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The Shunshanji site is one of the earliest archaeological sites identified in the middle reaches of Huai River region. Using phytolith analysis, 66 samples from 3 exposed profiles at the Shunshanji site were studied in order to contribute to the understanding of the nature of rice remains at the site and early farming information in the middle reaches of the Huai River region of China. The presence of rice phytoliths possibly from domesticated rice ( Oryza sativa ) in a sequence of sediments from Shunshanji site suggests that rice had been used and cultivated at Shunshanji, while dry farming had not reached the area between 8500 and 7000 BP. In addition, the continuous occurrence of a large percentage rice phytoliths that fall into wild or intermediate types and some domesticated rice phytoliths increased in percentage through time indicate the rice domestication was in the early stage, and the selective pressure changed the phytoliths morphologies gradually with time. This paper provides new evidence for understanding the origin and early development of rice agriculture in the Huai River region, and some clues for discovering the temporal-spatial route for the northward spread of rice cultivation and southward spread of dry farming in China. [ABSTRACT FROM AUTHOR]

The Xiaohuangshan site is an early Neolithic settlement in the lower Yangzi River dating to 9000–7000 BP. In this paper, starch grains extracted from the surfaces of 9 pottery sherds and 6 grinding slabs unearthed from the early Xiaohuangshan phase (9000–8500 cal. BP) are identified from Oryza , Triticeae Tribe, Coix lacryma-jobi , Nelumbo sp., Dioscorea opposita Trunb , Vigna and Quercus spp. Based on the statistical analysis of percentage presence and the minimum numbers of plants identified by starch grains on the grinding slabs and potteries, it can be found that rice has become one of the major staple foods together with Triticeae grasses, Job's tears and acorns, which indicates rice should have been cultivated intentionally at Xiaohuangshan. The results also suggest that grinding slabs from Xiaohuangshan were used mainly for processing wild plants other than rice, and plant residues extracted from their surfaces cannot be utilized independently to explore human's subsistence strategies in that time. In addition, acorns probably were cooked whole in the pottery vessels before they were shelled or ground on the grinding slabs in the Xiaohuangshan site. This paper provides new evidence for the beginning of rice cultivation during the early Neolithic in the Lower Yangtze River. [ABSTRACT FROM AUTHOR]

Phosphorus (P) is an important element in numerous metabolic reactions and signalling pathways, but the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome and metabolite analyses of apple leaves and roots were compared under different P conditions. The results showed that different P stresses influenced phenotypic characteristics, soil plant analytical development (SPAD) values and the contents of flavonoids and anthocyanins in apple seedlings. The contents of hydrogen peroxide (H 2 O 2) and malondialdehyde (MDA) and the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), acid phosphatase (ACP) and purple acid phosphatase (PAP) were also affected by different P stresses. In addition, RNA sequencing (RNA-seq) was used to characterize the influence of different P stresses on apple seedlings. Compared with control apple plants, there were 1246 and 1183 differentially expressed genes (DEGs) in leaves and roots under the low-P treatment and 60 and 1030 DEGs in leaves and roots under the high-P treatment, respectively. Gene Ontology (GO) analysis indicated that apple trees might change their responses to metabolic processes, cell proliferation, regulation of biological processes, reactive oxygen species metabolic processes and flavonoid metabolic processes under P stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that DEGs act on the mitogen-activated protein kinase (MAPK) signalling pathway, flavonoid biosynthesis, phenylpropanoid biosynthesis, and ATP-binding cassette (ABC) transporters. The metabolome analysis revealed that the levels of most amino acids and their derivatives, organic acids and flavonoids in roots treated with low-P stress were higher than those in roots of apple seedlings under control growth conditions. Apple seedlings regulate the flavonoid pathway to respond to different phosphorus environments. The results provide a framework for understanding the metabolic processes underlying different P responses and provide a foundation for improving the utilization efficiency of P in apple trees. • Physiological, transcriptome and metabolite analyses of apple leaves and roots were compared under different phosphorus conditions. • RNA-Seq was used to characterize the influence of different P tolerances in apple seedlings. • The metabolome analysis revealed that most amino acids and derivatives, organic acids and flavonoids in LP roots were higher than those in CK roots in apple seedlings under different P conditions. • Apple seedlings regulate the flavonoid pathway to respond to different phosphorus environments. [ABSTRACT FROM AUTHOR]

The site of Jiahu in the central plain of China is known for its early rice cultivation 9000 years ago. The preliminary starch analysis implies that the Jiahu grinding tools were used for processing various plants, including rice. This paper presents the use-wear analysis carried out on a sample of seventeen grinding tools from Jiahu, nine of which were previously analyzed for the presence of starch. Use-wear traces associated with processing cereal and wood-like material were identified. This result confirms important evidence of cereal processing in the early Neolithic period. It also reveals the diversity of functions in the grinding tool assemblage. Furthermore, the use-wear distribution indicates that grinding slabs without feet and cylindrical rollers were mainly associated with the processing of cereals while grinding slabs with feet were mainly related to the processing of wood-like material. Quantitative analysis of the starch data also indicates that grinding slabs without feet possess more starch grains than the grinding slabs with feet. Therefore, it is argued that specific types of grinding tools were used for processing specific kinds of material. This study highlights the different roles grinding tools may have played in early farming societies. [ABSTRACT FROM AUTHOR]

Trees are inevitably attacked by different kinds of pathogens in their life. However, little is known about the regulatory factors in poplar response to different pathogen infections. MicroRNA159 (miR159) is a highly conserved microRNA (miRNA) in plants and regulates plant development and stress responses. Here, transgenic poplar overexpressing pto-miR159a (OX-159) showed antagonistic regulation mode to poplar stem disease caused by fungi Cytospora chrysosperma and bacteria Lonsdalea populi. OX-159 lines exhibited a higher susceptibility after inoculation with bacterium L. populi , whereas enhanced disease resistance to necrotrophic fungi C. chrysosperma compared with wild-type (WT) poplars. Intriguingly, further disease assay found that OX159 line rendered the poplar susceptible to hemi-biotrophic fungi Colletotrichum gloeosporioide , exhibiting larger necrosis and lower ROS accumulation than WT lines. Transcriptome analyses revealed that more down-regulated differentially expressed genes with disease-resistant domains in OX-159 line compared with WT line. Moreover, the central mediator NPR1 of salicylic acid (SA) pathway showed a decrease in expression level, while jasmonic acid/ethylene (JA/ET) signal pathway marker genes ERF , as well as PR3 , MPK3 , and MPK6 genes showed an increase level in OX159-2 and OX159-5 compared with WT lines. Further spatio-temporal expression analysis revealed JA/ET signaling was involved in the dynamic response process to C. gloeosporioides in WT and OX159 lines. These results demonstrate that overexpression of pto-miR159a resulted in the crosstalk changes of the downstream hub genes, thereby controlling the disease resistance of poplars, which provides clues for understanding pto-miR159a role in coordinating poplar-pathogen interactions. • miR159a is involved in poplar disease resistance to different fungi and bacteria. • Transcriptome analyses revealed global down-regulation of genes with disease resistance domains in OX159 lines. • Overexpression of miR159a induced changes in downstream hormone pathway-related genes. • JA/ET signaling was involved in the dynamic response process to C. gloeosporioides in WT and OX159 lines. [ABSTRACT FROM AUTHOR]

• Physiological, transcriptome and metabolite analyses of apple leaves and roots were compared under different nitrogen conditions. • Different N stresses influenced plant growth and physiological characteristics. • RNA-Seq was used to characterize the influence of different N tolerance in apple seedlings. • The metabolome analysis revealed that most amino acids and derivatives, nucleotides and derivatives, and lipids decreased in LP leaves, but increased in roots compared with CK in apple seedlings. • Apple seedlings through regulated the carbon and nitrogen metabolism, and flavonoid pathway to respond to the different nitrogen environments. Nitrogen (N) is an essential element for plant growth and development. In this study, physiological, transcriptome and metabolite analyses of apple leaves and roots were compared under different N conditions. The results indicated that different N stresses influenced plant growth, the content of soil plant analytical development (SPAD) value and photosynthesis in apple seedlings. The content of hydrogen peroxide (H 2 O 2), and the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS) and glutamine antinotransferase (GOGAT) were also affected by different N stresses. RNA-Seq was used to analysis the influence of different N tolerances in apple seedlings. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) indicated that apple trees might affect the responses to photosynthesis, organic hydroxy compound biosynthetic process, and secondary metabolite biosynthetic process under N stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs focused on photosynthesis and secondary metabolite biosynthetic process. There were 527 differential metabolites in LNL/CKL, 157 in HNL/CKL, 477 in LNR/CKR, and 232 in HNR/CKR. The metabolome analysis indicated that total of 1004 and 389 significant differential metabolites were identified under low N and high N conditions in apple. Apple seedlings regulate the carbon metabolism, nitrogen metabolism and flavonoid pathway to adapt the different nitrogen environments. This research provide understanding for the metabolic processes underlying different N responses and provide a foundation for improving the efficiency of N use in apple trees. [ABSTRACT FROM AUTHOR]