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Shihuang Zhang

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Shihuang Zhang
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Shihuang Zhang

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    Heterotic grouping of maize inbred lines using RFLP and SSR markers
    (Institute of Crop Sciences, 2001) Yuan, L.X.; Fun Jun-Hua; Shihuang Zhang; Liu Xin-Zhi; Peng Ze-Bin; Xinhai Li; Warburton, M.; Khairallah, M.M.
    Publication
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    Zea mays (L.) P1 locus for cob glume color identified as a post-domestication selection target with an effect on temperate maize genomes
    (Elsevier, 2013) Chuanxiao Xie; Jianfeng Weng; Wenguo Liu; Cheng Zou; Zhuanfang Hao; Wenxue Li; Minshun Li; Xiaosen Guo; Gengyun Zhang; Yunbi Xu; Xinhai Li; Shihuang Zhang
    Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study (GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a ; log10P value for surrounding SNPs higher than the Bonferroni threshold ( < 0.001) when a mixed linear model (MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium (LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of ; and Tajima's D were significantly (P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing (180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.
    Publication
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    Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize
    (Public Library of Science, 2011) Yanli Lu; Shah, T.; Zhuanfang Hao; Taba, S.; Shihuang Zhang; Shibin Gao; Jian Liu; Moju Cao; Jing Wang; A. Bhanu Prakash; Tingzhao Rong; Yunbi Xu
    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.
    Publication
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    Maize in China: production systems, constraints, and research priorities
    (CIMMYT, 2006) Meng, E.; Ruifa Hu; Xiaohua Shi; Shihuang Zhang
    This report was undertaken as part of a seven-country project to promote the sustainable intensification of maize production systems in upland environments in Asia. Maize is cultivated throughout China and plays a key role in farm households through its contribution to food, feed, and income. As one of the primary sources of feed in China, it has played an important role in the rapid development of poultry and livestock industries. Maize production environments are characterized in the report using findings from primary farm and village level data collected across China’s maize belt. An assessment of technological constraints and needs of farm households is presented in the report, as well as the results of a maize research priority-setting workshop, where farm and village level information and experience were utilized to focus on the role of research and technology development in improving maize productivity. The identification of constraints to maize production highlighted differences in the surveyed regions, but also revealed many common problems encountered by maize farmers. Drought was targeted as a key constraint, along with others such as poor on-farm crop management, lack of technology and information dissemination, and poor seed quality. Participating farmers and scientists discussed a range of possible solutions to eliminate or minimize the effect of the constraints. Some of the constraints can largely be addressed through technological solutions, although the mere availability or development of technological solutions does not guarantee either their accessibility to farmers or their on-farm use. A challenging and unique mix of government intervention and liberalization of agricultural and market policies continue to influence maize production in China. Addressing the complex set of identified priority constraints to future maize production will necessarily involve a combination of science and policies to tackle the broader issues of markets, infrastructure, and farmer capacity.
    Publication