Comparative analysis of the dynamic proteomic profiles in berry skin between red and white grapes (Vitis vinifera L.) during fruit coloration

The aim of this study was to deepen our understanding of the proteomic profiles related to skin coloration at the whole proteome level through the analysis of multiple protein spots. A comparative proteomics analysis was conducted on the berry skins of red and white progeny derived from a single cross, 'Jingxiu' (red) x 'Muscat of Alexandria' (white), to minimize genetic background differences. Among the 1000-1800 spots assessed, the levels of 57, 70 and 26 proteins were lower in the skins of white progeny, compared to the skins of red progeny at about two weeks before veraison, at veraison and at maturity, respectively. Alternatively, the levels of 54, 50 and 23 proteins were higher at about two weeks before veraison, at veraison and at maturity, respectively. The levels of proteins involved in anthocyanin biosynthesis, especially UFGT and AOMT, were lower in the skins of white progeny at veraison and at maturity, and the levels of most proteins involved in amino acid metabolism were found to be lower before veraison. Almost all differentially accumulated proteins involved in energy production were found before and at veraison, while there was no difference detected in the levels of glycolysis, tricarboxylic acid cycle and photosynthesis between the skins of red and white progeny. The differential accumulation of enzyme proteins involved in anthocyanin synthesis had a decisive influence on the different skin colorization of red and white progeny. Many proteins related to metabolism and energy production were also differentially accumulated. In addition, many differences in the skin proteomes of white and red progeny were apparent before veraison, i.e. before skins developed coloration. (C) 2013 Elsevier B.V. All rights reserved

Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice

Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the N6-methyladenosine (m6A) and N5-methylcytosine (m5C) modifications on RNA, direct RNA sequencing (DRS) using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice. Approximately 94 million reads were generated, with an average length ranging from 619 nt to 1013 nt, and a total of 45,707 transcripts across 34,763 genes were detected. Expression profiles of transcripts at the isoform level were quantified among tissues. Transcriptome-wide mapping of m6A and m5C demonstrated that both modifications exhibited tissue-specific characteristics. The transcripts with m6A modifications tended to be modified by m5C, and the transcripts with modifications presented higher expression levels along with shorter poly(A) tails than transcripts without modifications, suggesting the complexity of gene expression regulation. Gene Ontology analysis demonstrated that m6A- and m5C-modified transcripts were involved in central metabolic pathways related to the life cycle, with modifications on the target genes selected in a tissue-specific manner. Furthermore, most modified sites were located within quantitative trait loci that control important agronomic traits, highlighting the value of cloning functional loci. The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome, improving our understanding of the rice genome

Agrobiodiversity and in situ conservation in ethnic minority communities of Xishuangbanna in Yunnan Province, Southwest China

Abstract Background Xishuangbanna of Yunnan Province, southwest of China belongs to a global biodiversity and cultural hotspot. Agrobiodiversity plays an essential role in local livelihoods and traditional culture in the region. However, preliminary studies suggest that diversity of crop plants and livestock species is declining. We hypothesized that agrobiodiversity and traditional means of preserving agrobiodiversity are threatened because of changes in government policy in favor of commercial plantations, land use change and changes in traditional agricultural practices. We investigated whether or not agrobiodiversity was declining, the specific causes, and signs of active biodiversity conservation practices in ethnic minority communities of Xishuangbanna which could form the basis for extensive in situ conservation programmes. Methods A series of field studies to document trends in agrobiodiversity were conducted in different ethnic minority communities in Menghai County, Mengla County and Jinghong City of Xishuangbanna of Yunnan Province, southwest of China between July 2015 and February 2016. Data was obtained through the use of semi-structured questionnaires, field observation and participatory rural appraisal (PRA) tools. A total of 360 ethnic households provided information on current status, functions, characteristics, changes, and threatened factors of farming crop and livestock resources. Some measures for in situ conservation of agricultural biological resources were also researched using PRA methods. Results Two hundred twenty-six crop varieties belonging to 31 families, 71 genera and 101 species were identified in Xishuangbanna, which included 83 vegetable crops, 77 food crops, 24 spice crops, 22 fruit crops, 13 cash crops, 6 oil crops, and 1 cloth crop, respectively. There were 15 livestock varieties, belonging to 6 major species: cattle, pigs, goats, chickens, ducks, and geese. Different crop and livestock resources had their own characteristics, functions and threatened factors. Since 2002, agroecosystem, crop diversity and livestock diversity have declined greatly over the Xishuangbanna region as a whole under implementation of the Sloping Land Conversion Program (SLCP). Swidden agriculture was completely eliminated under this program and gradually replaced by large land areas devoted to rubber, tea and banana plantations. Villager numbers engaging in farming production and population of crops and livestock were greatly decreased, particularly in terms of production of local traditional varieties. However, some in situ conservation measures such as seeds preservation, planting of traditional crops and raising livestock have played an important role in local agrobiodiversity conservation. Conclusion Abundant agricultural resources and agrobiodiversity are critical to the local livelihood and maintenance of traditional culture in Xishuangbanna. However, agrobiodiversity and related traditional culture have been greatly impacted by implementation of the SLCP since 2002. Therefore, in future conservation of agrobiodiversity, incorporating some sustainable protection measures based in local communities such as convening seed exchange fairs, conserving traditional varieties in permanent plots, making a visual documentary of indigenous cultivation, and providing traditional agricultural products to tourists should be carefully considered and adopted