Yu Li

Chinese Academy of Agricultural Sciences, Peping, Beijing, China

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Publications (35)85.72 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: To investigate the genetic structure of Chinese maize germplasm, the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs) was used to genotype a collection of 367 inbred lines widely used in maize breeding of China. A total of 41,819 informative SNPs with minor allele number of more than 0.05 were used to estimate the genetic diversity, relatedness, and linkage disequilibrium (LD) decay. Totally 1,015 SNPs evenly distributed in the genome were selected randomly to evaluate the population structure of these accessions. Results showed that two main groups could be determined i.e., the introduced germplasm and the local germplasm. Further, five subgroups corresponding to different heterotic groups, that is, Reid Yellow Dent (Reid), Lancaster Sure Crop (Lancaster), P group (P), Tang Sipingtou (TSPT), and Tem-tropic I group (Tem-tropic I), were determined. The genetic diversity of within subgroups was highest in the Tem-Tropic I and lowest in the P. Most lines in this panel showed limited relatedness with each other. Comparisons of gene diversity showed that there existed some conservative genetic regions in specific subgroups across the ten chromosomes, i.e., seven in the Lancaster, seven in the Reid, six in the TSPT, five in the P, and two in the Tem-Tropical I. In addition, the results also revealed that there existed fifteen conservative regions transmitted from Huangzaosi, an important foundation parent, to its descendants. These are important for further studies since the outcomes may provide clues to understand why Huangzaosi could become a foundation parent in Chinese maize breeding. For the panel of 367 elite lines, average LD distance was 391 kb and varied among different chromosomes as well as in different genomic regions of one chromosome. This analysis uncovered a high natural genetic diversity in the elite maize inbred set, suggesting that the panel can be used in association study, esp. for temperate regions.
    Theoretical and Applied Genetics 12/2013; 127(3). · 3.51 Impact Factor
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    ABSTRACT: SbSNAC1 is a member of the plant-specific NAC transcription factor superfamily that plays an important role in the abiotic stress response in sorghum. The SbSNAC1 protein consists of a typical NAC conserved domain at its N terminus and a diverse C-terminal region. The expression of SbSNAC1 was induced by various abiotic stresses, such as drought and salinity. SbSNAC1 is also expressed at a relatively higher concentration in roots and responds to the phytohormone abscisic acid. Transactivation analysis indicated that the transactivation activity of SbSNAC1 is located in the C-terminal region, whereas no activity was detected in the conserved NAC-domain, localized in the N-terminus. Subcellular localization assays using constructs of different SbSNAC1 fragments fused with green fluorescent protein revealed that the SbSNAC1 protein localized in the nucleus, and that the nuclear localization signal was present in the N-terminal section. Furthermore, transgenic plants overexpressing SbSNAC1 had an improved drought stress tolerance compared with wild-type plants, but no obvious retardation was detected in plant growth and development. These results suggest that SbSNAC1 has the potential to improve abiotic stress tolerance.
    Plant Cell Tissue and Organ Culture 12/2013; 115(3). · 2.61 Impact Factor
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    ABSTRACT: Grain yield is one of the most important and complex quantitative traits in maize breeding. In the present study, a total of 11 connected RIL populations, derived from crosses between elite inbreed “Huangzaosi” as the common parent and 11 elite inbreeds, were evaluated for five yield components and kernel-related traits under six environments. Quantitative trait loci (QTL) were detected for the traits under each environment and in joint analysis across all environments for each population. A total of 146 major QTL with R2 > 10 % in at least one environment and also detected based on joint analysis across all environments were identified in the 11 populations. Lqkwei4 conferring kernel weight and Lqklen4-1 conferring kernel length both located in the adjacent marker intervals in bin 4.05 were stably expressed in four environments and in joint analysis across six environments, with the largest R2 over 27 and 24 % in a single environment, respectively. Moreover, all major QTL detected in the 11 populations were aligned on the IBM2 2008 neighbors reference map. Totally 16 common QTL (CQTL) were detected. Seven important CQTL (CQTL1-2, CQTL1-3, CQTL4-1, CQTL4-2, CQTL4-3, CQTL4-4, and CQTL6-1) were located in bin 1.07, 1.10, 4.03, 4.05, 4.08, 4.09 and 6.01–6.02, respectively. These chromosomal regions could be targets for fine mapping and marker-assisted selection.
    Euphytica 10/2013; · 1.69 Impact Factor
  • ACTA AGRONOMICA SINICA 08/2013; 38(8):1435-1442.
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    ABSTRACT: Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.
    PLoS ONE 04/2013; 8(4):e59714. · 3.53 Impact Factor
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    ABSTRACT: Xylans are the major hemicelluloses in grasses, but their effects on biomass saccharification remain unclear. In this study, we examined the 79 representative Miscanthus accessions that displayed a diverse cell wall composition and varied biomass digestibility. Correlation analysis showed that hemicelluloses level has a strong positive effect on lignocellulose enzymatic digestion after NaOH or H(2)SO(4) pretreatment. Characterization of the monosaccharide compositions in the KOH-extractable and non-KOH-extractable hemicelluloses indicated that arabinose substitution degree of xylan is the key factor that positively affects biomass saccharification. The xylose/arabinose ratio after individual enzyme digestion revealed that the arabinose in xylan is partially associated with cellulose in the amorphous regions, which negatively affects cellulose crystallinity for high biomass digestibility. The results provide insights into the mechanism of lignocellulose enzymatic digestion upon pretreatment, and also suggest a goal for the genetic modification of hemicelluloses towards the bioenergy crop breeding of Miscanthus and grasses.
    Bioresource Technology 12/2012; 130C:629-637. · 5.04 Impact Factor
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    ABSTRACT: Simultaneous improvement in grain yield and related traits in maize hybrids and their parents (inbred lines) requires a better knowledge of genotypic correlations between family per se performance (FP) and testcross performance (TP). Thus, to understand the genetic basis of yield-related traits in both inbred lines and their testcrosses, two F (2:3) populations (including 230 and 235 families, respectively) were evaluated for both FP and TP of eight yield-related traits in three diverse environments. Genotypic correlations between FP and TP, [Formula: see text] (FP, TP), were low (0-0.16) for grain yield per plant (GYPP) and kernel number per plant (KNPP) in the two populations, but relatively higher (0.32-0.69) for the other six traits with additive effects as the primary gene action. Similar results were demonstrated by the genotypic correlations between observed and predicted TP values based on quantitative trait loci positions and effects for FP, [Formula: see text] (M (FP), Y (TP)). A total of 88 and 35 QTL were detected with FP and TP, respectively, across all eight traits in the two populations. However, the genotypic variances explained by the QTL detected in the cross-validation analysis were much lower than those in the whole data set for all traits. Several common QTL between FP and TP that accounted for large phenotypic variances were clustered in four genomic regions (bin 1.10, 4.05-4.06, 9.02, and 10.04), which are promising candidate loci for further map-based cloning and improvement in grain yield in maize. Compared with publicly available QTL data, these QTL were also detected in a wide range of genetic backgrounds and environments in maize. These results imply that effective selection based on FP to improve TP could be achieved for traits with prevailing additive effects.
    Theoretical and Applied Genetics 11/2012; 126(3). · 3.51 Impact Factor
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    ABSTRACT: NAC proteins are plant-specific transcription factors that play essential roles in stress responses. However, only little information regarding stress-related NAC genes is available in maize. In this study, a maize NAC gene, ZmSNAC1, was cloned and functionally characterized. Expression analysis revealed that ZmSNAC1 was strongly induced by low temperature, high-salinity, drought stress, and abscisic acid (ABA) treatment, but downregulated by salicylic acid treatment. Subcellular localization experiments in Arabidopsis protoplast cells indicated that ZmSNAC1 was localized in the nucleus. Transactivation assays demonstrated that ZmSNAC1 functioned as a transcriptional activator. Overexpression of ZmSNAC1 in Arabidopsis led to hypersensitivity to ABA and osmotic stress at the germination stage, but enhanced tolerance to dehydration compared to wild-type seedlings. These results suggest that ZmSNAC1 functions as a stress-responsive transcription factor in positive modulation of abiotic stress tolerance, and may have applications in the engineering of drought-tolerant crops. KEY MESSAGE: ZmSNAC1 functioned as a stress-responsive transcription factor in response to abiotic stresses, and might be useful for crop tolerance improvement.
    Plant Cell Reports 05/2012; 31(9):1701-11. · 2.94 Impact Factor
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    ABSTRACT: MADS-box genes encode a family of transcription factors, which control diverse developmental processes in flowering plants, with organs ranging from roots, flowers and fruits. In this study, six maize cDNAs encoding MADS-box proteins were isolated. BLASTX searches and phylogenetic analysis indicated that the six MADS-box genes belonging to the AGL2-like clade. qRT-PCR analysis revealed that these genes had differential expression patterns in different organs in maize. The results of yeast one-hybrid system indicated that the protein ZMM3-1, ZMM3-2, ZMM6, ZMM7-L, ZMM8-L and ZMM14-L had transcriptional activation activity. Subcellular localization of ZMM7-L demonstrated that the fluorescence of ZMM7-L-GFP was mainly detected in the nuclei of onion epidermal cells. qRT-PCR analysis for expression pattern of ZMM7-L showed that the gene was up-regulated by abiotic stresses and down-regulated by exogenous ABA. The germination rates of over-expression transgenic lines were lower than that of the wild type on medium with 150 mM NaCl, 350 mM mannitol. These results indicated that ZMM7-L might be a negative transcription factor responsive to abiotic stresses.
    Journal of plant physiology 03/2012; 169(8):797-806. · 2.50 Impact Factor
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    ABSTRACT: Plasma membrane protein 3 (PMP3), a class of small hydrophobic polypeptides with high sequence similarity, is responsible for salt, drought, cold, and abscisic acid. These small hydrophobic ploypeptides play important roles in maintenance of ion homeostasis. In this study, eight ZmPMP3 genes were cloned from maize and responsive to salt, drought, cold and abscisic acid. The eight ZmPMP3s were membrane proteins and their sequences in trans-membrane regions were highly conserved. Phylogenetic analysis showed that they were categorized into three groups. All members of group II were responsive to ABA. Functional complementation showed that with the exception of ZmPMP3-6, all were capable of maintaining membrane potential, which in turn allows for regulation of intracellular ion homeostasis. This process was independent of the presence of Ca(2+). Lastly, over-expression of ZmPMP3-1 enhanced growth of transgenic Arabidopsis under salt condition. Through expression analysis of deduced downstream genes in transgenic plants, expression levels of three ion transporter genes and four important antioxidant genes in ROS scavenging system were increased significantly in transgenic plants during salt stress. This tolerance was likely achieved through diminishing oxidative stress due to the possibility of ZmPMP3-1's involvement in regulation of ion homeostasis, and suggests that the modulation of these conserved small hydrophobic polypeptides could be an effective way to improve salt tolerance in plants.
    PLoS ONE 02/2012; 7(2):e31101. · 3.53 Impact Factor
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    ABSTRACT: With 2 figures and 4 tablesAbstractThe magnitude of genotypic correlations between family per se and testcross, r^g (per se, TC), is crucial for testing schemes in hybrid breeding as well as improvement of commercial hybrids. The objectives of this study were to identify the r^g (per se, TC), to examine the proportion of common QTL for both types of progenies and to determine the gene action of QTL identified for family per se and their value for the prediction of testcross progenies. Under multi-environments, r^g (per se, TC) were significant and higher than r^p (per se, TC), the phenotypic correlations between family per se and testcross for plant height and ear height in two maize crosses. The final fit for QTL explained 21.6–70.3% phenotypic variance and 24.4–79.4% genotypic variance for family per se. However, in cross-validation analysis (CV), the genotypic variance explained by all QTL was less than 60% for the two traits. Several common QTL (Chr. 1, Chr. 8 and Chr. 10) could be detected for both family per se and TC, which seems feasible to apply marker-assisted selection in maize breeding programmes.
    Plant Breeding 12/2011; 130(6). · 1.18 Impact Factor
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    ABSTRACT: In plants, the bZIP (basic leucine zipper) transcription factors regulate diverse functions, including processes such as plant development and stress response. However, few have been functionally characterized in maize (Zea mays). In this study, we cloned ZmbZIP72, a bZIP transcription factor gene from maize, which had only one copy in the maize genome and harbored three introns. Analysis of the amino acid sequence of ZmbZIP72 revealed a highly conserved bZIP DNA-binding domain in its C-terminal region, and four conserved sequences distributed in N- or C-terminal region. The ZmbZIP72 gene expressed differentially in various organs of maize plants and was induced by abscisic acid, high salinity, and drought treatment in seedlings. Subcellular localization analysis in onion epidermal cells indicated that ZmbZIP72 was a nuclear protein. Transactivation assay in yeast demonstrated that ZmbZIP72 functioned as a transcriptional activator and its N terminus (amino acids 23-63) was necessary for the transactivation activity. Heterologous overexpression of ZmbZIP72 improved drought and partial salt tolerance of transgenic Arabidopsis plants, as determined by physiological analyses of leaf water loss, electrolyte leakage, proline content, and survival rate under stress. In addition, the seeds of ZmbZIP72-overexpressing transgenic plants were hypersensitive to ABA and osmotic stress. Moreover, overexpression of ZmbZIP72 enhanced the expression of ABA-inducible genes such as RD29B, RAB18, and HIS1-3. These results suggest that the ZmbZIP72 protein functions as an ABA-dependent transcription factor in positive modulation of abiotic stress tolerance and may be a candidate gene with potential application in molecular breeding to enhance stress tolerance in crops.
    Planta 08/2011; 235(2):253-66. · 3.38 Impact Factor
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    ABSTRACT: SnRK2 (sucrose non-fermenting 1-related protein kinases 2) represents a unique family of protein kinase in regulating signaling transduction in plants. Although the regulatory mechanisms of SnRK2 have been well demonstrated in Arabidopsis thaliana, their functions in maize are still unknown. In our study, we cloned an SnRK2 gene from maize, ZmSAPK8, which encoded a putative homolog of the rice SAPK8 protein. ZmSAPK8 had two copies in the maize genome and harbored eight introns in its coding region. We demonstrated that ZmSAPK8 expressed differentially in various organs of maize plants and was up-regulated by high-salinity and drought treatment. A green fluorescent protein (GFP)-tagged ZmSAPK8 showed subcellular localization in the cell membrane, cytoplasm and nucleus. In vitro kinase assays indicated that ZmSAPK8 preferred Mn(2+) to Mg(2+) as cofactor for phosphorylation, and Ser-182 and Thr-183 in activation loop was important for its activity. Heterologous overexpression of ZmSAPK8 in Arabidopsis could significantly strengthen tolerance to salt stress. Under salt treatment, ZmSAPK8-overexpressed transgenic plants exhibited higher germination rate and proline content, low electrolyte leakage and higher survival rate than wild type. Further analysis indicated that transgenic plants showed increased transcription of the stress-related genes, RD29A, RD29B, RAB18, ABI1, DREB2A and P5CS1, under high-salinity conditions. The results demonstrated that ZmSAPK8 was involved in diverse stress signal transduction. Moreover, no obvious adverse effects on growth and development in the ZmSAPK8-overexpressed transgenic plants implied that ZmSAPK8 was potentially useful in transgenic breeding to improve salt tolerance in crops.
    Plant Cell Reports 06/2011; 30(9):1683-99. · 2.94 Impact Factor
  • ACTA AGRONOMICA SINICA 02/2011; 37(2):235-248.
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    ABSTRACT: Huangzaosi, Qi319, and Ye478 are foundation inbred lines widely used in maize breeding in China. To elucidate genetic base of yield components and kernel-related traits in these elite lines, two F(2:3) populations derived from crosses Qi319 × Huangzaosi (Q/H, 230 families) and Ye478 × Huangzaosi (Y/H, 235 families), as well as their parents were evaluated in six environments including Henan, Beijing, and Xinjiang in 2007 and 2008. Correlation and hypergeometric probability function analyses showed the dependence of yield components on kernel-related traits. Three mapping procedures were used to identify quantitative trait loci (QTL) for each population: (1) analysis for each of the six environments, (2) joint analysis for each of the three locations across 2 years, and (3) joint analysis across all environments. For the eight traits measured, 90, 89, and 58 QTL for Q/H, and 72, 76, and 51 QTL for Y/H were detected by the three QTL mapping procedures, respectively. About 70% of the QTL from Q/H and 90% of the QTL from Y/H did not show significant QTL × environment interactions in the joint analysis across all environments. Most of the QTL for kernel traits exhibited high stability across 2 years at the same location, even across different locations. Seven major QTL detected under at least four environments were identified on chromosomes 1, 4, 6, 7, 9, and 10 in the populations. Moreover, QTL on chr. 1, chr. 4, and chr. 9 were detected in both populations. These chromosomal regions could be targets for marker-assisted selection, fine mapping, and map-based cloning in maize.
    Theoretical and Applied Genetics 02/2011; 122(7):1305-20. · 3.51 Impact Factor
  • ACTA AGRONOMICA SINICA 01/2011; 37(1):58-66.
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    ABSTRACT: Breeding crops with the quality of broad-spectrum disease resistance using genetic resources is one of the principal goals of crop improvement. However, the molecular mechanism of broad-spectrum resistance remains largely unknown. Here, we show that GH3-2, encoding an indole-3-acetic acid (IAA)-amido synthetase, mediates a broad-spectrum resistance to bacterial Xanthomonas oryzae pv oryzae and Xanthomonas oryzae pv oryzicola and fungal Magnaporthe grisea in rice (Oryza sativa). IAA, the major form of auxin in rice, results in rice more vulnerable to the invasion of different types of pathogens, which is at least partly due to IAA-induced loosening of the cell wall, the natural protective barrier of plant cells to invaders. X. oryzae pv oryzae, X. oryzae pv oryzicola, and M. grisea secrete IAA, which, in turn, may induce rice to synthesize its own IAA at the infection site. IAA induces the production of expansins, the cell wall-loosening proteins, and makes rice vulnerable to pathogens. GH3-2 is likely contributing to a minor quantitative trait locus for broad-spectrum resistance. Activation of GH3-2 inactivates IAA by catalyzing the formation of an IAA-amino acid conjugate, which results in the suppression of expansin genes. Thus, GH3-2 mediates basal resistance by suppressing pathogen-induced IAA accumulation. It is expected that, regulated by a pathogen-induced strong promoter, GH3-2 alone may be used for breeding rice with a broad-spectrum disease resistance.
    Plant physiology 11/2010; 155(1):589-602. · 7.39 Impact Factor
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    ABSTRACT: In this paper, a full-length cDNA-encoding cytosolic nicotinamide adenine dinucleotide phosphate-dependent isocitrate dehydrogenase was isolated from maize and named ZmICDH. Analysis of the deduced protein sequence revealed that this gene had considerably high homologies with other plant ICDH genes such as those from rice, Arabidopsis and poplar. The gene was transcribed in all tissues tested, with the highest amount of transcript in root. Subcellular localization results indicated that ZmICDH was localized in cytosol. In an attempt to further understand the role of ZmICDH in maize, the functional characterization of the gene was conducted. The results indicated that the expression of ZmICDH was induced by drought and salt stresses. ZmICDH enhanced salt tolerance in transgenic Arabidopsis. Keywords ZmICDH -Salt-Drought-Stress-Transgenic Arabidopsis -Maize
    Journal of Plant Biology 04/2010; 53(2):107-112. · 1.28 Impact Factor
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    ABSTRACT: The cellulose synthase and cellulose synthase-like gene superfamily (CESA/CSL) is proposed to encode enzymes for cellulose and non-cellulosic matrix polysaccharide synthesis in plants. Although the rice (Oryza sativa L.) genome has been sequenced for a few years, the global expression profiling patterns and functions of the OsCESA/CSL superfamily remain largely unknown. A total of 45 identified members of OsCESA/CSL were classified into two clusters based on phylogeny and motif constitution. Duplication events contributed largely to the expansion of this superfamily, with Cluster I and II mainly attributed to tandem and segmental duplication, respectively. With microarray data of 33 tissue samples covering the entire life cycle of rice, fairly high OsCESA gene expression and rather variable OsCSL expression were observed. While some members from each CSL family (A1, C9, D2, E1, F6 and H1) were expressed in all tissues examined, many of OsCSL genes were expressed in specific tissues (stamen and radicles). The expression pattern of OsCESA/CSL and OsBC1L which extensively co-expressed with OsCESA/CSL can be divided into three major groups with ten subgroups, each showing a distinct co-expression in tissues representing typically distinct cell wall constitutions. In particular, OsCESA1, -3 & -8 and OsCESA4, -7 & -9 were strongly co-expressed in tissues typical of primary and secondary cell walls, suggesting that they form as a cellulose synthase complex; these results are similar to the findings in Arabidopsis. OsCESA5/OsCESA6 is likely partially redundant with OsCESA3 for OsCESA complex organization in the specific tissues (plumule and radicle). Moreover, the phylogenetic comparison in rice, Arabidopsis and other species can provide clues for the prediction of orthologous gene expression patterns. The study characterized the CESA/CSL of rice using an integrated approach comprised of phylogeny, transcriptional profiling and co-expression analyses. These investigations revealed very useful clues on the major roles of CESA/CSL, their potentially functional complement and their associations for appropriate cell wall synthesis in higher plants.
    BMC Plant Biology 01/2010; 10:282. · 3.94 Impact Factor
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    ABSTRACT: Early responsive to dehydration (ERD) genes could be rapidly induced to respond to dehydration and to various other abiotic stresses. Here, we report on an ERD gene (ZmERD4) from maize cloned by rapid amplification of complementary DNA (cDNA) ends. The ZmERD4 cDNA had a total length of 2,536bp with an open reading frame of 2,196bp, 5′-untranslated region (UTR) of 48 bp, and 3′-UTR of 292bp. The gene encoded a predicted polypeptide of 732 amino acids. The ZmERD4 protein shared a high amino acid sequence similarity with ERD4 of Oryza sativa and Arabidopsis thaliana. A reverse-transcription polymerase chain reaction analysis revealed that ZmERD4 was constitutively expressed in different tissues. RNA gel blot showed that ZmERD4 could be induced by both drought and salt stress and also responded to abscisic acid treatment, but it was not induced by low temperature (4°C). Transgenic Arabidopsis plants constitutively expressing the ZmERD4 gene under the control of the 35S cauliflower mosaic virus 35S promoter exhibited slightly smaller-sized leaves under normal growing conditions. Moreover, 35S::ZmERD4 transgenic plants displayed enhanced tolerance to water deficit and high salinity when compared to wild-type plants. Altogether, these findings suggested that ZmERD4 played an important role in early stages of plant adaptation to stress conditions and might be useful in improving plant tolerance to abiotic stress.
    Plant Molecular Biology Reporter 12/2009; 27(4):542-548. · 2.37 Impact Factor

Publication Stats

417 Citations
85.72 Total Impact Points

Institutions

  • 1995–2013
    • Chinese Academy of Agricultural Sciences
      • • Institute of Crop Sciences
      • • Institute of Crop Germplasm Resources
      Peping, Beijing, China
  • 2011
    • China Agricultural University
      • College of Biological Sciences
      Beijing, Beijing Shi, China
  • 2009
    • Huazhong Agricultural University
      • National Key Laboratory of Crop Genetic Improvement
      Wuhan, Hubei, China
  • 2008
    • French National Institute for Agricultural Research
      Lutetia Parisorum, Île-de-France, France