A genome‐wide association study reveals a quantitative trait locus for calf mortality on chromosome 9 in Japanese Black cattle

2021 ◽  
Author(s):  
S. Sasaki ◽  
T. Ibi
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Japanese Black Cattle ◽  
Genome Wide ◽  
A Genome ◽  
Calf Mortality ◽  
Trait Locus

scholarly journals Integration of genome-wide association study and expression quantitative trait locus mapping for identification of endometriosis-associated genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ya-Ching Chou ◽  
Ming-Jer Chen ◽  
Pi-Hua Chen ◽  
Ching-Wen Chang ◽  
Mu-Hsien Yu ◽  
...  
Keyword(s):  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Eqtl Analysis ◽  
Taiwanese Population ◽  
Genome Wide ◽  
A Genome

AbstractTo determine whether genetic predisposition to endometriosis varies depending on ethnicity and in association with expression quantitative trait loci (eQTL) in a Taiwanese population. We conducted a genome-wide association study (GWAS) and replicated it in 259 individuals with laparoscopy-confirmed stage III or IV endometriosis (cases) and 171 women without endometriosis (controls). Their genomic DNA was extracted from blood and evaluated by the GWAS of Taiwan Biobank Array. Novel genetic variants that predispose individuals to endometriosis were identified using GWAS and replication, including rs10739199 (P = 6.75 × 10−5) and rs2025392 (P = 8.01 × 10−5) at chromosome 9, rs1998998 (P = 6.5 × 10−6) at chromosome 14, and rs6576560 (P = 9.7 × 10−6) at chromosome 15. After imputation, strong signals were exhibited by rs10822312 (P = 1.80 × 10−7) at chromosome 10, rs58991632 (P = 1.92 × 10−6) and rs2273422 (P = 2.42 × 10−6) at chromosome 20, and rs12566078 (P = 2.5 × 10−6) at chromosome 1. We used the Genotype-Tissue Expression (GTEx) database to observe eQTL. Among these SNPs, the cis-eQTL rs13126673 of inturned planar cell polarity protein (INTU) showed significant association with INTU expression (P = 5.1 × 10–33). Moreover, the eQTL analysis was performed on endometriotic tissues from women with endometriosis. The expression of INTU in 78 endometriotic tissue of women with endometriosis is associated with rs13126673 genotype (P = 0.034). To our knowledge, this is the first GWAS to link endometriosis and eQTL in a Taiwanese population.

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.

Sign in / Sign up

Export Citation Format

Share Document