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Zhou D.,Guangdong Academy of Agricultural Sciences | Chen W.,Wenzhou University | Lin Z.,China Agricultural University | Chen H.,China Agricultural University | And 13 more authors.
Plant Biotechnology Journal

Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6× depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd. Source

Chen W.,Peking University | Chen H.,Peking University | Chen H.,Shenzhen Institute of Crop Molecular Design | Zheng T.,Chinese Academy of Agricultural Sciences | And 11 more authors.
Theoretical and Applied Genetics

Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 “high quality” SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays. © Springer-Verlag Berlin Heidelberg 2013. Source

Liu L.,National Center for Molecular Crop Design | Liu L.,Frontier Laboratories of Systems Crop Design Co. | Fan X.-D.,National Center for Molecular Crop Design | Fan X.-D.,Frontier Laboratories of Systems Crop Design Co.
Plant Molecular Biology

Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Recent advances with the RNA-mediated Cas9 endonuclease derived from clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) systems have dramatically transformed our ability to specifically modify intact genomes of diverse cells and organisms. The CRISPR-Cas system has been adapted as an efficient, facile, and robust gene-targeting technology with the potential for high-throughput and multiplexed genome engineering. Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its enormous potential for applications across basic science, agricultural and biotechnology. © 2014 Springer Science+Business Media Dordrecht. Source

Chen H.,Peking Yale Joint Center for Plant Molecular Genetics and Agro biotechnology | Xie W.,Huazhong Agricultural University | He H.,Peking Yale Joint Center for Plant Molecular Genetics and Agro biotechnology | Yu H.,China National Seed Group Co. | And 15 more authors.
Molecular Plant

A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecular breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the development of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for different objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies (GWAS) analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding. © The Author 2013. Source

Zhen G.,Peking University | Zhen G.,China Agricultural University | Zhang L.,Frontier Laboratories of Systems Crop Design Co. | Du Y.N.,Peking University | And 11 more authors.
Science China Life Sciences

Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs (76,336 unigenes), of which 100,648 contigs (66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes (DEGs) were upregulated (246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology (GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-CoA synthase (HMGS), mevalonate kinase (MVK), and squalene epoxidase (SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments. © 2015, The Author(s). Source

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