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Chen H.,Peking University | Chen H.,Shenzhen Institute of Crop Molecular Design | He H.,Peking University | He H.,Shenzhen Institute of Crop Molecular Design | And 5 more authors.
Current Opinion in Plant Biology | Year: 2013

Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding. © 2013 Elsevier Ltd.


Liu J.,Chinese University of Hong Kong | Cai Y.-Z.,Chinese University of Hong Kong | Cai Y.-Z.,China National Seed Group Company | Wong R.N.S.,Hong Kong Baptist University | And 5 more authors.
Journal of Agricultural and Food Chemistry | Year: 2012

Caffeoylquinic acids and lignans in the crude extracts of both roots and seeds from different burdock (Arctium lappa L.) genotypes were simultaneously characterized and systematically compared by LC-MS and matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS), and their antioxidant activities were also investigated. A total of 14 lignans were identified in burdock seeds and 12 caffeoylquinic acids in burdock roots. High levels of caffeoylquinic acids were also detected in burdock seeds, but only trace amounts of lignans were found in burdock roots. Burdock seeds contained higher concentrations of lignans and caffeoylquinic acids than burdock roots. Quantitative analysis of caffeoylquinic acids and lignans in roots and seeds of various burdock genotypes was reported for the first time. Great variations in contents of both individual and total phenolic compounds as well as antioxidant activities were found among different genotypes. Burdock as a root vegetable or medicinal plants possessed considerably stronger antioxidant activity than common vegetables and fruits. © 2012 American Chemical Society.


Gunaratne A.,Sabaragamuwa University of Sri Lanka | Gunaratne A.,University of Hong Kong | Wu K.,University of Hong Kong | Li D.,Huazhong Agricultural University | And 5 more authors.
Food Chemistry | Year: 2013

Proanthocyanidin-containing rice varieties have been rarely reported. Antioxidant capacity, major antioxidant components, and nutritional parameters of eight traditional red-grained rice varieties containing proanthocyanidins grown in Sri Lanka were investigated. The tested traditional red varieties, on the average, had over sevenfold higher both total antioxidant capacity and phenolic content than three light brown-grained new-improved rice varieties. Major antioxidant phenolic compounds identified in this study included proanthocyanidins, phenolic acids and γ-oryzanols (ferulic acid derivatives). Proanthocyanidins were detected only in the traditional red varieties, but not found in new-improved ones. Most traditional red varieties also contained significantly higher levels of protein with well balanced amino acids and higher contents of fat, fibre and vitamin E (tocopherols and tocotrienols) than the new-improved ones. Great variations in antioxidant capacity, major phenolics, and nutritional parameters were observed among different rice varieties. These Sri Lankan traditional red-grained rice varieties containing proanthocyanidins may be used as important genetic sources for rice breeding. © 2012 Elsevier Ltd. All rights reserved.


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 | Year: 2014

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.


Patent
China National Seed Group Co., Huazhong Agricultural University, Shenzhen Institute Of Molecular Crop Design and Frontier Laboratories of Systems Crop Design Co. | Date: 2013-02-07

The present invention provides a rice whole genome breeding chip and the application thereof. The rice whole genome breeding chip of the present invention is Rice60K, an SNP chip manufactured based on Infinium technique. Each chip can detect 24 samples simultaneously and contains 58,290 SNP sites. The marker sites have DNA sequences represented by SEQ ID NO.1-58290. The chip can be used in molecular marker fingerprint analysis of the rice variety resources, in genotype identification of the hybrid progeny population, in identification of the variety authenticity, in analysis and screening of the genetic background of the breeding materials, and in association analysis of the agronomic traits, having wide application prospects.


Qiao J.,Huazhong Agricultural University | Ma C.,China National Seed Group Co. | Wimmelbacher M.,Friedrich - Alexander - University, Erlangen - Nuremberg | Bornke F.,Friedrich - Alexander - University, Erlangen - Nuremberg | Luo M.,Huazhong Agricultural University
Plant and Cell Physiology | Year: 2011

Chloroplast development requires the coordinated action of various proteins, many of which remain to be identified. Here, we report two novel genes, Mesophyll-cell RNAi Library line 7 (MRL7) and MRL7-Like (MRL7-L), that are involved in this process. An Arabidopsis knock-down transgenic plant (MRL7-RNAi) with delayed-greening phenotype was isolated from an RNA interference (RNAi) transformant library. Cotyledons and young leaves of MRL7-RNAi were pale in seedlings and gradually greened as the plant matured, while a knock-out in the MRL7 gene was seedling lethal. The MRL7 protein was shown to co-localize with a marker protein for nucleoids in chloroplasts, indicative of a role for the protein in chloroplast nucleic acid metabolism. Accordingly, chloroplast development was arrested upon loss of MRL7 function and the expression of plastid-encoded genes transcribed by plastid-encoded RNA polymerase (PEP) was significantly reduced in MRL7 knock-down and knock-out plants. A paralog of MRL7 (MRL7-L) was identified in the Arabidopsis genome. Both MRL7 and MRL7-L are only found in land plants and encode previously uncharacterized proteins without any known conserved domain. Like MRL7, knock-down of MRL7-L also resulted in a virescent phenotype, and a similar effect on plastid gene expression. However, the MRL7-L protein was localized to the chloroplast stroma. Taken together, our data indicate that the two paralogous proteins MRL7 and MRL7-L have essential but distinct roles during early chloroplast development and are involved in regulation of plastid gene expression. © 2011 The Author.


Yu H.,China National Seed Group Co. | Xie W.,Huazhong Agricultural University | Li J.,China National Seed Group Co. | Zhou F.,China National Seed Group Co. | Zhang Q.,Huazhong Agricultural University
Plant Biotechnology Journal | Year: 2014

The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics-based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic background. We developed a whole-genome single nucleotide polymorphism (SNP) array, RICE6K, based on Infinium technology, using representative SNPs selected from more than four million SNPs identified from resequencing data of more than 500 rice landraces. RICE6K contains 5102 SNP and insertion-deletion (InDel) markers, about 4500 of which were of high quality in the tested rice lines producing highly repeatable results. Forty-five functional markers that are located inside 28 characterized genes of important traits can be detected using RICE6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs per 1 Mb and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups. Application tests of RICE6K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection. These results suggest that RICE6K provides an efficient and reliable genotyping tool for rice genomic breeding. © 2013 China National Seed Group Co. Ltd. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.


Li C.,China National Seed Group Company Ltd | Liu B.,China National Seed Group Company Ltd
Shengwu Gongcheng Xuebao/Chinese Journal of Biotechnology | Year: 2015

Insecticidal protein genes from Bacillus thuringiensis are currently the most widely used insect-resistant genes. They have been transferred to many crops for breeding and production. Among them, cotton, maize, potato and other insect-resistant crops are commercialized, creating considerable economic benefit. In this review, we summarized advances in identifying functional genes and transgenic crops for insect resistance, compared different strategies for enhancing vigor of insecticidal protein and utilizing gene stacking as well as listing valuable groups of stacked genes. In addition, the methods for multiple gene transformation was discussed. © 2015 Chin J Biotech, All rights reserved.


PubMed | Philips, China National Seed Group Co. and University of Auckland
Type: Journal Article | Journal: Journal of food science | Year: 2016

Buckwheat (BF) and millet (MF) are recommended as healthy foods due to their unique chemical composition and health benefits. This study investigated the thermal and rheological properties of BF-WF (wheat flour) and MF-WF flour blends at various ratios (0:100 to 100:0). Increasing BF or MF concentration led to higher cold paste viscosity and setback viscosity of pasting properties gel adhesiveness, storage modulus (G) and loss modulus (G) of dynamic oscillatory rheology, and yield stress (0 ) of flow curve of WF. BF and MF addition decreased peak viscosity and breakdown of pasting, gel hardness, swelling volume, and consistency coefficient (K) of flow curve of WF. Thermal properties of the blends appeared additive of that of individual flour. Nonadditive effects were observed for some property changes in the mixtures, and indicated interactions between flour components. This may provide a physicochemical basis for using BF and MF in formulating novel healthy products.


PubMed | China National Seed Group Co. and Huazhong Agricultural University
Type: Journal Article | Journal: TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik | Year: 2016

Pyramiding of S5 - n and f5 - n cumulatively improved seed-setting rate of indica-japonica hybrids, which provided an effective approach for utilization of inter-subspecific heterosis in rice breeding. Breeding for indica-japonica hybrid rice is an attractive approach to increase rice yield. However, hybrid sterility is a major obstacle in utilization of inter-subspecific heterosis. Wide-compatibility alleles can break the fertility barrier between indica and japonica subspecies, which have the potential to overcome inter-subspecific hybrid sterility. Here, we improved the compatibility of an elite indica restorer line 9311 to a broad spectrum of japonica varieties, by introducing two wide-compatibility alleles, S5-n and f5-n, regulating embryo-sac and pollen fertility, respectively. Through integrated backcross breeding, two near isogenic lines harboring either S5-n or f5-n and a pyramiding line carrying S5-n plus f5-n were obtained, with the recurrent parent genome recovery of 99.95, 99.49, and 99.44 %, respectively. The three lines showed normal fertility when crossed to typical indica testers. When testcrossed to five typical japonica varieties, these lines allowed significant increase of compatibility with constant agronomic performance. The introgressed S5-n could significantly improve 14.7-32.9 % embryo-sac fertility in indica-japonica hybrids. In addition, with the presence of f5-n fragment, S5-n would increase the spikelet fertility from 9.5 to 21.8 %. The introgressed f5-n fragment greatly improved anther dehiscence, embryo-sac and pollen fertility in indica-japonica hybrids, thus leading to improvement of spikelet fertility from 20.4 to 30.9 %. Moreover, the pyramiding line showed 33.6-46.7 % increase of spikelet fertility, suggesting cumulative effect of S5-n and f5-n fragment in seed-set improvement of inter-subspecific hybrids. Our results provided an effective approach for exploiting heterosis between indica and japonica subspecies, which had a profound implication in rice breeding.

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