Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

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.

Download Full-text

Dissection of Quantitative Trait Loci (QTL), annotation of Single Nucleotide Polymorphism (SNP), and Identification of Candidate Genes for Grain Yield in Triticum turgidum L. var durum

Advances in Science Technology and Engineering Systems Journal ◽

10.25046/aj0505125 ◽

2020 ◽

Vol 5 (5) ◽

pp. 1020-1027

Author(s):

Issame Farouk ◽

Ahmad Alsaleh ◽

Jihan Motowaj ◽

Fatima Gaboun ◽

Bouchra Belkadi ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Quantitative Trait Loci ◽

Grain Yield ◽

Candidate Genes ◽

Quantitative Trait ◽

Triticum Turgidum ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Trait Loci

Download Full-text

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

Acta Biológica Colombiana ◽

10.15446/abc.v21n1.49251 ◽

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

RESUMENLa yuca (Manihot esculenta) 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.ABSTRACTCassava (Manihot esculenta) 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.

Download Full-text

Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

Methods and Protocols ◽

10.3390/mps3020028 ◽

2020 ◽

Vol 3 (2) ◽

pp. 28 ◽

Cited By ~ 1

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.

Download Full-text