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genetic dissection of maize seedling root system architecture traits using an ultra-high density bin-map and a recombinant inbred line population

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Journal of Integrative Plant Biology 2016年第3期58卷 266-279页

作者： Weibin Song Baobao Wang Andrew L Hauck Xiaomei Dong Jieping Li Jinsheng Lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center of China Department of Plant Genetics and BreedingChina Agricultural University

Maize（Zea mays） root system architecture（RSA）mediates the key functions of plant anchorage and acquisition of nutrients and water. In this study,a set of 204 recombinant inbred lines（RILs） was derived from the widely adapted Chinese hybrid ZD958（Zheng58 Chang7-2）,genotyped by sequencing（gBS） and evaluated as seedlings for 24 RSA related traits divided into primary,seminal and total root classes. Signi ficant differences between the means of the parental phenotypes were detected for 18 traits,and extensive transgressive segregation in the RIL population was observed for all traits. Moderate to strong relationships among the traits were discovered. A total of 62 quantitative trait loci（QTL） were identi fied that individually explained from1.6% to 11.6%（total root dry weight/total seedling shoot dry weight） of the phenotypic variation. Eighteen,24 and 20 QTL were identi fied for primary,seminal and total root classes of traits,respectively. We found hotspots of 5,3,4 and 12 QTL in maize chromosome bins 2.06,3.02-03,9.02-04,and 9.05-06,respectively,implicating the presence of root gene clusters or pleiotropic effects. These results characterized the phenotypic variation and genetic architecture of seedling RSA in a population derived from a successful maize hybrid.

关键词： Maize root system architecture QTL bin map genotyping by sequencing(gBS)

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Efficiency and Inheritance of Targeted Mutagenesis in Maize Using CRISPR-Cas9

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Journal of genetics and genomics 2016年第1期43卷 25-36页

作者： Jinjie Zhu Ning Song Silong Sun Weilong Yang Haiming Zhao Weibin Song Jinsheng Lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University

CRISPR/Cas （clustered regularly interspaced short palindromic repeats/CR1SPR-associated proteins） is an adaptive immune system in bacteria and archaea to defend against invasion from foreign DNA fragments. Recently, it has been developed as a powerful targeted genome editing tool for a wide variety of species. However, its application in maize has only been tested with transiently expressed somatic cells or with a limited number of stable transgenic To plants. The exact efficiency and specificity of the CRISPR/Cas system in the highly complex maize genome has not been documented yet. Here we report an extensive study of the well-studied type II CRISPR-Cas9 system for targeted genome editing in maize, with the codon-optimized Cas9 protein and the short non-coding guide RNA generated through a functional maize U6 snRNA promoter. Targeted gene mutagenesis was detected for 90 loci by maize protoplast assay, with an average cleavage efficiency of 10.67 %. Stable knockout transformants for maize phytoene synthase gene （PSYI） were obtained. Mutations occurred in germ ceils can be stably inherited to the next generation. Moreover, no off-target effect was detected at the computationally predicted putative off-target loci. No significant difference between the transcriptomes of the Cas9 expressed and non-expressed lines was detected. Our results confirmed that the CRISPR-Cas9 could be successfully applied as a robust targeted genome editing system in maize.

关键词： CRISPR-Cas9 Targeted mutagenesis Heritability Maize

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genome-Wide Expression Profile of Maize Root Response to Phosphorus Deficiency Revealed by Deep Sequencing

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Journal of Integrative Agriculture 2014年第6期13卷 1216-1229页

作者： SU Shun-zhong WU Ling LIU Dan LU Yan-li LIN Hai-jian ZHANg Shu-zhi SHEN Ya-ou LIU Hai-lan ZHANg Zhi-ming RONg Ting-zhao ZHANg Xiao TIAN Yue-hui NIE Zhi gAO Shi-bin Key Laboratory of Biology and genetic Improvement of Maize in Southwest Region Ministry of Agriculture/Maize Research InstituteSichuan Agricultural University

Phosphorus （P） is one of the three primary macronutrients that are required in large amounts for plant growth and development. To better understand molecular mechanism of maize and identify relevant genes in response to phosphorus deficiency, we used Solexa/Illumina＇s digital gene expression （DgE） technology to investigate six genome-wide expression profiles of seedling roots of the low-P tolerant maize inbred line 178. DgE studies were conducted at 6, 24 and 72 h under both phosphorus deficient and sufficient conditions. Approximately 3.93 million raw reads for each sample were sequenced and 6 816 genes exhibited significant levels of differential expressions in at least one of three time points in response to P starvation. The number of genes with increased expression increased over time from 6 to 24 h, whereas genes with decreased expression were more abundant at 72 h, suggesting a gradual response process for P deficiency at different stages. gene annotations illustrated that most of differentially expressed genes （DEgs） are involved in different cellular and molecular processes such as environmental adaptation and carbohydrate metabolism. The expression of some known genes identified in other plants, such as those involved in root architecture, P metabolism and transport were found to be altered at least two folds, indicating that the mechanisms of molecular and morphological adaptation to P starvation are conserved in plants. This study provides insight into the general molecular mechanisms underlying plant adaptation to low-P stress and thus may facilitate molecular breeding for improving P utilization in maize.

关键词： maize phosphorus efficiency root digital gene expression

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The analysis of the eQTLs associated with the differential expression between maize two subgenomic duplicated genes

The analysis of the eQTLs associated with the differential e...

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第一届全国玉米生物学学术研讨会

作者：李恩 Shaojun Xie Jinsheng Lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center China Agricultural University

Whole genome duplications(WgDs)are a widespread feature during plant genome evolution,creating the types of single gene and duplicate genes by biased fractionation and genome *** the prevalence of these events,the mec...

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Population genomic analysis and genome wide association studies through the re-sequencing of 778 maize inbred lines

Population genomic analysis and Genome wide association stud...

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第一届全国玉米生物学学术研讨会

作者：史俊鹏 Zhipeng Liu Baobao Wang Xin Wang Andrew Hauck Shaojun Xie Hainan Zhao Mei Zhang Silong Sun Haiming Zhao Weibin Song Jinsheng Lai State Key Laboratory of Agrobiotechnology and National Maize Improvement Center China Agricultural University

Modern maize breeding process have generated enormous amount of genetic variants which may contribute to the phenotype *** top of re-sequencing data of 278 maize inbred lines,we expanded the population to 778 lines with.5x depth on average and identified 56 million *** 30%of the SNPs are novel and enriched in rare *** non-syn/syn ratio is 1.09 which is comparable with

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