Genotype-Environment Interactions at Quantitative Trait Loci Affecting Inflorescence Development in Arabidopsis thaliana

Genetics ◽  
2003 ◽  
Vol 165 (1) ◽  
pp. 353-365 ◽  
Author(s):  
Mark C Ungerer ◽  
Solveig S Halldorsdottir ◽  
Michael D Purugganan ◽  
Trudy F C Mackay
Keyword(s):  
Arabidopsis Thaliana ◽  
Quantitative Trait ◽  
Rank Order ◽  
Morphological Diversity ◽  
Inflorescence Development ◽  
High Resolution Mapping ◽  
Resolution Mapping ◽  
Trait Locus ◽  
Genomic Regions ◽  
Functional Capacities

Abstract Phenotypic plasticity and genotype-environment interactions (GEI) play a prominent role in plant morphological diversity and in the potential functional capacities of plant life-history traits. The genetic basis of plasticity and GEI, however, is poorly understood in most organisms. In this report, inflorescence development patterns in Arabidopsis thaliana were examined under different, ecologically relevant photoperiod environments for two recombinant inbred mapping populations (Ler × Col and Cvi × Ler) using a combination of quantitative genetics and quantitative trait locus (QTL) mapping. Plasticity and GEI were regularly observed for the majority of 13 inflorescence traits. These observations can be attributable (at least partly) to variable effects of specific QTL. Pooled across traits, 12/44 (27.3%) and 32/62 (51.6%) of QTL exhibited significant QTL × environment interactions in the Ler × Col and Cvi × Ler lines, respectively. These interactions were attributable to changes in magnitude of effect of QTL more often than to changes in rank order (sign) of effect. Multiple QTL × environment interactions (in Cvi × Ler) clustered in two genomic regions on chromosomes 1 and 5, indicating a disproportionate contribution of these regions to the phenotypic patterns observed. High-resolution mapping will be necessary to distinguish between the alternative explanations of pleiotropy and tight linkage among multiple genes.

Quantitative Trait Loci for Inflorescence Development in Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1133-1151 ◽  
Author(s):  
Mark C Ungerer ◽  
Solveig S Halldorsdottir ◽  
Jennifer L Modliszewski ◽  
Trudy F C Mackay ◽  
Michael D Purugganan
Keyword(s):  
Arabidopsis Thaliana ◽  
Quantitative Trait ◽  
Evolutionary Ecology ◽  
Genetic Correlations ◽  
Inflorescence Development ◽  
Meristem Identity ◽  
Trait Locus ◽  
The Many ◽  
Developmental Traits ◽  
Mapping Populations

Abstract Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler × Col and Cvi × Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi × Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.

scholarly journals High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.)

2019 ◽  
Vol 133 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Nian Liu ◽  
Jianbin Guo ◽  
Xiaojing Zhou ◽  
Bei Wu ◽  
Li Huang ◽  
...  
Keyword(s):  
High Resolution ◽  
Genetic Map ◽  
Quantitative Trait ◽  
Oil Content ◽  
Average Distance ◽  
Genomic Region ◽  
High Density ◽  
High Resolution Mapping ◽  
Resolution Mapping ◽  
Trait Locus

Key message ddRAD-seq-based high-density genetic map comprising 2595 loci identified a major and consensus QTL with a linked marker in a 0.8-Mb physical interval for oil content in peanut. Abstract Enhancing oil content is an important breeding objective in peanut. High-resolution mapping of quantitative trait loci (QTLs) with linked markers could facilitate marker-assisted selection in breeding for target traits. In the present study, a recombined inbred line population (Xuhua 13 × Zhonghua 6) was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing (ddRAD-seq). The resulting high-density genetic map contained 2595 loci, and spanned a length of 2465.62 cM, with an average distance of 0.95 cM/locus. Seven QTLs for oil content were identified on five linkage groups, including the major and stable QTL qOCA08.1 on chromosome A08 with 10.14–27.19% phenotypic variation explained. The physical interval of qOCA08.1 was further delimited to a ~ 0.8-Mb genomic region where two genes affecting oil synthesis had been annotated. The marker SNPOCA08 was developed targeting the SNP loci associated with oil content and validated in peanut cultivars with diverse oil contents. The major and stable QTL identified in the present study could be further dissected for gene discovery. Furthermore, the tightly linked marker for oil content would be useful in marker-assisted breeding in peanut.

scholarly journals Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population

Genetics ◽  
2005 ◽  
Vol 171 (3) ◽  
pp. 1341-1352 ◽  
Author(s):  
Johan D. Peleman ◽  
Crispin Wye ◽  
Jan Zethof ◽  
Anker P. Sørensen ◽  
Henk Verbakel ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
High Resolution ◽  
Quantitative Trait ◽  
Single Population ◽  
High Resolution Mapping ◽  
Resolution Mapping ◽  
Trait Locus

scholarly journals Epigenome-Wide Study Identified Methylation Sites Associated with the Risk of Obesity

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1984
Author(s):  
Majid Nikpay ◽  
Sepehr Ravati ◽  
Robert Dent ◽  
Ruth McPherson
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Rare Variants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Risk Snps ◽  
Trait Locus ◽  
Genomic Regions ◽  
Eqtl Data

Here, we performed a genome-wide search for methylation sites that contribute to the risk of obesity. We integrated methylation quantitative trait locus (mQTL) data with BMI GWAS information through a SNP-based multiomics approach to identify genomic regions where mQTLs for a methylation site co-localize with obesity risk SNPs. We then tested whether the identified site contributed to BMI through Mendelian randomization. We identified multiple methylation sites causally contributing to the risk of obesity. We validated these findings through a replication stage. By integrating expression quantitative trait locus (eQTL) data, we noted that lower methylation at cg21178254 site upstream of CCNL1 contributes to obesity by increasing the expression of this gene. Higher methylation at cg02814054 increases the risk of obesity by lowering the expression of MAST3, whereas lower methylation at cg06028605 contributes to obesity by decreasing the expression of SLC5A11. Finally, we noted that rare variants within 2p23.3 impact obesity by making the cg01884057 site more susceptible to methylation, which consequently lowers the expression of POMC, ADCY3 and DNAJC27. In this study, we identify methylation sites associated with the risk of obesity and reveal the mechanism whereby a number of these sites exert their effects. This study provides a framework to perform an omics-wide association study for a phenotype and to understand the mechanism whereby a rare variant causes a disease.

Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 224-234 ◽  
Author(s):  
C E Durel ◽  
L Parisi ◽  
F Laurens ◽  
W E Van de Weg ◽  
R Liebhard ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Malus Domestica ◽  
Quantitative Trait ◽  
Partial Resistance ◽  
Venturia Inaequalis ◽  
Genetic Dissection ◽  
Resistance Breakdown ◽  
Trait Locus ◽  
New Races ◽  
Genomic Regions

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus × domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has been inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles.Key words: Malus × domestica, partial resistance, Venturia inaequalis, resistance breakdown, quantitative trait locus.

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