Development of SCAR markers linked to zt-2, one of the genes controlling absence of tannins in faba bean

2008 ◽  
Vol 59 (1) ◽  
pp. 62 ◽  
Author(s):  
Natalia Gutierrez ◽  
C. M. Avila ◽  
M. T. Moreno ◽  
A. M. Torres
Keyword(s):  
Faba Bean ◽  
Bulked Segregant Analysis ◽  
Consensus Sequence ◽  
Flower Colour ◽  
Cost Effective ◽  
Tannin Content ◽  
Repulsion Phase ◽  
Protein Levels ◽  
F2 Population ◽  
Faba Beans

Faba beans (Vicia faba L.) have a great potential as a protein-rich fodder crop, but anti-nutritional factors such as condensed tannins reduce the biological value of their protein. Tannins can be removed from seeds by any of the two complementary genes, zt-1 and zt-2, which also determine white-flowered plants. The less common gene, zt-2, is also associated with increased protein levels and energy values and reduced fibre content of the seeds. To identify a cost-effective marker linked to zt-2, we analysed a segregating F2 population derived from the cross between the coloured flower and high tannin content genotype Vf6 and a zt-2 line. By using Bulked Segregant Analysis (BSA), five RAPD markers linked in coupling and repulsion phase to zt-2 were identified and their conversion into Sequence Characterised Amplified Regions (SCARs) was attempted. Amplification of the SCARS was more consistent, although the initial polymorphism was lost. Restriction digestion of SCAR SCAD16589 with AluI (SCAD16-A), Bsp120I (SCAD16-B) and HinfI (SCAD16-H) revealed clear differences due to the amplification of different loci. The consensus sequence of these CAPs (Cleavage Amplification Polymorphisms) markers allowed discrimination of three bands from which two new forward SCAR primers were developed based on specific sequences from zero tannin and high tannin content genotypes. To improve the efficiency of the marker screening, a multiplex PCR was developed that allowed the simultaneous amplification of the SCAR with the same advantages as a codominant marker. Marker validation was carried out with a new F2 population segregating for flower colour and tannin content, underscoring the potential of these markers in breeding selection to introgress the zt-2 gene for the development of new tannin free faba bean cultivars.

Molecular mapping of a thermosensitive genetic male sterility gene in rice using bulked segregant analysis

Genome ◽  
1997 ◽  
Vol 40 (2) ◽  
pp. 188-194 ◽  
Author(s):  
P. K. Subudhi ◽  
R. P. Borkakati ◽  
S. S. Virmani ◽  
N. Huang
Keyword(s):  
Male Sterility ◽  
Molecular Mapping ◽  
Bulked Segregant Analysis ◽  
Pcr Primers ◽  
Rflp Markers ◽  
Arbitrary Primers ◽  
Repulsion Phase ◽  
Genetic Male Sterility ◽  
True Breeding ◽  
Efficient Alternative

The thermosensitive genetic male sterility (TGMS) system is considered to be a more efficient alternative to the cytoplasmic male sterility (CMS) system for hybrid rice. An F2 population from a cross between a TGMS mutant line (IR32364TGMS) and IR68 was used to map the TGMS gene tms3(t). Fertile and sterile bulks were constructed following the classification of F2 plants into true breeding sterile, fertile, and segregating fertile plants based on F3 family studies. From the survey of 389 arbitrary primers in bulked segregant analysis, four RAPD markers were identified in which three, OPF182600, OPB19750, and OPAA7550, were linked to tms3(t) in repulsion phase and one, OPAC3640, was linked to tms3(t) in coupling phase. The tms3(t) gene was flanked by OPF182600 and OPAC3640 on one side and by OPAA7550 and OPB19750 on the other side. All four markers were low-copy sequences and two of them (OPF182600 and OPAC3640) detected polymorphism when the markers were used to probe the genomic blots. Subsequently, OPAC3640 was mapped to the short arm of chromosome 6 using a mapping population available at IRRI. However, no RFLP markers from this region showed linkage to tms3(t) owing to the lack of polymorphism between the parents. All RAPD fragments were cloned and partially sequenced from both ends. Thus, PCR primers can be designed to develop PCR markers for marker-assisted breeding to facilitate the transfer of tms3(t) from one genetic background to another.Key words: bulked segregant analysis, gene tagging, marker-assisted selection, RAPD, TGMS.

scholarly journals First Detection of Faba bean necrotic yellow virus in Spain

Plant Disease ◽  
2000 ◽  
Vol 84 (6) ◽  
pp. 707-707 ◽  
Author(s):  
M. Babin ◽  
V. Ortíz ◽  
S. Castro ◽  
J. Romero
Keyword(s):  
Faba Bean ◽  
Acyrthosiphon Pisum ◽  
Virus Disease ◽  
Epidemiological Data ◽  
Aphid Transmission ◽  
Enzyme Linked Immunosorbent Assay ◽  
Yellow Virus ◽  
Potential Threat ◽  
Bean Plants ◽  
Faba Beans

Faba bean necrotic yellow virus (FBNYV) was not detected during 1994 to 1996 field surveys of faba beans (Vicia faba L.) in Spain (1). In 1997, however, one sample with symptoms of necrosis, collected in Baleares, was tested using ELISA (enzyme-linked immunosorbent assay) and was positive for both Tomato spotted wilt virus (TSWV) and FBNYV. FBNYV is a single-strand DNA virus that is transmitted by aphids and is the main virus disease of broad bean in North Africa and West Asia (2). During 1997 to 1999, faba bean plants with symptoms of necrosis, yellowing, small leaves, and stunting were collected from several fields in the Murcia Region (Spain) and were analyzed using ELISA. To detect FBNYV, we used monoclonal 2E9 supplied by H. J. Vetten (Institute of Plant Virology, Microbiology and Biosafety, BBA, Braunschweig, Germany). Of 700 samples analyzed, 34 were positive for FBNYV. Of the 34 positive samples, 12 tested positive, using commercial antiserum from Loewe, Inc. (Munich) for mixed infections with TSWV. FBNYV was transmitted to healthy faba bean plants by aphids (Acyrthosiphon pisum) in greenhouse experiments and was confirmed by ELISA. Preliminary epidemiological data showed a gradual increase in the number of plants infected with time in the same field. Aphid transmission of FBNYV to faba beans has established the disease in Spain and is a potential threat to other leguminous crops. This is the first report of a nanovirus in Europe. References: (1) J. Fresno et al. Plant Dis. 81:112, 1997. (2) L. Katul et al. Ann. Appl. Biol. 123:629, 1993.

scholarly journals Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Chilling Tolerance ◽  
Pathway Enrichment Analysis ◽  
Potential Candidate ◽  
Rice Varieties ◽  
Booting Stage ◽  
F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

Portal vein, hepatic vein and circulating plasma amino acids in rats given diets based on lactalbumin, faba bean (Vicia faba) and chickpea (Cicer arietinum)

2003 ◽  
Vol 77 (1) ◽  
pp. 3-10 ◽  
Author(s):  
L. A. Rubiot
Keyword(s):  
Amino Acids ◽  
Portal Vein ◽  
Faba Bean ◽  
Plasma Concentrations ◽  
Portal Blood Flow ◽  
Hepatic Veins ◽  
Plasma Amino Acids ◽  
Synthetic Amino Acids ◽  
Male Wistar Rats ◽  
Faba Beans

AbstractThree experiments were carried out to determine plasma amino acids concentrations in circulating, portal and hepatic blood of growing male Wistar rats given diets containing lactalbumin, faba beans or chickpeas as the only protein source. Diets contained the same amount of digestible energy (15·5 kJ/g) and protein (lactalbumin in controls or legume proteins in the experimental diets; 100 g/kg). Appropriate amounts of essential synthetic amino acids were also added to legume-based diets taking into account their amino acid composition to equalize them to control (lactalbumin) diets. Portal blood flow (8·7±0·3 ml/min) was measured by using a transit-time ultrasound flow probe. Higher (P < 001) plasma concentrations of methionine than of controls were determined in hepatic veins of legume-fed rats. In contrast, lower (P < 001) concentrations of threonine, proline, valine, leucine, phenylalanine and lysine than those of controls were found in faba bean- and chickpea-fed rats. The same result as hepatic was obtained for portal and circulating plasma samples except that alanine and histidine values of legume-fed rats were also lower (P < 001) than controls. Calculated net afferent appearance rates of amino acids to the liver were lower (P < 001) than controls in rats given faba bean and chickpea diets for threonine, alanine, proline, valine, leucine, phenylalanine and lysine. This lower contribution of amino acids to the liver mainly via the portal vein in faba bean or chickpea-fed rats might explain previously reported differences in protein utilization and growth in comparison with animals given other protein sources (lactalbumin).

A baseline study of vicine–convicine levels in faba bean (Vicia faba L.) germplasm

2013 ◽  
Vol 11 (3) ◽  
pp. 250-257 ◽  
Author(s):  
Khalil Khamassi ◽  
Fayçal Ben Jeddi ◽  
Doug Hobbs ◽  
Jose Irigoyen ◽  
Fred Stoddard ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Faba Bean ◽  
Screening Method ◽  
Wild Type ◽  
Faba Beans ◽  
Collaborative Plant Breeding ◽  
Nutritional Compounds ◽  
The Uk ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Plant Breeding Programme

Vicine and convicine are anti-nutritional compounds that accumulate in the cotyledons of faba beans. When humans consume beans with high levels of these compounds, it can cause a condition called favism in individuals harbouring a deficiency in the activity of their glucose-6-phosphate dehydrogenase. When faba beans are used in animal feeds, there can be effects on performance. These concerns have resulted in increasing interest within plant breeding in developing low vicine and convicine faba bean germplasm. In order to facilitate this objective, we developed a rapid and robust screening method for vicine and convicine, capable of distinguishing between faba beans that are either high (wild type) or low in vicine and convicine. In the absence of reliable commercial reference materials, we report an adaptation of a previously published method where a biochemical assay and spectral data were used to confirm the identity of our analytes, vicine and convicine. This method could be readily adopted in other facilities and open the way to the efficient exploitation of diverse germplasm in regions where faba beans play a significant role in human nutrition. We screened a collection of germplasm of interest to a collaborative plant breeding programme developing between the National Institute for Agricultural Botany in the UK and L'Institut Nationale d'Agronomie de Tunisie in Tunisia. We report the results obtained and discuss the prospects for developing molecular markers for the low vicine and convicine trait.

scholarly journals Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Bhavna Hora ◽  
Naila Gulzar ◽  
Yue Chen ◽  
Konstantinos Karagiannis ◽  
Fangping Cai ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Vaccine Development ◽  
Consensus Sequence ◽  
Cost Effective ◽  
Recombination Analysis ◽  
Genome Sequences ◽  
Single Genome ◽  
Hiv 1

ABSTRACT High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).

Quantitative genetic studies of yield, yield components, and phenological and agronomic characters in spring faba bean

Genome ◽  
1987 ◽  
Vol 29 (1) ◽  
pp. 169-173 ◽  
Author(s):  
H. M. Kao ◽  
P. B. E. McVetty
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Yield Components ◽  
Harvest Index ◽  
Dry Matter ◽  
Diallel Analysis ◽  
Diallel Cross ◽  
Agronomic Characters ◽  
Vicia Faba L ◽  
Faba Beans

Hayman's diallel cross analysis was employed to investigate the nature of the genetic control and heritability of yield, yield components, and phenological and agronomic characters in F1 and F2 generations of spring faba beans (Vicia faba L.). High-yielding S4 inbred lines from five open-pollinated faba bean cultivars were used as parents to generate complete F1 and F2 diallels. The S5 inbred line parents and the 20 cross combinations were planted in randomized complete block experiments with six replications. All characters in the F1 diallel and in the F2 diallel with the exception of days from planting to maturity met all of the assumptions required for Hayman's diallel analysis. Yield, total dry matter, harvest index, and pods per plant exhibited significant apparent overdominance in both the F1 and F2 diallels. It is concluded that substantial immediate increases in yield and total dry matter could be expected from exploiting the apparent overdominant gene action found for these characters in these crosses via F1 hybrids or synthetics. Key words: total dry matter, harvest index, diallel crosses, inheritance, Vicia faba L.

Screening of Faba Bean (Vicia faba L.) Germplasm Accessions against Grey Mould Disease Caused by Botrytis fabae Sard

2020 ◽  
Author(s):  
Ibrahim Elkhalil Benzohra ◽  
Hakima Belaidi
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Grey Mould ◽  
Grain Legume ◽  
Sources Of Resistance ◽  
Significant Difference ◽  
Botrytis Fabae ◽  
Vicia Faba L ◽  
Faba Beans ◽  
Chocolate Spot Disease

Background: Faba bean (Vicia faba L.) is thirst most important grain legume in the world and the first one in Algeria. The chocolate spot disease caused by Botrytis fabae Sard (BF), is the major constraint of this culture in Algeria when caused a destructive damages.Methods: The aim of this study is to find the sources of resistance for Seven varieties of faba beans (Giza 02, Giza 40, Giza 461, Sakha 02, Sakha 03, Precoce de Seville), by using the detached leaflet inoculation test for resistance to the two isolates from BF represent two different regions of northwest Algeria (Mascara and Relizane). Result: A significant difference (P less than 0.05) was observed in the reaction of the varieties which manifest themselves by a different reaction vis-à-vis the isolates of BF. Total sensitivity was observed in the four (4) varieties Giza02, Sakha01, Sakha02 and Sakha03, two (2) varieties (Giza40 and Ziban), are tolerant, while the variety named ‘Precoce de Seville’ showed significant resistance to both isolates from BF. These results showed a similar pathogenic behavior of two isolates of BF and variability in the level of reactions of the varieties of beans. The variety ‘Precoce de Seville’ showed promising results to be valued and cultivated in order to reduce the damage caused by this disease and reduce the use of chemicals.

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