Xiaohong Yang

Xiaohong Yang
China Agricultural University | CAU · National Maize Improvement Center of China

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176
Publications
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Publications

Publications (176)
Article
A better understanding of the extent of convergent selection among crops could greatly improve breeding programs. We found that the quantitative trait locus KRN2 in maize and its rice ortholog, OsKRN2, experienced convergent selection. These orthologs encode WD40 proteins and interact with a gene of unknown function, DUF1644, to negatively regulate...
Article
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Background Maize ( Zea mays L. ssp. mays ) was domesticated from teosinte ( Zea mays ssp. parviglumis ) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication and adaptation processes over the past two decades, but efforts have been limited either in sample siz...
Article
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Starch is the most abundant storage carbohydrate in maize kernels and provides calories for humans and other animals as well as raw materials for various industrial applications. Decoding of the genetic basis of natural variation in kernel starch content is needed to manipulate starch quantity and quality via molecular breeding to meet future needs...
Preprint
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Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wil...
Article
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Plant seed germination is a crucial developmental event that has significant effects on seedling establishment and yield production. This process is controlled by multiple intrinsic signals, particularly phytohormones. The gaseous hormone ethylene stimulates seed germination; however, the genetic basis of ethylene production in maize during seed ge...
Article
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Carotenoids, which serve as precursors of vitamin A and antioxidants, play important roles in human health. Breeding to increase carotenoid levels in cereal grains is an economically feasible way to address nutritional deficiency. Here, we performed quantitative trait–locus (QTL) mapping of 5 primary and 12 derived carotenoid-related traits in maiz...
Article
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Plastid isoprenoids, a diverse group of compounds that includes carotenoids, chlorophylls, tocopherols, and multiple hormones, are essential for plant growth and development. Here, we identified and characterized SEED CAROTENOID DEFICIENT (SCD), which encodes an enzyme that functions in the biosynthesis of plastid isoprenoids in maize (Zea mays). S...
Article
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Background Plant architecture is a critical factor that affects planting density and, consequently, grain yield in maize. The genes or loci that determine organ size are the key regulators of plant architecture. Thus, understanding the genetic and molecular mechanisms of organ size will inform the use of a molecular manipulation approach to improve...
Data
Figure S1 Phenotypic distribution of tocopherol contents in the 11 parents of the six RIL populations. Figure S2 Box‐plot showing the distribution of tocopherol‐related traits in the six RIL populations. Figure S3 Comparative results between GWAS and QTL analysis for three tocopherol traits. Figure S4 Quantile‐quantile plots of GWAS results. Fi...
Data
Table S1 Statistical analysis for tocopherol traits in six RIL populations. Table S2 QTL information mapped in each RIL population. Table S3 Percent variation explained by epistasis between pairs of QTLs. Table S4 Eighty‐one a priori candidate genes identified in a previous study. Table S5 Candidate genes in the QTL region on chromosome 8. Tab...
Data
Principal coordinate analysis plot for 481 maize inbred lines. Blue, green, red, and black color represent Stiff Stalk, Tropical-Subtropical, Non-Stiff Stalk, and the mixed subgroup, respectively.
Data
Boxplots of summary statistics for 425,597 SNPs in all inbred lines from the diversity panel and in each subpopulation. (A) Minor allele frequency, (B) Gene diversity, (C) PIC.
Data
Quantile-quantile plots of estimated −log10(P-value) from association analysis for haploid male fertility using six methods, (A) across genetic backgrounds, and within the (B) “Mo17” and (C) “Zheng58” backgrounds. The gray solid line is the expected line under the null distribution where there are few true marker associations. The observed P-values...
Data
The distribution of minor allele frequency for the 425,597 high quality SNPs.
Data
ANOVA for the arcsine transformed haploid male fertility values.
Data
Manhattan plots for haploid male fertility across genetic backgrounds assessed with six models. The dashed horizontal line indicates the genome-wide significance threshold.
Data
Manhattan plots for haploid male fertility in the “Zheng58” background assessed with six models. The dashed horizontal line indicates the genome-wide significance threshold.
Data
Average linkage disequilibrium between marker pairs according to their physical distance, shown for all 10 chromosomes.
Data
Linkage disequilibrium (LD) across the 10 chromosomes in the maize diversity panel of 481 lines. The X-axis indicates the physical distance between SNPs within the same chromosome and the Y-axis indicates the LD (r2).
Data
Manhattan plots for haploid male fertility in the “Mo17” background assessed with six models. The dashed horizontal line indicates the genome-wide significance threshold.
Data
Physical positions of 6 SNPs significantly associated with HFM based on Q model under Zheng58 background and the predicted function or homology of adjacent candidate genes.
Article
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Alternative splicing (AS) enhances transcriptome diversity and plays important roles in regulating plant processes. Although widespread natural variation in AS has been observed in plants, how they are regulated and contribute to phenotypic variation is poorly understood. Here, we report a population-level transcriptome assembly and genome-wide ass...
Article
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Large-scale application of the doubled haploid (DH) technology by in vivo haploid induction has greatly improved the efficiency of maize breeding. While the haploid induction rate and the efficiency of identifying haploid plants have greatly improved in recent years, the low efficiency of doubling of haploid plants has remained and currently presen...
Article
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Key message: Genetic relationships among Chinese maize germplasms reveal historical trends in heterotic patterns from Chinese breeding programs and identify line Dan340 as a potential genome donor for elite inbred line Zheng58. The characterization of the genetic relationships, heterotic patterns and breeding history of lines in maize breeding pro...
Article
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Background: Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited. Results: A set of 2196 heterogeneous inbred family (HIF) maize lines derived from 12 recombinant inbred line (RIL) populat...
Article
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Although tocopherols play an important role in plants and animals, the genetic architecture of tocopherol content in maize kernels has remained largely unknown. In this study, linkage and association analyses were conducted to examine the genetic architecture of tocopherol content in maize kernels. Forty-one unique quantitative trait loci (QTLs) we...
Article
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Maize was domesticated from lowland teosinte (Zea mays ssp. parviglumis), but the contribution of highland teosinte (Zea mays ssp. mexicana, hereafter mexicana) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-...
Article
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Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitativ...
Article
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Key message: We identified 11 SAD genes, and mined their natural variations associated with the conservation of stearic to oleic acid, especially ZmSAD1 supported by both the QTL and an expression QTL. Maize oil is generally regarded as a healthy vegetable oil owing to its low abundance of saturated fatty acids. Stearoyl-ACP desaturase (SAD) is a...
Article
Full-text available
Maize production is threatened by drought stress worldwide. Identification of the genetic components underlying drought tolerance in maize is of great importance. Here we report a genome-wide association study (GWAS) of maize drought tolerance at the seedling stage that identified 83 genetic variants, which were resolved to 42 candidate genes. The...
Article
Full-text available
Violaxanthin de-epoxidase (VDE) has a critical role in the carotenoid biosynthesis pathway, which is involved in protecting the photosynthesis apparatus from damage caused by excessive light. Here, a VDE gene in maize, ZmVDE1, was cloned and shown to have functional domains in common with the gramineous VDE protein. Candidate gene association analy...