Improved conditions for silver–ammonia staining of DNA in polyacrylamide gel

Cong, Weitao; He, Hong‐Zhang; Zhu, Zhongxin; Ye, Cai-Xue; Yang, Xuyi; Choi, Jung-Kap; Jin, Litai; Li, Xiaokun

doi:10.1002/elps.200900786

Cited by 5 publications

(4 citation statements)

References 12 publications

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“…In contrast, traditional polyacrylamide gel electrophoresis and silver staining methods are complex to operate, time-consuming, and exhibit poor reproducibility in staining. Additionally, they have limited sensitivity and cannot accurately perform quantitative analysis [ 75 , 76 ].…”

Section: Discussionmentioning

confidence: 99%

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Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers

Liu,

Cheng,

et al. 2023

PLoS ONE

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Polygonatum cyrtonema Hua is a perennial herbaceous plant of the Polygonatum genus, belonging to the Liliaceae family, with significant medicinal and nutritional value. In China, this species is a traditional medicinal and edible herb with a long history of application and is widely appreciated by the people. However, as the demand for medicinal herbs continues to grow, excessive harvesting has led to the depletion of wild resources and the risk of genetic erosion. In addition, the chaotic cultivation of varieties and the lack of high quality germplasm resources have led to inconsistent quality of medical materials. Therefore, it is urgent to conduct genetic diversity evaluation of this species and establish a sound conservation plan. This study assessed the genetic diversity and population structure of 96 samples collected from seven regions in China using the simple sequence repeat (SSR) molecular marker technology. In this study, a total of 60 alleles (Na) were detected across the 10 polymorphic SSR markers used, with an average of 6.0 alleles generated per locus. The values of polymorphic information content (PIC) values ranged from 0.3396 to 0.8794, with an average value of 0.6430. The average value of the effective number of alleles (Ne) was 2.761, and the average value of the Shannon’s information index (I) was 1.196. The population structure analysis indicates that the Polygonatum cyrtonema Hua germplasm can be classified into three subpopulations (JZ, QY, JD) at the molecular level, which corresponds to the previous subgroups identified based on individual plant phenotypic traits. Analysis of Molecular Variance (AMOVA) showed that 74% of the genetic variation was between individuals within populations in different regions. The phylogenetic analysis of the 96 germplasm samples divided them into three main populations. The QY and JD subpopulations are largely clustered together, which could be attributed to their mountainous distribution and the local climate environment. The genetic differentiation coefficient (Fst) value was low at 0.065, indicating relatively low population differentiation. The ratio of the genetic differentiation coefficient (Fst) between the JZ population and the other two populations (QY and JD) is much higher than the ratio between the QY and JD populations. Based on the clustering results and the ratio of the genetic differentiation coefficient (Fst), it can be inferred that the genetic relationship between the QY and JD subpopulations is closer, with a certain degree of genetic differentiation from the JZ subpopulation. This study supports the conservation of germplasm resources of Polygonatum cyrtonema Hua in China and provides new parental material for germplasm genetic improvement and breeding programs.

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Section: Discussionmentioning

confidence: 99%

“…staining. Additionally, they have limited sensitivity and cannot accurately perform quantitative analysis [75,76]. Fluorescence labeled capillary electrophoresis technology does not require gel making and silver staining, which saves time and effort and realizes automated data processing and reduces human errors.…”

Section: Plos Onementioning

confidence: 99%

Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers

Liu,

Cheng,

et al. 2023

PLoS ONE

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“…In contrast, acidic methods impregnate with silver nitrate in a weakly acidic milieu and use formaldehyde to reduce silver under alkaline conditions (3). The silver staining methods are too many for the investigator to choose one suited for the research goals, thus, numerous comparisons of silver staining methods have been reported for polyacrylamide gels unbound to any backing surface (1, 5, 6, 8, 15), such as glass plate or plastic, but to our knowledge relatively few have been published for backed gels (3, 9). Moreover, the silver staining methods suited for unbacked gel may be not available for backed gel since the backing film serves as a surface for silver deposition and restricts diffusion of reagents in and out of the gel to one face only (3).…”

mentioning

confidence: 99%

“…After electrophoresis, gels were silver stained using eight protocols according to the steps described in Table 1. The protocols included the procedures devised by Bassam et al (2, 3), Creste et al (9), Benbouza et al (5), An et al (1), Cong et al (8), the protocol described by the manufacturer of TGGE system (method 3) and its simplified procedure (method 4). All chemicals used for staining were analytical grade from Sinopharm (Shanghai, China).…”

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confidence: 99%

A comparison of silver staining protocols for detecting DNA in polyester-backed polyacrylamide gel

Shanlian¹,

Chen²,

Lin³

et al. 2012

Braz. J. Microbiol.

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Agarose Gel Electrophoresis and Polyacrylamide Gel Electrophoresis for Visualization of Simple Sequence Repeats

Anderson

Wright

Meksem

2013

Methods in Molecular Biology

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In the modern age of genetic research there is a constant search for ways to improve the efficiency of plant selection. The most recent technology that can result in a highly efficient means of selection and still be done at a low cost is through plant selection directed by simple sequence repeats (SSRs or microsatellites). The molecular markers are used to select for certain desirable plant traits without relying on ambiguous phenotypic data. The best way to detect these is the use of gel electrophoresis. Gel electrophoresis is a common technique in laboratory settings which is used to separate deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) by size. Loading DNA and RNA onto gels allows for visualization of the size of fragments through the separation of DNA and RNA fragments. This is achieved through the use of the charge in the particles. As the fragments separate, they form into distinct bands at set sizes. We describe the ability to visualize SSRs on slab gels of agarose and polyacrylamide gel electrophoresis.

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Improved conditions for silver–ammonia staining of DNA in polyacrylamide gel

Cited by 5 publications

References 12 publications

Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers

Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers

A comparison of silver staining protocols for detecting DNA in polyester-backed polyacrylamide gel

Agarose Gel Electrophoresis and Polyacrylamide Gel Electrophoresis for Visualization of Simple Sequence Repeats

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