Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

La démocratisation des outils de la génomique et plus particulièrement du séquençage à haut débit a permis le séquençage du génome du canard commun. Des projets complémentaires sont déjà initiés pour prolonger et exploiter au mieux ces premiers acquis. En tout premier lieu, il s’agit de poursuivre la description de la structure du génome et d’en exploiter les connaissances : cartes d’hybrides irradiés pour ordonner la séquence le long des chromosomes ; génomique comparée avec le génome de la poule pour bénéficier des connaissances sur ce génome modèle ; recherche de SNP (Single Nucleotide Polymorphism) pour les études et la gestion de populations ; carte génétique pour la détection des QTL (Quantitative Trait Locus). La première détection de QTL influençant les performances du mulard, réalisée à l’aide de marqueurs microsatellites chez la cane commune, sera complétée par une seconde étude utilisant des marqueurs SNP développés spécifiquement et permettant une bien meilleure couverture du génome. Par ailleurs, il est important de réaliser une annotation fonctionnelle du génome, ce qui peut être abordé par le séquençage de transcrits. A terme, le génome annoté sera utilisé pour analyser son expression dans différents tissus et/ou conditions d’élevage, la connaissance des modèles de transcrits et de protéines facilitant les études en transcriptomique et protéomique. Le canard mulard, produit du croisement de la cane commune avec le canard de Barbarie, devra également être étudié en raison de son intérêt agronomique, lié à ses performances exceptionnelles dans la filière des palmipèdes gras.

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Regulation of Janus Kinase 2 by an Inflammatory Bowel Disease Causal Non-coding Single Nucleotide Polymorphism

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz213 ◽

2020 ◽

Vol 14 (5) ◽

pp. 646-653

Author(s):

Christopher J Cardinale ◽

Michael E March ◽

Xiang Lin ◽

Yichuan Liu ◽

Lynn A Spruce ◽

...

Keyword(s):

Inflammatory Bowel Disease ◽

Quantitative Trait Locus ◽

Single Nucleotide Polymorphism ◽

Bowel Disease ◽

Quantitative Trait ◽

Janus Kinase ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Inflammatory Bowel ◽

Trait Locus

Abstract Background and Aims Among the >240 genetic loci described to date which confer susceptibility to inflammatory bowel disease, a small subset have been fine-mapped to an individual, non-coding single nucleotide polymorphism [SNP]. To illustrate a model mechanism by which a presumed-causal non-coding SNP can function, we analysed rs1887428, located in the promoter region of the Janus kinase 2 [JAK2] gene. Methods We utilized comparative affinity purification-mass spectrometry, DNA–protein binding assays, CRISPR/Cas9 genome editing, transcriptome sequencing and methylome quantitative trait locus methods to characterize the role of this SNP. Results We determined that the risk allele of rs1887428 is bound by the transcription factor [TF] RBPJ, while the protective allele is bound by the homeobox TF CUX1. While rs188748 only has a very modest influence on JAK2 expression, this effect was amplified downstream through the expression of pathway member STAT5B and epigenetic modification of the JAK2 locus. Conclusion Despite the absence of a consensus TF-binding motif or expression quantitative trait locus, we have used improved methods to characterize a putatively causal SNP to yield insight into inflammatory bowel disease mechanisms. Podcast This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast

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Molecular Mapping of the Major Resistance Quantitative Trait Locus qHS2.09 with Simple Sequence Repeat and Single Nucleotide Polymorphism Markers in Maize

Phytopathology ◽

10.1094/phyto-12-11-0330 ◽

2012 ◽

Vol 102 (7) ◽

pp. 692-699 ◽

Cited By ~ 19

Author(s):

Jianfeng Weng ◽

Xianjun Liu ◽

Zhenhua Wang ◽

Jianjun Wang ◽

Lin Zhang ◽

...

Keyword(s):

Quantitative Trait Locus ◽

Single Nucleotide Polymorphism ◽

Quantitative Trait ◽

Nucleotide Polymorphism ◽

Head Smut ◽

Maize Breeding ◽

Single Nucleotide ◽

Breeding Programs ◽

Trait Locus ◽

Major Qtl

The major quantitative trait locus (QTL) qHS2.09 plays an important role in resistance to head smut during maize breeding and production. In this study, a near-isogenic line (NIL), L34, which harbors the major QTL qHS2.09 in bin 2.09, was developed using a resistant donor ‘Mo17’ in a susceptible genetic background ‘Huangzao4’. Using 18,683 genome-wide polymorphic loci, this major QTL was finely mapped into an interval of ≈1.10 Mb, flanked by single nucleotide polymorphism (SNP) markers PZE-102187307 and PZE-102188421. Moreover, the favorable allele from ‘Mo17’ for SNP PZE-102187611 in this interval that was most significantly associated with resistance to head smut (P = 1.88 E-10) and accounted for 39.7 to 44.4% of the phenotypic variance in an association panel consisting of 80 inbred lines. With combined linkage and association mapping, this major QTL was finally located between SNP PZE-102187486 and PZE-102188421 with an interval of ≈1.00 Mb. Based on the pedigrees of ‘Mo17’ and its derivatives widely used in temperate maize breeding programs, the favorable haplotype from ‘Mo17’ is shown to be the main source of resistance to head smut in these lines. Therefore, the SNPs closely linked to the major QTL qHS2.09, detected in both linkage and association mapping, and could be useful for marker-assisted selection in maize breeding programs.

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Comparing Genotyping-by-Sequencing and Single Nucleotide Polymorphism Chip Genotyping for Quantitative Trait Loci Mapping in Wheat

Crop Science ◽

10.2135/cropsci2015.06.0389 ◽

2016 ◽

Vol 56 (1) ◽

pp. 232-248 ◽

Cited By ~ 20

Author(s):

Prabin Bajgain ◽

Matthew N. Rouse ◽

James A. Anderson

Keyword(s):

Single Nucleotide Polymorphism ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genotyping By Sequencing ◽

Quantitative Trait Loci Mapping ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Single Nucleotide Polymorphism Chip ◽

Trait Loci

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A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus

BMC Genomics ◽

10.1186/s12864-015-1559-4 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 12

Author(s):

Guangqin Cai ◽

Qingyong Yang ◽

Bin Yi ◽

Chuchuan Fan ◽

Chunyu Zhang ◽

...

Keyword(s):

Quantitative Trait Locus ◽

Single Nucleotide Polymorphism ◽

Brassica Napus ◽

Single Nucleotide Polymorphism Array ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Filtering Method ◽

Trait Locus ◽

Locus Mapping

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Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽

10.3390/d13040144 ◽

2021 ◽

Vol 13 (4) ◽

pp. 144

Author(s):

Nohra Castillo Rodríguez ◽

Xingbo Wu ◽

María Isabel Chacón ◽

Luz Marina Melgarejo ◽

Matthew Wohlgemuth Blair

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Genotyping By Sequencing ◽

Passion Fruit ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Passiflora Edulis ◽

Tropical Fruit ◽

Commercial Cultivars ◽

Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

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