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Diversity in metagenomic sequences reveals new pathogenic fungus associated with smut in Job’s tears
LI Xiang-dong, SHI Ming, PAN Hong, LU Xiu-juan, WEI Xin-yuan, LU Ping, LIAN Qi-xian, FU Yu-hua
2020, 19 (9): 2257-2264.   DOI: 10.1016/S2095-3119(20)63164-1
Abstract128)      PDF in ScienceDirect      
Smut is a serious disease in Job’s tears, also known as adlay, and contributes to the reduction of crop yield in agricultural fields.  In this study, the key pathogenic fungi in adlay smut disease were first identified by internal transcribed spacer region (ITS) high-throughput sequencing and then used to elucidate the composition and diversity of the fungal community in adlay smut.  Results indicate that an abundance of operational taxonomic units (OTUs) were detected in the infected involucres of flowering plants and the OTUs were classified to nine phyla, 20 classes, 45 orders, 90 families and 119 genera.  A total of 4 986 OTUs clustered together, sharing six core OTUs in all samples, while 145 OTUs were shared among four geographical groups.  The Shannon and Simpson indices ranged from 0.137–1.629 and 0.357–0.970, respectively.  Community diversity ranked as Anshun (AS)>Qinglong (QL)>Xingren (XR)>Xingyi (XY) among the four geographical groups by Shannon and Simpson indices, exhibiting complex community diversities among accessions and geographical groups.  The richness and diversity data imply a weak relationship between the accession community richness and geographical origins of samples.  Two closely related fungal genera, Sporisorium and Ustilago, were implicated as causes of smut disease.  The genus Sporisorium appears to be more commonly found among accessions and thus is more likely to be the fungal pathogen causing smut in adlay.  This work can facilitate strategies to control and prevent smut infection to improve adlay yield.
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Morphological diversity and correlation analysis of phenotypes and quality traits of proso millet (Panicum miliaceum L.) core collections
ZHANG Da-zhong, Rabia Begum Panhwar, LIU Jia-jia, GONG Xiang-wei, LIANG Ji-bao, LIU Minxuan, LU Ping, GAO Xiao-li, FENG Bai-li
2019, 18 (5): 958-969.   DOI: 10.1016/S2095-3119(18)61997-5
Abstract208)      PDF in ScienceDirect      
Genetic diversity and comprehensive performance are the basis for the discovery and efficient use of proso millet (Panicum miliaceum L.) core collections.  In this study, 386 proso millet core collections were used as materials to observe inflorescence color, leaf phase, inflorescence density, axis shape, branched spike length, panicle type, trichome, measured area of the top3 leaves, and chlorophyll content of the top3 leaves at filling stage.  These core collections were also used to record growth period, plant height, diameter of main stem, plant tiller number, branch number, panicle length, panicle number per plant, and panicle weight per plant at the maturation stage.  Starch, fat, protein, and yellow pigment contents in the grain and 1 000-seed weight were also measured after harvest.  Then, quantitative traits were used for diversity analysis and comprehensive evaluation of each collection.  Correlations between all traits were also analyzed.  Results showed that among the 8 quality traits, the Shannon index (H´) of hull color was the highest (1.588) followed by the H´ of inflorescence density (0.984).  However, inflorescence color and axis shape were lower.  The H´ of 16 quantitative traits were significantly higher than the quality traits with the following traits having the highest indices: fat content (2.092), 1 000-seed weight (2.073), top3 leaves area (2.070), main stem diameter (2.056), and plant height (2.052).  Furthermore, all other traits had a diversity higher than 1.900.  After a comprehensive evaluation of phenotypic traits, plant height, diameter of main stem, plant tiller number, leaf area of top3 leaves, and 1 000-seed weight were the biggest contributors to the principal components.  Six high-fat and high-protein cultivars, including Nuoshu, A75-2, Zhiduoaosizhi, Panlonghuangmi, Xiaobaishu, and Xiaohongshu were also screened.  Correlations between the quantitative traits were significant, including the correlation between quality traits and quantitative traits.  In conclusion, the core collections can be used as basis for discriminating among proso millet cultivars based on related traits and for further studies on millet with rich genetic diversity, good representation, and significant collection between traits.
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Molecular mapping of YrTZ2, a stripe rust resistance gene in wild emmer accession TZ-2 and its comparative analyses with Aegilops tauschii
WANG Zhen-zhong, XIE Jing-zhong, GUO Li, ZHANG De-yun, LI Gen-qiao, FANG Ti-lin, CHEN Yongxing, LI Jun, WU Qiu-hong, LU Ping, LI Miao-miao, WU Hai-bin, ZHANG Huai-zhi, ZHANG Yan, YANG Wu-yun, LUO Ming
2018, 17 (06): 1267-1275.   DOI: 10.1016/S2095-3119(17)61846-X
Abstract475)      PDF in ScienceDirect      
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease that can cause severe yield losses.  Identification and utilization of stripe rust resistance genes are essential for effective breeding against the disease.  Wild emmer accession TZ-2, originally collected from Mount Hermon, Israel, confers near-immunity resistance against several prevailing Pst races in China.  A set of 200 F6:7 recombinant inbred lines (RILs) derived from a cross between susceptible durum wheat cultivar Langdon and TZ-2 was used for stripe rust evaluation.  Genetic analysis indicated that the stripe rust resistance of TZ-2 to Pst race CYR34 was controlled by a single dominant gene, temporarily designated YrTZ2.  Through bulked segregant analysis (BSA) with SSR markers, YrTZ2 was located on chromosome arm 1BS flanked by Xwmc230 and Xgwm413 with genetic distance of 0.8 cM (distal) and 0.3 cM (proximal), respectively.  By applying wheat 90K iSelect SNP genotyping assay, 11 polymorphic loci (consisting of 250 SNP markers) closely linked to YrTZ2 were identified.  YrTZ2 was further delimited into a 0.8-cM genetic interval between SNP marker IWB19368 and SSR marker Xgwm413, and co-segregated with SNP marker IWB28744 (co-segregated with 28 SNP).  Comparative genomics analyses revealed high level of collinearity between the YrTZ2 genomic region and the orthologous region of Aegilops tauschii 1DS.  The genomic region between loci IWB19368 and IWB31649 harboring YrTZ2 is orthologous to a 24.5-Mb genomic region between AT1D0112 and AT1D0150, spanning 15 contigs on chromosome 1DS.  The genetic and comparative maps of YrTZ2 provide a framework for map-based cloning and marker-assisted selection of YrTZ2.
 
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Evaluation of selenium and carotenoid concentrations of 200 foxtail millet accessions from China and their correlations with agronomic performance
LIU Min-xuan, ZHANG Zong-wen, REN Gui-xing, ZHANG Qi, WANG Yin-yue, LU Ping
2016, 15 (7): 1449-1457.   DOI: 10.1016/S2095-3119(15)61160-1
Abstract1950)      PDF in ScienceDirect      
    As selenium and carotenoids are essential micronutrients, the determination of their concentrations in different varieties is important in the breeding of foxtail millet (Setaria italica L. P. Beauv.). To identify selenium- and carotenoid-enriched foxtail millet varieties and to analyze correlations between trace elements and agronomic traits, we measured the selenium and carotenoid concentrations of 200 Chinese accessions by high-performance liquid chromatography and atomic fluorescence spectrometry. Our analysis revealed that lutein concentration in 200 foxtail millet accessions followed normal distribution and average was 3.1 μg g–1. The mean value of zeaxanthin concentration in 200 accessions was 8.6 μg g–1. Lutein and zeaxanthin concentrations were higher in the foxtail millet from Liaoning than in varieties from other locations, with averages of 10.0 and 3.5 μg g–1, respectively. The average measured selenium concentration was 100.3 μg kg–1. The highest average selenium concentration, 110.3 μg kg–1, was found in varieties from Shanxi. Varieties from Inner Mongolia had the lowest average selenium concentration, 84.7 μg kg–1, which was significantly lower (P<0.05) than that of Shanxi. Selenium concentrations of 23 varieties were higher than 117.9 μg kg–1, accounting for 11.5% of the total, thereby were considered to be enriched in selenium. In addition, we identified 29 lutein-enriched varieties (>4.27 μg g–1) and 30 zeaxanthin-enriched ones (>12.63 μg g–1), which corresponded to 14.5 and 15% of tested accessions, respectively. Correlation analysis revealed that selenium concentration was significantly positively correlated with spikelet length (P<0.01), while zeaxanthin concentration was significantly correlated with grass weight (P<0.05) and spikelet length (P<0.01). No correlation was found between lutein concentration and agronomic characters, selenium content or zeaxanthin content. Our results should contribute substantially to the selection of suitable varieties for the development of plants with desired levels of these nutritionally important elements. These results will significantly contribute towards selection of the most suitable varieties for obtaining plants with desired levels of these nutritionally important elements.
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Soil Insect Diversity and Abundance Following Different Fertilizer Treatments on the Loess Plateau of China
LIN Ying-hua, LU Ping, YANG Xue-yun , ZHANG Fu-dao
2013, 12 (9): 1644-1651.   DOI: 10.1016/S2095-3119(13)60562-6
Abstract1539)      PDF in ScienceDirect      
The presence of abundant and diverse communities of macro-arthropods is considered an indicator of sustainability in agroecosystems. This study was designed to investigate the effects of different fertilizer treatments on abundance and diversity of insects of arable loess soil on the Loess Plateau of China. These regimes included a control with no fertilizer addition or manure, treatments with application of mineral fertilizers (N, NK, NP, PK, NPK), treatments with NPK in combination with organic materials such as wheat straw or maize stalk, treatments with two rates of organic manure application; and different crop rotations (Rot.1: winter wheat summer maize; Rot.2: winter wheat summer maize soybean intercropping; and Rot.3: winter wheat or rapeseed summer maize soybean intercropping). Soil macro-arthropods were collected from the plough layer (0-20 cm) and sorted by hand after each harvest in June and October 2001 and 2002. A total of 3 132 individuals were collected, from 7 orders and 55 families, dominated by Formicidae (61.72%) and Staphylinidae (14.24%). The results showed that individuals and groups were significantly influenced by sampling dates, while groups were significantly influenced by the fertilization treatments. Soil insect biodiversity, as determined by the Shannon index, was significantly influenced by fertilization and sampling dates. The abundance of soil insects was positively and significantly correlated with soil moisture content in October 2002. Nitrogen, phosphorus and potassium fertilizers and incorporation of organic materials were favorable factors for abundance and diversity in arable loess soil.
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