Yong-Ming Gao

Publications (11)23.62 Total impact

• Source

  Available from: Jauhar Ali

  Article: Three genetic systems controlling growth, development and productivity of rice (Oryza sativa L.): a reevaluation of the 'Green Revolution'

  Fan Zhang, Yun-Zhu Jiang, Si-Bin Yu, J Ali, A H Paterson, G S Khush, Jian-Long Xu, Yong-Ming Gao, Bin-Ying Fu, R Lafitte, Zhi-Kang Li
  [show abstract] [hide abstract]
  ABSTRACT: The Green Revolution (GR-I) included worldwide adoption of semi-dwarf rice cultivars (SRCs) with mutant alleles at GA20ox2 or SD1 encoding gibberellin 20-oxidase. Two series of experiments were conducted to characterize the pleiotropic effects of SD1 and its relationships with large numbers of QTLs affecting rice growth, development and productivity. The pleiotropic effects of SD1 in the IR64 genetic background for increased height, root length/mass and grain weight, and for reduced spikelet fertility and delayed heading were first demonstrated using large populations derived from near isogenic IR64 lines of SD1. In the second set of experiments, QTLs controlling nine growth and yield traits were characterized using a new molecular quantitative genetics model and the phenotypic data of the well-known IR64/Azucena DH population evaluated across 11 environments, which revealed three genetic systems: the SD1-mediated, SD1-repressed and SD1-independent pathways that control rice growth, development and productivity. The SD1-mediated system comprised 43 functional genetic units (FGUs) controlled by GA. The SD1-repressed system was the alternative one comprising 38 FGUs that were only expressed in the mutant sd1 backgrounds. The SD1-independent one comprised 64 FGUs that were independent of SD1. GR-I resulted from the overall differences between the former two systems in the three aspects: (1) trait/environment-specific contributions; (2) distribution of favorable alleles for increased productivity in the parents; and (3) different responses to (fertilizer) inputs. Our results suggest that at 71.4 % of the detected loci, a QTL resulted from the difference between a functional allele and a loss-of-function mutant, whereas at the remaining 28.6 % of loci, from two functional alleles with differentiated effects. Our results suggest two general strategies to achieve GR-II (1) by further exploiting the genetic potential of the SD1-repressed and SD1-independent pathways and (2) by restoring the SD1-mediated pathways, or 'back to the nature' to fully exploit the genetic diversity of those loci in the SD1-mediated pathways which are virtually inaccessible to most rice-breeding programs worldwide that are exclusively based on sd1.
  Theoretical and Applied Genetics 02/2013; · 3.30 Impact Factor
• Article: Pyramiding Xa23 and Rxo1 for resistance to two bacterial diseases into an elite indica rice variety using molecular approaches

  Yong-Li Zhou, Jian-Long Xu, Shao-Chuan Zhou, Jing Yu, Xue-Wen Xie, Mei-Rong Xu, Yong Sun, Ling-Hua Zhu, Bin-Ying Fu, Yong-Ming Gao, Zhi-Kang Li
  [show abstract] [hide abstract]
  ABSTRACT: Rice bacterial leaf blight (BB) caused by Xanthomonas oryzae pv. oryzae and bacterial leaf streak (BLS) caused by X. oryzae pv. oryzicola (Xoc) are two important diseases of rice that often outbreak simultaneously and constrain rice production in much of Asia and parts of Africa. Developing resistant cultivars has been the most effective approach to control BB, however, most single resistance genes have limited value in breeding programs because of their narrow-spectrum of resistance to the races of the pathogen. By contrast, there is little progress in breeding varieties resistant to Xoc since BLS resistance in rice was a quantitative trait and so far only a few quantitative resistance loci have been identified. We reported here the development of a high yield elite line, Lu-You-Zhan highly resistant to both BB and BLS by pyramiding Xa23 with a wide-spectrum resistance to BB derived from wild rice and a non-host maize resistance gene, Rxo1, using both marker assisted selection (MAS) and genetic engineering. Our study has provided strong evidence that non-host R genes could be a valuable source of resistance in combating those plant diseases where no single R gene controlling high level of resistance exists and demonstrated that MAS combined with transgenic technologies are an effective strategy to achieve high level of resistance against multiple plant diseases.
  Molecular Breeding 04/2012; 23(2):279-287. · 2.85 Impact Factor
• Source

  Available from: Zhi-Kang Li

  Article: Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.).

  Haodong Chen, Hang He, Yanjiao Zou, Wei Chen, Renbo Yu, Xia Liu, Yang Yang, Yong-Ming Gao, Jian-Long Xu, Liu-Min Fan, Yi Li, Zhi-Kang Li, Xing Wang Deng
  [show abstract] [hide abstract]
  ABSTRACT: Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica-Japonica subspecific differentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice genome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica-Japonica and Indica-Indica crosses.
  Theoretical and Applied Genetics 06/2011; 123(6):869-79. · 3.30 Impact Factor
• Source

  Available from: Jauhar Ali

  Article: Dissecting genetic networks underlying complex phenotypes: the theoretical framework.

  Fan Zhang, Hu-Qu Zhai, Andrew H Paterson, Jian-Long Xu, Yong-Ming Gao, Tian-Qing Zheng, Rong-Ling Wu, Bin-Ying Fu, Jauhar Ali, Zhi-Kang Li
  [show abstract] [hide abstract]
  ABSTRACT: Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many 'downstream' loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and "co-adapted" gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis.
  PLoS ONE 01/2011; 6(1):e14541. · 4.09 Impact Factor
• Article: Identification of functional candidate genes for drought tolerance in rice.

  Bin-Ying Fu, Jian-Hua Xiong, Ling-Hua Zhu, Xiu-Qin Zhao, Hua-Xue Xu, Yong-Ming Gao, Yang-Sheng Li, Jian-Long Xu, Zhi-Kang Li
  [show abstract] [hide abstract]
  ABSTRACT: Drought tolerance (DT) in rice is known to be controlled by many quantitative trait loci (QTLs) and involved differential expression of large numbers of genes, but linking QTLs with their underlying genes remains the most challenging issue in plant molecular biology. To shed some light on this issue, differential gene expression in response to PEG simulated drought in 3 unique genetic materials (a lowland rice, IR64 and its derived line, PD86 which has 11 introgressed DT QTLs, and a upland rice IRAT109) was investigated using a PCR-based subtractive hybridization strategy. More than 300 unique subtracted cDNA sequences, covering genes of diverse cellular activities and functions, were identified and confirmed by semi-quantitative and quantitative RT-PCR. Detailed bioinformatics analyses of the data revealed two interesting results. First, the levels and mechanisms of DT of the three rice lines were associated with the number and types of differentially expressed genes, suggesting different DT mechanisms in rice are controlled by different sets of genes and different metabolic pathways, and most differentially expressed genes under drought were able to contribute to DT. Second, there appeared a high correspondence in genomic location between DT QTLs and clusters of differentially expressed genes in rice, suggesting some DT QTLs may represent clusters of co-regulated and functionally related genes. Thus, differential gene expression analyses using genetically characterized materials can provide additional insights into the molecular basis of QTLs and convergent evidence to shortlist the candidate genes for target QTLs.
  Molecular and General Genetics 01/2008; 278(6):599-609. · 2.63 Impact Factor
• Source

  Available from: ricedata.cn

  Article: Mapping QTLs with digenic epistasis under multiple environments and predicting heterosis based on QTL effects.

  Yong-Ming Gao, Jun Zhu
  [show abstract] [hide abstract]
  ABSTRACT: Mixed linear model approach was proposed for mapping QTLs with the digenic epistasis and QTL by environment (QE) interaction as well as additive and dominant effects. Monte Carlo simulations indicated that the proposed method could provide unbiased estimations for both positions and genetic main effects of QTLs, as well as unbiased predictions for QE interaction effects. A method was suggested for predicting heterosis based on individual QTL effects. The immortalized F(2) (IF(2)) population constructed by random mating among RI or DH lines is appropriate for mapping QTLs with epistasis and their QE interaction. Based on the models and methodology proposed, we developed a QTL mapping software, QTLMapper 2.0 on the basis of QTLmapper 1.0, which is suitable for analyzing populations of DH, RIL, F(2) and IF(2). Data of thousand grain weight of IF(2) population with 240 lines derived from elite hybrid rice Shanyou 63 were analyzed as a worked example.
  Theoretical and Applied Genetics 09/2007; 115(3):325-33. · 3.30 Impact Factor
• Source

  Available from: Jauhar Ali

  Article: Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.).

  Zhi-Kang Li, Bin-Ying Fu, Yong-Ming Gao, Jian-Long Xu, J Ali, H R Lafitte, Yun-Zhu Jiang, J Domingo Rey, C H M Vijayakumar, R Maghirang, Tian-Qing Zheng, Ling-Hua Zhu
  [show abstract] [hide abstract]
  ABSTRACT: Tremendous efforts have been taken worldwide to develop genome-wide genetic stocks for rice functional genomic (FG) research since the rice genome was completely sequenced. To facilitate FG research of complex polygenic phenotypes in rice, we report the development of over 20,000 introgression lines (ILs) in three elite rice genetic backgrounds for a wide range of complex traits, including resistances/tolerances to many biotic and abiotic stresses, morpho-agronomic traits, physiological traits, etc., by selective introgression. ILs within each genetic background are phenotypically similar to their recurrent parent but each carries one or a few traits introgressed from a known donor. Together, these ILs contain a significant portion of loci affecting the selected complex phenotypes at which allelic diversity exists in the primary gene pool of rice. A forward genetics strategy was proposed and demonstrated with examples on how to use these ILs for large-scale FG research. Complementary to the genome-wide insertional mutants, these ILs opens a new way for highly efficient discovery, candidate gene identification and cloning of important QTLs for specific phenotypes based on convergent evidence from QTL position, expression profiling, functional and molecular diversity analyses of candidate genes, highlights the importance of genetic networks underlying complex phenotypes in rice that may ultimately lead to more complete understanding of the genetic and molecular bases of quantitative trait variation in rice.
  Plant Molecular Biology 10/2005; 59(1):33-52. · 4.15 Impact Factor
• Source

  Available from: zju.edu.cn

  Article: Analysis of digenic epistatic effects and QE interaction effects QTL controlling grain weight in rice.

  Yong-ming Gao, Jun Zhu, You-shen Song, Ci-xin He, Chun-hai Shi, Yong-zhong Xing
  [show abstract] [hide abstract]
  ABSTRACT: Immortalized F(2) population of rice (Oryza sativa L.) was developed by randomly mating F(1) among recombinant inbred (RI) lines derived from (Zhenshan 97B x Minghui 63), which allowed replications within and across environments. QTL (quantitative trait loci) mapping analysis on kilo-grain weight of immortalized F(2) population was performed by using newly developed software for QTL mapping, QTLMapper 2.0. Eleven distinctly digenic epistatic loci included a total of 15 QTL were located on eight chromosomes. QTL main effects of additive, dominance, and additive x additive, additive x dominance, and dominance x dominance interactions were estimated. Interaction effects between QTL main effects and environments (QE) were predicted. Less than 40% of single effects, most of which were additive effects, for identified QTL were significant at 5% level. The directional difference for QTL main effects suggested that these QTL were distributed in parents in the repulsion phase. This should make it feasible to improve kilo-grain weight of both parents by selecting appropriate new recombinants. Only few of the QE interaction effects were significant. Application prospect for QTL mapping achievements in genetic breeding was discussed.
  Journal of Zhejiang University SCIENCE 05/2004; 5(4):371-7.
• Article: [Studies of marker screening efficiency and corresponding influencing factors in QTL composite interval mapping].

  Yong-Ming Gao, Ping Wan
  [show abstract] [hide abstract]
  ABSTRACT: Screening markers efficiently is the foundation of mapping QTLs by composite interval mapping. Main and interaction markers distinguished, besides using background control for genetic variation, could also be used to construct intervals of two-way searching for mapping QTLs with epistasis, which can save a lot of calculation time. Therefore, the efficiency of marker screening would affect power and precision of QTL mapping. A doubled haploid population with 200 individuals and 5 chromosomes was constructed, with 50 markers evenly distributed at 10 cM space. Among a total of 6 QTLs, one was placed on chromosome I, two linked on chromosome II, and the other three linked on chromosome IV. QTL setting included additive effects and epistatic effects of additive x additive, the corresponding QTL interaction effects were set if data were collected under multiple environments. The heritability was assumed to be 0.5 if no special declaration. The power of marker screening by stepwise regression, forward regression, and three methods for random effect prediction, e.g. best linear unbiased prediction (BLUP), linear unbiased prediction (LUP) and adjusted unbiased prediction (AUP), was studied and compared through 100 Monte Carlo simulations. The results indicated that the marker screening power by stepwise regression at 0.1, 0.05 and 0.01 significant level changed from 2% to 68%, the power changed from 2% to 72% by forward regression. The larger the QTL effects, the higher the marker screening power. While the power of marker screening by three random effect prediction was very low, the maximum was only 13%. That suggested that regression methods were much better than those by using the approaches of random effect prediction to identify efficient markers flanking QTLs, and forward selection method was more simple and efficient. The results of simulation study on heritability showed that heightening of both general heritability and interaction heritability of genotype x environments could enhance marker screening power, the former had a greater influence on QTLs with larger main and/or epistatic effects, while the later on QTLs with small main and/or epistatic effects. The simulation of 100 times was also conducted to study the influence of different marker number and density on marker screening power. It is indicated that the marker screening power would decrease if there were too many markers, especially with high density in a mapping population, which suggested that a mapping population with definite individuals could only hold limited markers. According to the simulation study, the reasonable number of markers should not be more than individuals. The simulation study of marker screening under multiple environments showed high total power of marker screening. In order to relieve the problem that marker screening power restricted the efficiency of QTL mapping, markers identified in multiple environments could be used to construct two search intervals.
  Acta Genetica Sinica 07/2002; 29(6):555-61.
• Source

  Available from: Zhi-Kang Li

  Article: Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.)

  Haodong Chen, bullet Hang, He @bullet, Yanjiao Zou, bullet Wei, Chen @bullet, Renbo Yu, Xia Liu, bullet Yang, Yang @bullet, Yong-Ming Gao, Jian-Long Xu, bullet Liu, Min Fan, bullet Yi, Li @bullet, Zhi-Kang Li, bullet Xing, Wang Deng
  [show abstract] [hide abstract]
  ABSTRACT: Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 represen-tative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica–Japonica subspecific dif-ferentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice gen-ome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica–Japonica and Indica–Indica crosses.
• Source

  Available from: Zhi-Kang Li

  Article: QTLs affecting morph-physiological traits related to drought tolerance detected in overlapping introgression lines of rice (Oryza sativa L.)

  Xiu-Qin Zhao, Jian-Long Xu, Ming Zhao, Renee Lafitte, Ling-Hua Zhu, Bin-Ying Fu, Yong-Ming Gao, Zhi-Kang Li
  [show abstract] [hide abstract]
  ABSTRACT: Plant photosynthetic traits such as net photosynthetic rate (Pn), stomata conductance (gs), transpiration rate (Tr), and intercellular CO2 concentration (Ci), are known to relate to drought tolerance in plants, but the genetic basis of these traits remains largely uncharacterized because of the difficulty in phenotyping physiological traits in a large mapping population. In this study, a set of 55 overlapping introgression lines (ILs) in the Teqing (indica) background were used to genetically dissect several morph-physiological traits and their relationship with grain yield under water stress and non-stress conditions. These traits included specific leaf weight (SLW), chlorophyll content (CC), leaf stomata frequency (SF), Pn, gs, Tr, and Ci. A total of 40 QTLs affecting the measured traits were identified and mapped to 21 genomic regions in the rice genome. Clustered QTLs affecting Pn, gs, Tr, and Ci in the same genomic regions suggest common genetic bases for the physiological traits. Low or no phenotypic correlations between leaf morphological traits and photosynthetic traits and between morph-physiological traits and grain yield (GY) appeared to be due to inconsistence in QTL effect for clustered QTLs, unlinked QTLs affecting different traits, and to possible epistasis that could not be adequately addressed in this study. Our results indicate that improving drought tolerant (DT) of rice by selecting any single secondary traits is not expected to be effective and the identified QTLs for GY and related morph-physiological traits should be carefully confirmed before to be used for improving DT in rice by MAS.
  Plant Science.