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Using UAV-Based Temporal Spectral Indices to Dissect Changes in the Stay-Green trait in Wheat

Plant Phenomics 2024年第3期6卷 517-531页

作者： Rui Yu Xiaofeng Cao Jia Liu Ruiqi Nie Chuanliang Zhang Meng Yuan Yanchuan Huang Xinzhe Liu Weijun Zheng Changfa Wang Tingting Wu Baofeng Su Zhensheng Kang Qingdong Zeng Dejun Han Jianhui Wu College of Agronomy Northwest A&F UniversityYanglingShaanxi 712100China State Key Laboratory of Crop Stress Resistance and High-Efficiency Production Northwest A&F UniversityYanglingShaanxi 712100China College of Mechanical and Electronic Engineering Northwest A&F UniversityYanglingShaanxi 712100China College of Plant Protection Northwest A&F UniversityYanglingShaanxi 712100China

Stay-green(SG)in wheat is a beneficial trait that increases yield and stress ***,conventional phenotyping techniques limited the understanding of its genetic *** indices(SIs)as non-destructive tools to evaluate crop temporal senescence provide an alternative ***,we applied Sls to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages over 2 field *** Sis(normalized difference vegetation index,green normalized difference vegetation index,normalized difference red edge index,and optimized soil-adjusted vegetation index)were normalized to develop relative stay-green scores(RSGS)as the SG *** RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci(QTL)harboring 3,079 single-nucleotide polymorphisms associated with SG and 1,085 corresponding candidate *** them,15 QTL overlapped or were adjacent to known SG-related QTL/genes,while the remaining QTL were ***,a set of favorable haplotypes of SG-related candidate genes such as TraesCS2A03G1081100,TracesCS6B03G0356400,and TracesCS2B03G1299500 are increasing following the Green Revolution,further validating the feasibility of the *** study provided a valuable reference for further quantitative SG and genetic research in diverse wheat panels.

关键词： changes dissect indices spectral stay-green temporal trait uav-based using wheat

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Sequential Recommendation via Cross-Domain Novelty Seeking trait Mining

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Journal of Computer Science & Technology 2020年第2期35卷 305-319页

作者： Fu-Zhen Zhuang Ying-Min Zhou Hao-Chao Ying Fu-Zheng Zhang Xiang Ao Xing Xie Qing He Hui Xiong Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences Institute of Computing Technology Chinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China School of Public Health Zhejiang University School of MedicineHangzhou 310027China Meituan-Dianping Group Beijing 100102China Microsoft Research Asia Beijing 100080China Department of Management Science and Information Systems Rutgers UniversityNew Jersey 07102U.S.A.

Transfer learning has attracted a large amount of interest and research in last decades, and some effort has been made to build more precise recommendation systems. Most previous transfer recommendation systems assume that the target domain shares the same/similar rating patterns with the auxiliary source domain, which is used to improve the recommendation performance. However, almost all existing transfer learning work does not consider the characteristics of sequential data. In this paper, we study the new cross-domain recommendation scenario by mining novelty-seeking trait. Recent studies in psychology suggest that novelty-seeking trait is highly related to consumer behavior, which has a profound business impact on online recommendation. Previous work performed on only one single target domain may not fully characterize users' novelty-seeking trait well due to the data scarcity and sparsity, leading to the poor recommendation performance. Along this line, we propose a new cross-domain novelty-seeking trait mining model (CDNST for short) to improve the sequential recommendation performance by transferring the knowledge from auxiliary source domain. We conduct systematic experiments on three domain datasets crawled from Douban to demonstrate the effectiveness of our proposed model. Moreover, we analyze the directed influence of the temporal property at the source and target domains in detail.

关键词： sequential recommendation novelty-seeking trait transfer learning

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trait associations in common bean genotypes grown under drought stress and field infestation by BSM bean fly

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The Crop Journal 2015年第4期3卷 305-316页

作者： Daniel Ambachew Firew Mekbib Asrat Asfaw Stephen E.Beebe Matthew W.Blair South Agricultural Research Institute(SARI) Haramaya University International Potato Center (CIP) International Center for Tropical Agriculture (CIAT) Tennessee State University (TSU)

Understanding functional relations among plant traits and their modulation by growing conditions is imperative in designing selection strategies for breeding programs. This study assessed trait relationships among 196 common bean genotypes exposed to stresses for drought and field infestation of bean fly or bean stem maggot(BSM). The study was carried out at two locations and data was analyzed with linear correlation, path coefficient and genotype × trait biplot analyses. Multiple trait data related to mechanisms of drought and bean fly tolerance were collected on 196 genotypes grown under i) water deficit at mid-pod fill, or ii) unprotected against bean fly; iii) irrigated, well watered conditions, or iv) bean fly protection with chemicals. Seed yield exhibited positive and significant correlations with leaf chlorophyll content, vertical root pulling resistance, pod harvest index, pods per plant and seeds per pod at both phenotypic and genotypic levels under stress and non-stress conditions. Genotypic correlations of traits with seed yield were greater than their respective phenotypic correlations across environments indicating the greater contribution of genotypic factors to the trait correlation. Pods per plant and seeds per pod had high positive direct effects on seed yield both under stress and non-stress whereas pods per plant had the highest indirect effect on seed yield through pod harvest index under *** general, our results suggest that vertical root pulling resistance and pod harvest index are important selection objectives for improving seed yield in common beans under non-stress and stress conditions, and particularly useful for drought and BSM tolerance evaluation.

关键词： Bean stem maggot(BSM) Path coefficient Selection objective trait linkage Pleiotropism

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Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony (Paeonia suffruticosa Andrews) breeding population

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Horticulture Research 2023年第7期10卷 206-220页

作者： Liping Peng Yang Li Wanqing Tan Shangwei Wu Qing Hao Ningning Tong Zhanying Wang Zheng’an Liu Qingyan Shu Key Laboratory of Plant Resources Institute of Botanythe Chinese Academy of SciencesBeijing 100093China China National Botanical Garden Beijing 100093China College of Life Science University of Chinese Academy of SciencesBeijing 100049China College of Landscape Architecture and Forestry Qingdao Agricultural UniversityQingdao 266109China Peony Research Institute Luoyang Academy of Agricultural and Forestry SciencesLuoyang 471000China

Great progress has been made in our understanding of floral organ identity determination and its regulatory network in many species;however,the quantitative genetic basis of floral organ number variation is far less well understood for species-specific traits from the perspective of population ***,using a tree peony(Paeonia suffruticosa Andrews,Paeoniaceae)cultivar population as a model,the phenotypic polymorphism and genetic variation based on genome-wide association studies(GWAS)and expression quantitative trait locus(eQTL)analysis were *** on 24 phenotypic traits of 271 representative cultivars,the transcript profiles of 119 cultivars were obtained,which indicated abundant genetic variation in tree *** total,86 GWAS-related cis-eQTLs and 3188 trans-eQTL gene pairs were found to be associated with the numbers of petals,stamens,and *** addition,19 floral organ number-related hub genes with 121 cis-eQTLs were obtained by weighted gene co-expression network analysis,among which five hub genes belonging to the ABCE genes of the MADS-box family and their spatial–temporal co-expression and regulatory network were *** results not only help our understanding of the genetic basis of floral organ number variation during domestication,but also pave the way to studying the quantitative genetics and evolution of flower organ number and their regulatory network within populations.

关键词： cultivar breeding trait

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trait complementarity between fine roots of Stipa purpurea and their associated arbuscular mycorrhizal fungi along a precipitation gradient in Tibetan alpine steppe

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Journal of Mountain Science 2019年第3期16卷 542-547页

作者： ZHANG Jing WANG Ping XUE Ka HAO Yan-bin WANG Yan-fen CUI Xiao-yong College of Life Sciences University of Chinese Academy of Sciences College of Forestry Beijing Forestry University College of Resources and Environment University of Chinese Academy of Sciences

Development of fine roots and formation of symbiosis with arbuscular mycorrhizal(AM) fungi represent two strategies for plants to acquire nutrient and water from soil. Here, we elucidated how fine root development and symbolized mycorrhizal fungi with Stipa purpurea responded to the precipitation change in Tibetan alpine steppe ecosystem across a precipitation gradient from 50 mm to 400 mm. As precipitation increased, the proportion of thinner fine roots(diameter < 0.4 mm) in total roots increased significantly; while the mycorrhizal colonization percentage, either associated with thinner or thicker roots, decreased. This phenomenon indicated that fine root development and symbolized mycorrhizal fungi are likely alternative, and plant preferred to develop fine root rather than build a symbiotic relationship with mycorrhizal fungi in more benign niches with higher precipitation. Also, root diameter was negatively correlated with specific root length(SRL), but positively correlated with AM fungal colonization percentage, indicating thicker-root species rely more on mycorrhizal fungi in alpine steppe. The complementarity between fine root and mycorrhizal fungi of S. purpurea is mediated by precipitation in Tibetan alpine steppe.

关键词： Arbuscular mycorrhizal fungal colonization Root diameter trait complementarity Precipitation Stipa purpurea Alpine steppe

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Fine-Mapping of qTGW1.2a, a Quantitative trait Locus for 1000-Grain Weight in Rice

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Rice science 2019年第4期26卷 220-228,I0002-I0004,I0010,I0015页

作者： WANG Wenhui WANG Linlin ZHU Yujun FAN Yeyang ZHUANG Jieyun State Key Laboratory of Rice Biology/Chinese National Center for Rice Improvement China National Rice Research Institute

Thousand-grain weight (TGW) is a key component of grain yield in rice. This study was conducted to validate and fine-map qTGW1.2a, a quantitative trait locus for grain weight and grain size previously located in a 933.6-kb region on the long arm of rice chromosome 1. Firstly, three residual heterozygotes (RHs) were selected from a BC2F11 population of the indica rice cross Zhenshan 97 (ZS97)///ZS97//ZS97/Milyang 46. The heterozygous segments in these RHs were arranged successively in physical positions, forming one set of sequential residual heterozygotes (SeqRHs). In each of the populations derived, non-recombinant homozygotes were identified to produce near isogenic lines (NILs) comprising the two homozygous genotypes. The NILs were tested for grain weight, grain length and grain width. QTL analyses for the three traits were performed. Then, the updated QTL location was followed for a new run of SeqRHs identification-NIL development-QTL mapping. Altogether, 11 NIL populations derived from four sets of SeqRHs were developed and used. qTGW1.2a was finally delimitated into a 77.5-kb region containing 13 annotated genes. In the six populations segregating this QTL, which were in four generations and were tested across four years, the allelic direction of qTGW1.2a remained consistent and the genetic effects were stable. For TGW, the additive effects ranged from 0.23 to 0.38 g and the proportions of phenotypic variance explained ranged from 26.15% to 41.65%. These results provide a good foundation for the cloning and functional analysis of qTGW1.2a.

关键词： fine mapping grain weight minor effect quantitative trait locus rice grain length grain width

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Interval mapping of quantitative trait loci by molecular markers in rice (Oryza sativa L.)

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Science China Chemistry 1995年第4期38卷 422-428页

作者：徐云碧申宗坦徐吉臣朱衡陈英朱立煌 Department of Agronomy Zhejiang Agricultural University Hangzhou 310029 China Institute of Genetics Chinese Academy of Sciences Beijing 100101 China

Using an F2 as the mapping population derived from indica Zhaiyeqing 8 and japonica Jingxi 17 of rice, a linkage map was constructed, which consisted of 54 restriction fragment length polymorphism (RFLP) markers. By using the interval mapping procedure based on 2 flanking markers, 11 quantitative trait loci (QTLs) were mapped for 4 traits: days to heading (Dth1), tiller angle (Ta1), spikelet number per panicle (Sn1, Sn2, Sn3) and spikelet density (Sdn1-Sdn6). An example was taken for QTL mapping of rice, and the interval mapping was shown to be able to detect the QTL located between 2 flanking markers. For a specific trait, more than one QTL could be found on one chromosome. Genetically related traits could be controlled by the same group of QTLs or polygenic system.

关键词： rice (Oryza sativa L.) restriction fragment length polymorphism (RFLP) quantitative trait loci (QTLs) linkage mapping.

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Identification of Stable Quantitative trait Loci for Sheath Blight Resistance Using Recombinant Inbred Line

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Rice science 2019年第5期26卷 331-338页

作者： CHEN Yuan ZENG Yuxiang JI Zhijuan LIANG Yan WEN Zhihua YANG Changdeng State Key Laboratory of Rice Biology China National Rice Research Institute

To identify stable quantitative trait loci(QTLs)responsible for sheath blight resistance,a recombinant inbred line mapping population consisting of 219 lines was developed by crossing Lemont and Yangdao *** disease rating,average lesion length,maximum disease rating and maximum lesion length were assayed in six different environments.A total of 128 minor effect QTLs were detected by multiple interval *** QTLs explained less than 11.2%of the phenotypic variations individually,and 106 QTLs were clustered in 20 QTL-rich regions/putative *** QTL×environment interactions were detected at three putative loci(qSBR11.1,qSBR11.2 and qSBR11.3),indicating that these three loci were not *** other 17 stable loci(qSBR1.1,qSBR1.2,qSBR2.1,qSBR2.3,qSBR3.1,qSBR3.2,qSBR3.5,qSBR3.6,qSBR5.1,qSBR7.1,qSBR8.1,qSBR9.1,qSBR9.2,qSBR9.3,qSBR12.1,qSBR12.2 and qSBR12.4)provided a foundation for marker-assisted selection in *** of allelic effect on the 20 putative loci identified 7 highly stable loci,including qSBR3.2,qSBR7.1,qSBR8.1,qSBR9.2,qSBR9.3,qSBR12.1 and qSBR12.2.

关键词： rice sheath blight resistance quantitative trait locus recombinant inbred line

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Association Mapping of Quantitative trait Loci for Grain Size in Introgression Line Derived from Oryza rufipogon

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Rice science 2020年第3期27卷 246-254页

作者： Kashif HUSSAIN ZHANG Yingxing Workie ANLEY Aamir RIAZ Adil ABBAS MdHasanuzzaman RANI WANG Hong SHEN Xihong CAO Liyong CHENG Shihua Key Laboratory for Zhejiang Super Rice Research&State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China Southern Rice Research Institute Thatta Agriculture Research WingGovernment of SindhSindh 73130Pakistan Department of Plant Sciences University of GondarP.O.Box 196Ethiopia Bangladesh Institute of Nuclear Agriculture Dhaka 2202Bangladesh

Grain size is one of the critical agronomic traits governing grain yield and quality in ***,the underlying genetic mechanisms that control grain size in rice are poorly *** used an introgression line derived from Zhonghui 8015 and Oryza rufipogon *** introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain ***-wide association study(GWAS)was performed using 28193 SNPs through a general linear model,and 56 significant SNPs on different loci associated with the 4 grain size traits were *** genes including GS3 and q GL3 showed substantial effects on grain length and *** new stable loci were identified with pleiotropic effects on grain ***,gene expression analyses,combined gene-based associations,and functional annotations permitted the shortlisting of important dominant genes including GS3 and q GL3.

关键词： grain size association mapping Oryza sativa Oryza rufipogon quantitative trait locus genome-wide association analysis

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High-density SNP genetic linkage map construction and quantitative trait locus mapping for resistance to cucumber mosaic virus in tobacco(Nicotiana tabacum L.)

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The Crop Journal 2019年第4期7卷 539-547页

作者： Lirui Cheng Xiaocui Chen Caihong Jiang Bing Ma Min Ren Yazeng Cheng Dan Liu Ruimei Geng Aiguo Yang Key Laboratory of Tobacco Genetic Improvement and Biotechnology Tobacco Research Institute Chinese Academy of Agricultural Sciences Qingdao 266100 Shandong China Key Laboratory of Zunyi Crop Gene Resource and Germplasm Innovation Zunyi Academy of Agricultural Sciences Zunyi 563006 Guizhou China

Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco.

关键词： Single nucleotide polymorphism Genetic linkage map Tobacco Cucumber mosaic virus Quantitative trait loci

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