Genetic variation of Bmy1 alleles in barley (Hordeum vulgare L.) investigated by CAPS analysis

Zhang, Wen Sheng; Li, Xia; Liu, Jian Bing

doi:10.1007/s00122-006-0497-6

Cited by 23 publications

(16 citation statements)

References 34 publications

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“…Several studies have found associations with lower enzyme activity and the presence of the 126-bp indel (Coventry et al 2003;Erkkilä 1999;Gunkel et al 2002) and between lower enzyme thermostability and the presence of the 126-bp indel (Coventry et al 2003;Kaneko et al 2000). However, recently, Zhang et al (2007) reported that absence of the 126-bp indel is not a good indicator of elite malt quality.…”

Section: Resultsmentioning

confidence: 91%

“…There have been several reports regarding the use of Bmy1 intron III as a potential predictor of good or bad malting quality (Erkkilä et al 1998;Erkkilä 1999;Kaneko et al 2000;Gunkel et al 2002;Coventry et al 2003;Zhang et al 2007). One predictor of malt quality is DP, which requires the barley to be malted before conducting the assay.…”

Section: β-Amylase Activitymentioning

confidence: 98%

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Utilization of Different Bmy1 Intron III Alleles for Predicting β-Amylase Activity and Thermostability in Wild and Cultivated Barley

2010

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The third intron of barley (Hordeum vulgare L.) β-amylase 1 (Bmy1) is extremely polymorphic. The use of specific insertion/deletions (indels) in the third intron as markers for cultivar development has been recommended based on associations with β-amylase activity and thermostability. The third intron of Bmy1 in 40 barley genotypes was sequenced and aligned with 15 Bmy1 intron III sequences from GenBank and four alleles (Bmy1.a, Bmy1.b, Bmy1.c, and Bmy1.d) were identified based on indels of 126, 38, 11, and 21 bp. β-Amylase activity and thermostability were assayed in 22 North American cultivars and 12 wild barley genotypes. Cultivars carrying the Bmy1.a and Bmy1.b alleles had β-amylase activity ranges calculated on a fresh weight (FW) basis of 1.8-and 1.5-fold, respectively, and thermostability ranges of 8.8-and 1.2-fold, respectively. β-Amylase activity calculated on a protein basis yielded a 2.4-and 1.4-fold range for Bmy1.a and Bmy1.b, respectively. Significantly different activities were observed in cultivars carrying either Bmy1.a or the Bmy1.b allele when calculated on a FW basis and the Bmy1.a allele when calculated on a protein basis. Significantly different thermostabilities were observed in cultivars carrying the Bmy1.a allele. Wild barleys were found to carry Bmy1.a, Bmy1.b, and Bmy1.c alleles with β-amylase activity ranges calculated on a FW basis of 1.7-, 1.7-, and 2.6-fold, respectively, and thermostability ranges of 1.3-, 1.4-, and 2.1-fold, respectively. β-Amylase activity measured on a protein basis identified a 1.3-, 1.4-, and 2.1-fold range for Bmy1.a, Bmy1.b, and Bmy1.c, respectively. Significantly different activities were found in genotypes with any of these three alleles when calculated on a FW basis yet only in those with the Bmy1.c allele when calculated on a protein basis. Significantly different thermostabilities in genotypes carrying either the Bmy1.b or Bmy1.c allele were observed. In the germplasm studied here, the Bmy1 intron III alleles are not reliable predictors of β-amylase activity and thermostability.

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Section: Resultsmentioning

confidence: 91%

Section: β-Amylase Activitymentioning

confidence: 98%

Utilization of Different Bmy1 Intron III Alleles for Predicting β-Amylase Activity and Thermostability in Wild and Cultivated Barley

2010

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“…A further advantage of the SNaPshot platform over TDI-FRET is that it relies on sequencing software (rather than real-time PCR software), which tends to be quite widely available. The method is relatively cost-effective and, unlike the cleaved amplified polymorphic site assay that differentiates between two high thermostability allele types and the alleles associated with low and intermediate thermostability (Malysheva et al 2004;Zhang et al 2007), TDI-FRET can differentiate all isoforms and identify heterozygotes.…”

Section: Pcr Amplificationmentioning

confidence: 99%

“…Cultivars and genetic resources were analysed by different methods, providing insight into the diversity of the encoding sequence and revealing other haplotypes (Kihara et al 1998;Polakova et al 2003;Zhang et al 2004; as a detection platform. Subsequently, a simpler assay, cleaved amplified polymorphic site was developed, which was able to discriminate between the two high and the low/intermediate thermostability haplotypes, and this method has been widely used in later years (Malysheva et al 2004;Sjakste & Roder 2004;Zhang et al 2007). Pyrosequencing has been suggested as an alternative haplotype detection platform (Polakova et al 2003;Malysheva-Otto & Roder 2006), but it suffers from a requirement for rather expensive equipment and consumables.…”

Section: Introductionmentioning

confidence: 99%

Haplotyping barley bmy1 using the SNaPshot assay

et al. 2010

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Abstract:The allelic status at bmy1, which encodes the enzyme β-amylase 1 in the barley grain, has an important influence over a cultivar's malting quality. Changes in the malting process have been responsible for the need to improve the thermostability of this enzyme. We have compared a published bmy1 haplotyping assay based on TDI-FRET (templatedirected dye-terminator incorporation fluorescence resonance energy transfer) with a SNaPshot protocol by jointly analysing a set of 21 cultivars of known haplotype. The two methods gave the same result, but the SNaPshot assay was easier to interpret. The SNaPshot assay was therefore used to haplotype the Czech malting barley core collection with respect to bmy1. The old Czech cultivar Kasticky was the only entry identified as carrying the high thermostability haplotype, with the remainder carrying either the intermediate or the low thermostability haplotypes. Older materials were the most variable in terms of bmy1 haplotype, but the majority carried the intermediate type. Most of the descendants of cv. Diamant carried the low thermostability haplotype. The most recently released cultivars recommended for the brewing of Czech beer tend to carry the intermediate allele.

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“…After sequencing confirmation (Fig. 8), SNPs were detected using cleaved amplification polymorphisms (38). The PCR products were treated in the reaction mixture directly after amplification with the corresponding restriction enzyme for at least 12 h at 37˚C (Table IV), according to the manufacturers' instructions.…”

Section: Screening Of Nucleotide Polymorphisms and Assessment Of Codomentioning

confidence: 99%

Molecular Characterization of Caveolin-1 in Pigs Infected with Haemophilus parasuis

Liu

Chen

Tong

et al. 2011

The Journal of Immunology

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Caveolin-1 (Cav1) plays a critical role in the invasion of pathogenic microbes into host cells, yet little is known about porcine Cav1. In this study, we provide the molecular characterization of Cav1 in pigs following stimulation with LPS/polyinosinic-polycytidylic acid as well as during infection with Haemophilus parasuis. The porcine Cav1 gene is 35 kb long and is located at SSC18q21; two isoforms (Cav1-α and Cav1-β) are produced by alternative splicing. Three point mutations were identified in the coding region of the gene, two of which were significantly associated with nine immunological parameters in Landrace pigs, including the Ab response against porcine reproductive and respiratory syndrome virus and lymphocyte counts. Promoter analysis indicated that NF-κB activates both Cav1 transcripts, but the forkhead gene family specifically regulates Cav1-β in the pig. Porcine Cav1 is expressed ubiquitously, with Cav1-α more abundantly expressed than Cav1-β in all tissues investigated. Basal expression levels of Cav1 in PBMCs are relatively similar across different pig breeds. LPS and polyinosinic-polycytidylic acid markedly induced the expression of Cav1 in porcine kidney-15 cells in vitro, likely through NF-κB activation. Pigs infected with H. parasuis exhibited decreased expression of Cav1, particularly in seriously impaired organs such as the brain. This study provides new evidence that supports the use of Cav1 as a potential diagnostic and genetic marker for disease resistance in animal breeding. In addition, our results suggest that Cav1 may be implicated in the pathogenesis of Glasser’s disease, which is caused by H. parasuis.

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Genetic variation of Bmy1 alleles in barley (Hordeum vulgare L.) investigated by CAPS analysis

Cited by 23 publications

References 34 publications

Utilization of Different Bmy1 Intron III Alleles for Predicting β-Amylase Activity and Thermostability in Wild and Cultivated Barley

Utilization of Different Bmy1 Intron III Alleles for Predicting β-Amylase Activity and Thermostability in Wild and Cultivated Barley

Haplotyping barley bmy1 using the SNaPshot assay

Molecular Characterization of Caveolin-1 in Pigs Infected with Haemophilus parasuis

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