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Yunbi Xu

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Yunbi Xu
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Yunbi Xu

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Now showing 1 - 9 of 9
  • 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 Xu
    Genomic 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.
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  • Maize (Zea mays L.) genome size indicated by 180-bp knob abundance is associated with flowering time
    (Nature Publishing Group, 2017) Yinqiao Jian; Cheng Xu; Zifeng Guo; Shanhong Wang; Yunbi Xu; Cheng Zou
    Flowering time is considered one of the most important agronomic traits in maize (Zea mays L.), and previous studies have indicated that this trait is correlated with genome size. We observed a significant difference in genome size between tropical and temperate inbred lines and a moderate positive correlation between genome size and 180-bp knob abundance determined by high-throughput sequencing in maize inbred lines in this study. We assembled the reads that were mapped to 180-bp knob sequences and found that the top ten abundant 180-bp knob sequences are highly variable. Moreover, our results indicate that genome size is associated with the flowering time of both male and female flowers, in both tropical and temperate inbred lines and under both tropical and temperate environments. To identify loci associated with genome size, we performed a genome-wide association study. The analysis identified three genomic regions associated with genome size, of which two were novel while the third one is located close to the known knobs K8L1 and K8L2. Overall, our results indicate that selection for breeding materials with earlier flowering times can be assisted by choosing germplasms with smaller genome sizes and that genome size can be determined based on the abundance of 180-bp knobs
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  • Fast diffusion of domesticated maize to temperate zones
    (Nature Publishing Group, 2017) Xiaolong Li; Yinqiao Jian; Chuanxiao Xie; Jun Wu; Yunbi Xu; Cheng Zou
    Adaptation 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.
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  • Identification and functional characterization of the AGO1 ortholog in maize
    (Wiley, 2016) Dongdong Xu; Hailong Yang; Cheng Zou; Wen-Xue Li; Yunbi Xu; Chuanxiao Xie
    Eukaryotic 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.
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  • 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 Li
    Background 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.
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  • Bulked sample analysis in genetics, genomics and crop improvement
    (Wiley Open Access, 2016) Cheng Zou; Pingxi Wang; Yunbi Xu
    Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
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  • 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 Xu
    Various 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.
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  • 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 Zou
    With 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 Zhang
    Artificial 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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