Shihuang Zhang

Chinese Academy of Agricultural Sciences, Beijing, Beijing Shi, China

Are you Shihuang Zhang?

Claim your profile

Publications (24)73.5 Total impact

  • [show abstract] [hide abstract]
    ABSTRACT: Maize rough dwarf disease (MRDD), caused by the Maize rough dwarf virus (MRDV) is highly prevalent across summer at maize-growing areas in China. To investigate the genetic architecture underlying this viral disease, a set of 236 Chinese maize inbred lines was evaluated for resistance to MRDD in 2010 and 2011. Based on 41,101 single-nucleotide polymorphism (SNP) markers with minor allele frequencies (MAF) greater than 5 %, a genome-wide association study (GWAS) was employed to identify genomic loci for resistance to MRDD. A total of 73 SNPs were found to be associated with resistance to MRDD at a significance threshold of -log10 (P) > 4 controlling the false discovery rate (FDR) at α = 0.1. Fourteen of these SNPs were detected in both of the two environments tested. A total of 48 SNPs were identified in linkage disequilibrium (LD) blocks containing candidate resistance genes, including protein kinase genes. Using the pedigree information and whole-genome SNP analysis of five highly resistant inbred lines derived from the hybrid ‘P78599’, nine derivative fragments harbouring SNPs associated with MRDD resistance were detected. One 81.57 Mb fragment in particular located in bin 8.03, which contained six SNPs associated with MRDD resistance, and included the major quantitative trait loci (QTL) that had been identified in the previous study. These results suggest that the SNPs and fragments associated with MRDD resistance, especially those in bin 8.03, could be used for fine mapping of resistance genes and developing resistant varieties in maize.
    European Journal of Plant Pathology 05/2014; 139(1). · 1.61 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: The recessive opaque-2 mutant gene (o2) reduces α-zeins accumulation in maize endosperm, changes the amino acid composition of maize kernels, induces an opaque endosperm, and increases the lysine content of kernels. The quality protein maize (QPM) inbred line CA339 (o2o2) and an elite normal inbred line liao2345 (O2O2) were used to construct o2 near-isogenic lines (NILs) by marker-assisted selection (MAS) using the co-dominant SSR marker phi057. Two specific o2 NILs were constructed, named liao2345/o2-1 and liao2345/o2-2. However, the kernel phenotypes of the two o2 NILs were different from each other. liao2345/o2-1 had the wild-type vitreous endosperm, which is similar to its recurrent parent liao2345, while the endosperm of liao2345/o2-2 was opaque, identical to typical o2 mutant individuals. In comparison to their recurrent parent liao2345, the lysine concentration of liao2345/o2-1 was similar and the lysine concentration in liao2345/o2-2 was doubled. SDS-PAGE analysis indicated that liao2345/o2-1 had the same zeins ratio as liao2345, whereas the zeins concentration of liao2345/o2-2 was markedly lower. Sequence and transcript abundance analyses indicated that the CDS of two o2 NILs are derived from CA339, but they have different promoters. The O2 transcript of liao2345/o2-2 is largely inhibited because of an rbg transposable element inserted between the TATA box and initiator codon of liao2345/o2-2. We concluded that different crossing-over patterns during the process of o2 NIL construction resulted in the different kernel phenotypes of the two o2 NILs. We surmise that the reversion of liao2345/o2-1 to wild type was due to the recombination with the wild type liao2345 promoter during introgression and backcrossing. The o2 mutant gene of donor (CA339) is a null mutant because of low O2 expression. However, its CDS probably encodes a protein with normal function which can maintain the normal accumulation of zeins in maize endosperm.
    PLoS ONE 01/2014; 9(1):e85159. · 3.73 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: Kernel weight, controlled by quantitative trait loci (QTL), is an important component of grain yield in maize. Cytokinins (CKs) participate in determining grain morphology and final grain yield in crops. ZmIPT2, which is expressed mainly in the basal transfer cell layer, endosperm, and embryo during maize kernel development, encodes an isopentenyl transferase (IPT) that is involved in CK biosynthesis. The coding region of ZmIPT2 was sequenced across a panel of 175 maize inbred lines that are currently used in Chinese maize breeding programs. Only 16 single nucleotide polymorphisms (SNPs) and seven haplotypes were detected among these inbred lines. Nucleotide diversity (pi) within the ZmIPT2 window and coding region were 0.347 and 0.0047, respectively, and they were significantly lower than the mean nucleotide diversity value of 0.372 for maize Chromosome 2 (P < 0.01). Association mapping revealed that a single nucleotide change from cytosine (C) to thymine (T) in the ZmIPT2 coding region, which converted a proline residue into a serine residue, was significantly associated with hundred kernel weight (HKW) in three environments (P <0.05), and explained 4.76% of the total phenotypic variation. In vitro characterization suggests that the dimethylallyl diphospate (DMAPP) IPT activity of ZmIPT2-T is higher than that of ZmIPT2-C, as the amounts of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) consumed by ZmIPT2-T were 5.48-, 2.70-, and 1.87-fold, respectively, greater than those consumed by ZmIPT2-C. The effects of artificial selection on the ZmIPT2 coding region were evaluated using Tajima's D tests across six subgroups of Chinese maize germplasm, with the most frequent favorable allele identified in subgroup PB (Partner B). These results showed that ZmIPT2, which is associated with kernel weight, was subjected to artificial selection during the maize breeding process. ZmIPT2-T had higher IPT activity than ZmIPT2-C, and this favorable allele for kernel weight could be used in molecular marker-assisted selection for improvement of grain yield components in Chinese maize breeding programs.
    BMC Plant Biology 07/2013; 13(1):98. · 4.35 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: Maize rough dwarf disease (MRDD, a viral disease) results in significant grain yield losses, while genetic basis of which is largely unknown. Based on comparative genomics, eukaryotic translation initiation factor 4E (eIF4E) was considered as a candidate gene for MRDD resistance, validation of which will help to understand the possible genetic mechanism of this disease. ZmeIF4E (orthologs of eIF4E gene in maize) encodes a protein of 218 amino acids, harboring five exons and no variation in the cDNA sequence is identified between the resistant inbred line, X178 and susceptible one, Ye478. ZmeIF4E expression was different in the two lines plants treated with three plant hormones, ethylene, salicylic acid, and jasmonates at V3 developmental stage, suggesting that ZmeIF4E is more likely to be involved in the regulation of defense gene expression and induction of local and systemic resistance. Moreover, four cis-acting elements related to plant defense responses, including DOFCOREZM, EECCRCAH1, GT1GAMSCAM4, and GT1CONSENSUS were detected in ZmeIF4E promoter for harboring sequence variation in the two lines. Association analysis with 163 inbred lines revealed that one SNP in EECCRCAH1 is significantly associated with CSI of MRDD in two environments, which explained 3.33 and 9.04 % of phenotypic variation, respectively. Meanwhile, one SNP in GT-1 motif was found to affect MRDD resistance only in one of the two environments, which explained 5.17 % of phenotypic variation. Collectively, regulatory motifs respectively harboring the two significant SNPs in ZmeIF4E promoter could be involved in the defense process of maize after viral infection. These results contribute to understand maize defense mechanisms against maize rough dwarf virus.
    MGG Molecular & General Genetics 03/2013; · 2.58 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: The major quantitative trait locus (QTL) qHS2.09 plays an important role in resistance to head smut during maize breeding and production. In this study, a near-isogenic line (NIL), L34, which harbors the major QTL qHS2.09 in bin 2.09, was developed using a resistant donor 'Mo17' in a susceptible genetic background 'Huangzao4'. Using 18,683 genome-wide polymorphic loci, this major QTL was finely mapped into an interval of ≈1.10 Mb, flanked by single nucleotide polymorphism (SNP) markers PZE-102187307 and PZE-102188421. Moreover, the favorable allele from 'Mo17' for SNP PZE-102187611 in this interval that was most significantly associated with resistance to head smut (P = 1.88 E-10) and accounted for 39.7 to 44.4% of the phenotypic variance in an association panel consisting of 80 inbred lines. With combined linkage and association mapping, this major QTL was finally located between SNP PZE-102187486 and PZE-102188421 with an interval of ≈1.00 Mb. Based on the pedigrees of 'Mo17' and its derivatives widely used in temperate maize breeding programs, the favorable haplotype from 'Mo17' is shown to be the main source of resistance to head smut in these lines. Therefore, the SNPs closely linked to the major QTL qHS2.09, detected in both linkage and association mapping, and could be useful for marker-assisted selection in maize breeding programs.
    Phytopathology 03/2012; 102(7):692-9. · 2.97 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: The recessive mutant allele of the opaque2 gene (o2) alters the endosperm protein pattern and increases the kernel lysine content of maize (Zea mays L.). In this study, sequencing results showed that the o2 mutant was successfully introgressed into 12 elite normal maize inbred lines by marker assisted selection (MAS). The average genetic similarity between these normal inbred lines and their o2 near-isogenic lines (NILs) was more than 95%. Kernel lysine content increased significantly in most of o2 NILs lines relative to normal elite inbreds, but remained unchanged in the genetic backgrounds Dan598o2 and Liao2345o2. Moreover, the kernel characteristics of these two o2 NILs did not differ from the other inbred lines. The results of lysine content analysis in the F1 hybrids between Liao2345o2 and Dan598o2 and other o2 NILs demonstrated that gene(s) other than opaque2 may control kernel lysine content in these two o2 NILs. The results of zein analysis showed that 22-kD α-zein synthesis was reduced or absent, and the 19-kD α-zein synthesis was greatly reduced compared with the recurrent parents in most o2 NILs except for Dan598o2 and Liao2345o2. Our results indicate that gene(s) other than opaque2 may play more important roles in zein synthesis and kernel lysine content in some maize genetic backgrounds.
    Planta 08/2011; 235(1):205-15. · 3.35 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: Single nucleotide polymorphism (SNP) is a common form of genetic variation and popularly exists in maize genome. An Illumina GoldenGate assay with 1 536 SNP markers was used to genotype maize inbred lines and identified the functional genetic variations underlying drought tolerance by association analysis. Across 80 lines, 1 006 polymorphic SNPs (65.5% of the total) in the assay with good call quality were used to estimate the pattern of genetic diversity, population structure, and familial relatedness. The analysis showed the best number of fixed subgroups was six, which was consistent with their original sources and results using only simple sequence repeat markers. Pairwise linkage disequilibrium (LD) and association mapping with phenotypic traits investigated under water-stressed and well-watered regimes showed rapid LD decline within 100-500 kb along the physical distance of each chromosome, and that 29 SNPs were associated with at least two phenotypic traits in one or more environments, which were related to drought-tolerant or drought-responsive genes. These drought-tolerant SNPs could be converted into functional markers and then used for maize improvement by marker-assisted selection.
    Journal of Integrative Plant Biology 05/2011; 53(8):641-52. · 3.75 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: With 2 tablesAbstractRecombination frequency greatly affects selection efficiency in plant breeding. A high-density single-nucleotide polymorphism (SNP) map integrated with physical map and other molecular maps is very useful for characterizing genetic recombination variation. In this study, recombination frequency in maize was investigated through SNP linkage maps constructed with three recombinant inbred line populations. The integrated map consisted of 1443 molecular markers, including 1155 SNPs, spanning 1346 cM. A 100-fold difference in recombination frequency was observed between different chromosomal regions, ranging from an average of 0.09 cM/Mb for pericentromeric regions to 7.08 cM/Mb for telomeric regions. Recombination suppression in non-centromeric regions identified nine recombination-suppressed regions, one of which likely contained condensed heterochromatin (knobs). Recombination variation along chromosomes was highly predictable for pericentromeric and telomeric regions, but population-specific with 4.5-fold difference for the same marker interval across the three populations or specific chromosome regions because of the presence of knobs. As recombination variation can be identified and well characterized as shown in this study, the related information will facilitate future genetic studies, gene cloning and marker-assisted plant breeding.
    Plant Breeding 04/2011; 130(5):533 - 539. · 1.18 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: Plant invertases catalyze the conversion of sucrose to glucose and fructose, which are distinct signals of widely varied stress-tolerance processes, including the biosynthesis and detection of hormones under water deficit. In the invertase gene family, the candidate gene ivr2 encoding plant acid-soluble invertase plays a vital role in drought tolerance. In this study, a putative genomic sequence of ivr2 including three exons and two introns was acquired and genetically analyzed using bioinformatics and statistics, based on a partial ivr2 gene sequence of the GenBank library. The ivr2 genomic sequence data from 106 maize inbred lines were obtained using five nested primer pairs. Further analysis showed that the detected polymorphic sites were mainly located in exon-1, intron-1 and exon-2 regions; High linkage disequilibrium level and low nucleotide diversity were identified at this ivr2 locus. Association mapping combined the genotypic and phenotypic data, and a total of 48 associations showed high contributions to the variations in grain yield and its components under well-watered and water-stressed conditions over 2 years of experiments. This suggested that functional polymorphisms in ivr2 were possibly associated with maize drought tolerance. This provides reference information for efficient marker-assisted selection of superior alleles in drought tolerance breeding programs.
    Genetica 03/2011; 139(4):479-87. · 1.68 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: The harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05-5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS). A total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives. The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P=8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production.
    PLoS ONE 01/2011; 6(12):e29229. · 3.73 Impact Factor
  • Source
    Molecular Breeding 01/2011; 28(1):135-135. · 3.25 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: Drought often delays developmental events so that plant height and above-ground biomass are reduced, resulting in yield loss due to inadequate photosynthate. In this study, plant height and biomass measured by the Normalized Difference Vegetation Index (NDVI) were used as criteria for drought tolerance. A total of 305 lines representing temperate, tropical and subtropical maize germplasm were genotyped using two single nucleotide polymorphism (SNP) chips each containing 1536 markers, from which 2052 informative SNPs and 386 haplotypes each constructed with two or more SNPs were used for linkage disequilibrium (LD) or association mapping. Single SNP- and haplotype-based LD mapping identified two significant SNPs and three haplotype loci [a total of four quantitative trait loci (QTL)] for plant height under well-watered and water-stressed conditions. For biomass, 32 SNPs and 12 haplotype loci (30 QTL) were identified using NDVIs measured at seven stages under the two water regimes. Some significant SNP and haplotype loci for NDVI were shared by different stages. Comparing significant loci identified by single SNP- and haplotype-based LD mapping, we found that six out of the 14 chromosomal regions defined by haplotype loci each included at least one significant SNP for the same trait. Significant SNP haplotype loci explained much higher phenotypic variation than individual SNPs. Moreover, we found that two significant SNPs (two QTL) and one haplotype locus were shared by plant height and NDVI. The results indicate the power of comparative LD mapping using single SNPs and SNP haplotypes with QTL shared by plant height and biomass as secondary traits for drought tolerance in maize. KeywordsMaize–Drought tolerance–Secondary traits–Plant height–Biomass–Single nucleotide polymorphism (SNP)–Haplotype–LD mapping–Association mapping
    Molecular Breeding 01/2011; 30(1):1-12. · 3.25 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: Nitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation. In this study, we used the SmartArray™ and GeneChip® microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize. Nine miRNA families (miR164, miR169, miR172, miR397, miR398, miR399, miR408, miR528, and miR827) were identified in leaves, and nine miRNA families (miR160, miR167, miR168, miR169, miR319, miR395, miR399, miR408, and miR528) identified in roots. They were verified by real time stem loop RT-PCR, and some with additional time points of nitrate limitation. The miRNAs identified showed overlapping or unique responses to chronic and transient nitrate limitation, as well as tissue specificity. The potential target genes of these miRNAs in maize were identified. The expression of some of these was examined by qRT-PCR. The potential function of these miRNAs in responding to nitrate limitation is described. Genome-wide miRNAs responding to nitrate limiting conditions in maize leaves and roots were identified. This provides an insight into the timing and tissue specificity of the transcriptional regulation to low nitrate availability in maize. The knowledge gained will help understand the important roles miRNAs play in maize responding to a nitrogen limiting environment and eventually develop strategies for the improvement of maize genetics.
    PLoS ONE 01/2011; 6(11):e28009. · 3.73 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436-0.566) were generally much higher than individual SNPs (0.247-0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2-100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10-100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5-10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.
    PLoS ONE 01/2011; 6(9):e24861. · 3.73 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: This paper describes two joint linkage-linkage disequilibrium (LD) mapping approaches: parallel mapping (independent linkage and LD analysis) and integrated mapping (datasets analyzed in combination). These approaches were achieved using 2,052 single nucleotide polymorphism (SNP) markers, including 659 SNPs developed from drought-response candidate genes, screened across three recombinant inbred line (RIL) populations and 305 diverse inbred lines, with anthesis-silking interval (ASI), an important trait for maize drought tolerance, as the target trait. Mapping efficiency was improved significantly due to increased population size and allele diversity and balanced allele frequencies. Integrated mapping identified 18 additional quantitative trait loci (QTL) not detected by parallel mapping. The use of haplotypes improved mapping efficiency, with the sum of phenotypic variation explained (PVE) increasing from 5.4% to 23.3% for single SNP-based analysis. Integrated mapping with haplotype further improved the mapping efficiency, and the most significant QTL had a PVE of up to 34.7%. Normal allele frequencies for 113 of 277 (40.8%) SNPs with minor allele frequency (<5%) in 305 lines were recovered in three RIL populations, three of which were significantly associated with ASI. The candidate genes identified by two significant haplotype loci included one for a SET domain protein involved in the control of flowering time and the other encoding aldo/keto reductase associated with detoxification pathways that contribute to cellular damage due to environmental stress. Joint linkage-LD mapping is a powerful approach for detecting QTL underlying complex traits, including drought tolerance.
    Proceedings of the National Academy of Sciences 10/2010; 107(45):19585-90. · 9.74 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.
    Theoretical and Applied Genetics 10/2009; 120(1):93-115. · 3.66 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: This study analyzes population structure and linkage disequilibrium (LD) among 187 com-monly used Chinese maize inbred lines, representing the genetic diversity among public, commercial and historically important lines for corn breeding. Seventy SSR loci, evenly distributed over 10 chromosomes, were assayed for polymorphism. The identified 290 alleles served to estimate population structure and analyze the genome-wide LD. The population of lines was highly structured, showing 6 subpopulations: BSSS (American BSSS including Reid), PA (group A germplasm derived from modern U.S. hybrids in China), PB (group B germplasm derived from modern U.S. hybrid in China), Lan (Lancaster Surecrop), LRC (derivative lines from Lvda Reb Cob, a Chinese landrace) and SPT (derivative lines from Si-ping-tou, a Chinese landrace). Forty lines, which formerly had an unknown and/or miscellaneous origin and pedigree record, were assigned to the appropriate group. Rela-tionship estimates based on SSR marker data were quantified in a Q matrix, and this information will inform breeder's decisions regarding crosses. Exten-sive inter-and intra-chromosomal LD was detected between 70 microsatellite loci for the investigated maize lines (2109 loci pairs in LD with D 0 [ 0.1 and 93 out of them at P \ 0.01).This suggests that rapidly evolving microsatellites may track recent population structure. Interlocus LD decay among the diverse maize germplasm indicated that association studies in QTLs and/or candidate genes might avoid nonfunc-tional and spurious associations since most of the LD blocks were broken between diverse germplasm. The defined population structure and the LD analysis present the basis for future association mapping. Keywords Association mapping Á Linkage disequilibrium Á Maize (Zea mays L.) Á Population structure Abbreviations CTAB Cetyltrimethylammonium bromide LD Linkage disequilibrium PCR Polymerase chain reaction PIC Polymorphic information content QTL Quantitative trait locus Electronic supplementary material The online version of this article (doi:10.1007/s11032-007-9140-8) contains supple-mentary material, which is available to authorized users.
    Molecular Breeding 01/2008; 21:407-418. · 3.25 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: The inference of genome ancestry and the estimation of molecular relatedness are of great importance for breeding efficiency and association studies. Seventy SSR loci, evenly distributed in 10 chromosomes, were assayed for polymorphism among 187 commonly used maize (Zea mays L.) inbreds which represent the genetic diversity in China. The identified 290 alleles served as raw data for estimating population structure using the coalescent linked loci, based on the ADMIXTURE model. Population number, K, has been inferred to be between five and seven. Specifying five subpopulations (K = 5) led to a distinct decrease and specifying K to be greater than six resulted in only minimal increases in the likelihood value. Therefore, population number, K, has been inferred into six subpopulations, which are PA, BSSS (includes Reid), PB, Lan (Lancaster Sure Crop), LRC (Luda Reb Cob, a Chinese landrace, and its derivatives), and SPT (Si-ping-tou, a Chinese landrace and its derivatives). The Kullback-Leibler distance of pairwise subpopulation was also inferred as n xp (187 x 6) Q matrices, which gave a detailed percentage of genetic composition of six subpopulations and molecular relatedness of each line. The genome-wide linkage disequilibrium (LD) indicated that the association studies in QTLs and/or candidate genes might avoid nonfunctional and spurious associations, as most of the LD blocks were broken among diverse germplasm. The defined population structure has given us a clear genetic structure of these lines for breeding practice and established a good basis for association analysis.
    Journal of Genetics and Genomics 09/2007; 34(8):738-48. · 2.08 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: Limited information is available on genetic variation in low-nitrogen (low-N) stress tolerance and N-use efficiency (NUE) among maize inbreds. To unveil this information, a panel of 189 diverse maize inbred lines was evaluated under contrasting levels of N availability over 2years. Low-N agronomic efficiency (LNAE), absolute grain yield (GY) at low-N conditions, and the ratio between GY at low-N and optimum-N conditions were taken into account to represent low-N tolerance. Additionally, N-agronomic efficiency (NAE) along with other agronomic traits was also analyzed. Analysis of variance revealed significant effects of genotype on LNAE, NAE, and GY. The estimated broad-sense heritability was 0.38 for LNAE while it was only 0.11 for NAE, implying that selection based on LNAE should be more effective than NAE. LNAE exhibited highly positive genotypic and phenotypic correlations with GY, ear kernel number (EKN), kernel weight, plant height (PH), and chlorophyll content at low-N conditions, while it was negatively correlated with grain-N content and anthesis-silking interval. Path analysis indicated that the EKN at low-N stress had the highest positive effects on LNAE. KeywordsGenetic variation–Low-N stress tolerance–N-agronomic efficiency–N-use efficiency–Maize
    Euphytica 180(2):281-290. · 1.64 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: Retrospective analyses may provide an understanding of unexploited genetic potential and indicate possible pathways for future yield improvement. The objectives of this study were to present maize(Zea mays L.)yield trends and plant traits changes for maize cultivars from the 1950s to the 2000s in China. Trials were conducted at three locations in 2007 and 2008, and at four locations in 2009. Twenty-seven single hybrids, four double-cross hybrids, and four open-pollinated varieties, were grown at three densities at each location each year. 56% of total yield gain was contributed to breeding from 1950 to 2000. New hybrids had more resistance to compound stress. Levels of response of all hybrids to higher-yielding environments were similar, and greater than that of OPVs. All maize cultivars showed morphological changes for all characteristics tested in a volatile manner from 1950 to 2000, except for relatively stable leaf number. ASI decreased and tolerance to root lodging improved, which were enhanced at higher plant densities. There were no trends for other characteristics at higher densities. Shorter maturity, smaller plant size and more tolerance to root and stalk lodging will be required for further yield improvement. Chinese maize yield improvement can benefit from agronomic strategies at higher plant densities.
    Euphytica 185(3). · 1.64 Impact Factor

Publication Stats

162 Citations
207 Downloads
2k Views
73.50 Total Impact Points

Institutions

  • 2009–2013
    • Chinese Academy of Agricultural Sciences
      • Institute of Crop Sciences
      Beijing, Beijing Shi, China
    • International Maize and Wheat Improvement Center
      Tezcoco, México, Mexico
  • 2010–2011
    • Sichuan Agricultural University
      Hua-yang, Sichuan, China