF in ScienceDirect

Partial substitution of chemical fertilizers by organic amendments is adopted widely for promoting the availability of soil phosphorus (P) in agricultural production. However, few studies have comprehensively evaluated the effects of long-term organic substitution on soil P availability and microbial activity in greenhouse vegetable fields. A 10-year (2009–2019) field experiment was carried out to investigate the impacts of organic fertilizer substitution on soil P pools, phosphatase activities and the microbial community, and identify factors that regulate these soil P transformation characteristics. Four treatments included 100% chemical N fertilizer (4CN), 50% substitution of chemical N by manure (2CN+2MN), straw (2CN+2SN), and combined manure with straw (2CN+1MN+1SN). Compared with the 4CN treatment, organic substitution treatments increased celery and tomato yields by 6.9−13.8% and 8.6−18.1%, respectively, with the highest yields being in the 2CN+1MN+1SN treatment. After 10 years of fertilization, organic substitution treatments reduced total P and inorganic P accumulation, increased the concentrations of available P, organic P, and microbial biomass P, and promoted phosphatase activities (alkaline and acid phosphomonoesterase, phosphodiesterase, and phytase) and microbial growth in comparison with the 4CN treatment. Further, organic substitution treatments significantly increased soil C/P, and the partial least squares path model (PLS-PM) revealed that the soil C/P ratio directly and significantly affected phosphatase activities and the microbial biomass and positively influenced soil P pools and vegetable yield. Partial least squares (PLS) regression demonstrated that arbuscular mycorrhizal fungi positively affected phosphatase activities. Our results suggest that organic fertilizer substitution can promote soil P transformation and availability. Combining manure with straw was more effective than applying these materials separately for developing sustainable P management practices.

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Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs

WANG Kai, WU Ping-xian, WANG Shu-jie, JI Xiang, CHEN Dong, JIANG An-an, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing

2022, 21 (6): 1731-1739. DOI: 10.1016/S2095-3119(21)63814-5

Abstract （271） PDF in ScienceDirect

Chenghua (CH) pig and Qingyu (QY) pig are typical Chinese native fatty breeds. CH pig is mainly distributed in Chengdu Plain, while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin. There are significant differences in their phenotypic traits, including body image, growth performance, and meat quality. This study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing (RRBS). It was observed that the pH at 45 min (pH_45min, P=5.22e–13), lightness at 45 min (L*_45min, P=4.85e–5), and lightness at 24 h (L*_24h, P=3.57e–5) of CH pigs were higher than those of QY pigs. We detected 10 699 differentially methylated cytosines (DMCs) and 2 760 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway, Type II diabetes mellitus, Insulin signaling pathway, mTOR signaling pathway, and Insulin resistance. Furthermore, 15 DMGs were associated with fat metabolism (ACACA, CAB39, CRADD, CRTC2, FASN, and GCK), muscle development (HK2, IKBKB, MTOR, PIK3CD, PPARGC1A, and RPTOR), or meat quality traits (PCK1, PRKAG2, and SLC2A4). The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs.

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Source–sink relations and responses to sink–source manipulations during grain filling in wheat

WU Xiao-li, LIU Miao, LI Chao-su, Allen David (Jack) MCHUGH, LI Ming, XIONG Tao, LIU Yu-bin, TANG Yong-lu

2022, 21 (6): 1593-1605. DOI: 10.1016/S2095-3119(21)63640-7

Abstract （232） PDF in ScienceDirect

The source–sink ratio during grain filling is a critical factor that affects crop yield in wheat, and the main objective of this study was to determine the source–sink relations at both the canopy scale and the individual culm level under two nitrogen (N) levels at the post-jointing stage. Nine widely-used cultivars were chosen for analyzing source–sink relations in southwestern China; and three typical cultivars of different plant types were subjected to artificial manipulation of the grain-filling source–sink ratio to supplement crop growth measurements. A field experiment was conducted over two consecutive seasons under two N rates (N+, 150 kg ha^–1; N–, 60 kg ha^–1), and three manipulations were imposed after anthesis: control (Ct), removal of flag and penultimate leaves (Lr) and removal of spikelets on one side of each spike (Sr). The results showed that the single grain weights in the three cultivars were significantly decreased by Lr and increased by Sr, which demonstrated that wheat grain yield potential seems more source-limited than sink-limited during grain filling, but the source–sink balance was obviously changed by climatic variations and N deficient environments. Grain yield was highly associated with sink capacity (SICA), grain number, biomass, SPAD values, and leaf area index during grain filling, indicating a higher degree of source limitation with an increase in sink capacity. Therefore, source limitation should be taken into account by breeders when SICA is increased, especially under non-limiting conditions. Chuanmai 104, a half-compact type with a mid-sized spike and a long narrow upper leaf, showed relatively better performance in source–sink relations. Since this cultivar showed the characteristics of a lower reduction in grain weight after Lr, a larger increase after Sr, and a lower reduction in post-anthesis dry matter accumulation, then the greater current photosynthesis during grain filling contributed to the grain after source and sink manipulation.

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The Nutrient Expert decision support system improves nutrient use efficiency and environmental performance of radish in North China

ZHANG Jia-jia, DING Wen-cheng, CUI Rong-zong, LI Ming-yue, Sami ULLAH, HE Ping

2022, 21 (5): 1501-1512. DOI: 10.1016/S2095-3119(21)63660-2

Abstract （143） PDF in ScienceDirect

Excessive fertilization has led to nutrient use inefficiency and serious environmental consequences for radish cultivation in North China. The Nutrient Expert (NE) system is a science-based, site-specific fertilization decision support system, but the updated NE system for radish has rarely been evaluated. This study aims to validate the feasibility of NE for radish fertilization management from agronomic, economic, and environmental perspectives. A total of 46 field experiments were conducted over four seasons from April 2018 to November 2019 across the major radish growing regions in North China. The results indicated that NE significantly reduced N, P₂O₅, and K₂O application rates by 98, 110, and 47 kg ha⁻¹ relative to those in the farmers’ practice (FP), respectively, and reduced N and P₂O₅ inputs by 48 and 44 kg ha⁻¹, respectively, while maintaining the same K₂O rate as soil testing (ST). Relative to FP and ST, NE significantly increased radish yield by 2.7 and 2.6 t ha⁻¹ (4.2 and 4.0%) and net returns by 837 and 432 USD ha⁻¹, respectively. On average, NE significantly improved the agronomic efficiency (AE) of N, P, and K (relative to FP and ST) by 42.4 and 31.0, 67.4 kg kg⁻¹and 50.9, and 20.3 and 12.3 kg kg⁻¹; enhanced the recovery efficiency (RE) of N, P, and K by 11.4 and 7.0, 14.1 and 7.5, and 11.3 and 6.3 percentage points; and increased the partial factor productivity (PFP) of N, P, and K by 162.9 and 96.8, 488.0 and 327.3, and 86.9 and 22.4 kg kg⁻¹, respectively. Furthermore, NE substantially reduced N and P₂O₅ surpluses by 105.1 and 115.1 kg ha⁻¹, respectively, and decreased apparent N loss by 110.8 kg ha⁻¹ compared to FP. These results indicated that the NE system is an effective and feasible approach for improving NUE and promoting cleaner radish production in North China.

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Detection of quantitative trait loci (QTL) associated with spring regrowth in alfalfa (Medicago sativa L.)

JIANG Xue-qian, ZHANG Fan, WANG Zhen, LONG Rui-cai, LI Ming-na, HE Fei, YANG Xi-jiang, YANG Chang-fu, JIANG Xu, YANG Qing-chuan, WANG Quan-zhen, KANG Jun-mei

2022, 21 (3): 812-818. DOI: 10.1016/S2095-3119(21)63671-7

Abstract （231）

Spring regrowth is an important trait for perennial plants including alfalfa, the most cultivated forage legume worldwide. However, the genetic and genomic basis of the trait is largely unknown in alfalfa due to its complex genetic background of the tetroploid genome. The objective of this study was to identify quantitative trait loci (QTLs) associated with spring regrowth using high-resolution genetic linkage maps we constructed previously. In total, 36 significant additive effect QTLs for the trait were detected. Among them, 10 QTLs individually explained more than 10% of the phenotypic variation (PVE) with four in P1 and six in P2. Six overlapped QTLs intervals were detected with two and four intervals distributed in P1 and P2, respectively. In P1, both overlapped genomic regions were located on homolog 7D. In P2, the four QTLs with PVE>10% were co-localized on homolog 6D. Meanwhile, six pairs of significant epistatic QTLs were identified in P2. Screening of potential candidate genes associated with four overlapped QTLs (qCP2019-8, qLF2019-5, qLF2020-4, and qBLUP-3) narrowed down one candidate annotated as MAIL1. The Arabidopsis homolog gene has been reported to play an important role in plant growth. Therefore, the detected QTLs are valuable resources for genetic improvement of alfalfa spring vigor using marker-assisted selection (MAS), and further identification of the associated genes would provide insights into genetic control of spring regrowth in alfalfa.

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Factors influencing seed reserve utilization during seedling establishment in maize inbred lines

LI Min, WEN Da-xing, SUN Qing-qing, WU Cheng-lai, LI Yan, ZHANG Chun-qing

2022, 21 (3): 677-684. DOI: 10.1016/S2095-3119(21)63608-0

Abstract （158） PDF in ScienceDirect

Strong seedlings are essential for high yield. To explore the foundation of strong seedlings, we investigated various factors influencing the conversion and distribution of seed storage reserves during seedling establishment in maize inbred lines. Three maize inbred lines were used to explore the effects of seed size, seed vigor, illumination duration, temperature, water content, and salt concentration of the seedling medium on the utilization of seed storage reserves during seedling establishment. The results showed that the conversion rate of small seeds was 3.69 to 17.71% higher than that of large seeds. Moreover, prolonged illumination time was conducive to the formation of strong seedlings. However, low temperature, drought stress and salt stress reduced the conversion rate of seed storage reserves and increased the root/shoot ratio. These results could be used to guide field management during seedling emergence and develop improved germplasm with a high conversion rate of seed storage reserves.

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Response of carbohydrate metabolism-mediated sink strength to auxin in shoot tips of apple plants

SU Jing, CUI Wei-fang, ZHU Ling-cheng, LI Bai-yun, MA Feng-wang, LI Ming-jun

2022, 21 (2): 422-433. DOI: 10.1016/S2095-3119(20)63593-6

Abstract （213） PDF in ScienceDirect

Auxin (indole-3-acetic acid, IAA) has a considerable impact on the regulation of plant carbohydrate levels and growth, but the mechanism by which it regulates sugar levels in plants has received little attention. In this study, we found that exogenous IAA altered fructose (Fru), glucose (Glc), and sucrose (Suc) concentrations in shoot tips mainly by regulating MdSUSY1, MdFRK2, MdHxK1 and MdSDH2 transcript levels. Additionally, we used 5-year-old ‘Royal Gala’ apple trees to further verify that these genes play primary roles in regulating sink strength. The results showed that MdSUSY1, MdFRK2, MdHxK1/3 and MdSDH2 might be major contributors to sink strength regulation. Taken together, these results provide new insight into the regulation of the carbohydrate metabolism mechanism, which will be helpful for regulating sink strength and yield.

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Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

WU Ping-xian, ZHOU Jie, WANG Kai, CHEN De-juan, YANG Xi-di, LIU Yi-hui, JIANG An-an, SHEN Lin-yuan, JIN Long, XIAO Wei-hang, JIANG Yan-zhi, LI Ming-zhou, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Xue-wei, TANG Guo-qing

2021, 20 (9): 2483-2490. DOI: 10.1016/S2095-3119(20)63474-8

Abstract （130） PDF in ScienceDirect

Birth weight (BW) and days to 100 kg (D100) are important economic traits that are both affected by polygenes. However, the genetic architecture of these quantitative traits is still elusive. Genotyping-by-sequencing (GBS) data containing a large number of single nucleotide polymorphisms (SNPs) have become a powerful tool in genomic analysis. To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology. After quality control, 279 787 SNPs were generated for subsequent genome-wide association study (GWAS). A total of 30 genome-wide SNPs (P<1.79E–07) were identified for D100. Furthermore, a total of 22 and 2 suggestive SNPs (P<3.57E–06) were detected for D100 and BW, respectively. Of these, one locus located on SSC12 (position: 46 226 512 bp) were evaluated to affect both BW and D100 in Yorkshire pigs, indicating the pleiotropism in different traits. Considering the function of candidate genes, two genes, NSRP1 and DOCK7, were suggested as the most promising candidate genes involved in growth traits. Thus, use of GBS is able to identify novel variants and potential candidate genes for BW and D100, and provide an opportunity for improving pig growth traits using genomic selection in pigs.

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Genome-wide identification, molecular evolution, and expression divergence of the hexokinase gene family in apple

ZHU Ling-cheng, SU Jing, JIN Yu-ru, ZHAO Hai-yan, TIAN Xiao-cheng, ZHANG Chen, MA Feng-wang, LI Ming-jun, MA Bai-quan

2021, 20 (8): 2112-2125. DOI: 10.1016/S2095-3119(20)63562-6

Abstract （157） PDF in ScienceDirect

Hexokinase (HXK) is the first irreversible catalytic enzyme in the glycolytic pathway, which not only provides energy for plant growth and development but also serves as a signaling molecule in response to environmental changes. However, the evolutionary pattern of the HXK gene family in apple remains unknown. In this study, a total of nine HXK genes were identified in the Malus×domestica genome GDDH13 v1.1. The physiological and biochemical properties, exon-intron structures, conserved motifs, and cis-elements of the MdHXK genes were determined. Predicted subcellular localization indicated that the MdHXK genes were mainly distributed in the mitochondria, cytoplasm, and nucleus. Gene duplication revealed that whole-genome duplication (WGD) and segmental duplication played vital roles in MdHXK gene family expansion. The ω values of pairwise MdHXK genes indicated that this family was subjected to strong purifying selection during apple domestication. Additionally, five subfamilies were classified, and recent/old duplication events were identified based on phylogenetic tree analysis. Different evolutionary rates were estimated among the various HXK subfamilies. Moreover, divergent expression patterns of the MdHXK genes in four source-sink tissues and at five different apple fruit developmental stages indicated that they play vital roles in apple fruit development and sugar accumulation. Our study provides a theoretical basis for future elucidation of the biological functions of the MdHXK genes during apple fruit development.

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Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs

WANG Kai, WU Ping-xian, CHEN De-juan, ZHOU Jie, YANG Xi-di, JIANG An-an, MA Ji-deng, TANG Qian-zi, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing

2021, 20 (7): 1898-1906. DOI: 10.1016/S2095-3119(20)63488-8

Abstract （161） PDF in ScienceDirect

We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs. Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST (Z(FST)) method, and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity (ZHp) method. The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism, disease resistance, cellular processes, and biochemical signals, and several were related to body morphology and organs. They included PPP3CA, which plays an essential role in the transduction of intracellular Ca²⁺-mediated signals, and WWTR1, which plays a pivotal role in organ size control and tumor suppression. These results suggest that genes associated with body morphology were subject to selection pressure during domestication, whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding. Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.

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Aggregate-associated changes in nutrient properties, microbial community and functions in a greenhouse vegetable field based on an eight-year fertilization experiment of China

LUAN Hao-an, GAO Wei, TANG Ji-wei, LI Ruo-nan, LI Ming-yue, ZHANG Huai-zhi, CHEN Xin-ping, Dainius MASILIUNAS, HUANG Shao-wen

2020, 19 (10): 2530-2548. DOI: 10.1016/S2095-3119(20)63269-5

Abstract （149） PDF in ScienceDirect

Soil aggregation, microbial community, and functions (i.e., extracellular enzyme activities; EEAs) are critical factors affecting soil C dynamics and nutrient cycling. We assessed soil aggregate distribution, stability, nutrients, and microbial characteristics within >2, 0.25–2, 0.053–0.25, and <0.053 mm aggregates, based on an eight-year field experiment in a greenhouse vegetable field in China. The field experiment includes four treatments: 100% N fertilizer (CF), 50% substitution of N fertilizer with manure (M), straw (S), and manure plus straw (MS). The amounts of nutrient (N, P₂O₅, and K₂O) input were equal in each treatment. Results showed higher values of mean weight diameter in organic-amended soils (M, MS, and S, 2.43–2.97) vs. CF-amended soils (1.99). Relative to CF treatment, organic amendments had positive effects on nutrient (i.e., available N, P, and soil organic C (SOC)) conditions, microbial (e.g., bacterial and fungal) growth, and EEAs in the >0.053 mm aggregates, but not in the <0.053 mm aggregates. The 0.25–0.053 mm aggregates exhibited better nutrient conditions and hydrolytic activity, while the <0.053 mm aggregates had poor nutrient conditions and higher oxidative activity among aggregates, per SOC, available N, available P, and a series of enzyme activities. These results indicated that the 0.25–0.053 mm (<0.053 mm) aggregates provide suitable microhabitats for hydrolytic (oxidative) activity. Interestingly, we found that hydrolytic and oxidative activities were mainly impacted by fertilization (58.5%, P<0.01) and aggregate fractions (50.5%, P<0.01), respectively. The hydrolytic and oxidative activities were significantly (P<0.01) associated with nutrients (SOC and available N) and pH, electrical conductivity, respectively. Furthermore, SOC, available N, and available P closely (P<0.05) affected microbial communities within >0.25, 0.25–0.053, and <0.053 mm aggregates, respectively. These findings provide several insights into microbial characteristics within aggregates under different fertilization modes in the greenhouse vegetable production system in China.

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Early selection of bread wheat genotypes using morphological and photosynthetic attributes conferring drought tolerance

Hafiz Ghulam Muhu-Din Ahmed, Abdus Salam khan, LI Ming-ju, Sultan Habibullah Khan, Muhammad Kashif

2019, 18 (11): 2483-2491. DOI: 10.1016/S2095-3119(18)62083-0

Abstract （125） PDF in ScienceDirect

Genetic diversity is the base of any genetic improvement breeding program aimed at stress breeding. The variability among breeding materials is of primary importance in the achievements of a good crop production. Herein, 105 wheat genotypes were screened against drought stress using factorial completely randomized design at seedling stage to determine the genetic diversity and traits association conferring drought tolerance. Analysis of variances revealed that all the studied parameters differed significantly among all genotypes, indicating the significance genetic variability existed among all genotypes for studied indices. The 10 best performance genotypes G1, G6, G11, G16, G21, G26, G39, G44, G51, and G61 were screened as drought tolerant, while five lowest performance genotypes G3, G77, G91, G98, and G105 were screened as drought susceptible. Root length, chlorophyll a, chlorophyll b, and carotenoid contents were significantly correlated among themselves which exhibited the importance of these indices for rainfed areas in future wheat breeding scheme. Shoot length exhibited non-significant and negative association with other studied traits, and its selection seems not to be a promising criteria for this germplasm for drought stress. Best performance genotypes under drought stress conditions will be useful in future wheat breeding program and early selection will be effective for developing high yielding and drought tolerant wheat varieties.

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Transcriptome analysis reveals the effects of alkali stress on root system architecture and endogenous hormones in apple rootstocks

LIU Xuan, LIANG Wei, LI Yu-xing, LI Ming-jun, MA Bai-quan, LIU Chang-hai, MA Feng-wang, LI Cui-ying

2019, 18 (10): 2264-2271. DOI: 10.1016/S2095-3119(19)62706-1

Abstract （144） PDF in ScienceDirect

Soil alkalinity is a major factor that restricts the growth of apple roots. To analyze the response of apple roots to alkali stress, the root structure and endogenous hormones of two apple rootstocks, Malus prunifolia (alkali-tolerant) and Malus hupehensis (alkali-sensitive), were compared. To understand alkali tolerance of M. prunifolia at the molecular level, transcriptome analysis was performed. When plants were cultured in alkaline conditions for 15 d, the root growth of M. hupehensis with weak alkali tolerance decreased significantly. Analysis of endogenous hormone levels showed that the concentrations of indole-3-acetic acid (IAA) and zeatin riboside (ZR) in M. hupehensis under alkali stress were lower than those in the control. However, the trend for IAA and ZR in M. prunifolia was the opposite. The concentration of abscisic acid (ABA) in the roots of the two apple rootstocks under alkali stress increased, but the concentration of ABA in the roots of M. prunifolia was higher than that in M. hupehensis. The expression of IAA-related genes ARF5, GH3.6, SAUR36, and SAUR32 and the Cytokinin (CTK)-related gene IPT5 in M. prunifolia was higher than those in the control, but the expression of these genes in M. hupehensis was lower than those in the control. The expression of ABA-related genes CIPK1 and AHK1 increased in the two apple rootstocks under alkali stress, but the expression of CIPK1 and AHK1 in M. prunifolia was higher than in M. hupehensis. These results demonstrated that under alkali stress, the increase of IAA, ZR, and ABA in roots and the increase of the expression of related genes promoted the growth of roots and improved the alkali tolerance of apple rootstocks.

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Multivariate analysis between meteorological factor and fruit quality of Fuji apple at different locations in China

ZHANG Qiang, ZHOU Bei-bei, LI Min-ji, WEI Qin-ping, HAN Zhen-hai

2018, 17 (06): 1338-1347. DOI: 10.1016/S2095-3119(17)61826-4

Abstract （453） PDF in ScienceDirect

China has the largest apple planting area and total yield in the world, and the Fuji apple is the major cultivar, accounting for more than 70% of apple planting acreage in China. Apple qualities are affected by meteorological conditions, soil types, nutrient content of soil, and management practices. Meteorological factors, such as light, temperature and moisture are key environmental conditions affecting apple quality that are difficult to regulate and control. This study was performed to determine the effect of meteorological factors on the qualities of Fuji apple and to provide evidence for a reasonable regional layout and planting of Fuji apple in China. Fruit samples of Fuji apple and meteorological data were investigated from 153 commercial Fuji apple orchards located in 51 counties of 11 regions in China from 2010 to 2011. Partial least-squares regression and linear programming were used to analyze the effect model and impact weight of meteorological factors on fruit quality, to determine the major meteorological factors influencing fruit quality attributes, and to establish a regression equation to optimize meteorological factors for high-quality Fuji apples. Results showed relationships between fruit quality attributes and meteorological factors among the various apple producing counties in China. The mean, minimum, and maximum temperatures from April to October had the highest positive effects on fruit qualities in model effect loadings and weights, followed by the mean annual temperature and the sunshine percentage, the temperature difference between day and night, and the total precipitation for the same period. In contrast, annual total precipitation and relative humidity from April to October had negative effects on fruit quality. The meteorological factors exhibited distinct effects on the different fruit quality attributes. Soluble solid content was affected from the high to the low row preface by annual total precipitation, the minimum temperature from April to October, the mean temperature from April to October, the temperature difference between day and night, and the mean annual temperature. The regression equation showed that the optimum meteorological factors on fruit quality were the mean annual temperature of 5.5–18°C and the annual total precipitation of 602–1 121 mm for the whole year, and the mean temperature of 13.3–19.6°C, the minimum temperature of 7.8–18.5°C, the maximum temperature of 19.5°C, the temperature difference of 13.7°C between day and night, the total precipitation of 227 mm, the relative humidity of 57.5–84.0%, and the sunshine percentage of 36.5–70.0% during the growing period (from April to October).

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Transcriptomes of early developing tassels under drought stress reveal differential expression of genes related to drought tolerance in maize

WANG Nan, LI Liang, GAO Wen-wei, WU Yong-bo, YONG Hong-jun, WENG Jian-feng, LI Ming-shun, ZHANG De-gui, HAO Zhuan-fang, LI Xin-hai

2018, 17 (06): 1276-1288. DOI: 10.1016/S2095-3119(17)61777-5

Abstract （462） PDF in ScienceDirect

Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered (control) and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ‘RNA transcript’ and ‘mRNA surveillance’ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.

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Structure and expression analysis of the sucrose synthase gene family in apple

TONG Xiao-lei, WANG Zheng-yang, MA Bai-quan, ZHANG Chun-xia, ZHU Ling-cheng, MA Feng-wang, LI Ming-jun

2018, 17 (04): 847-856. DOI: 10.1016/S2095-3119(17)61755-6

Abstract （628） PDF in ScienceDirect

Sucrose synthases (SUS) are a family of enzymes that play pivotal roles in carbon partitioning, sink strength and plant development. A total of 11 SUS genes have been identified in the genome of Malus domestica (MdSUSs), and phylogenetic analysis revealed that the MdSUS genes were divided into three groups, named as SUS I, SUS II and SUS III, respectively. The SUS I and SUS III groups included four homologs each, whereas the SUS II group contained three homologs. SUS genes in the same group showed similar structural characteristics, such as exon number, size and length distribution. After assessing four different tissues, MdSUS1s and MdSUS2.1 showed the highest expression in fruit, whereas MdSUS2.2/2.3 and MdSUS3s exhibit the highest expression in shoot tips. Most MdSUSs showed decreased expression during fruit development, similar to SUS enzyme activity, but both MdSUS2.1 and MdSUS1.4 displayed opposite expression profiles. These results suggest that different MdSUS genes might play distinct roles in the sink-source sugar cycle and sugar utilization in apple sink tissues.

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Complete genome sequences of four isolates of Citrus leaf blotch virus from citrus in China

LI Ping, LI Min, ZHANG Song, WANG Jun, YANG Fang-yun, CAO Meng-ji, LI Zhong-an

2018, 17 (03): 712-715. DOI: 10.1016/S2095-3119(17)61860-4

Abstract （806） PDF in ScienceDirect

Citrus leaf blotch virus (CLBV) is a member of the genus Citrivirus, in the family Betaflexiviridae. It has been reported CLBV could infect kiwi, citrus and sweet cherry in China. Of 289 citrus samples from six regions of China, 15 were detected to be infected with CLBV in this study. The complete genome of four isolates of CLBV was obtained from Reikou in Sichuan (CLBV-LH), Yura Wase in Zhejiang (CLBV-YL), Bingtangcheng in Hunan (CLBV-BT), Fengjie 72-1 in Chongqing (CLBV-FJ), respectively. While they all represented 8 747 nucleotides in monopartite size, excluding the poly(A) tail, each of the isolates coded three open reading frames (ORFs). Identity of the four isolates ranged from 98.9 to 99.8% to each other and from 96.8 to 98.1% to the citrus references in GenBank by multiple alignment of genomes. A phylogenetic tree based on the genome sequences of available CLBV isolates indicated that the four isolates were clustered together, suggesting that CLBV isolates from citrus in China did not have obvious variation. This is the first report of the complete nucleotide sequences of CLBV isolates infecting citrus in China.

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GmNAC15 overexpression in hairy roots enhances salt tolerance in soybean

LI Ming, HU Zheng, JIANG Qi-yan, SUN Xian-jun, GUO Yuan, QI Jun-cang, ZHANG Hui

2018, 17 (03): 530-538. DOI: 10.1016/S2095-3119(17)61721-0

Abstract （1099） PDF in ScienceDirect

The NAC (NAM, ATAF1/2 and CUC2) transcription factor family plays a key role in plant development and responses to abiotic stress. GmNAC15 (Glyma15g40510.1), a member of the NAC transcription factor family in soybean, was functionally characterized, especially with regard to its role in salt tolerance. In the present study, qRT-PCR (quantitative reverse transcription PCR) analysis indicated that GmNAC15 was induced by salt, drought, low temperature stress, and ABA treatment in roots and leaves. GmNAC15 overexpression in soybean (Glycine max) hairy roots enhanced salt tolerance. Transgenic hairy roots improved the survival of wild leaves; however, overexpression of GmNAC15 in hairy root couldn’t influnce the expression level of GmNAC15 in leaf. GmNAC15 regulates the expression levels of genes responsive to salt stress. Altogether, these results provide experimental evidence of the positive effect of GmNAC15 on salt tolerance in soybean and the potential application of genetic manipulation to enhance the salt tolerance of important crops.

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Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq

LI Ming-na, LONG Rui-cai, FENG Zi-rong, LIU Feng-qi, SUN Yan, ZHANG Kun, KANG Jun-mei, WANG Zhen, CAO Shi-hao

2018, 17 (01): 184-196. DOI: 10.1016/S2095-3119(17)61749-0

Abstract （700） PDF in ScienceDirect

Carex rigescens (Franch.) V. Krecz is a wild turfgrass perennial species in the Carex genus that is widely distributed in salinised areas of northern China. To investigate genome-wide salt-response gene networks in C. rigescens, transcriptome analysis using high-throughput RNA sequencing on C. rigescens exposed to a 0.4% salt treatment (Cr_Salt) was compared to a non-salt control (Cr_Ctrl). In total, 57 742 546 and 47 063 488 clean reads were obtained from the Cr_Ctrl and Cr_Salt treatments, respectively. Additionally, 21 954 unigenes were found and annotated using multiple databases. Among these unigenes, 34 were found to respond to salt stress at a statistically significant level with 6 genes up-regulated and 28 down-regulated. Specifically, genes encoding an EF-hand domain, ZFP and AP2 were responsive to salt stress, highlighting their roles in future research regarding salt tolerance in C. rigescens and other plants. According to our quantitative RT-PCR results, the expression pattern of all detected differentially expressed genes were consistent with the RNA-seq results. Furthermore, we identified 11 643 simple sequence repeats (SSRs) from the unigenes. A total of 144 amplified successfully in the C. rigescens cultivar Lüping 1, and 69 of them reflected polymorphisms between the two genotypes tested. This is the first genome-wide transcriptome study of C. rigescens in both salt-responsive gene investigation and SSR marker exploration. Our results provide further insights into genome annotation, novel gene discovery, molecular breeding and comparative genomics in C. rigescens and related grass species.

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Modulation of protein expression in alfalfa (Medicago sativa L.) root and leaf tissues by Fusarium proliferatum

CONG Li-li, SUN Yan, LONG Rui-cai, KANG Jun-mei, ZHANG Tie-jun, LI Ming-na, WANG Zhen, YANG Qing-chuan

2017, 16 (11): 2558-2572. DOI: 10.1016/S2095-3119(17)61690-3

Abstract （725） PDF in ScienceDirect

Alfalfa (Medicago sativa L.) is an important forage crop and is also a target of many fungal diseases including Fusarium spp. As of today, very little information is available about molecular mechanisms that contribute to pathogenesis and defense responses in alfalfa against Fusarium spp. and specifically against Fusarium proliferatum, the causal agent of alfalfa root rot. In this study, we used a proteomic approach to identify inducible proteins in alfalfa during a compatible interaction with F. proliferatum strain YQC-L1. Samples used for the two-dimensional gel electrophoresis (2-DE) and MALDI-TOF/TOF mass spectrometry were from roots and leaves of alfalfa cultivar AmeriGraze 401+Z and WL656HQ. Plants were grown in hydroponic conditions and at 4 days post inoculation with YQC-L1. Our disease symptom assays indicated that AmeriGraze 401+Z was tolerant to YQC-L1 infection while WL656HQ was highly susceptible. Analysis of differentially expressed proteins found in the 2-DE was further characterized using the MASCOT MS/MS ion search software and associated databases to identify multiple proteins that might be involved in F. proliferatum resistance. A total of 66 and 27 differentially expressed proteins were found in the roots and leaves of the plants inoculated with YQC-L1, respectively. These identified proteins were placed in various categories including defense and stress response related metabolism, photosynthesis and protein synthesis. Thirteen identified proteins were validated for their expressions by quantitative reverse transcription (qRT)-PCR. Our results suggested that some of the identified proteins might play important roles in alfalfa resistance against Fusarium spp. These finding could facilitate further dissections of molecular mechanisms controlling root rot disease in alfalfa and potentially other legume crops.

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Molecular characterization and tissue expression profile of the Dnmts gene family in pig

LUO Zong-gang, ZHANG Kai, CHEN Lei, YANG Yuan-xin, FU Peng-hui, WANG Ke-tian, WANG Ling, LI Ming-zhou, LI Xue-wei, ZUO Fu-yuan, WANG Jin-yong

2017, 16 (06): 1367-1374. DOI: 10.1016/S2095-3119(16)61512-5

Abstract （803） PDF in ScienceDirect

DNA methyltransferases (Dnmts) comprise a family of proteins which involved in the establishment and maintenance of DNA methylation patterns. In pig, the molecular characterization and tissue expression profile of Dnmt gene family are not clear. To solve this problem, reverse transcriptase PCR and rapid amplification of cDNA ends were used to clone the sequences of the porcine Dnmt2 and Dnmt3b genes. Furthermore, the mRNA expression profiles of Dnmt1, Dnmt2, Dnmt3a and Dnmt3b genes from 54 adult tissues and 2 entire fetuses of Rongchang pig were analyzed by quantitative real-time PCR (qRT-PCR). As a result, the lengths of porcine Dnmt2 and Dnmt3b gene cDNAs were 1 227 and 2 559 bp with cytosine-C5 specific DNA methylase domain, respectively. The four Dnmt genes were highly expressed in longissimus dorsi muscle (P<0.01). Dnmt1 is highly expressed in heart (P<0.01) and Dnmt 2 shows its preference in liver and seminal vesicle tissue (P<0.01). Dnmt3a and Dnmt3b are highly expressed in the two fetus stages (P<0.01). All these results suggested that each gene has its specific expression profile, and deeper study is required to dig more details between the methylation level and Dnmt family mRNA expressions in different tissues.

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Soil N transformation and microbial community structure as affected by adding biochar to a paddy soil of subtropical China

LI Ming, LIU Ming, LI Zhong-pei, JIANG Chun-yu, WU Meng

2016, 15 (1): 209-219. DOI: 10.1016/S2095-3119(15)61136-4

Abstract （2068） PDF in ScienceDirect

We have had little understanding on the effects of different types and quantities of biochar amendment on soil N transformation process and the microbial properties. In this study, various biochars were produced from straw residues and wood chips, and then added separately to a paddy soil at rates of 0.5, 1 and 2% (w/w). The effects of biochar application on soil net N mineralization and nitrification processes, chemical and microbial properties were examined in the laboratory experiment. After 135 d of incubation, addition of straw biochars increased soil pH to larger extent than wood biochars. The biochar-amended soils had 37.7, 7.3 and 227.6% more soil organic carbon (SOC), available P and K contents, respectively, than the control soil. The rates of net N mineralization and nitrification increased significantly as biochars quantity rose, and straw biochars had greater effect on N transformation rate than wood biochars. Soil microbial biomass carbon increased by 14.8, 45.5 and 62.5% relative to the control when 0.5, 1 and 2% biochars (both straw- and wood-derived biochars), respectively, were added. Moreover, biochars amendments significantly enhanced the concentrations of phospholipid fatty acids (PLFAs), as the general bacteria abundance increased by 161.0% on average. Multivariate analysis suggested that the three rice straw biochar (RB) application levels induced different changes in soil microbial community structure, but there was no significant difference between RB and masson pine biochar (MB) until the application rate reached 2%. Our results showed that biochars amendment can increase soil nutrient content, affect the N transformation process, and alter soil microbial properties, all of which are biochar type and quantity dependent. Therefore, addition of biochars to soil may be an appropriate way to disposal waste and improve soil quality, while the biochar type and addition rate should be taken into consideration before its large-scale application in agro-ecosystem.

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Development of a Vehicle-Mounted Crop Detection System

ZHONG Zhen-jiang, SUN Hong, LI Min-zan, ZHANG Feng , LI Xiu-hua

2014, 13 (6): 1284-1292. DOI: 10.1016/S2095-3119(13)60617-6

Abstract （1631） PDF in ScienceDirect

In order to monitor plant chlorophyll content in real-time, a new vehicle-mounted detection system was developed to measure crop canopy spectral characteristics. It was designed to work as a wireless sensor network with one control unit and one measuring unit. The control unit included a personal digital assistant (PDA) device with a ZigBee wireless network coordinator. As the coordinator of the whole wireless network, the control unit was used to receive, display and store all the data sent from sensor nodes. The measuring unit consisted of several optical sensor nodes. All the sensor nodes were mounted on an on-board mechanical structure so that the measuring unit could collect the canopy spectral data while moving. Each sensor node contained four optical channels to measure the light radiation at the wavebands of 550, 650, 766, and 850 nm. The calibration tests verified a good performance in terms of the wireless transmission ability and the sensor measurement precision. Both stationary and moving field experiments were also conducted in a winter wheat experimental field. There was a high correlation between chlorophyll content and vegetation index, and several estimation models of the chlorophyll content were established. The highest R2 of the estimation models was 0.718. The results showed that the vehicle-mounted crop detection system has potential for field application.

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