Multilocus evolution

2019 ◽  
pp. 117-144
Author(s):  
Glenn-Peter Sætre ◽  
Mark Ravinet
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Disequilibrium ◽  
Qtl Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genetic Evolution ◽  
Highly Active ◽  
Genome Wide ◽  
Trait Locus

Most phenotypic traits are affected by a multitude of genes, which may interact in complex ways. This means that the single locus model explored in chapters 3 and 4 is not always able to capture the full complexity of genetic evolution. In many cases, multiple genes are involved and so this chapter formalizes the analysis of multilocus evolution. Concepts such as linkage disequilibrium and epistasis are introduced, both of which are necessary to properly understand multilocus evolution. The currently highly active field emerging as a result of a crossover between quantitative genetics and genomics is further explored, including methods such as quantitative trait locus (QTL) analysis and genome wide association study (GWAS) that allow phenotypic variation to be associated with likely causative genes and that have made important advances in our understanding of the genetic underpinnings of disease.

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.

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