Integrating a molecular network hypothesis and QTL results for heterosis in Arabidopsis thaliana
0
Citation
0
Reference
20
Related Paper
Abstract:
Integrating a molecular network hypothesis and QTL results for heterosis in Arabidopsis thalianaCite
A comprehensive linkage atlas for seed yield in rapeseed. Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.
Family-based QTL mapping
Trait
Genetic architecture
Cite
Citations (78)
Heterosis-a complex process that has not been fully deciphered yet-has been observed and used in many plant and animal species. Some studies suggest that differential gene expression in the hybrids compared to their parents can be correlated with heterosis and hybrid performances. eQTL analyses, that were conducted with maize notably, are efficient approaches to identify loci that act in cis or trans to regulate variation in gene expression. They can lead to the identification of candidate genes, which can affect phenotypic variation. eQTL analyses can also be used to build gene regulatory networks that can contribute to our understanding of the molecular mechanisms underlying phenotypic variation. In particular, eQTL analyses have the potential to identify those regulatory factors at which variation is likely to have direct and/or strong impacts on the phenotype. Thus, eQTL approaches have the potential to help decipher the molecular mechanisms underlying heterosis. However, because transcript accumulation is not the only regulatory level affecting the phenotype of an individual, the use of structural genomic, proteomic, metabolomic, and epigenetic analyses is expected to be required to gain a full understanding of causes of phenotypic variation. Hence, to gain a better understanding of the mechanisms responsible for heterosis, the different regulatory levels that lead to the phenotype need to be assessed by integrating "omics" approaches.
Candidate gene
Cite
Citations (0)
Family-based QTL mapping
Candidate gene
Cite
Citations (36)
Genetic architecture
Cite
Citations (0)
Epistasis
Family-based QTL mapping
Genome-wide Association Study
Cite
Citations (63)
Abstract Epistasis seems to play a significant role in the manifestation of heterosis. However, the power of detecting epistatic interactions among quantitative trait loci (QTL) in segregating populations is low. We studied heterosis in Arabidopsis thaliana hybrid C24 × Col-0 by testing near-isogenic lines (NILs) and their triple testcross (TTC) progenies. Our objectives were to (i) provide the theoretical basis for estimating different types of genetic effects with this experimental design, (ii) determine the extent of heterosis for seven growth-related traits, (iii) map the underlying QTL, and (iv) determine their gene action. Two substitution libraries, each consisting of 28 NILs and covering ∼61 and 39% of the Arabidopsis genome, were assayed by 110 single-nucleotide polymorphism (SNP) markers. With our novel generation means approach 38 QTL were detected, many of which confirmed heterotic QTL detected previously in the same cross with TTC progenies of recombinant inbred lines. Furthermore, many of the QTL were common for different traits and in common with the 58 QTL detected by a method that compares triplets consisting of a NIL, its recurrent parent, and their F1 cross. While the latter approach revealed mostly (75%) overdominant QTL, the former approach allowed separation of dominance and epistasis by analyzing all materials simultaneously and yielded substantial positive additive × additive effects besides directional dominance. Positive epistatic effects reduced heterosis for growth-related traits in our materials.
Epistasis
Inbred strain
Dominance (genetics)
Cite
Citations (100)
Epistasis
Genetic architecture
Pleiotropy
Family-based QTL mapping
Cape verde
Cite
Citations (70)
Bulked segregant analysis
Family-based QTL mapping
Identification
Cite
Citations (17)
Epistasis
Plant biochemistry
Family-based QTL mapping
Cite
Citations (25)
Abstract A long‐standing and fundamental question in biology is how genes influence complex phenotypes. Combining near‐isogenic line mapping with genome expression profiling offers a unique opportunity for exploring the functional relationship between genotype and phenotype and for generating candidate genes for future study. We used a whole‐genome microarray produced with ink‐jet technology to measure the relative expression level of over 21 500 genes from an Arabidopsis thaliana near‐isogenic line (NIL) and its recurrent parent. The NIL material contained two introgressions (bottom of chromosome II and top of chromosome III) of the Cvi‐1 ecotype in a L er ‐2 ecotype genome background. Each introgression ‘captures’ a Cvi allele of a physiological quantitative trait loci (QTL) that our previous studies have shown increases transpiration and reduces water‐use efficiency at the whole‐plant level. We used a mixed model anova framework for assessing sources of expression variability and for evaluating statistical significance in our array experiment. We discovered 25 differentially expressed genes in the introgression at a false‐discovery rate (FDR) cut‐off of 0.20 and identified new candidate genes for both QTL regions. Several differentially expressed genes were confirmed with QRT–PCR (quantitative reverse transcription–polymerase chain reaction) assays. In contrast, we found no statistically significant differentially expressed genes outside of the QTL introgressions after controlling for multiple tests. We discuss these results in the context of candidate genes, cloning QTL, and phenotypic evolution.
Introgression
Candidate gene
Ecotype
Family-based QTL mapping
Cite
Citations (39)