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Genome-wide identification, evolutionary selection, and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea

AN Feng, ZHANG Kang, ZHANG Ling-kui, LI Xing, CHEN Shu-min, WANG Hua-sen, CHENG Feng

2022, 21 (6): 1620-1632. DOI: 10.1016/S2095-3119(21)63827-3

Abstract （213） PDF in ScienceDirect

DNA methylation plays an important role in plant growth and development, and in regulating the activity of transposable elements (TEs). Research on DNA methylation-related (DMR) genes has been reported in Arabidopsis, but little research on DMR genes has been reported in Brassica rapa and Brassica oleracea, the genomes of which exhibit significant differences in TE content. In this study, we identified 78 and 77 DMR genes in Brassica rapa and Brassica oleracea, respectively. Detailed analysis revealed that the numbers of DMR genes in different DMR pathways varied in B. rapa and B. oleracea. The evolutionary selection pressure of DMR genes in B. rapa and B. oleracea was compared, and the DMR genes showed differential evolution between these two species. The nucleotide diversity (π) and selective sweep (Tajima’s D) revealed footprints of selection in the B. rapa and B. oleracea populations. Transcriptome analysis showed that most DMR genes exhibited similar expression characteristics in B. rapa and B. oleracea. This study dissects the evolutionary differences and genetic variations of the DMR genes in B. rapa and B. oleracea, and will provide valuable resources for future research on the divergent evolution of DNA methylation between B. rapa and B. oleracea.

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Identification and validation of stable and novel quantitative trait loci for pod shattering in soybean [Glycine max (L.) Merr.]

JIA Jia, WANG Huan, CAI Zhan-dong, WEI Ru-qian, HUANG Jing-hua, XIA Qiu-ju, XIAO Xiao-hui, MA Qi-bin, NIAN Hai, CHENG Yan-bo

2022, 21 (11): 3169-3184. DOI: 10.1016/j.jia.2022.08.082

Abstract （218） PDF in ScienceDirect

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

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Spatial variation of technical efficiency of cereal production in China at the farm level

ZHOU Wen-bin, WANG Huai-yu, HU Xi, DUAN Feng-ying

2021, 20 (2): 470-481. DOI: 10.1016/S2095-3119(20)63579-1

Abstract （139） PDF in ScienceDirect

Rice, wheat and maize are the main staple food crops to ensure the food security in China with diversified climate condition, cropping system and environmental and socio-economic factors across provinces. Spatial variation of technical efficiency in farmers’ field is helpful to understand the potential to improve farmers’ yield given the inputs level and reduce the yield gap. The study is based on a large-scale farm household survey which covered 1 218 rice farmers, 3 566 wheat farmers and 2 111 maize farmers in the main producing areas. The results indicate that rice farmers are with very high technical efficiency level, nearly 0.9 on average, with little room to improve the efficiency of agricultural inputs. Similar results have been found in wheat and maize farmers’ fields, although the technical efficiency levels are lower than that of rice farmers while still at a high level with obvious variation across regions. Farmers with higher yield level also achieve better technical efficiency in most locations. Both local environmental and socio-economic factors significantly affect farmers’ technical efficiency. In the context of urbanization and economic development, improved and new agricultural technologies need to be prioritized and facilitated to improve cereal yield at farm level.

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Field identification of morphological and physiological traits in two special mutants with strong tolerance and high sensitivity to drought stress in upland rice (Oryza sativa L.)

HUANG Min, XU Yu-hui, WANG Hua-qi

2019, 18 (5): 970-981. DOI: 10.1016/S2095-3119(18)61909-4

Abstract （334） PDF in ScienceDirect

The two mutants idr1-1 and 297-28, which were obtained from the radiation mutation of HD297 and IAPAR9, were used as experimental materials in this study for a 2-year (2012 and 2013) experiment about field drought resistance identification in Beijing, China. Key agronomic traits and water-related physiological indexes were observed and measured, including the leaf anti-dead level (LADL), days to heading, plant height, setting percentage, aboveground biomass, leaf water potential (LWP), net photosynthetic rate (Pn) and transpiration rate. The results showed that the mutant idr1-1 that was under drought stress (DS) conditions for 2 years had the highest LADL grades (1.3 and 2.0) among all the materials, and they were 2–3 grades stronger than the wild-type IAPAR9 with an average that was 21.4% higher for the setting percentage than the wild type. Compared with the IAPAR9 for the 2-year average delay in the days to heading and the reduction rates in the plant height, setting percentage, and aboveground biomass under DS compared with the well-watered (WW) treatment, idr1-1 showed 3.2% less delay and 19.1, 16.4, and 6.1% less reduction, respectively. The idr1-1 in the LWP always exhibited the highest performance among all the materials. The Pn of idr1-1 under severe and mild DS comparing with that under WW was slightly decreased and even slightly increased, respectively, leading to an average reduction rate of only 0.92%, which was 26.93% less than that of IAPAR9. Under the severe DS, idr1-1 still showed the highest value of 16.88 μmol CO2 m–2 s–1 among all the materials and was significantly higher than that of IAPAR9 (11.66 μmol CO2 m–2 s–1). Furthermore, only idr1-1 had the increased and the highest transpiration rate values (7.6 and 6.04 mmol H2O m–2 s–1) under both mild and severe DS compared with the values under WW, when the transpiration rate of all the other materials significantly decreased. By contrast, the 297-28 in terms of the LADL grade under DS was the lowest (7.0), and it was four grades weaker than its wild-type HD297 and even one grade weaker than the drought-sensitive paddy rice SN265. For the 2-year average reduction rates in aboveground biomass and plant heights under DS compared with those under the WW, 297-28 was 31.6 and 31.8% higher than HD297, respectively. Meanwhile, 297-28 showed the worst performance for the LWP, Pn, and transpiration rate. These results suggest that idr1-1 might be a superior drought tolerant mutant of upland rice found in China. It has a strong ability to maintain and even enhance leaf transpiration while maintaining a high plant water potential under DS, thus supporting a high Pn and alleviating the delay in agronomic trait development and yield loss effectively. 297-28 is a much more highly drought-sensitive mutant that is even more sensitive than paddy rice varieties. The two mutants could be used as drought tolerance controls for rice germplasm identification and the drought resistant mechanism studies in the future. idr1-1 is also suitable for breeding drought-tolerant and lodging-resistant high-yield rice varieties.

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Molecular identification and enzymatic properties of laccase2 from the diamondback moth Plutella xylostella (Lepidoptera: Plutellidae)

LIU Zhen-gang, WANG Huan-huan, XUE Chao-bin

2018, 17 (10): 2310-2319. DOI: 10.1016/S2095-3119(17)61764-7

Abstract （322） PDF in ScienceDirect

Laccase (EC 1.10.3.2) is known to oxidize various aromatic and nonaromatic compounds via a radical-catalyzed reaction, which generally includes two types of laccase, Lac1 and Lac2. Lac1 oxidizes toxic compounds in the diet, and Lac2 is known to play an important role in melanizing the insect exoskeleton. In this study, we cloned and sequenced the cDNA of the diamondback moth, Plutella xylostella Lac2 (PxLac2), from the third instar larvae using polymerase chain reaction (PCR) and rapid amplification of cDNA ends techniques. The results showed that the full-length PxLac2 cDNA was 1 944 bp long and had an open reading frame of 1 794 bp. PxLac2 encoded a protein with 597 amino acids and had a molecular weight of 66.09 kDa. Moreover, we determined the expression levels of PxLac2 in different stages by quantitative PCR (qPCR). The results indicated that PxLac2 was expressed differently in different stages. We observed the highest expression level in pupae and the lowest expression level in fourth instar larvae. We also investigated the enzymatic properties of laccase, which had optimal activity at pH 3.0 and at 35°C. Under these optimal conditions, laccase had a Michaelis constant (K_m) of 0.97 mmol L⁻¹, maximal reaction speed (V_m) of 56.82 U mL⁻¹, and activation energy (E_a) of 17.36 kJ mol⁻¹ to oxidize 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid ammonium salt). Type II copper enhanced laccase activity below 0.8 mmol L⁻¹ and reduced enzyme activity above 0.8 mmol L⁻¹ with an IC₅₀ concentration of 1.26 mmol L⁻¹. This study provides insights into the biological function of laccase.

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Insecticide induction of O-demethylase activity and expression of cytochrome P450 genes in the red imported fire ant (Solenopsis invicta Buren)

ZHANG Bai-zhong, KONG Fan-chao, WANG Hua-tang, GAO Xi-wu, ZENG Xin-nian, SHI Xue-yan

2016, 15 (1): 135-144. DOI: 10.1016/S2095-3119(15)61072-3

Abstract （2119） PDF in ScienceDirect

The red imported fire ant (Solenopsis invicta) is a global major invasive pest, and has caused significant economic, social and environmental impacts since its invasion to mainland of China in 2004. To date, chemical control has been the most effective measure. However, the long-term use of chemicals would lead to an unexpected rebound. To understand the risks and explore the mechanisms of detoxification or induction to insecticides in S. invicta, the O-demethylase activity and expression of cytochrome P450 genes of workers and queens, and the effects of chlorpyrifos and fipronil exposure in workers were investigated. Biochemical assays showed the O-demethylase activity of cytochrome P450 was significantly higher in workers than in queens (1.66-fold), and was significantly induced in workers exposed to chlorpyrifos and fipronil, reaching a maximum (3.00- and 1.95-fold) at 48 h and then decreasing dramatically compared to controls (exposed to acetone counterpart). The relative expression levels of 12 cytochrome P450 expressed sequence tags (ESTs) in workers were significantly higher than in queens (from 2.3- to 36.4-fold). Multiple cytochrome P450 genes (except 9E4) were co-up-regulated (from 1.5- to 2.86-fold) in workers exposed to fipronil. These results indicated that the increased O-demethylase activity may result from the increased transcription levels of cytochrome P450 related to detoxification of insecticides in S. invicta. It appears that cytochrome P450 plays an important role in enhanced metabolic detoxification of insecticides. At the same time, it also provides the theoretical basis for resistance management and rational usage of insecticides to control S. invicta.

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Expression patterns of OCT4, NANOG, and SOX2 in goat preimplantation embryos from in vivo and in vitro

YU Xiao-li, ZHAO Xiao-e, WANG Hua-yan, MA Bao-hua

2015, 14 (7): 1398-1406. DOI: 10.1016/S2095-3119(14)60923-0

Abstract （2255） PDF in ScienceDirect

The transcription factors, including OCT4, NANOG, and SOX2, played crucial roles in the maintenance of self-renewal and pluripotency in embryonic stem cells (ESCs). They expressed in preimplantation mammalian development with spatio- temporal pattern and took part in regulation of development. However, their expression and roles in goat had not been reported. In the present study, the expression of OCT4, NANOG, and SOX2 in goat preimplantation embryos both in vivo and in vitro were detected by real-time RCR and immunofluorescence. For in vivo fertilized embryos, the transcripts of OCT4, NANOG, and SOX2 could be detected from oocytes to blastocyst stage, their expression in morula and blastocyst stages was much higher than other stage. OCT4 protein was detected from oocyte to blastocyst, but the fluorescence was more located-intensive with nuclei from 8-cell stage, its expression present in both inner cell mass (ICM) and trophoblast cells (TE) at blastocyse stage. NANOG protein was similar to OCT4, the signaling of fluorescence completely focused on cell nuclei, while the SOX2 firstly showed nuclei location in morula. Comparing to in vivo fertilized embryo, the mRNA of these three transcription factors could be detected at 8-cell stage in parthenogenetic embryos (in vitro). Thereafter, the expressional level rose gradually along with embryo development. The locations of OCT4 and NANOG proteins were similar to in vivo fertilized embryos, and they located in cell nuclei from morula to blastocyst stage, while SOX2 protein firstly could be detected in cell nuclei at 8-cell stage. These differences suggested that OCT4, NANOG, and SOX2 played different function in regulating development of goat preimplantation embryos. These results may provide a novel insight to goat embryo development and be useful for goat ESCs isolation.

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Virulence and Diversity of Blumeria graminis f. sp. tritici Populations in China

ZENG Fan-song, YANG Li-jun, GONG Shuang-jun, SHI Wen-qi, ZHANG Xue-jiang, WANG　Hua , XIANG Li-bo, XUE Min-Feng , YU Da-zhao

2014, 13 (11): 2424-2437. DOI: 10.1016/S2095-3119(13)60669-3

Abstract （1244） PDF in ScienceDirect

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, is an important disease in China. To characterize the virulence and diversity of the pathogen, 1082 isolates were obtained from 8 major wheat-growing regions during the spring growing season in 2011. The virulence test was performed by inoculation on detached leaves of 22 differential lines with known Pm genes. Frequencies of virulence on these genotypes ranged from 0 to 97.4%. None of the 1 082 isolates was compatible to Pm21 and less than 20.0% were virulent to the genotype carrying Pm13. In contrast, the virulence frequencies of each population was more than 50.0% to differentials carrying Pm1a, Pm3b, Pm3c, Pm3f, Pm5a, Pm6 and Pm8. In total, 1028 pathotypes were detected, of which 984 were unique. Phenotypic diversity indices revealed a high level of diversity within populations. Genetic distance between different populations correlated significantly with geographical distance (R2=0.494, P 0.001). In addition, isolates from Xinjiang appear to form a separate group. Significant positive or negative associations between alleles at pairs of virulence loci were detected in 57 allele pairs to Pm genes. Virulence and diversity of the 8 populations suggested that varieties with effective resistance gene combinations should be developed at a regional level.

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The Defined siRNAs Suppress Nanog and Sox2 Expressions in Mouse ES Cells

LEI Lei, DOU Lin , WANG Hua-yan

2011, 10 (9): 1475-1481. DOI: 10.1016/S1671-2927(11)60141-7

Abstract （2868） PDF in ScienceDirect

Nanog, Oct4 and Sox2 are important transcription factors that are expressed in embryonic stem (ES) cells or embryoniccarcinoma (EC) cells, but in most cases they are absent in somatic cells. These factors play a key role to maintain embryonic stemcell self-renew and pluripotency. Down-regulation of Nanog and Sox2 gene expression can change multiple gene expressionpatterns and signal transduction pathways, and will initiate ES cell differentiation. This study was designed to select theefficient small interfering RNA (siRNA) fragments that inhibit Nanog and Sox2 gene expression in mouse J1 ES cells and P19 ECcells. Among synthesized siRNAs we screened out the siRNA N301 for Nanog and siRNA S720 for Sox2, which not only downregulatedof Nanog and Sox2 gene expression, but also interfered embryoid bodies formation. Our study provided the definedsiRNA fragments that could be used to investigate the epigenetic function of Nanog and Sox2 genes.

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