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Wu Z.,Zhongkai University of Agriculture and Engineering | Cheng J.,South China Agricultural University | Qin C.,Zunyi Institute of Agricultural science | Qin C.,Sichuan Agricultural University | And 4 more authors.
International Journal of Molecular Sciences | Year: 2013

Cytoplasmic male sterility (CMS), widely used in the production of hybrid seeds, is a maternally inherited trait resulting in a failure to produce functional pollen. In order to identify some specific proteins associated with CMS in pepper, two-dimensional gel electrophoresis (2-DE) was applied to proteomic analysis of anthers/buds between a CMS line (designated NA3) and its maintainer (designated NB3) in Capsicum annuum L. Thirty-three spots showed more than 1.5-fold in either CMS or its maintainer. Based on mass spectrometry, 27 spots representing 23 distinct proteins in these 33 spots were identified. Proteins down-regulated in CMS anthers/buds includes ATP synthase D chain, formate dehydrogenase, alpha-mannosidas, RuBisCO large subunit-binding protein subunit beta, chloroplast manganese stabilizing protein-II, glutathione S-transferase, adenosine kinase isoform 1T-like protein, putative DNA repair protein RAD23-4, putative caffeoyl-CoA 3-O-methyltransferase, glutamine synthetase (GS), annexin Cap32, glutelin, allene oxide cyclase, etc. In CMS anthers/buds, polyphenol oxidase, ATP synthase subunit beta, and actin are up-regulated. It was predicted that male sterility in NA3 might be related to energy metabolism turbulence, excessive ethylene synthesis, and suffocation of starch synthesis. The present study lays a foundation for future investigations of gene functions associated with pollen development and cytoplasmic male sterility, and explores the molecular mechanism of CMS in pepper. © 2013 by the authors; licensee MDPI, Basel, Switzerland. Source

Qu J.,Sichuan Agricultural University | Liu J.,Sichuan Agricultural University | Liu J.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region
BMC Research Notes | Year: 2013

Abstract. Background: Maize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world. Simple sequence repeats (SSRs) are widely used as molecular markers in maize genetics and breeding, but only two thousands pairs of SSRs have been published currently, which hardly satisfies for the increasing needs of geneticists and breeders. Furthermore, the increasing studies have revealed that SSRs also play a vital role in functional regulation and evolution. It is fortunate that the development of sequencing technology and bio-software provides the basis for characterization and development of SSRs in maize. Results: In this study, MISA was applied to identify overall 179,681 SSRs in maize reference genome B73, with an average distance of 11.46 Kbp. Their distributions within the genome in different regions were non-random, and the density followed in a descending order of UTR, promotor, intron, intergenic and CDS. Meanwhile, 82,694 (46.02%) SSRs with unique flanking sequences were selected, and then applied to analyze the polymorphism of next-generation sequencing data from 345 maize inbred lines and data from maize reference genome B73. There were 58,946 SSRs with length information results in ten or more than ten genomes, accounting for 71.28% of SSRs with unique flanking sequences, while 55,621 SSRs had polymorphism, with an average PIC value of 0.498. 250 pairs of SSR primers in different genomic regions covering all maize chromosomes were randomly chosen for the experimental validation, with an average PIC value of 0.63 in 11 elite maize inbred lines. Conclusions: Our work provided insight into the non-random distribution spatterns and compositions of SSRs in different regions of maize genome, and also developed more polymorphic SSR markers using next-generation sequencing reads. The genome-wide SSRs polymorphism markers could be useful for genetic analysis and marker-assisted selection in breeding practice, and it was also proved to be high efficient for molecular marker development via next-generation sequencing reads. © 2013 Qu and Liu; licensee BioMed Central Ltd. Source

Farkhari M.,University of Tehran | Farkhari M.,University of Agriculture and Natural Resources Ramin | Farkhari M.,International Maize and Wheat Improvement Center | Krivanek A.,International Maize and Wheat Improvement Center | And 9 more authors.
Plant Breeding | Year: 2013

Large-scale selective genotyping and high-throughput analysis are two important strategies for low-cost and high-effective genetic mapping. In this study, selective genotyping was applied to four maize F2 populations. Thirty plants were selected from each of the two tails of the original F2 populations to represent extreme resistant and susceptible plants to root lodging, and genotyped individually with 1536 single nucleotide polymorphisms (SNPs). A quantitative trait locus (QTL) was declared when at least three closely linked SNPs showed significant allele frequency difference between the two tails. Nine QTL were identified for root lodging across the four populations, which were located on chromosomes 2, 4, 5, 7, 8 and 10 and one of them was shared between two populations. A total of 20 segregation distortion regions (SDRs) were identified across the four populations, one of which was co-localized with a QTL on chromosome 4. The tightly linked SNPs identified in this study can be used for marker-assisted selection for root lodging. Selective genotyping, when combined with pooled DNA analysis, can be used to develop strategies for high-throughput genetic mapping for all crops. © 2012 Blackwell Verlag GmbH. Source

Xu J.,Sichuan Agricultural University | Xu J.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region | Liu Y.,Sichuan Agricultural University | Liu J.,Sichuan Agricultural University | And 15 more authors.
Journal of Integrative Plant Biology | Year: 2012

The control of flowering is not only important for reproduction, but also plays a key role in the processes of domestication and adaptation. To reveal the genetic architecture for flowering time and photoperiod sensitivity, a comprehensive evaluation of the relevant literature was performed and followed by meta analysis. A total of 25 synthetic consensus quantitative trait loci (QTL) and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development. Besides, a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits. Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize (Zea mays L.). Our results suggest that the combination of literature review, meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering. Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection, such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation. © 2012 Institute of Botany, Chinese Academy of Sciences. Source

Xu J.,Sichuan Agricultural University | Xu J.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region | Liu L.,Sichuan Agricultural University | Liu L.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region | And 19 more authors.
DNA Research | Year: 2013

Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study. © The Author 2013. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Source

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