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1. Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines
HUO Dong-ao, ZHU Bin, TIAN Gui-fu, DU Xu-ye, GUO Juan, CAI Meng-xian
Journal of Integrative Agriculture    2019, 18 (7): 1541-1546.   DOI: 10.1016/S2095-3119(19)62635-3
摘要217)      PDF    收藏
The economically valuable oil crop Brassica napus (AACC, 2n=38), which arose from interspecific hybridization between the diploid ancestors Brassica rapa (AA, 2n=20) and Brassica oleracea (CC, 2n=18), has a complex genome.  More than 10% of the assembled sequences, most of which belong to the C subgenome, have not been anchored to the corresponding chromosome.  Previously, a complete set of monosomic alien addition lines (MAALs, C1–C9) with each of the nine C-subgenome chromosomes added to the extracted A subgenome was obtained from the allotetraploid B. napus donor Oro, after the ancestral B. rapa (RBR Oro) genome was restored.  These MAALs effectively reduced the complexity of the B. napus genome.  Here, we determined the expression values of genes on unanchored scaffolds in the MAALs and RBR Oro.  Then, multiple comparisons of these gene expression values were used to determine the affiliations of the non-anchored scaffolds on which the genes were located.  In total, 54.68% (44.11 Mb) of the 80.67 Mb of non-anchored scaffolds belonging to the C subgenome were assigned to corresponding C chromosomes.  This work highlights the potential value of these MAALs in improving the genome quality of B. napus.
 
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2. Functional analysis of a wheat pleiotropic drug resistance gene involved in Fusarium head blight resistance
WANG Gui-ping, HOU Wen-qian, ZHANG Lei, WU Hong-yan, ZHAO Lan-fei, DU Xu-ye, MA Xin, LI An-fei, WANG Hong-wei, KONG Ling-rang
Journal of Integrative Agriculture    2016, 15 (10): 2215-2227.   DOI: 10.1016/S2095-3119(16)61362-X
摘要1708)      PDF    收藏
    The pleiotropic drug resistance (PDR) sub-family of adenosine triphosphate (ATP)-binding cassette (ABC) transporter had been reported to participate in diverse biological processes of plant. In this study, we cloned three novel PDR genes in Fusarium head blight (FHB) resistant wheat cultivar Ning 7840, which were located on wheat chromosomes 6A, 6B and 6D. In phylogeny, these genes were members of cluster I together with AePDR7 and BdPDR7. Subcellular localization analysis showed that TaPDR7 was expressed on the plasmalemma. The quantitative real time PCR (RT-PCR) analysis showed that this gene and its probable orthologues in chromosomes 6B and 6D were both up-regulated sharply at 48 h after infected by Fusarium graminearum and trichothecene deoxynivalenol (DON) in spike. When knocking down the transcripts of all TaPDR7 members by barely stripe mosaic virus-induced gene silencing (BSMV-VIGS) system, it could promote the F. graminearum hyphae growth and made larger pathogen inoculation points in Ning 7840, which suggested that TaPDR7 might play an important role in response to F. graminearum. Although salicylic acid (SA), methyl jasmonate (MeJA) and abscisic acid (ABA) had been reported to possibly regulate wheat FHB resistance, here, we found that the three members of TaPDR7 were negatively regulated by these three hormones but positively regulated by indoleacetic acid (IAA).
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3. Cloning and characterization of a novel UDP-glycosyltransferase gene induced by DON from wheat
MA Xin, DU Xu-ye, LIU Guo-juan, YANG Zai-dong, HOU Wen-qian, WANG Hong-wei, FENG De-shun
Journal of Integrative Agriculture    2015, 14 (5): 830-838.   DOI: 10.1016/S2095-3119(14)60857-1
摘要2424)      PDF    收藏
Fusarium head blight (FHB), caused primarily by Fusarium graminearum, is a destructive disease of wheat throughout the world. However, the mechanisms of host resistance to FHB are still largely unclear. Deoxynivalenol (DON) produced by F. graminearum which enhances the pathogen to spread could be converted into inactive form D3G by UDP-glycosyltransferases (UGTs). A DON responsive UGT gene, designated as TaUGT4, was first cloned from wheat in this study. The putative open reading frame (ORF) of TaUGT4 was 1 386 bp, encoding 461 amino acids protein. TaUGT4 was placed on chromosome 2D using a set of nulli-tetrasomic lines of wheat cultivar Chinese Spring (CS). When fused with eGFP at C terminal, TaUGT4 was shown to localize in cytoplasm of the transformed tobacco cells. The transcriptional analysis revealed that TaUGT4 was strongly induced by F. graminearum or DON in both of FHB-resistant cultivar Sumai 3 and susceptible cultivar Kenong 199, especially in Sumai 3 under DON treatment. Similar increase of TaUGT4 expression was observed in Sumai 3 and Kenong 199 in response to salicylic acid (SA) treatment. But interestingly, the transcripts level of TaUGT4 in Sumai 3 showed significantly higher than that in Kenong 199 after treated with methyl jasmonate (MeJA). According to the expression patterns, TaUGT4 might lead to different effects between FHB-resistant genotype and susceptible genotype in the process against F. graminearum inoculation. It had also been discussed in this paper that JA signaling pathway might play a significant role in the resistance against F. graminearum compared to SA signaling pathway.
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4. Association analysis of grain traits with SSR markers between Aegilops tauschii and hexaploid wheat (Triticum aestivum L.)
ZHAO Jing-lan, WANG Hong-wei, ZHANG Xiao-cun, DU Xu-ye, LI An-fei, KONG Ling-rang
Journal of Integrative Agriculture    2015, 14 (10): 1936-1948.   DOI: 10.1016/S2095-3119(15)61070-X
摘要1348)      PDF    收藏
Seven important grain traits, including grain length (GL), grain width (GW), grain perimeter (GP), grain area (GA), grain length/width ratio (GLW), roundness (GR), and thousand-grain weight (TGW), were analyzed using a set of 139 simple sequence repeat (SSR) markers in 130 hexaploid wheat varieties and 193 Aegilops tauschii accessions worldwide. In total, 1 612 alleles in Ae. tauschii and 1 360 alleles in hexaploid wheat (Triticum aestivum L.) were detected throughout the D genome. 197 marker-trait associations in Ae. tauschii were identified with 58 different SSR loci in 3 environments, and the average phenotypic variation value (R2) ranged from 0.68 to 15.12%. In contrast, 208 marker-trait associations were identified in wheat with 66 different SSR markers in 4 environments and the average phenotypic R2 ranged from 0.90 to 19.92%. Further analysis indicated that there are 6 common SSR loci present in both Ae. tauschii and hexaploid wheat, which are significantly associated with the 5 investigated grain traits (i.e., GA, GP, GR, GL, and TGW) and in total, 16 alleles derived from the 6 aforementioned SSR loci were shared by Ae. tauschii and hexaploid wheat. These preliminary data suggest the existence of common alleles may explain the evolutionary process and the selection between Ae. tauschii and hexaploid wheat. Furthermore, the genetic differentiation of grain shape and thousand-grain weight were observed in the evolutionary developmental process from Ae. tauschii to hexaploid wheat.
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