scholarly journals CerealsDB—new tools for the analysis of the wheat genome: update 2020

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Paul A Wilkinson ◽  
Alexandra M Allen ◽  
Simon Tyrrell ◽  
Luzie U Wingen ◽  
Xingdong Bian ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Quantitative Trait Loci ◽  
Open Access ◽  
Quantitative Trait ◽  
Hexaploid Wheat ◽  
Marker Assisted Selection ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

Abstract CerealsDB (www.cerealsdb.uk.net) is an online repository of mainly hexaploid wheat (Triticum aestivum) single nucleotide polymorphisms (SNPs) and genotyping data. The CerealsDB website has been designed to enable wheat breeders and scientists to select the appropriate markers for research breeding tasks, such as marker-assisted selection. We report a large update of genotyping information for over 6000 wheat accessions and describe new webtools for exploring and visualizing the data. We also describe a new database of quantitative trait loci that links phenotypic traits to CerealsDB SNP markers and allelic scores for each of those markers. CerealsDB is an open-access website that hosts information on wheat SNPs considered useful for both plant breeders and research scientists. The latest CerealsDB database is available at https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php.

scholarly journals Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle

2007 ◽  
Vol 89 (4) ◽  
pp. 215-220 ◽  
Author(s):  
B. J. HAYES ◽  
A. J. CHAMBERLAIN ◽  
H. McPARTLAN ◽  
I. MACLEOD ◽  
L. SETHURAMAN ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Single Nucleotide Polymorphisms ◽  
Quantitative Trait ◽  
Marker Assisted Selection ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Angus Cattle ◽  
Genome Wide

SummaryA key question for the implementation of marker-assisted selection (MAS) using markers in linkage disequilibrium with quantitative trait loci (QTLs) is how many markers surrounding each QTL should be used to ensure the marker or marker haplotypes are in sufficient linkage disequilibrium (LD) with the QTL. In this paper we compare the accuracy of MAS using either single markers or marker haplotypes in an Angus cattle data set consisting of 9323 genome-wide single nucleotide polymorphisms (SNPs) genotyped in 379 Angus cattle. The extent of LD in the data set was such that the average marker–marker r2 was 0·2 at 200 kb. The accuracy of MAS increased as the number of markers in the haplotype surrounding the QTL increased, although only when the number of markers in the haplotype was 4 or greater did the accuracy exceed that achieved when the SNP in the highest LD with the QTL was used. A large number of phenotypic records (>1000) were required to accurately estimate the effects of the haplotypes.

scholarly journals IDENTIFICACIÓN DE QTLs ASOCIADOS A CARACTERES DE ARQUITECTURA VEGETAL EN YUCA (Manihot esculenta)

2015 ◽  
Vol 21 (1) ◽  
Author(s):  
Camilo López ◽  
Ruben Eduardo Mora Moreno ◽  
Johana Carolina Soto
Keyword(s):  
Quantitative Trait Loci ◽  
Leaf Area ◽  
Plant Height ◽  
Quantitative Trait ◽  
Manihot Esculenta ◽  
Root Weight ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Number Of Shoots

<p class="p1"><strong>RESUMEN</strong></p><p class="p2">La yuca (<em>Manihot esculenta</em>) es el cuarto cultivo en importancia a nivel mundial como fuente de calorías para la población humana después del arroz, el azúcar y el maíz, posicionándose por esta razón como un cultivo primordial para la seguridad alimentaria. Su arquitectura ha sido considerada como un factor clave que subyace a la fisiología del rendimiento, relacionando características morfológicas con productividad. En este trabajo se evaluaron diferentes características de arquitectura vegetal en yuca. Los caracteres fueron evaluados en una población F1 compuesta por 133 hermanos completos (familia K) sembrados en dos lugares biogeográficamente diferentes: La Vega (Cundinamarca) y Arauca (Arauca) en Colombia. Las características evaluadas relacionadas con la arquitectura vegetal fueron altura de la planta (AT), número de brotes (NB), longitud entrenudos (LE), número de raíces (NR), peso de raíces (PR), pigmentación del peciolo (PP), área de la hoja (AH) y tipo de hoja (TH). A partir de los datos obtenidos y empleando un mapa genético de alta densidad basado en SNPs (Single Nucleotide Polymorphisms) se llevó a cabo un análisis de QTLs (Quantitative Trait Loci). Se lograron identificar tres QTLs para La Vega asociados con los caracteres altura total, número de brotes y área de la hoja. Para Arauca se detectaron tres QTLs asociados con altura total, longitud de entrenudos y número de brotes. Los QTLs se distribuyeron en cuatro grupos de ligamiento y explicaron entre 18,93 y 41,92 % de la variación genética.</p><p class="p1"><strong>ABSTRACT</strong></p><p class="p2">Cassava (<em>Manihot esculenta</em>) is the fourth most important crop worldwide as a source of calories for the human population after rice, sugar and corn and therefore it is considered as a staple crop. Cassava’s architecture has been considered as a key factor underlying the physiology of yield, relating morphological traits with productivity. In this work different characteristics of plant architecture were evaluated in a cassava F1 population composed by 133 complete siblings (family K) planted in two biogeographically different zones: La Vega (Cundinamarca) and Arauca (Arauca) in Colombia. The characteristics evaluated related to the vegetal architecture were plant height (AT), number of shoots (NB), internodes length (LE), number of roots (NR), root weight (PR), petiole pigmentation (PP), leaf area (AH) and leaf type (TH). From the data obtained and using a SNP- (Single Nucleotide Polymorphism) high-density genetic map a QTLs analysis (Quantitative Trait Loci) was carried out. It was possible to identify three QTLs for La Vega associated with characters plant height, internodes length and leaf area. From the Arauca’s dataset, three QTLs were detected associated with plant height, number of shoots and internodes length. The QTLs were distributed into four linkage groups and explained between 18.93 and 41.92 % of genetic variation.</p><p class="p2"> </p>

scholarly journals Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

2020 ◽  
Vol 3 (2) ◽  
pp. 28 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Trait Loci ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.

Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.)

2002 ◽  
Vol 105 (6) ◽  
pp. 921-936 ◽  
Author(s):  
A. Börner ◽  
E. Schumann ◽  
A. Fürste ◽  
H. Cöster ◽  
B. Leithold ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Hexaploid Wheat ◽  
Triticum Aestivum L ◽  
Trait Loci

scholarly journals Single Nucleotide Polymorphisms: A Modern Tool to Screen Plants for Desirable Traits

2021 ◽  
Author(s):  
Lovina I. Udoh ◽  
Willie Peggy Obaseojei ◽  
Chiebuka Uzoebo
Keyword(s):  
Marker Assisted Selection ◽  
Target Genes ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Modern Tool

Single nucleotide polymorphism (SNP) represent a change in a single nucleotide within the genome. This can alter the phenotype of an individual within the same species if it occurs in a coding region of the gene. The change in nucleotide can produce desirable characteristic in plants and can become an object for selection. New SNPs have been discovered and subsequently converted to molecular markers using various non-gel based and next generation sequencing platforms. Considering that SNP markers are based on target genes, its abundance in the genome, high automation and multiplexability, has made it a marker of choice and an effective tool for screening plant germplasm for desirable traits. This chapter considers SNP as molecular marker, their discovery and different SNP genotyping methods was documented. A few case studies of SNP as allele specific markers and their association with traits of interest was considered. Thus, highlighting their efficacy as useful tool for marker assisted selection and plant germplasms screening.

scholarly journals Detection of Quantitative Trait Loci (QTL) associated with the spring regrowth vigor trait in alfalfa (Medicago sativa L.)

2020 ◽  
Author(s):  
Xueqian Jiang ◽  
Fan Zhang ◽  
Zhen Wang ◽  
Ruicai Long ◽  
Mingna Li ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Medicago Sativa ◽  
Quantitative Trait ◽  
Female Parent ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Phenotypic Data ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Medicago Sativa L

Abstract Background: Alfalfa ( Medicago sativa L.) is a perennial forage legume with a reputation as being the “queen of forage”. Spring regrowth vigor refers to the process of perennial alfalfa returning to growth after winter survival. The objective of this research was to identify candidate genes significantly associated with spring regrowth vigor.Results: We used a tetraploid alfalfa F1 population comprised of 392 progenies to identify quantitative trait loci (QTL) that control this trait. The F1 population phenotypic data were collected using a total of three environmental phenotypic data. The mapping population was genotyped using Genotyping-by-sequencing (GBS), and linkage maps were developed based on single nucleotide polymorphism (SNP) markers. Fifteen significant QTL for spring regrowth vigor were detected in both parents. Five QTL were identified in the male genetic map, while ten QTL were identified in the female. Four QTL were located on homolog 7D of the male parent, and two QTL were colocalized. Five QTL were mapped on homolog 6D of the female parent, and two QTL were colocalized.Conclusions: The QTL presented in this study can be used to improve the efficiency of alfalfa breeding programs and provide valuable resources for the genetic improvement of alfalfa using marker-assisted selection (MAS).β These authors contributed equally to this research. *Correspondence:Junmei [email protected]

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