A genome-wide association study for equine recurrent airway obstruction in European Warmblood horses reveals a suggestive new quantitative trait locus on chromosome 13

2017 ◽  
Vol 48 (6) ◽  
pp. 691-693 ◽  
Author(s):  
D. Schnider ◽  
S. Rieder ◽  
T. Leeb ◽  
V. Gerber ◽  
M. Neuditschko
Keyword(s):  
Quantitative Trait Locus ◽  
Airway Obstruction ◽  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Recurrent Airway Obstruction ◽  
Genome Wide ◽  
A Genome ◽  
Trait Locus

scholarly journals Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato

DNA Research ◽  
2019 ◽  
Vol 26 (5) ◽  
pp. 399-409 ◽  
Author(s):  
Rumi Sasai ◽  
Hiroaki Tabuchi ◽  
Kenta Shirasawa ◽  
Kazuki Kishimoto ◽  
Shusei Sato ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Association Study ◽  
Meloidogyne Incognita ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Single Nucleotide ◽  
Genome Wide ◽  
F1 Progeny ◽  
Trait Locus

Abstract The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita.

scholarly journals Genome-Wide Association Study Reveals a New Quantitative Trait Locus in Rice Related to Resistance to Brown Planthopper Nilaparvata lugens (Stål)

Insects ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 836
Author(s):  
Longqing Shi ◽  
Meng Dong ◽  
Ling Lian ◽  
Junian Zhang ◽  
Yongsheng Zhu ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Durable Resistance ◽  
Brown Planthopper ◽  
Genome Wide Association ◽  
Rice Varieties ◽  
Genome Wide ◽  
Trait Locus

The brown planthopper (BPH) is one of the main pests endangering rice yields. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. To identify new BPH resistance-related genes, a total of 123 rice varieties were assessed for resistance and durable resistance. Three varieties were immune, and nine were highly resistant to BPH. After whole-genome resequencing of all 123 varieties, 1,897,845 single nucleotide polymorphisms (SNPs) were identified. Linkage disequilibrium (LD) decay analysis showed that the average LD of the SNPs at 20 kb was 0.30 (r2) and attenuated to half value (~0.30) at a distance of about 233 kb. A genome-wide association study (GWAS) of durable resistance to BPH was conducted using the Fast-MLM model. One quantitative trait locus, identified on chromosome 2, included 13 candidate genes. Two candidate genes contained a leucine-rich repeat and CC-NBS-LRR or NB-ARC domains, which might confer resistance to pests or diseases. Interestingly, LOC_Os02g27540 was highly expressed and was induced by BPH; GWAS identified potential rice genes coding for durable resistance to BPH. This study helps to elucidate the mechanism of durable resistance to BPH in rice and provides essential genetic information for breeding and functional verification of resistant varieties.

Genetic dissection of 2-heptenal content in soybean (Glycine max) seed through genome-wide association study

2020 ◽  
Vol 71 (10) ◽  
pp. 884
Author(s):  
Zhikun Wang ◽  
Mingming Yang ◽  
Yuanzhuo Wang ◽  
Chao Yang ◽  
Xue Zhao ◽  
...  
Keyword(s):  
Glycine Max ◽  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Fatty Acid Content ◽  
Soybean Seed ◽  
Genome Wide Association ◽  
Quality Characteristic ◽  
Genome Wide ◽  
A Genome

Association analysis is an alternative to conventional, family-based methods for detecting the location of gene(s) or quantitative trait loci (QTLs), and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Flavour is an essential quality characteristic of soymilk; however, soymilk contains volatile compounds unacceptable to consumers. One of main constituents in the volatiles of normal soymilk is 2-heptenal, which is thought to be a degradative oxidation product of polyunsaturated acids. In this study, a genome-wide association study using 24651 single-nucleotide polymorphisms (SNPs) was performed to identify quantitative trait nucleotides (QTNs) controlling 2-heptenal content in soybean (Glycine max (L.) Merr.) seed from a natural population of 110 soybean germplasm accessions. We detected 62 significant QTNs located on 18 different chromosomes that are significantly associated with 2-heptenal content in soybean seed. Among these, 17 QTNs co-localised with QTLs previously found to be related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in lipid metabolism. These findings further our understanding of the genetic basis of 2-heptenal content in soybean seed and the improvement of marker-assisted breeding efficiency, which will be important for breeding soybean cultivars with low 2-heptenal content.

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