Gel electrophoresis for the identification of plant varieties

The association between hordein polypeptide banding and agronomic traits in partitioning genetic diversity in six-rowed Ethiopian barley lines (Hordeum vulgare L.)

BACKGROUND

Evaluation of the extent of genetic variation within and between the populations of crop genetic resources are of paramount importance in any breeding program. An experiment aimed at assessing the extent of variation among barley lines and the degree of association between hordein polypeptide and agronomic traits was hence executed.

METHODS

Field experiment was conducted in six environments between 2017-2019 involving 19 barley lines. Hordein bands were separated using vertical Sodium Dodecyl Sulphate Poly- acrylamide Gel Electrophoresis (SDS-PAGE).

RESULTS

The analysis of variance revealed significant variation among lines and wider range units were observed for the agronomic traits. The line (Acc# 16,811-6) was superior, producing the highest grain yield (2.97 ton ha^-1) across environments, 3.6 ton ha^-1 at Holleta, and 1.93 ton ha^-1 at Chefedonsa. At Arsi Negelle a different line Acc# 17146-9 was the highest yielding (3.15ton ha^-1). SDS-PAGE-based analysis of barley lines separated 12 hordein bands between C (four bands) and B (eight bands) subunits. Interestingly bands 52, 46a, and 46b were uniquely conserved in the four naked barley lines (Acc#16809-14,16956-11, 17240-3, 17244-19). A considerably high proportion of genetic diversity within the populations than among the populations could be a repercussion of high gene flow which substantiates the longstanding and dominant informal seed exchange system among the farmers. The significant positive association between grain yield and band 50 evocates the expression of this allele may code for higher grain yield. The negative association between days to maturity and band 52 perhaps stipulates earliness in barely lines upon the manifestation of the band. Band 52 and 60 appeared to be associated with more than one agronomic trait (days to maturity and thousand kernel weight; grain filling period and grain yield respectively) and could be the result of pleiotropic characteristics of the genes residing in these banding regions.

CONCLUSION

The barley lines exhibited substantial variation for hordein protein and agronomic traits. However, imparted the need for the implementation of decentralized breeding as a consequence of genotype-by-environment interaction. Significant hordein polypeptide and agronomic traits association advocated the utilization of hordein as a protein marker and perhaps consider them in the parental line selection.

A Machine Learning Method for Classification and Identification of Potato Cultivars Based on the Reaction of MOS Type Sensor-Array

In response to one of the most important challenges of the century, i.e., the estimation of the food demands of a growing population, advanced technologies have been employed in agriculture. The potato has the main contribution to people’s diet worldwide. Therefore, its different aspects are worth studying. The large number of potato varieties, lack of awareness about its new cultivars among farmers to cultivate, time-consuming and inaccurate process of identifying different potato cultivars, and the significance of identifying potato cultivars and other agricultural products (in every food industry process) all necessitate new, fast, and accurate methods. The aim of this study was to use an electronic nose, along with chemometrics methods, including PCA, LDA, and ANN as fast, inexpensive, and non-destructive methods for detecting different potato cultivars. In the present study, nine sensors with the best response to VOCs were adopted. VOCs sensors were used at various VOCs concentrations (1 to 10,000 ppm) to detect different gases. The results showed that a PCA with two main components, PC1 and PC2, described 92% of the total samples’ dataset variance. In addition, the accuracy of the LDA and ANN methods were 100 and 96%, respectively.

Agro-morphological description, genetic diversity and population structure of sugarcane varieties from sub-tropical India

Genetic diversity in 92 sugarcane varieties of sub-tropical India was assessed using 30 morphological descriptors and 643 simple sequence repeat (SSR) marker loci. Out of the 30 morphological descriptors, 14 were found polymorphic, and significant variability was recorded for plant height, cane diameter and number of millable canes. Grouping traits like plant growth habit, leaf blade curvature and leaf sheath adherence were found to be predominantly monomorphic. There were a few pairs of varieties (e.g., CoP 9702 and CoP 9302, CoP 9301 and CoSe 01424, UP 05 and Co 1336, CoS 96258 and CoH 110) that showed similar DUS profiles except differing for a few descriptors. The STRUCTURE profile suggest that all the 92 sugarcane varieties had admixtures and no sub-group had a pure unblemished structure profile. An average Nei's genetic distance of 0.49 was found to be a better measure of diversity, whereas, the average band informativeness (Ib_av) value of all the 80 SSR primers was 0.434. Although, the mean Ib_av values for EST-SSR and genomic-SSR primers were same (0.43), the range of Ib_av of EST-SSR (0.04-0.85) was more compared to genomic-SSR (0.12-0.63) primers. The segregation of the varieties based on morphological traits was not in accordance with their geographical distribution or maturity groups, but principal component analysis was able to group the sugarcane varieties that had similar pedigree together. Results indicate that the SSRs have a potential use in the DNA fingerprinting of varieties to prevent any malpractice like unauthorised re-registration of a previously registered sugarcane variety under PPV&FR Act. The marker profiles could also be utilised for variety identification and release, since at present, it has been made mandatory to include it in addition to the morphological descriptors.

Food processing and breeding strategies for coeliac-safe and healthy wheat products

A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients. The first approach is based on food processing strategies, which aim to remove gliadins or all gluten from edible products. We find that several of the candidate food processing techniques to produce low gluten-immunogenic products from wheat already exist. The second approach focuses on wheat breeding strategies to remove immunogenic epitopes from the gluten proteins, while maintaining their food-processing properties. A combination of breeding strategies, including mutation breeding and possibly genome editing, will be necessary to produce coeliac-safe wheat. Individuals suffering from CD and people genetically susceptible who may develop CD after prolonged gluten consumption would benefit from reduced CD-immunogenic wheat. Although the production of healthy and less CD-toxic wheat varieties and food products will be challenging, increasing global demand may require these issues to be addressed in the near future by food processing and cereal breeding companies.

Application of proteomics to hordein screening in the malting process

This study was undertaken to investigate the effect of the malting process on hordein composition. For this purpose, combination of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and the method of isotopic peptides labeling iTRAQ was used. Barley proteins are essential components determining the quality of both malt and beer. Since hordeins represent the most abundant proteins accounting for about 40-50% of total protein fraction of mature barley grain, our research was focused on them. In this respect, the proteins of interest were extracted from milled samples of barley grain, germinated barley grain (samples collected at different time intervals), green malt and malt, respectively. Particular hordein extracts were firstly fractionated via SDS- PAGE, which was used as a relatively rapid and reliable technique providing information about hordein profile of analyzed samples. Then, separated proteins were in-gel digested and resulting peptides were measured by mass spectrometry. In addition, the chosen proteins, after in-gel digestion, were subjected to the iTRAQ method and the screening of proteins during malting process was evaluated. Our results have revealed that most of the hordein components present in the barley grain can be found in all stages of the malting process as well as in the final malt. The amount of hordeins decreases during the malting process; in the case of C hordein, the protein decrease is approximately 65%. On the other hand, significant degradation of D hordein was detected. The suggested procedure can be used to follow the development of the hordein profile during germination, which is of great technological importance in beer production.

MALDI-TOF mass spectrometry of hordeins: rapid approach for identification of malting barley varieties

A procedure for identification of malting barley varieties using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of ethanol-soluble barley proteins (hordeins) is described. The hordeins were first extracted from milled barley grains by several extraction protocols (using different extraction agents and conditions). Hordein extracts were then analyzed directly via MALDI-TOF MS without any preliminary purification or separation step, and the protein profiles of analyzed hordein extracts were compared in order to find out the most suitable extraction procedure for mass spectrometric analysis. The optimized procedure was successfully applied to identification of 13 malting barley varieties. Our results revealed that the proposed mass spectrometry-based approach provides characteristic mass patterns of extracted hordeins, which can be advantageously used for barley variety identification.

On-site variety discrimination of tomato plant using visible-near infrared reflectance spectroscopy

The use of visible-near infrared (NIR) spectroscopy was explored as a tool to discriminate two new tomato plant varieties in China (Zheza205 and Zheza207). In this study, 82 top-canopy leaves of Zheza205 and 86 top-canopy leaves of Zheza207 were measured in visible-NIR reflectance mode. Discriminant models were developed using principal component analysis (PCA), discriminant analysis (DA), and discriminant partial least squares (DPLS) regression methods. After outliers detection, the samples were randomly split into two sets, one used as a calibration set (n=82) and the remaining samples as a validation set (n=82). When predicting the variety of the samples in validation set, the classification correctness of the DPLS model after optimizing spectral pretreatment was up to 93%. The DPLS model with raw spectra after multiplicative scatter correction and Savitzky-Golay filter smoothing pretreatments had the best satisfactory calibration and prediction abilities (correlation coefficient of calibration (R(c))=0.920, root mean square errors of calibration=0.196, and root mean square errors of prediction=0.216). The results show that visible-NIR spectroscopy might be a suitable alternative tool to discriminate tomato plant varieties on-site.

Early prediction of wheat quality: analysis during grain development using mass spectrometry and multivariate data analysis

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and multivariate data analysis have been used for the determination of wheat quality at different stages of grain development. Wheat varieties with one of two different end-use qualities (i.e. suitable or not suitable for bread-making purposes) were investigated. The samples were collected from grains from 15 until 45 days post-anthesis (dpa). Gluten proteins from wheat grains were extracted and subsequently analysed by mass spectrometry. Discrimination partial least-squares regression and soft independent modelling of class analogy were used to determine the quality of new and unknown wheat samples. With these methods, we were able to predict correctly the end-use qualities at every stage investigated. This new fast technique, based on the rapidity of mass spectrometry combined with the objectivity of multivariate data analysis, offers a method that can replace the traditional rather time-consuming ones such as gel electrophoresis. This study focused on the determination of wheat quality at 15 dpa, when the grain is due for harvest 1 month later.

Identification of barley and rye varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks

Cereal varieties are normally identified using time-consuming methods such as visual examination of either the intact grain or one-dimensional electrophoretic patterns of the grain storage proteins. A fast method for identification of wheat (Triticum aestivum L.) varieties has previously been developed, which combines analysis of alcohol-soluble wheat proteins (gliadins) using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks. Here we have applied the same method for the identification of both barley (Hordeum vulgare L.) and rye (Secale cereale L.) varieties. For barley, 95% of the mass spectra were correctly classified. This is an encouraging result, since in earlier experiments only a grouping into subsets of varieties was possible. However, the method was not useful in the classification of rye, due to the strong similarity between mass spectra of different varieties.

Isoelectric focusing in the vegetable seed industry

Different types of electrophoretic procedures were developed for hybrid purity testing based on starch gel electrophoresis (SGE), vertical polyacrylamide gel electrophoresis (PAGE), and isoelectric focusing (IEF). For the most important vegetables these methods are much faster than plant grow-outs and relatively inexpensive. Compared to SGE and PAGE methods, horizontal IEF proved to be more efficient for large-scale hybrid purity testing. These developments were made possible by the basic work of Harry Rilbe and improvements that were initiated as a result of Rilbe's work. The present paper describes a number of milestones during this developmental period, starting with the isoelectric focusing concept of Harry Rilbe up to the large-scale application of IEF. Further, a comparison of IEF with DNA fingerprinting methods along with the future of both techniques is discussed with respect to hybrid purity testing in the vegetable seed industry. When it comes to a choice between the use of either IEF or a DNA-based method, efficiency and efficacy determines the method which is best suited for hybrid purity testing. It is also concluded that in the future we will see an increased use of both IEF as well as DNA-based methods for hybrid purity testing because expectations of growers has increased; consequently they will accept fewer inbreds in a hybrid variety, especially when growing in a greenhouse.

Horizontal ultrathin-layer multi-zonal electrophoresis of DNA: an efficient tool for large-scale polymerase chain reaction (PCR) fragment analysis

A rapid and efficient procedure for large-scale analysis of polymerase chain reaction (PCR) fragments in the range of 200-3000 base pairs is presented. The procedure is based on horizontal ultrathin-layer multi-zonal (HUME) electrophoresis of PCR fragments in polyacrylamide gels followed by silver staining. HUME gels can be prepared rapidly using a simple procedure called the flap technique. The electrophoretic set-up allows the use of multi-channel pipettes for sample loading. Separation and detection of the PCR fragments from sample preparation to silver staining can be carried out in 2 h. Using four electrophoresis units, one technician can analyze 400 PCR fragment samples in 2 h.

High-performance separations in isolation and characterization of allergens

The present state of the use of separation techniques in the identification and characterization of allergens and in the monitoring of the quality of allergenic preparations is critically surveyed. After a brief summary of the range of problems encountered in obtaining and in the application of allergenic preparations and of the principal physico-chemical properties of allergens, chromatographic and electromigration methods of separation of components of these systems and their combinations with immunochemical procedures are discussed, with selected examples of application to real materials. Emphasis is placed on evaluation of the most important analytical parameters, such as reliability of the results, separation efficiency and resolution, and on the most recent results in the field.

DNA profiling and plant variety registration: 1. The use of random amplified DNA polymorphisms to discriminate between varieties of oilseed rape

Before they can be marketed in the UK, newly bred varieties of crop species have to undergo a process of statutory testing, part of which involves the examination of the distinctness, uniformity and stability (DUS) of the variety. DUS testing is also used as the basis for the award of Plant Breeders' Rights. This paper examines the potential of DNA polymorphisms, amplified using arbitrary primers (RAPDs) for use in DUS testing of varieties of oilseed rape. RAPDs using suitable primers can produce high levels of discrimination (> 95%) between varieties, although there are certain problems in gel 'scoring' that are only partially resolved by computerised gel scanning/evaluation techniques. Varieties of oilseed rape are also heterogeneous in their RAPD profiles using certain primers, which could cause problems in the DUS testing context. DNA profiling with RAPDs could be used for discrimination between and identification of oilseed rape varieties, but its use for DUS testing needs to be considered carefully.