SNP high-throughput screening in grapevine using the SNPlex genotyping system.

Abstract:

BACKGROUND:Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP) discovery and genotyping in grapevine (Vitis vinifera L.). However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs) thus providing a valuable source for high-throughput genotyping methods. RESULTS:Herein we report the first application of the SNPlexgenotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah x Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA) methods were used for preparation of genomic DNA for the SNPlex assay. CONCLUSION:Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA), is a good solution for future applications in well-equipped laboratories.

journal_name

BMC Plant Biol

journal_title

BMC plant biology

authors

Pindo M,Vezzulli S,Coppola G,Cartwright DA,Zharkikh A,Velasco R,Troggio M

doi

10.1186/1471-2229-8-12

subject

Has Abstract

pub_date

2008-01-28 00:00:00

pages

12

issn

1471-2229

pii

1471-2229-8-12

journal_volume

8

pub_type

杂志文章
  • Genetic basis of unstable expression of high gamma-tocopherol content in sunflower seeds.

    abstract:BACKGROUND:Tocopherols are natural antioxidants with both in vivo (vitamin E) and in vitro activity. Sunflower seeds contain predominantly alpha-tocopherol (>90% of total tocopherols), with maximum vitamin E effect but lower in vitro antioxidant action than other tocopherol forms such as gamma-tocopherol. Sunflower ger...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-12-71

    authors: García-Moreno MJ,Fernández-Martínez JM,Velasco L,Pérez-Vich B

    更新日期:2012-05-18 00:00:00

  • Environmental and genetic regulation of plant height in soybean.

    abstract:BACKGROUND:Shoot architecture is fundamentally crucial to crop growth and productivity. As a key component of shoot architecture, plant height is known to be controlled by both genetic and environmental factors, though specific details remain scarce. RESULTS:In this study, 308 representative soybean lines from a core ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-021-02836-7

    authors: Yang Q,Lin G,Lv H,Wang C,Yang Y,Liao H

    更新日期:2021-01-25 00:00:00

  • Transcriptome analysis provides new insights into the transcriptional regulation of methyl jasmonate-induced flavonoid biosynthesis in pear calli.

    abstract:BACKGROUND:Flavonoid biosynthesis is strongly influenced by phytohormones. For example, methyl jasmonate (MeJA) enhances the flavonoid accumulation in pear. However, the molecular mechanism underlying the MeJA-induced flavonoid biosynthesis in pear is largely uncharacterized. Therefore, the transcriptome of pear calli ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02606-x

    authors: Premathilake AT,Ni J,Shen J,Bai S,Teng Y

    更新日期:2020-08-25 00:00:00

  • Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata).

    abstract:BACKGROUND:Pongamia (Millettia pinnata syn. Pongamia pinnata), an oilseed legume species, is emerging as potential feedstock for sustainable biodiesel production. Breeding Pongamia for favorable traits in commercial application will rely on a comprehensive understanding of molecular mechanism regulating oil accumulatio...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-018-1356-8

    authors: Huang J,Hao X,Jin Y,Guo X,Shao Q,Kumar KS,Ahlawat YK,Harry DE,Joshi CP,Zheng Y

    更新日期:2018-07-09 00:00:00

  • Tartaric acid pathways in Vitis vinifera L. (cv. Ugni blanc): a comparative study of two vintages with contrasted climatic conditions.

    abstract:BACKGROUND:The acid component of grape berries, originating in the metabolism of malate and tartrate, the latter being less well-known than the former, is a key factor at play in the microbiological stability of wines destined for distillation. Grape acidity is increasingly affected by climate changes. The ability to c...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-016-0833-1

    authors: Cholet C,Claverol S,Claisse O,Rabot A,Osowsky A,Dumot V,Ferrari G,Gény L

    更新日期:2016-06-28 00:00:00

  • Nitrogen-fixing bacteria and Oxalis - evidence for a vertically inherited bacterial symbiosis.

    abstract:BACKGROUND:Plant-endophyte symbioses often revolve around nitrogen metabolism, and involve varying degrees of intimacy. Although evidence for vertical inheritance of nitrogen-fixing endophytic bacteria is increasing, it is confined mostly to crop plants, and to date no such system has been reported for geophytes. METH...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-019-2049-7

    authors: Jooste M,Roets F,Midgley GF,Oberlander KC,Dreyer LL

    更新日期:2019-10-23 00:00:00

  • Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels.

    abstract:BACKGROUND:Dissecting the genetic basis and regulatory mechanisms for the biosynthesis and accumulation of nutrients in maize could lead to the improved nutritional quality of this crop. Gene expression is regulated at the genomic, transcriptional, and post-transcriptional levels, all of which can produce diversity amo...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-017-1119-y

    authors: Xu X,Wang M,Li L,Che R,Li P,Pei L,Li H

    更新日期:2017-10-16 00:00:00

  • Cytological evidence of BSD2 functioning in both chloroplast division and dimorphic chloroplast formation in maize leaves.

    abstract:BACKGROUND:Maize bsd2 (bundle sheath defective2) is a classical C4 mutant with defective C4 photosynthesis, accompanied with reduced accumulation of Rubisco (ribulose bisphosphate carboxylase oxygenase) and aberrant mature chloroplast morphology in the bundle sheath (BS) cells. However, as a hypothetical chloroplast ch...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-019-2219-7

    authors: Li H,Bai M,Jiang X,Shen R,Wang H,Wang H,Wu H

    更新日期:2020-01-09 00:00:00

  • Global analysis of the MATE gene family of metabolite transporters in tomato.

    abstract:BACKGROUND:Species in the Solanaceae family are known for producing plethora of specialized metabolites. In addition to biosynthesis pathways, a full comprehension of secondary metabolism must also take into account the transport and subcellular compartmentalization of substances. Here, we examined the MATE (Multidrug ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-017-1115-2

    authors: Santos ALD,Chaves-Silva S,Yang L,Maia LGS,Chalfun-Júnior A,Sinharoy S,Zhao J,Benedito VA

    更新日期:2017-10-30 00:00:00

  • Natural diversity of potato (Solanum tuberosum) invertases.

    abstract:BACKGROUND:Invertases are ubiquitous enzymes that irreversibly cleave sucrose into fructose and glucose. Plant invertases play important roles in carbohydrate metabolism, plant development, and biotic and abiotic stress responses. In potato (Solanum tuberosum), invertases are involved in 'cold-induced sweetening' of tu...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-271

    authors: Draffehn AM,Meller S,Li L,Gebhardt C

    更新日期:2010-12-09 00:00:00

  • CRISPR/Cas9-mediated mutation of OsSWEET14 in rice cv. Zhonghua11 confers resistance to Xanthomonas oryzae pv. oryzae without yield penalty.

    abstract:BACKGROUND:Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease in Southeast Asia and West Africa. OsSWEET14, encoding a sugar transporter, is known to be a major susceptible gene of bacterial blight targeted by four different transcription activator-like (TAL) effector...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02524-y

    authors: Zeng X,Luo Y,Vu NTQ,Shen S,Xia K,Zhang M

    更新日期:2020-07-03 00:00:00

  • Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize.

    abstract:BACKGROUND:Modifications of DNA and histones in various combinations are correlated with many cellular processes. In this study, we investigated the possible relationship between histone H4 tetraacetylation, DNA methylation and histone H3 dimethylation at lysine 9 during mitosis in maize root meristems. RESULTS:Treatm...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-178

    authors: Yang F,Zhang L,Li J,Huang J,Wen R,Ma L,Zhou D,Li L

    更新日期:2010-08-18 00:00:00

  • Characterization, sub-cellular localization and expression profiling of the isoprenylcysteine methylesterase gene family in Arabidopsis thaliana.

    abstract:BACKGROUND:Isoprenylcysteine methylesterases (ICME) demethylate prenylated protein in eukaryotic cell. Until now, knowledge about their molecular information, localization and expression pattern is largely unavailable in plant species. One ICME in Arabidopsis, encoded by At5g15860, has been identified recently. Over-ex...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-212

    authors: Lan P,Li W,Wang H,Ma W

    更新日期:2010-09-27 00:00:00

  • Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships.

    abstract:BACKGROUND:The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02696-7

    authors: Ren T,Li ZX,Xie DF,Gui LJ,Peng C,Wen J,He XJ

    更新日期:2020-11-13 00:00:00

  • Characterization of the glutathione S-transferase gene family through ESTs and expression analyses within common and pigmented cultivars of Citrus sinensis (L.) Osbeck.

    abstract:BACKGROUND:Glutathione S-transferases (GSTs) represent a ubiquitous gene family encoding detoxification enzymes able to recognize reactive electrophilic xenobiotic molecules as well as compounds of endogenous origin. Anthocyanin pigments require GSTs for their transport into the vacuole since their cytoplasmic retentio...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-14-39

    authors: Licciardello C,D'Agostino N,Traini A,Recupero GR,Frusciante L,Chiusano ML

    更新日期:2014-02-03 00:00:00

  • What makes for sound science?

    abstract::The inclusive threshold policy for publication in BMC journals including BMC Plant Biology means that editorial decisions are largely based on the soundness of the research presented rather than the novelty or potential impact of the work. Here we discuss what is required to ensure that research meets the requirement ...

    journal_title:BMC plant biology

    pub_type: 社论

    doi:10.1186/s12870-017-1139-7

    authors: Costa F,Cramer G,Finnegan EJ

    更新日期:2017-11-10 00:00:00

  • Modification of the fatty acid composition in Arabidopsis and maize seeds using a stearoyl-acyl carrier protein desaturase-1 (ZmSAD1) gene.

    abstract:BACKGROUND:Stearoyl-acyl carrier protein desaturase (SAD) is a key enzyme that catalyses the conversion of stearoyl-acyl carrier protein (ACP) to oleoyl-ACP, a precursor for the biosynthesis of polyunsaturated fatty acids. ZmSAD1 (GenBank: KU949326) is a major QTL for stearic acid content in maize seeds. To investigate...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-016-0827-z

    authors: Du H,Huang M,Hu J,Li J

    更新日期:2016-06-14 00:00:00

  • Calmodulin-dependent and calmodulin-independent glutamate decarboxylases in apple fruit.

    abstract:BACKGROUND:The ubiquitous, non-proteinaceous amino acid GABA (γ-aminobutyrate) accumulates in plants subjected to abiotic stresses such as chilling, O2 deficiency and elevated CO2. Recent evidence indicates that controlled atmosphere storage causes the accumulation of GABA in apple (Malus x domestica Borkh.) fruit, and...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-13-144

    authors: Trobacher CP,Zarei A,Liu J,Clark SM,Bozzo GG,Shelp BJ

    更新日期:2013-09-28 00:00:00

  • Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus.

    abstract:BACKGROUND:Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. na...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02752-2

    authors: Zhu W,Guo Y,Chen Y,Wu D,Jiang L

    更新日期:2020-12-04 00:00:00

  • Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models.

    abstract:BACKGROUND:Maize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we exa...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-016-0874-5

    authors: Bracco M,Cascales J,Hernández JC,Poggio L,Gottlieb AM,Lia VV

    更新日期:2016-08-26 00:00:00

  • Identification of differentially expressed genes induced by Bamboo mosaic virus infection in Nicotiana benthamiana by cDNA-amplified fragment length polymorphism.

    abstract:BACKGROUND:The genes of plants can be up- or down-regulated during viral infection to influence the replication of viruses. Identification of these differentially expressed genes could shed light on the defense systems employed by plants and the mechanisms involved in the adaption of viruses to plant cells. Differentia...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-286

    authors: Cheng SF,Huang YP,Wu ZR,Hu CC,Hsu YH,Tsai CH

    更新日期:2010-12-27 00:00:00

  • Developmental features of cotton fibre middle lamellae in relation to cell adhesion and cell detachment in cultivars with distinct fibre qualities.

    abstract:BACKGROUND:Cotton fibre quality traits such as fibre length, strength, and degree of maturation are determined by genotype and environment during the sequential phases of cotton fibre development (cell elongation, transition to secondary cell wall construction and cellulose deposition). The cotton fibre middle lamella ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-017-1017-3

    authors: Hernandez-Gomez MC,Runavot JL,Meulewaeter F,Knox JP

    更新日期:2017-03-31 00:00:00

  • The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population.

    abstract:BACKGROUND:The improvement of fruit aroma is currently one of the most sought-after objectives in peach breeding programs. To better characterize and assess the genetic potential for increasing aroma quality by breeding, a quantity trait locus (QTL) analysis approach was carried out in an F1 population segregating larg...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-14-137

    authors: Sánchez G,Martínez J,Romeu J,García J,Monforte AJ,Badenes ML,Granell A

    更新日期:2014-05-19 00:00:00

  • Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications.

    abstract:BACKGROUND:Western white pine (WWP, Pinus monticola Douglas ex D. Don) is of high interest in forest breeding and conservation because of its high susceptibility to the invasive disease white pine blister rust (WPBR, caused by the fungus Cronartium ribicola J. C. Fisch). However, WWP lacks genomic resource development ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-014-0380-6

    authors: Liu JJ,Sniezko RA,Sturrock RN,Chen H

    更新日期:2014-12-30 00:00:00

  • Application of the thermal time model for different Typha domingensis populations.

    abstract:BACKGROUND:Cattail (Typha domingensis Pers.) is a perennial emergent plant which is used in Green Floating Filters (GFFs), one of the most innovative systems of wastewater treatment to bioremediate eutrophic waters and produce biomass as biofuel feedstocks. The establishment of cattails in GFFs depends on the seed germ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02573-3

    authors: Carhuancho León FM,Aguado Cortijo PL,Morató Izquierdo MDC,Castellanos Moncho MT

    更新日期:2020-08-17 00:00:00

  • Characterization of histological changes at the tillering stage (Z21) in resistant and susceptible wheat plants infected by Tilletia controversa Kühn.

    abstract:BACKGROUND:Dwarf bunt, which is caused by Tilletia controversa Kühn, is a soilborne and seedborne disease that occurs worldwide and can lead to 70% or even total losses of wheat crops. However, very little information is available about the histological changes that occur in dwarf bunt-resistant and dwarf bunt-suscepti...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02819-0

    authors: Xu T,Qin D,Muhae Ud Din G,Liu T,Chen W,Gao L

    更新日期:2021-01-18 00:00:00

  • The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana.

    abstract:BACKGROUND:Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection. RESULT...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-016-0895-0

    authors: Wang L,Bei X,Gao J,Li Y,Yan Y,Hu Y

    更新日期:2016-09-26 00:00:00

  • Molecular mechanism of seed dormancy release induced by fluridone compared with cod stratification in Notopterygium incisum.

    abstract:BACKGROUND:Notopterygium incisum is an important Chinese medicinal plant. Its mature seeds have underdeveloped embryos and are physiological dormant. We found the seeds with full developed embryos can germinate after treated by fluridone (FL), an inhibitor of abscisic acid (ABA). In order to understand the molecular me...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-018-1333-2

    authors: Aihua L,Shunyuan J,Guang Y,Ying L,Na G,Tong C,Liping K,Luqi H

    更新日期:2018-06-11 00:00:00

  • An endogenous artificial microRNA system for unraveling the function of root endosymbioses related genes in Medicago truncatula.

    abstract:BACKGROUND:Legumes have the unique capacity to undergo two important root endosymbioses: the root nodule symbiosis and the arbuscular mycorrhizal symbiosis. Medicago truncatula is widely used to unravel the functions of genes during these root symbioses. Here we describe the development of an artificial microRNA (amiR)...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-13-82

    authors: Devers EA,Teply J,Reinert A,Gaude N,Krajinski F

    更新日期:2013-05-16 00:00:00

  • Annotation of gene function in citrus using gene expression information and co-expression networks.

    abstract:BACKGROUND:The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world's most economically important fruit crops. With increasing volumes of transcriptomics data available for these species, Gene Co-expression Network (GCN) analysis is a viable option for p...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-14-186

    authors: Wong DC,Sweetman C,Ford CM

    更新日期:2014-07-15 00:00:00