Genetic purity and testing technologies for seed quality: a company perspective

1998 ◽  
Vol 8 (2) ◽  
pp. 285-294 ◽  
Author(s):  
J. S. C. Smith ◽  
J. C. Register III
Keyword(s):  
Single Molecule ◽  
Seed Quality ◽  
Genetic Purity ◽  
Biochemical Methods ◽  
Crop Varieties ◽  
Select Group ◽  
Purity Testing ◽  
Length Polymorphisms ◽  
Micro Array ◽  
High Level

AbstractA high level of genetic purity in crop varieties must be achieved and maintained for agronomic performance as well as to encourage investment and innovation in plant breeding and to ensure that the improvements in productivity and quality imparted by breeders are delivered to the farmer and, ultimately, to the consumer. Traditionally, morphological comparisons have formed the basis for genetic purity evaluations. However, replicated field observations are time-consuming, expensive and unreliable. Morphology cannot provide information on the purity of specific genetic attributes that relate to grain quality or to pest or herbicide resistance bred into varieties. Biochemical assays, including isozymes, can distinguish varieties within several species. Isozymes have been routinely used in checking seed-lot purity in maize (Zea mays L.) for the past 20 years. Newer DNA-based technologies such as restriction fragment length polymorphisms and more recently developed methods that use the polymerase chain reaction can allow even more discriminative and faster identification of varieties. However, none of the DNA methods have replaced biochemical methods for seed purity assays, other than in a relatively select group of crops with very high seed value, due to their high datapoint cost. It will require further miniaturization, automation and enhanced capabilities to process numerous samples simultaneously before newly developed methods supplant biochemical methods for routine usage in purity testing. New varieties that have major genes for herbicide or insect resistance incorporated within them require purity assays during product development and following seed production of the commercial variety. Immunological or DNA sequence assays can be developed and automated systems are required to process hundreds of thousands of individuals. Ultra-high, micro-array technologies and single-molecule detection systems are now under development. These technologies offer the promise that adequate distinction and high sample throughput will be combined. New methods may eclipse the capabilities of biochemical methodologies, thereby potentially raising genetic purity standards and enabling farmers and consumers better to utilize and benefit from increasingly productive varieties that are bred from a more diverse base of genetic resources.

scholarly journals Seed genetic purity testing of F1 Benincasa hispida var. chieh-qua hybrids using SSR molecular marker analysis

2020 ◽  
Vol 48 (3) ◽  
pp. 345-353
Author(s):  
J.Y. Chen ◽  
Q.M. Chen ◽  
Z.G. Liu ◽  
C.L. Wang ◽  
L.L. Ma ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Seed Quality ◽  
Accurate Method ◽  
Whole Genome Sequence ◽  
Genetic Purity ◽  
Purity Testing ◽  
Benincasa Hispida ◽  
Ssr Primers ◽  
Hybrid Seeds ◽  
Molecular Marker Analysis

To ensure that farmers can access high-quality seeds, it is essential to find a simple, rapid and accurate method to assess seed purity. In recent years, heterosis in chieh-qua has been widely applied to production. Using the whole genome sequence of chieh-qua, we designed simple sequence repeat (SSR) primers specific for chieh-qua. The parental lines of nine hybrids were screened using 200 SSR primers, seven of which exhibited polymorphisms. The bands were clear, stable and reproducible. We found dominant and co-dominant bands between the parents of the nine hybrids. The seven pairs of SSR primers were successfully used to assess genetic purity of the nine chieh-qua hybrids. The SSR molecular marker purity assessment results were consistent with the results obtained from a field grow-out test (GOT). However, the use of SSR markers provided a more accurate, reliable and faster method for seed purity testing than the GOT. We propose using SSR molecular marker technology to assess the genetic purity of chieh-qua hybrid seeds. With this method, the seed quality can be determined faster, which may help to accelerate the chieh-qua breeding process.

scholarly journals Sequence-characterized amplified region (SCAR) technique used for variety discrimination in vinca (Catharanthus roseus (L.) G.Don)

2002 ◽  
Vol 24 (1) ◽  
pp. 299-305 ◽  
Author(s):  
Carlos C.E Menezes ◽  
Tara Vantoai ◽  
Miller B McDonald ◽  
Tocio Sediyama
Keyword(s):  
Catharanthus Roseus ◽  
Seed Quality ◽  
Sequence Information ◽  
Genetic Purity ◽  
Banding Patterns ◽  
Sequence Characterized Amplified Region ◽  
Purity Testing ◽  
Polymorphic Bands ◽  
Scar Primers

Sequence-Characterized Amplified Region (SCAR) appears as a useful technique for genetic purity testing and variety discrimination, applicable to species in which some other techniques have failed. In particular, this technique is very attractive with species in which RAPD results were not consistent. The RAPD polymorphic bands were cloned, sequenced and from the sequence information, primers pairs for normal PCR were developed. Since the probability of obtaining successful SCAR primers from RAPD polymorphic bands was about 50%, a larger number of RAPD polymorphic bands are needed to develop sufficient SCAR primers for varietal discrimination in vinca. In addition, the efficiency of the SCAR technique is strongly affected by the quality of DNA extracted from seeds. The SCAR banding patterns obtained from vinca seed were consistent and repeatable making the results reliable for genetic purity testing and variety discrimination. The SCAR technique is simple, fast, relatively inexpensive and allows the use of DNA extracted from dry seeds, which is very important in a seed-quality evaluating program

Fatal Respiratory Diphtheria Caused by ß-Lactam–Resistant Corynebacterium diphtheriae

2020 ◽  
Author(s):  
Brian M Forde ◽  
Andrew Henderson ◽  
Elliott G Playford ◽  
David Looke ◽  
Belinda C Henderson ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genomic Analysis ◽  
Carbapenem Resistance ◽  
Corynebacterium Diphtheriae ◽  
Penicillin Binding Protein ◽  
Long Read ◽  
Amoxicillin Clavulanic Acid ◽  
Resistance To Penicillin ◽  
High Level

Abstract Background Diphtheria is a potentially fatal respiratory disease caused by toxigenic Corynebacterium diphtheriae. Although resistance to erythromycin has been recognized, β-lactam resistance in toxigenic diphtheria has not been described. Here, we report a case of fatal respiratory diphtheria caused by toxigenic C. diphtheriae resistant to penicillin and all other β-lactam antibiotics, and describe a novel mechanism of inducible carbapenem resistance associated with the acquisition of a mobile resistance element. Methods Long-read whole-genome sequencing was performed using Pacific Biosciences Single Molecule Real-Time sequencing to determine the genome sequence of C. diphtheriae BQ11 and the mechanism of β-lactam resistance. To investigate the phenotypic inducibility of meropenem resistance, short-read sequencing was performed using an Illumina NextSeq500 sequencer on the strain both with and without exposure to meropenem. Results BQ11 demonstrated high-level resistance to penicillin (benzylpenicillin minimum inhibitory concentration [MIC] ≥ 256 μg/ml), β-lactam/β-lactamase inhibitors and cephalosporins (amoxicillin/clavulanic acid MIC ≥ 256 μg/mL; ceftriaxone MIC ≥ 8 μg/L). Genomic analysis of BQ11 identified acquisition of a novel transposon carrying the penicillin-binding protein (PBP) Pbp2c, responsible for resistance to penicillin and cephalosporins. When strain BQ11 was exposed to meropenem, selective pressure drove amplification of the transposon in a tandem array and led to a corresponding change from a low-level to a high-level meropenem-resistant phenotype. Conclusions We have identified a novel mechanism of inducible antibiotic resistance whereby isolates that appear to be carbapenem susceptible on initial testing can develop in vivo resistance to carbapenems with repeated exposure. This phenomenon could have significant implications for the treatment of C. diphtheriae infection, and may lead to clinical failure.

scholarly journals Use of molecular marker techniques in seed testing by Brazilian seed companies

1998 ◽  
Vol 55 (spe) ◽  
pp. 79-82 ◽  
Author(s):  
P.T. Della Vecchia ◽  
C.A.R. da Silva ◽  
P. Terenciano-Sobrinho
Keyword(s):  
Molecular Marker ◽  
New Technologies ◽  
Seed Quality ◽  
Genetic Purity ◽  
Process Step ◽  
Seed Testing ◽  
Routine Basis ◽  
Seed Market ◽  
Key Issues ◽  
High Quality Seed

Seed market is becoming global and globalization is growing very fast. To compete favourably in this new global seed world, quality and cost are and will be certanly the key issues. High seed quality can only be obtained by a thorough control of the entire seed production process, step by step from planning to final delivery. That requires science, technology, expertise, experience, good management and certanly, the most important, an absolute and unconditional commitment with quality. Seed testing for quality assurance is one important step in the process of production of high quality seed. In the late years a considerable amount of research has been published, particularly on the use of some Polymerase Chain Reaction DNA based new technologies (RAPD, microsatelites, AFLP) for genetic purity determinations in seed testing. As far as we know, no Brazilian seed company is using, on regular basis, RAPD or other molecular marker techniques in the determination of genetic purity in seed testing. Most of these are using morphological or physiological traits expressed by seed, seedling or mature plant and/or electrophoresis of seed or seedling proteins/isoenzymes for that purpose. Main reasons for that are: DNA molecular marker techniques are relatively new; lack of specialized personnel to run DNA molecular marker assays on routine basis; higher cost/sample when compared to proteins/isoenzymes electrophoresis.

Genetic variation in Eruca vesicaria (L.) Cav.

2007 ◽  
Vol 5 (03) ◽  
pp. 142-153 ◽  
Author(s):  
S. I. Warwick ◽  
R. K. Gugel ◽  
C. Gómez-Campo ◽  
T. James
Keyword(s):  
Field Trial ◽  
Seed Quality ◽  
Quality Data ◽  
Oilseed Crop ◽  
Aflp Data ◽  
Cruciferous Vegetable ◽  
Western Africa ◽  
Length Polymorphisms ◽  
Western Asia ◽  
Agronomic Potential

Eruca vesicariasubsp.sativa(syn.E. sativa) is a cruciferous vegetable and oilseed crop that is high in erucic acid. It occurs throughout the Mediterranean region and western Asia, and has been naturalized elsewhere as a crop/weed escape. It is closely related to subsp.vesicariaand subsp.pinnatifida, which are endemic to Spain and north-western Africa, respectively. This study evaluated patterns and levels of diversity in the three subspecies based on 234 amplified fragment length polymorphisms (AFLP), and evaluated agronomic and seed quality data in a field trial in western Canada. AFLP data revealed three main clusters: ‘Sativa’ (33 accessions of subsp.sativa), ‘Vesicaria’ (nine accessions of subsp.vesicaria) and a ‘Pinnatifida’ cluster (one accession of subsp.pinnatifidaand three Moroccan accessions of subsp.sativa). The Sativa cluster separated into Mediterranean and Asian groups, likely reflecting differences in origin (wild versus cultivated) or primary usage, vegetable versus seed oil. The origin of the introduced Mexican population was confirmed as subsp.sativa. The highest levels of diversity were found in the Sativa cluster (88% AFLP polymorphisms) and the least in the Vesicaria (56%) and Pinnatifida (39%) clusters. Extensive variation was observed among the 159 subsp.sativaaccessions evaluated in the field trial, and overall findings indicated a favourable agronomic potential.

EFFECTS OF ISOLATION DISTANCE ON CONTAMINATION IN SWEETCLOVER

1972 ◽  
Vol 52 (4) ◽  
pp. 517-524 ◽  
Author(s):  
B. P. GOPLEN ◽  
D. A. COOKE ◽  
P. PANKIW
Keyword(s):  
Honey Bees ◽  
Genetic Purity ◽  
Isolation Distance ◽  
Isolation Distances ◽  
Contamination Levels ◽  
High Level

The recessive low coumarin gene cu was used as a marker to study the effects of isolation distance on contamination levels in sweetclover pollinated by honey bees. A 46-m isolation distance was found inadequate to maintain a high level of genetic purity. Considerable contamination from crossing resulted with isolation distances from 46 to 804 m when there was little competitive bloom from other entomophilous crops. A highly attractive and competitive crop of rapeseed appeared to serve as a very effective isolation barrier to minimize contamination. A higher amount of contamination occurred in the borders of the low-coumarin isolation plots of one test. The results of this study are sufficient to question the existing isolation standards for sweetclover, but are not adequate to formulate new standards.

scholarly journals Pengujian Kemurnian Genetik Benih Padi Galur F3 (Pandanwangi x PTB33) Terseleksi Menggunakan Marka Molekuler Simple Sequence Repeats (SSR)

Agrikultura ◽  
2015 ◽  
Vol 26 (2) ◽  
Author(s):  
Syindy Raffini Nasihin ◽  
Wieny H. Rizky ◽  
Nono Carsono
Keyword(s):  
Simple Sequence Repeats ◽  
Simple Sequence Repeat ◽  
Brown Planthopper ◽  
Plant Analysis ◽  
Current Experiment ◽  
Genetic Purity ◽  
Experimental Station ◽  
Purity Testing ◽  
Brown Planthopper Resistance ◽  
Simple Sequence

ABSTRACTSeed Purity Testing of F3 Progeny of Rice Lines Derived from a Cross between Pandanwangi x PTB-33 Estimated by Simple Sequence Repeat MarkersSeeds with high purity is required to produce maximum crop yield. Genetic purity of selected F3rice seed progenies derived from a cross between Pandanwangi x PTB33 was estimated by SSR(simple sequence repeats) molecular markers. Objective of current experiment was to obtain riceseed with high genetic purity (100%) in terms of homogeneity of alleles. The experiment wasconducted at Laboratory of Plant Analysis and Biotechnology, meanwhile field experiment wasperformed at Ciparanje Experimental Station, Faculty of Agriculture, Universitas Padjadjaran.Based on primer designed by Bradbury (aromatic trait) and primers RM589 and RM586 (supposedto correlate with brown planthopper resistance gene), seeds of F3 selected had 100% geneticpurity. SSR markers applied for each offspring were able to demonstrate the purity of the seed.Genotypes with 100% genetic purity can be continued for propagating their seeds.Keywords: F3, seed purity, seed rice, SSR markersABSTRAKBenih dengan kemurnian genetik tinggi sangat diperlukan untuk produksi tanaman yangmaksimal. Kemurnian genetik padi generasi F3 hasil persilangan Pandanwangi x PTB-33 diestimasidengan menggunakan marka molekuler SSR. Percobaan ini bertujuan untuk mendapatkan generasiF3 yang memiliki kemurnian genetik 100%. Penelitian dilaksanakan di Kebun PercobaanCiparanje, Fakultas Pertanian Universitas Padjadjaran dan Laboratorium Analisis dan BioteknologiTanaman. Hasil analisis menggunakan primer Bradbury menunjukkan 100% benih murniberdasarkan karakter aromatik, begitupun berdasarkan karakter ketahanan terhadap wereng(primer RM589 dan RM586) menunjukkan 100% benih murni. Marka molekuler SSR yangdigunakan untuk verifikasi kemurnian mampu menunjukkan kemurnian genetik benih padi yangtinggi. Genotip PP dapat dilanjutkan untuk pengujian dan atau perbanyakan benih sumber.Kata kunci: benih padi, F3, marka SSR, uji kemurnian genetik

scholarly journals A compendium of novel genomics technologies provides a chromosome-scale assembly and insights into the sex determining system of the Greenland Halibut

2021 ◽  
Author(s):  
Anne-Laure Ferchaud ◽  
Claire Merot ◽  
Eric Normandeau ◽  
Ioannis Ragoussis ◽  
Charles Babin ◽  
...  
Keyword(s):  
Sex Determination ◽  
Single Molecule ◽  
Sex Chromosome ◽  
Major Effect ◽  
Whole Genome Sequence ◽  
Greenland Halibut ◽  
Long Reads ◽  
Full Picture ◽  
High Conservation ◽  
High Level

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. In this study, we combined single molecule sequencing of long reads (Pacific Sciences) with Chromatin Conformation Capture sequencing (Hi-C) data to provide the first chromosome-level genome reference for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96 % of its total length distributed among 24 chromosomes. The investigation of its syntenic relationships with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that flatfishes do not escape the rule applied to other teleost fish and exhibit a high level of plasticity and turnover in sex-determination mechanisms. A whole-genome sequence analysis of 198 individuals allowed us to draw a full picture of the molecular sex determination (SD) system for Greenland Halibut, revealing that this species possesses a very nascent male heterogametic XY system, with a putative major effect of the sox2 gene, also described as the main SD driver in two other flatfishes. Interestingly, our study also suggested for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of early steps of sex chromosome evolution.

scholarly journals Identification and characterization of popular rice (Oryza sativa L.) varieties through chemical tests

2020 ◽  
pp. 82-85
Author(s):  
M.S. Nagendra ◽  
P. Selvaraju ◽  
R. Jerlin ◽  
K. Ganesamurthy ◽  
N. Senthil
Keyword(s):  
Tamil Nadu ◽  
Oryza Sativa L ◽  
Colour Change ◽  
Gelatinization Temperature ◽  
Genetic Purity ◽  
Rice Varieties ◽  
Seed Supply ◽  
Crop Varieties ◽  
Identification And Characterization

Identification and characterization of crop varieties are crucial for ensuring the genetic purity of seeds. The present investigation was carried out to identify suitable chemical methods that are fast, reliable and easy for seed analysts, breeders and seed producers for identification of a variety. Twenty-five popular rice varieties in the seed supply chain of Tamil Nadu were subjected to phenol, modified phenol, NaOH, aroma, gelatinization temperature (alkali spreading value), GA3 and 2,4-D tests. The results of the experiment revealed that phenol and modified phenol tests changed the colour of TKM 9 and TRY 1 variety to brown but no colour change was observed in the variety I.W. Ponni variety. The NaOH test is useful for the identification of TKM 9 variety as it changed the colourless solution to red. GA3 and 2,4-D tests characterized the varieties based on the shoot growth into two and three groups respectively. However, all the variety lacked aroma and exhibited a high gelatinization temperature.

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