A combinatorial strategy to identify various types of QTLs for quantitative traits using extreme phenotype individuals in an F2 population.
Plant Commun
; 3(3): 100319, 2022 05 09.
Article
em En
| MEDLINE
| ID: mdl-35576159
ABSTRACT
Theoretical and applied studies demonstrate the difficulty of detecting extremely over-dominant and small-effect genes for quantitative traits via bulked segregant analysis (BSA) in an F2 population. To address this issue, we proposed an integrated strategy for mapping various types of quantitative trait loci (QTLs) for quantitative traits via a combination of BSA and whole-genome sequencing. In this strategy, the numbers of read counts of marker alleles in two extreme pools were used to predict the numbers of read counts of marker genotypes. These observed and predicted numbers were used to construct a new statistic, Gw, for detecting quantitative trait genes (QTGs), and the method was named dQTG-seq1. This method was significantly better than existing BSA methods. If the goal was to identify extremely over-dominant and small-effect genes, another reserved DNA/RNA sample from each extreme phenotype F2 plant was sequenced, and the observed numbers of marker alleles and genotypes were used to calculate Gw to detect QTGs; this method was named dQTG-seq2. In simulated and real rice dataset analyses, dQTG-seq2 could identify many more extremely over-dominant and small-effect genes than BSA and QTL mapping methods. dQTG-seq2 may be extended to other heterogeneous mapping populations. The significance threshold of Gw in this study was determined by permutation experiments. In addition, a handbook for the R software dQTG.seq, which is available at https//cran.r-project.org/web/packages/dQTG.seq/index.html, has been provided in the supplemental materials for the users' convenience. This study provides a new strategy for identifying all types of QTLs for quantitative traits in an F2 population.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Oryza
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Locos de Características Quantitativas
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Plant Commun
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
China