Additional file 1: Table S1. Information for accessions used in this study. Table S2. Quality assessment of genome sequencing data. Table S3. Genome mapping quality and genome coverage of genome sequencing data. Table S4. Genomic variations for 517 indica rice accessions against the MSU reference genome. Table S5. Number of deleterious variations in subpopulation of landrace and cultivar. Table S6. Genotyping results 319 quantitative trait nucleotidesof the 212 vital gene in rice from RiceNavi database. Table S7. Genomic segments that identified as breeding signatures between Ind IV and Ind II. Table S8. Genomic segments that identified as breeding signatures between Ind I and Ind II. Table S9. QTLs and known genes that identified by GWAS of eleven agronomic traits for Guangdong indica rice. Table S10. Allele combinations of plant heightgenes of Guangdong indica rice germplasm. Table S11. Allele combinations of thousand grain weight, grain length, grain widthand grain length width ratiogenes of Guangdong indica rice germplasm. Table S12. Phenotypic effect assessment of known QTNs that genotyped by RiceNavi. Table S13. Genotyping of 4 eating quality genes.
To evaluate the soil quality in the main cotton growing regions of Xinjiang, 11 soil quality indices were measured in representative locations: Hami, Bole, Changji, Shihezi, Aksu, Kashgar and Kuitun. The indices included soil pH, salt, organic matter, total N, available P and available K for soil physicochemical properties, and Cr, Cu, Zn, As, and Pb for soil heavy metal pollution. Based on these indices, a comprehensive soil quality index (SQI) was developed to analyze the soil quality in the cotton fields of Xinjiang. The results showed that the soils in Xinjiang's cotton fields were alkaline, with an average pH of 7.87. The soils were mildly saline, with an average salt content of 3.44 g·kg-1. Soil organic matter and total N concentrations were generally low, whereas available P and available K concentrations were relatively high. Soil available P concentrations were significantly higher than that of the second national soil survey, whereas soil pH, salt content, organic matter, and total N were less. Soil available K was greater in some regions but lower in others compared with the second national soil survey. The average heavy metal concentrations were as follows: Cr, 45.88 mg·kg-1; Cu, 40.66 mg·kg-1; Zn, 68.30 mg·kg-1; As, 12.88 mg·kg-1; and Pb, 16.68 mg·kg-1. These values were all below the national standards. However, the Cu, Zn, and As concentrations were greater than the background values in Xinjiang, indicating the accumulation of those elements in the soils. When the Nemerow comprehensive pollution index (PN) of heavy metals was less than 0.5, the comprehensive soil quality improved as the soil physicochemical properties improved. Soil organic matter, total N, Cu, Zn, As and Pb were the main variables affecting soil quality in the main cotton cropping regions of Xinjiang. The cotton growing areas in Xinjiang generally had medium soil quality. Changji and Kuitun had the highest SQI (0.52) whereas Aksu had the lowest value (0.31). Soil quality was generally highest in northern Xinjiang, followed by western area, and then southern area.以新疆主要棉区为研究对象,测定了哈密、博乐、昌吉、奎屯、石河子、阿克苏及喀什棉田土壤耕层的pH、盐分、有机质、全氮、速效磷、速效钾及Cr、Cu、Zn、As、Pb 共计11个指标,综合分析土壤理化性质和重金属含量,采用土壤质量综合指数(SQI)对新疆主要棉区棉田土壤质量进行综合评价.结果表明: 新疆棉区棉田土壤呈碱性,pH均值为7.87,盐分含量均值为3.44 g·kg-1,为轻度盐化土壤,有机质和全氮含量均偏低,速效磷、速效钾含量较为丰富,与第二次全国土壤普查数据相比,土壤pH、盐分含量、有机质和全氮均呈下降趋势,土壤速效磷明显增长,部分地区土壤速效钾呈现出不同程度的升高趋势;Cr、Cu、Zn、As、Pb 5种重金属含量分别为45.88、40.66、68.30、12.88、16.68 mg·kg-1,均未超过国家二级标准,但与新疆土壤元素背景值相比,Cu、Zn、As均有累积现象.当重金属内梅罗综合污染指数(PN)小于0.5时,土壤理化性质越好,土壤综合质量越好.土壤有机质、全氮、Cu、Zn和As是影响新疆棉区棉田土壤质量的重要因素.新疆棉区棉田土壤质量总体属于中等水平,昌吉、奎屯质量最高,SQI为0.52,阿克苏质量最低,SQI为0.31,不同棉区土壤质量呈现为:北疆>东疆>南疆.
Lily (Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases (CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellular space, are key enzymes participating in sucrose allocation in higher plants. Previous studies have shown that CWINs play an essential role in bulblet initiation process in bulbous crops, but the underlying molecular mechanism remains unclear. Here, a CWIN gene of Lilium brownii var. giganteum (Lbg) was identified and amplified from genomic DNA. Quantitative RT-PCR assays revealed that the expression level of LbgCWIN1 was highly upregulated exactly when the endogenous starch degraded in non-sucrose medium during in vitro bulblet initiation in Lbg. Phylogenetic relationship, motif, and domain analysis of LbgCWIN1 protein and CWINs in other plant species showed that all sequences of these CWIN proteins were highly conserved. The promoter sequence of LbgCWIN1 possess a number of alpha-amylase-, phytohormone-, light- and stress-responsive cis-elements. Meanwhile, β-glucuronidase (GUS) assay showed that the 459 bp upstream fragment from the translational start site displayed maximal promoter activity. These results revealed that LbgCWIN1 might function in the process of in vitro bulblet initiation and be in the response to degradation of endogenous starch.
Soil organic carbon (SOC) largely influences soil quality and sustainability. The effects of no-till (NT) and crop straw return practices (SR) on soil organic carbon sequestration have been well documented. However, the mechanism of soil bacterial community in regulating soil organic carbon under NT and SR remains unclear. In this study, we investigated the impacts of tillage (conventional tillage (CT) and NT) and crop straw return practices (crop straw removal (NS) and SR) on topsoil layer (0–5 cm) bacterial community, CH4 and CO2 emissions and SOC fractions in rice-wheat cropping system. Overall, in the wheat season following the annual rice-wheat rotation in two cycles, NT significantly increased SOC by 4.4% for 1–2 mm aggregates in the 0–5 cm soil layer, but decreased CO2 emissions by 7.4%. Compared with NS, SR notably increased the contents of SOC in the topsoil layer by 6.5% and in macro-aggregate by 17.4% in 0–5 cm soil layer, and promoted CH4 emissions (by 22.3%) and CO2 emissions (by 22.4%). The combination of NT and NS resulted in relatively high SOC and low CH4 emissions along with high bacterial community abundance. The most abundant genus under different treatments was Gp6, which significant impacted SOC and MBC. Bacterial communities like Subdivision3 had the most impact on CH4 emissions. Structural equation modeling further suggested that the soil bacterial community indirectly mediated the SOC through balancing SOC in 1–2 mm aggregates and CH4 emissions. This study provides a new idea to reveal the mechanism of short-term tillage and straw return on SOC.
Trehalose-6-phosphate phosphatase (TPP) is a pivotal enzyme in trehalose biosynthesis which plays an essential role in plant development and in the abiotic stress response. However, little is currently known about TPPs in groundnut. In the present study, a total of 16 AhTPP genes were identified, and can be divided into three phylogenetic subgroups. AhTPP members within the same subgroups generally displayed similar exon–intron structures and conserved motifs. Gene collinearity analysis revealed that segmental duplication was the primary factor driving the expansion of the AhTPP family. An analysis of the upstream promoter region of AhTPPs revealed eight hormone- and four stress-related responsive cis-elements. Transcriptomic analysis indicated high expression levels of AhTPP genes in roots or flowers, while RT-qPCR analysis showed upregulation of the six tested genes under different abiotic stresses, suggesting that AhTPPs play roles in growth, development, and response to various abiotic stresses. Subcellular localization analysis showed that AhTPP1A and AhTPP5A were likely located in both the cytoplasm and the nucleus. To further confirm their functions, the genes AhTPP1A and AhTPP5A were individually integrated into yeast expression vectors. Subsequent experiments demonstrated that yeast cells overexpressing these genes displayed increased tolerance to osmotic and salt stress compared to the control group. This study will not only lay the foundation for further study of AhTPP gene functions, but will also provide valuable gene resources for improving abiotic stress tolerance in groundnut and other crops.
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