Yaou Shen

Latest Publications

1. JHM

   Effects of ZmHIPP on lead tolerance in maize seedlings: Novel ideas for soil bioremediation

   Ma, Langlang, An, Rong, Jiang, Li, Zhang, Chen, Li, Zhaoling, Zou, Chaoying, Yang, Cong, Pan, Guangtang, Lübberstedt, Thomas, and Shen, Yaou

   Journal of Hazardous Materials May 2022

   Abs HTML PDF

   Extensive lead (Pb) absorption by plants affects their growth and development and causes damage to the human body by entering the food chain. In this study, we cloned ZmHIPP, a gene associated with Pb tolerance and accumulation in maize, using combined linkage mapping and weighted gene co-expression network analysis. We show that ZmHIPP, which encodes a heavy metal-associated isoprenylated plant protein, positively modulated Pb tolerance and accumulation in maize seedlings, Arabidopsis, and yeast. The genetic variation locus (A/G) in the promoter of ZmHIPP contributed to the phenotypic disparity in Pb tolerance among different maize inbred lines by altering the expression abundance of ZmHIPP. Knockdown of ZmHIPP significantly inhibited growth and decreased Pb accumulation in maize seedlings under Pb stress. ZmHIPP facilitated Pb deposition in the cell wall and prevented it from entering the intracellular organelles, thereby alleviating Pb toxicity in maize seedlings. Compared to that in the mutant zmhipp, the accumulated Pb in the wild-type line mainly consisted of the low-toxicity forms of Pb. Our study increases the understanding of the mechanism underlying Pb tolerance in maize and provides new insights into the bioremediation of Pb-polluted soil.

2. PJ

   Genetic variations in ZmSAUR15 contribute to the formation of immature embryo-derived embryonic calluses in maize

   Wang, Yanli, He, Shijiang, Long, Yun, Zhang, Xiaoling, Zhang, Xiaoxiang, Hu, Hongmei, Li, Zhaoling, Hou, Fengxia, Ge, Fei, Gao, Shibin, Pan, Guangtang, Ma, Langlang, and Shen, Yaou

   The Plant Journal Feb 2022

   Abs HTML PDF

   The ability of immature maize (Zea mays) embryos to form embryonic calluses (ECs) is highly genotype dependent, which limits transgenic breeding development in maize. Here, we report the association map-based cloning of ZmSAUR15 using an association panel (AP) consisting of 309 inbred lines with diverse formation abilities for ECs. We demonstrated that ZmSAUR15, which encodes a small auxin-upregulated RNA, acts as a negative effector in maize EC induction. Polymorphisms in the ZmSAUR15 promoter that influence the expression of ZmSAUR15 transcripts modulate the EC induction capacity in maize. ZmSAUR15 is involved in indole-3-acetic acid biosynthesis and cell division in immature embryo-derived callus. The ability of immature embryos to induce EC formation can be improved by the knockout of ZmSAUR15, which consequently increases the callus regeneration efficiency. Our study provides new insights into overcoming the genotypic limitations associated with EC formation and improving genetic transformation in maize.

3. TAG

   GWAS and transcriptome analysis reveal MADS26 involved in seed germination ability in maize

   Ma, Langlang, Wang, Chen, Hu, Yu, Dai, Wei, Liang, Zhenjuan, Zou, Chaoying, Pan, Guangtang, Lübberstedt, Thomas, and Shen, Yaou

   Theoretical and Applied Genetics Mar 2022

   Abs HTML PDF

   MADS26 affecting maize seed germination was identified by GWAS and transcriptomics. Gene-based association analyses revealed three variations within MADS26 regulating seed germination traits. Overexpressed MADS26 in Arabidopsis improved seed germination.

4. PBJ

   Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping

   Liu, Min, Tan, Xiaolong, Yang, Yan, Liu, Peng, Zhang, Xiaoxiang, Zhang, Yinchao, Wang, Lei, Hu, Yu, Ma, Langlang, Li, Zhaoling, Zhang, Yanling, Zou, Chaoying, Lin, Haijian, Gao, Shibin, Lee, Michael, Lübberstedt, Thomas, Pan, Guangtang, and Shen, Yaou

   Plant Biotechnology Journal Mar 2020

   Abs HTML PDF

   Kernel size-related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P \textless 2.25 × 10−6) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P \textless 1 × 10−3) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable-effect SNPs and the co-localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co-localized SNPs, of which zma-miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma-miR164e resulted in the down-regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker-assisted selection (MAS) for high-yield breeding in maize.

5. CJ

   Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

   Ge, Fei, Qu, Jingtao, Liu, Peng, Pan, Lang, Zou, Chaoying, Yuan, Guangsheng, Yang, Cong, Pan, Guangtang, Huang, Jianwei, Ma, Langlang, and Shen, Yaou

   The Crop Journal Aug 2021

   Abs HTML PDF

   The current assembled maize genomes cannot represent the broad genetic diversity of maize germplasms. Acquiring more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in maize. Here we describe the genome sequence and annotation of A188, a maize inbred line with high phenotypic variation relative to other lines, acquired by single-molecule sequencing and optical genome mapping. We assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to 9.73 Mb for B73 and 10.2 Mb for Mo17. Based on the B73_RefGen_V4 genome, 295 scaffolds (2084.35 Mb, 94.30% of the final genome assembly) were anchored and oriented on ten chromosomes. Comparative analysis revealed that ∼30% of the predicted A188 genes showed large structural divergence from B73, Mo17, and W22 genomes, which causes high protein divergence and may lead to phenotypic variation among the four inbred lines. As a line with high embryonic callus (EC) induction capacity, A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in maize. Combining our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.

6. BMC

   Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

   Liu, Peng, Zhang, Yinchao, Zou, Chaoying, Yang, Cong, Pan, Guangtang, Ma, Langlang, and Shen, Yaou

   BMC Genomics Aug 2022

   Abs HTML PDF

   Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance.

7. TAG

   A combination of linkage mapping and GWAS brings new elements on the genetic basis of yield-related traits in maize across multiple environments

   Zhang, Xiaoxiang, Guan, Zhongrong, Li, Zhaoling, Liu, Peng, Ma, Langlang, Zhang, Yinchao, Pan, Lang, He, Shijiang, Zhang, Yanling, Li, Peng, Ge, Fei, Zou, Chaoying, He, Yongcong, Gao, Shibin, Pan, Guangtang, and Shen, Yaou

   Theoretical and Applied Genetics Oct 2020

   Abs HTML PDF

   Using GWAS and QTL mapping identified 100 QTL and 138 SNPs, which control yield-related traits in maize. The candidate gene GRMZM2G098557 was further validated to regulate ear row number by using a segregation population.

8. MP

   The Coix Genome Provides Insights into Panicoideae Evolution and Papery Hull Domestication

   Guo, Chao, Wang, Yanan, Yang, Aiguo, He, Jun, Xiao, Chaowen, Lv, Shanhua, Han, Fengming, Yuan, Yibing, Yuan, Yuan, Dong, Xiaolong, Guo, Juan, Yang, Yawen, Liu, Hailan, Zuo, Ningzhi, Hu, Yaxi, Zhao, Kangxu, Jiang, Zhengbo, Wang, Xing, Jiang, Tingting, Shen, Yaou, Cao, Moju, Wang, Yuan, Long, Zhaobo, Rong, Tingzhao, Huang, Luqi, and Zhou, Shufeng

   Molecular Plant Feb 2020

   Abs HTML PDF

   Coix is a grass crop domesticated as early as the Neolithic era. It is still widely cultivated for both highly nutritional food and medicinal use. However, the genetic study and breeding of this crop are hindered by the lack of a sequenced genome. Here, we report de novo sequencing and assembly of the 1619-Mb genome of Coix, and annotation of 75.39% repeats and 39 629 protein-coding genes. Comparative genomics analysis showed that Coix is more closely related to sorghum than maize, but intriguingly only Coix and maize had a recent genome duplication event, which was not detected in sorghum. We further constructed a genetic map and mapped several important traits, especially the strength of hull. Selection of papery hull (thin: easy dehulling) from the stony hull (thick: difficult dehulling) in wild progenitors was a key step in Coix domestication. The papery hull makes seed easier to process and germinate. Anatomic and global transcriptome analysis revealed that the papery hull is a result of inhibition of cell division and wall biogenesis. We also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci (QTLs), which are associated with hull thickness and color, respectively. The two QTLs were further fine mapped within intervals of 250 kb and 146 kb, respectively. These resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop.

9. TB

   Haploid Strategies for Functional Validation of Plant Genes

   Shen, Yaou, Pan, Guangtang, and Lübberstedt, Thomas

   Trends in Biotechnology Oct 2015

   Abs HTML PDF

   Increasing knowledge of plant genome sequences requires the development of more reliable and efficient genetic approaches for genotype–phenotype validation. Functional identification of plant genes is generally achieved by a combination of creating genetic modifications and observing the according phenotype, which begins with forward-genetic methods represented by random physical and chemical mutagenesis and move towards reverse-genetic tools as targeted genome editing. A major bottleneck is time need to produce modified homozygous genotypes that can actually be used for phenotypic validation. Herein, we comprehensively address and compare available experimental approaches for functional validation of plant genes, and propose haploid strategies to reduce the time needed and cost consumed for establishing gene function.

10. PNAS

    Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

    Qin, Cheng, Yu, Changshui, Shen, Yaou, Fang, Xiaodong, Chen, Lang, Min, Jiumeng, Cheng, Jiaowen, Zhao, Shancen, Xu, Meng, Luo, Yong, Yang, Yulan, Wu, Zhiming, Mao, Likai, Wu, Haiyang, Ling-Hu, Changying, Zhou, Huangkai, Lin, Haijian, González-Morales, Sandra, Trejo-Saavedra, Diana L., Tian, Hao, Tang, Xin, Zhao, Maojun, Huang, Zhiyong, Zhou, Anwei, Yao, Xiaoming, Cui, Junjie, Li, Wenqi, Chen, Zhe, Feng, Yongqiang, Niu, Yongchao, Bi, Shimin, Yang, Xiuwei, Li, Weipeng, Cai, Huimin, Luo, Xirong, Montes-Hernández, Salvador, Leyva-González, Marco A., Xiong, Zhiqiang, He, Xiujing, Bai, Lijun, Tan, Shu, Tang, Xiangqun, Liu, Dan, Liu, Jinwen, Zhang, Shangxing, Chen, Maoshan, Zhang, Lu, Zhang, Li, Zhang, Yinchao, Liao, Weiqin, Zhang, Yan, Wang, Min, Lv, Xiaodan, Wen, Bo, Liu, Hongjun, Luan, Hemi, Zhang, Yonggang, Yang, Shuang, Wang, Xiaodian, Xu, Jiaohui, Li, Xueqin, Li, Shuaicheng, Wang, Junyi, Palloix, Alain, Bosland, Paul W., Li, Yingrui, Krogh, Anders, Rivera-Bustamante, Rafael F., Herrera-Estrella, Luis, Yin, Ye, Yu, Jiping, Hu, Kailin, and Zhang, Zhiming

    Proceedings of the National Academy of Sciences Apr 2014

    HTML PDF