Yong-Ming Gao

Chinese Academy of Agricultural Sciences, Peping, Beijing, China

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Publications (34)28.99 Total impact

  • No preview · Article · Jan 2015 · ACTA AGRONOMICA SINICA
  • [Show abstract] [Hide abstract] ABSTRACT: Abnormal heading in hybrid rice production has caused great economic loss in recent years, but the genetic basis of this phenomenon remains elusive. In this study, we developed four testcross populations using 38 introgression lines (ILs) from Shuhui 527 (SH527)/Fuhui 838 (FH838)//SH527 population as male parents and four male sterile lines (MSLs; namely II-32A, Xieqingzao A, Gang 46A and Jin 23A) as female parents. Progeny testing allowed us to identify 55 abnormal heading combinations in Hefei, but had late heading date in Hangzhou and Guangzhou of China. By one- and two-way analysis of variance, a total of 21 QTLs and 31 pairs of epistatic QTLs associated with photosensitivity were identified in the four populations, respectively. Genotypic analysis showed that the IL parent of most abnormal heading combinations showed some introgressions at markers RM331 and RM3395 on chromosome 8 (strongly associated with the known genes OsHAP3H/DTH8/Ghd8/LHD1) of donor FH838 alleles, and these two markers were also identified as affecting photosensitivity. The observation that the recipient parent (SH527), donor parent (FH838), their testcross combinations with four MSLs, and the IL parents of abnormal heading combinations had normal heading date in Hefei suggested that OsHAP3H/DTH8/Ghd8/LHD1 showed no independent regulation on abnormal heading in the abnormal heading combinations. It is noteworthy that complex epistasis among RM331 or RM3395 with other loci, including dominant × additive, additive × dominant, and dominant × dominant epistases, were identified only in the four testcross populations of the current study, but not in the SH527/FH838//SH527 population, suggesting the cause of abnormal heading in abnormal heading combinations in Hefei and delayed heading in Hangzhou and Guangzhou.
    No preview · Article · Jul 2014 · Rice Science
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    [Show abstract] [Hide abstract] ABSTRACT: The 3,000 rice genomes project The 3,000 rice genomes project 1,2,3* Abstract Background: Rice, Oryza sativa L., is the staple food for half the world's population. By 2030, the production of rice must increase by at least 25% in order to keep up with global population growth and demand. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land, as well as to ensure a stable global food supply. Findings: We resequenced a core collection of 3,000 rice accessions from 89 countries. All 3,000 genomes had an average sequencing depth of 14×, with average genome coverages and mapping rates of 94.0% and 92.5%, respectively. From our sequencing efforts, approximately 18.9 million single nucleotide polymorphisms (SNPs) in rice were discovered when aligned to the reference genome of the temperate japonica variety, Nipponbare. Phylogenetic analyses based on SNP data confirmed differentiation of the O. sativa gene pool into 5 varietal groups – indica, aus/boro, basmati/sadri, tropical japonica and temperate japonica. Conclusions: Here, we report an international resequencing effort of 3,000 rice genomes. This data serves as a foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or genetic approaches. It also serves to understand the genomic diversity within O. sativa at a higher level of detail. With the release of the sequencing data, the project calls for the global rice community to take advantage of this data as a foundation for establishing a global, public rice genetic/genomic database and information platform for advancing rice breeding technology for future rice improvement.
    Full-text · Article · May 2014
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    Fan Zhang · Xiu-Fang Ma · Yong-Ming Gao · Xian-Bin Hao · Zhi-Kang Li
    [Show abstract] [Hide abstract] ABSTRACT: Cold stress is an important factor limiting rice yield in many areas of high latitude and altitude. Considerable efforts have been taken to genetically dissect cold tolerance (CT) in rice using DNA markers. Because of possible epistasis and gene × environment interactions associated with identified quantitative trait loci, the results of these genetic studies have unfortunately not been directly applicable to marker-assisted selection for improved rice CT. In this study, we demonstrated the utility of a selective introgression strategy for simultaneous improvement and genetic dissection of rice seedling CT. A set of japonica introgression lines (ILs) with significantly improved seedling CT were developed from four backcross populations based on two rounds of selection. Genetic characterization of these cold-tolerant ILs revealed two important aspects of genome-wide responses to strong phenotypic selection for rice CT: (1) significant over-introgression of donor alleles at 57 loci in 29 functional genetic units (FGUs) across the rice genome and (2) pronounced non-random associations between or among alleles at many unlinked CT loci. Linkage disequilibrium analyses of the detected CT loci allowed us to construct putative genetic networks (multi-locus structures) underlying the seedling CT of rice. Each network consisted of a single FGU, with high introgression as the putative regulator plus two to three groups of highly associated downstream FGUs. A bioinformatics search of rice genomic regions harboring these putative regulators identified a small set of candidate regulatory genes that are known to be involved in plant stress response. Our results suggest that CT in rice is controlled by multiple pathways. Genetic complementarity between parental-derived functional alleles at many loci within a given pathway provides an appropriate explanation for the commonly observed hidden diversity and transgressive segregation of CT and other complex traits in rice.
    Full-text · Article · May 2014 · BMC Genetics
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    [Show abstract] [Hide abstract] ABSTRACT: How to overcome yield stagnation is a big challenge to rice breeders. An effective method for quickly developing new cultivars is to further improve an outstanding cultivar. In this study, three advanced backcross populations under yield selection that consist of 123 BC2F2:4 introgression lines (ILs) were developed by crossing Minghui 86 (recurrent parent, RP) with three high-yielding varieties (donors), namely, ZDZ057, Fuhui 838, and Teqing, respectively. The progeny testing allowed the identification of 12 promising ILs that had significantly higher mean grain yields than Minghui 86 in two environments. A total of 55 QTLs that affect grain yield and its related traits were identified, which included 50 QTLs that were detected using the likelihood ratio test based on stepwise regression (RSTEP-LRT) method, and eight grain yield per plant (GY) QTLs were detected using chi-squared (c2) test. Among these QTLs, five QTLs were simultaneously detected in different populations and 22 QTLs were detected in both environments. The beneficial donor alleles for increased GY and its related traits were identified in 63.6% (35 out of 55) of the QTLs. These promising ILs and QTLs identified will provide the elite breeding materials and genetic information for further improvement of the grain yield for Minghui 86 through pyramiding breeding.
    Full-text · Article · Apr 2013 · Agricultural Sciences in China
  • Chao XIANG · Li-jun QU · Yong-ming GAO · Ying-yao SHI
    [Show abstract] [Hide abstract] ABSTRACT: Floral transition, which is referred to as a plant's transition from vegetative stage to reproductive stage, is considered to be a critical developmental switch in higher plants, for a timely flowering is a major factor of reproductive success. Endogenous and environmental cues, such as photoperiod, light quality, plant hormones concentrations and temperature, provide information to the plants whether the environment is favorable for flowering. These cues promote, or prevent, flowering through a complex genetic network, mediated by a careful orchestration of temporal and spatial gene expression. One of such cues is photoperiod. Rice (Oryza sativa L.) serves as a powerful model species for the understanding of flowering in higher plants, including flower development and photoperiodic control of flowering. In this review, we overviewed and discussed the flower development and its model. We also overviewed the photoperiodic pathways in rice flowering control, and summarized the pathways at molecular level.
    No preview · Article · Mar 2013 · Rice Science
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    [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.
    Full-text · Article · Feb 2013 · Theoretical and Applied Genetics
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    Full-text · Article · Jan 2013 · Plant Pathology
  • No preview · Article · Sep 2011 · ACTA AGRONOMICA SINICA
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    [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.
    Full-text · Article · Jun 2011 · Theoretical and Applied Genetics
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    Dataset: Table S2
    [Show abstract] [Hide abstract] ABSTRACT: Quantitative genetics presentation of multilocus zygote genotypes and their corresponding phenotypic effect, aij (assuming complete dominance) of three unlinked segregating loci of a single functional genetic unit (FGU) in an F2 population with two alleles at each of the loci, one functional allele (the capital letter) and the other nonfunctional mutant (the small letter). (0.05 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Table S9
    [Show abstract] [Hide abstract] ABSTRACT: Expected population parameters, μ (mean) and σ2G (variance), of segregating loci in a signaling pathway of model (2) resulting from positive and negative selection under the seven scenarios of biparental populations defined in Table 1. (0.28 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Table S11
    [Show abstract] [Hide abstract] ABSTRACT: Genetic parameters of 16 QTLs in seven groups (QG) affecting plant heights identified in the IR64/Azucena DH population evaluated in 1994 wet season at IRRI [36]. (0.07 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Table S1
    [Show abstract] [Hide abstract] ABSTRACT: Nature of allelic diversity at 26 cloned QTLs. (0.07 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Table S5
    [Show abstract] [Hide abstract] ABSTRACT: Comparison between the estimated epistatic effects of four digenic genotypes for each epistatic loci pair under scenario 3 (Figure 1B and Table 1) and their phenotypic values assigned based on model (2) in an F2 or RI (DH) population. (0.06 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Table S6
    [Show abstract] [Hide abstract] ABSTRACT: The genetic expectations and phenotypic values of digenic genotypes in trait X based on model (2) and the classic quantitative genetics model under scenario 3 (Figure 1B and Table 1) in a RI or DH population. (0.10 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Table S7
    [Show abstract] [Hide abstract] ABSTRACT: The genetic expectations and phenotypic values of digenic genotypes in trait X predicted based on model (2) and the classic quantitative genetic model under scenario 3 (Figure 1B and Table 1) in an F2 (complete dominance) population. (0.10 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Table S12
    [Show abstract] [Hide abstract] ABSTRACT: Inferred effects on plant height (cm) of the SD1 mediated downstream pathways (QG1-3, QPh8a and QPh9b) based on the theoretical expectations and observed plant heights (in cm) of the tri-locus genotypes at the corresponding QTLs. (0.06 MB DOC)
    Full-text · Dataset · Jan 2011
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    Dataset: Figure S4
    [Show abstract] [Hide abstract] ABSTRACT: The expected cumulated frequency shifts of functional alleles in response to positive and negative selection under the seven scenarios defined in Table 1 (A) under complete dominance at all segregating loci in an F2 population, (B) under mixed gene action (complete dominance for the regulatory S and T loci and additivity for the downstream B loci) in an F2 population, (C) complete additivity in an F2 population, and (D) RI or DH population. In the steps of selection, 1, 2, …, 8 represent the selection trait thresholds of ≥4.0 or ≤4.0, …, ≥32.0 or ≤32.0 for positive or negative selection defined in Table S9. (0.51 MB PDF)
    Full-text · Dataset · Jan 2011
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    Dataset: Figure S3
    [Show abstract] [Hide abstract] ABSTRACT: The expected mid-parental trait heterosis (HMP) under three types of gene actions under scenarios 3–7 of Table 1 regarding the type and number of segregating loci in a signaling pathway defined in Figure 1B. In the mixed gene action, all segregating loci at regulatory (S and T) levels are completely dominant, and all loci at the downstream level B act additively. r and n are the numbers of segregating loci and possible distributions of the segregating loci in the parents. (1.64 MB TIF)
    Full-text · Dataset · Jan 2011