Person: Chuanxiao Xie
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Chuanxiao Xie
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Chuanxiao Xie
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0000-0003-3425-0211 10 results
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- Pollen self-elimination CRISPR–Cas genome editing prevents transgenic pollen dispersal in maize(Cell Press, 2023) Honglin Wang; Xiantao Qi; Jinjie Zhu; Changlin Liu; Hongwei Fan; Xuecai Zhang; Xinhai Li; Qin Yang; Chuanxiao Xie
Publication - Crop genome editing: a way to breeding by design(Elsevier, 2020) Chuanxiao Xie; Yunbi Xu; Jianmin Wan
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 - Fast diffusion of domesticated maize to temperate zones(Nature Publishing Group, 2017) Xiaolong Li; Yinqiao Jian; Chuanxiao Xie; Jun Wu; Yunbi Xu; Cheng ZouAdaptation to a temperate climate was a prerequisite for the spread of maize across a broad geographical range. To explicitly explore the demographic process underlying maize adaptation, we used a diffusion-based method to model the differentiation between temperate and tropical populations using the Non-Stiff Stalk group as a proxy for temperate maize. Based on multiple sequential Markovian coalescent approaches, we estimate that tropical and temperate maize diverged approximately 3‚000 to 5‚000 years ago and the population size shrank after the split. Using composite likelihood approaches, we identified a distinct tropical-temperate divergence event initiated 4‚958 years ago (95% confidence interval (CI): 4‚877–5‚039) from an ancestral population whose effective size was 24,162 (95% CI: 23,914–24,409). We found that continuous gene flow between tropical and temperate maize accompanied the differentiation of temperate maize. Long identical-by-descent tracts shared by tropical and temperate inbred lines have been identified, which might be the result of gene flow between tropical and temperate maize or artificial selection during domestication and crop improvement. Understanding the demographic history of maize diffusion not only provides evidence for population dynamics of maize, but will also assist the identification of regions under selection and the genetic basis of complex traits of agronomic importance.
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 - Development of a maize 55 K SNP array with improved genome coverage for molecular breeding(Springer Verlag, 2017) Cheng Xu; Yonghong Ren; Yinqiao Jian; Zifeng Guo; Zhang, Y.; Chuanxiao Xie; Junjie Fu; Hongwu Wang; Guoying Wang; Yunbi Xu; Zhang Li-Ping; Cheng ZouWith the decrease of cost in genotyping, single nucleotide polymorphisms (SNPs) have gained wide acceptance because of their abundance, even distribution throughout the maize (Zea mays L.) genome, and suitability for high-throughput analysis. In this study, a maize 55 K SNP array with improved genome coverage for molecular breeding was developed on an Affymetrix® Axiom® platform with 55,229 SNPs evenly distributed across the genome, including 22,278 exonic and 19,425 intronic SNPs. This array contains 451 markers that are associated with 368 known genes and two traits of agronomic importance (drought tolerance and kernel oil biosynthesis), 4067 markers that are not covered by the current reference genome, 734 markers that are differentiated significantly between heterotic groups, and 132 markers that are tags for important transgenic events. To evaluate the performance of 55 K array, we genotyped 593 inbred lines with diverse genetic backgrounds. Compared with the widely-used Illumina® MaizeSNP50 BeadChip, our 55 K array has lower missing and heterozygous rates and more SNPs with lower minor allele frequency (MAF) in tropical maize, facilitating in-depth dissection of rare but possibly valuable variation in tropical germplasm resources. Population structure and genetic diversity analysis revealed that this 55 K array is also quite efficient in resolving heterotic groups and performing fine fingerprinting of germplasm. Therefore, this maize 55 K SNP array is a potentially powerful tool for germplasm evaluation (including germplasm fingerprinting, genetic diversity analysis, and heterotic grouping), marker-assisted breeding, and primary quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) for both tropical and temperate maize.
Publication - Zea mays (L.) P1 locus for cob glume color identified as a post-domestication selection target with an effect on temperate maize genomes(Elsevier, 2013) Chuanxiao Xie; Jianfeng Weng; Wenguo Liu; Cheng Zou; Zhuanfang Hao; Wenxue Li; Minshun Li; Xiaosen Guo; Gengyun Zhang; Yunbi Xu; Xinhai Li; Shihuang ZhangArtificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study (GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a ; log10P value for surrounding SNPs higher than the Bonferroni threshold ( < 0.001) when a mixed linear model (MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium (LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of ; and Tajima's D were significantly (P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing (180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.
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