scholarly journals Genome-wide association study reveals a quantitative trait locus and two candidate genes on Sus scrofa chromosome 5 affecting intramuscular fat content in Suhuai pigs

animal ◽  
2021 ◽  
Vol 15 (9) ◽  
pp. 100341
Author(s):  
B.B. Wang ◽  
L.M. Hou ◽  
W.D. Zhou ◽  
H. Liu ◽  
W. Tao ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Association Study ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Sus Scrofa ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Trait Locus ◽  
Intramuscular Fat Content

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.

scholarly journals A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 96 ◽  
Author(s):  
Fucheng Guo ◽  
Liang Ming ◽  
Rendalai Si ◽  
Li Yi ◽  
Jing He ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Gobi Desert ◽  
Camelus Bactrianus ◽  
Genome Wide ◽  
A Genome ◽  
Bactrian Camels

Bactrian camels (Camelus bactrianus) are one of the few large livestock species that can survive in the Gobi Desert. Animal immunity and disease resistance are related to hematological traits, which are also associated with tolerance observed in Bactrian camels. However, no genome-wide association studies have examined the genetic mechanism of the immune capability of Bactrian camels. In the present study, we used genotyping-by-sequencing data generated from 366 Bactrian camel accessions to perform a genome-wide association study for 17 hematological traits. Of the 256,616 single-nucleotide polymorphisms (SNPs) obtained, 1,635 trait–SNP associations were among the top quantitative trait locus candidates. Lastly, 664 candidate genes associated with 13 blood traits were identified. The most significant were ZNF772, MTX2, ESRRG, MEI4, IL11, FRMPD4, GABPA, NTF4, CRYBG3, ENPP5, COL16A1, and CD207. The results of our genome-wide association study provide a list of significant SNPs and candidate genes, which offer valuable information for further dissection of the molecular mechanisms that regulate the camel’s hematological traits to ultimately reveal their tolerance mechanisms.

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