Person: Wen-Xue Li
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Wen-Xue Li
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Wen-Xue Li
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0000-0002-5652-7560 7 results
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- Factors affecting genomic selection revealed by empirical evidence in maize(Elsevier, 2018) Xiaogang Liu; Hongwu Wang; Hui Wang; Zifeng Guo; Xiaojie Xu; Jiacheng Liu; Shanhong Wang; Wen-Xue Li; Cheng Zou; Prasanna, B.M.; Olsen, M.; Changling Huang; Yunbi XuGenomic selection (GS) as a promising molecular breeding strategy has been widely implemented and evaluated for plant breeding, because it has remarkable superiority in enhancing genetic gain, reducing breeding time and expenditure, and accelerating the breeding process. In this study the factors affecting prediction accuracy (rMG) in GS were evaluated systematically, using six agronomic traits (plant height, ear height, ear length, ear diameter, grain yield per plant and hundred-kernel weight) evaluated in one natural and two biparental populations. The factors examined included marker density, population size, heritability, statistical model, population relationships and the ratio of population size between the training and testing sets, the last being revealed by resampling individuals in different proportions from a population. Prediction accuracy continuously increased as marker density and population size increased and was positively correlated with heritability; rMG showed a slight gain when the training set increased to three times as large as the testing set. Low predictive performance between unrelated populations could be attributed to different allele frequencies, and predictive ability and prediction accuracy could be improved by including more related lines in the training population. Among the seven statistical models examined, including ridge regression best linear unbiased prediction (RR-BLUP), genomic BLUP (GBLUP), BayesA, BayesB, BayesC, Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), and reproducing kernel Hilbert space (RKHS), the RKHS and additive-dominance model (Add + Dom model) showed credible ability for capturing non-additive effects, particularly for complex traits with low heritability. Empirical evidence generated in this study for GS-relevant factors will help plant breeders to develop GS-assisted breeding strategies for more efficient development of varieties.
Publication - Large-scale evaluation of maize germplasm for low-phosphorus tolerance(Public Library of Science, 2015) Hongwei Zhang; Ruineng Xu; Chuanxiao Xie; Changling Huang; Hong Liao; Yunbi Xu; Jiankang Wang; Wen-Xue LiLow-phosphorus (LP) stress is a global problem for maize production and has been exacerbated by breeding activities that have reduced the genetic diversity of maize. Although LP tolerance in maize has been previously evaluated, the evaluations were generally performed with only a small number of accessions or with samples collected from a limited area. In this research, 826 maize accessions (including 580 tropical/subtropical accessions and 246 temperate accessions) were evaluated for LP tolerance under field conditions in 2011 and 2012. Plant height (PH) and leaf number were measured at three growth stages. The normalized difference vegetation index (NDVI) and fresh ear weight (FEW) were also measured. Genetic correlation analysis revealed that FEW and NDVI were strongly correlated with PH, especially at later stages. LP-tolerant and -sensitive accessions were selected based on the relative trait values of all traits using principal component analysis, and all the 14 traits of the tolerant maize accessions showed less reduction than the sensitive accessions under LP conditions. LP tolerance was strongly correlated with agronomic performance under LP stress conditions, and both criteria could be used for genetic analysis and breeding of LP tolerance. Temperate accessions showed slightly better LP tolerance than tropical/subtropical ones, although more tolerant accessions were identified from tropical/subtropical accessions, which could be contributed by their larger sample size. This large-scale evaluation provides useful information, LP-tolerant germplasm resources and evaluation protocol for genetic analysis and developing maize varieties for LP tolerance.
Publication - Identification and functional characterization of the AGO1 ortholog in maize(Wiley, 2016) Dongdong Xu; Hailong Yang; Cheng Zou; Wen-Xue Li; Yunbi Xu; Chuanxiao XieEukaryotic Argonaute proteins play primary roles in miRNA and siRNA pathways that are essential for numerous developmental and biological processes. However, the functional roles of the four ZmAGO1 genes have not yet been characterized in maize (Zea mays L.). In the present study, ZmAGO1a was identified from four putative ZmAGO1 genes for further characterization. Complementation of the Arabidopsis ago1-27 mutant with ZmAGO1a indicated that constitutive overexpression of ZmAGO1a could restore the smaller rosette, serrated leaves, later flowering and maturation, lower seed set, and darker green leaves at late stages of the mutant to the wild-type phenotype. The expression profiles of ZmAGO1a under five different abiotic stresses indicated that ZmAGO1a shares expression patterns similar to those of Argonaute genes in rice, Arabidopsis, and wheat. Further, variation in ZmAGO1a alleles among diverse maize germplasm that resulted in several amino acid changes revealed genetic diversity at this locus. The present data suggest that ZmAGO1a might be an important AGO1 ortholog in maize. The results presented provide further insight into the function of ZmAGO1a.
Publication - Strand-specific RNA-Seq transcriptome analysis of genotypes with and without low-phosphorus tolerance provides novel insights into phosphorus-use efficiency in maize(BioMed Central, 2016) Qingguo Du; Kai Wang; Cheng Xu; Cheng Zou; Chuanxiao Xie; Yunbi Xu; Wen-Xue LiBackground Phosphorus (P) stress is a global problem in maize production. Although macro/microarray technologies have greatly increased our general knowledge of maize responses to P stress, a greater understanding of the diversity of responses in maize genotypes is still needed. Results In this study, we first evaluated the tolerance to low P of 560 accessions under field conditions, and selected the low P-tolerant line CCM454 and the low P-sensitive line 31778 for further research. We then generated 24 strand-specific RNA libraries from shoots and roots of CCM454 and 31778 that had been subjected to P stress for 2 and 8 days. The P deficiency-responsive genes common to CCM454 and 31778 were involved in various metabolic processes, including acid phosphatase (APase) activity. Determination of root-secretory APase activities showed that the induction of APase by P stress occurred much earlier in CCM454 than that in 31778. Gene Ontology analysis of differentially expressed genes (DEGs) and CAT/POD activities between CCM454 and 31778 under P-sufficient and -deficient conditions demonstrated that CCM454 has a greater ability to eliminate reactive oxygen species (ROS) than 31778. In addition, 16 miRNAs in roots and 12 miRNAs in shoots, including miRNA399s, were identified as DEGs between CCM454 and 31778. Conclusions The results indicate that the tolerance to low P of CCM454 is mainly due to the rapid responsiveness to P stress and efficient elimination of ROS. Our findings increase the understanding of the molecular events involved in the diversity of responses to P stress among maize accessions.
Publication - An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design(Nature Publishing Group, 2016) Yongping Zhao; Congsheng Zhang; Wenwen Liu; Wei Gao; Changlin Liu; Gaoyuan Song; Wen-Xue Li; Long Mao; Beijiu Cheng; Yunbi Xu; Xinhai Li; Chuanxiao XiePrecision DNA/gene replacement is a promising genome-editing tool that is highly desirable for molecular engineering and breeding by design. Although the CRISPR/Cas9 system works well as a tool for gene knockout in plants, gene replacement has rarely been reported. Towards this end, we first designed a combinatory dual-sgRNA/Cas9 vector (construct #1) that successfully deleted miRNA gene regions (MIR169a and MIR827a). The deletions were confirmed by PCR and subsequent sequencing, yielding deletion efficiencies of 20% and 24% on MIR169a and MIR827a loci, respectively. We designed a second structure (construct #2) that contains sites homologous to Arabidopsis TERMINAL FLOWER 1 (TFL1) for homology-directed repair (HDR) with regions corresponding to the two sgRNAs on the modified construct #1. The two constructs were co-transformed into Arabidopsis plants to provide both targeted deletion and donor repair for targeted gene replacement by HDR. Four of 500 stably transformed T0 transgenic plants (0.8%) contained replaced fragments. The presence of the expected recombination sites was further confirmed by sequencing. Therefore, we successfully established a gene deletion/replacement system in stably transformed plants that can potentially be utilized to introduce genes of interest for targeted crop improvement.
Publication - Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize(Nature Publishing Group, 2017) Hui Wang; Cheng Xu; Xiaogang Liu; Zifeng Guo; Xiaojie Xu; Shanhong Wang; Chuanxiao Xie; Wen-Xue Li; Cheng Zou; Yunbi XuVarious types of populations have been used in genetics, genomics and crop improvement, including bi- and multi-parental populations and natural ones. The latter has been widely used in genome-wide association study (GWAS). However, inbred-based GWAS cannot be used to reveal the mechanisms involved in hybrid performance. We developed a novel maize population, multiple-hybrid population (MHP), consisting of 724 hybrids produced using 28 temperate and 23 tropical inbreds. The hybrids can be divided into three subpopulations, two diallels and NC (North Carolina Design) II. Significant genetic differences were identified among parents, hybrids and heterotic groups. A cluster analysis revealed heterotic groups existing in the parental lines and the results showed that MHPs are well suitable for GWAS in hybrid crops. MHP-based GWAS was performed using 55 K SNP array for flowering time traits, days to tassel, days to silk, days to anthesis and anthesis-silking interval. Two independent methods, PEPIS developed for hybrids and TASSEL software designed for inbred line populations, revealed highly consistent results with five overlapping chromosomal regions identified and used for discovery of candidate genes and quantitative trait nucleotides. Our results indicate that MHPs are powerful in GWAS for hybrid-related traits with great potential applications in the molecular breeding era.
Publication - Cloning and characterization of maize miRNAs involved in responses to nitrogen deficiency(Public Library of Science, 2012) Meng Zhao; Huanhuan Tai; Suzhen Sun; Fusuo Zhang; Yunbi Xu; Wen-Xue LiAlthough recent studies indicated that miRNAs regulate plant adaptive responses to nutrient deprivation, the functional significance of miRNAs in adaptive responses to nitrogen (N) limitation remains to be explored. To elucidate the molecular biology underlying N sensing/signaling in maize, we constructed four small RNA libraries and one degradome from maize seedlings exposed to N deficiency. We discovered a total of 99 absolutely new loci belonging to 47 miRNA families by small RNA deep sequencing and degradome sequencing, as well as 9 new loci were the paralogs of previously reported miR169, miR171, and miR398, significantly expanding the reported 150 high confidence genes within 26 miRNA families in maize. Bioinformatic and subsequent small RNA northern blot analysis identified eight miRNA families (five conserved and three newly identified) differentially expressed under the N-deficient condition. Predicted and degradome-validated targets of the newly identified miRNAs suggest their involvement in a broad range of cellular responses and metabolic processes. Because maize is not only an important crop but is also a genetic model for basic biological research, our research contributes to the understanding of the regulatory roles of miRNAs in plant adaption to N-deficiency stress.
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