Quantitative Trait Loci × Maternal Cytoplasmic Environment Interaction for Development Rate in <i>Oncorhynchus mykiss</i>

Nichols, Krista M.; Broman, Karl W.; Sundin, Kyle; Young, Jennifer M.; Wheeler, Paul; Thorgaard, Gary H.

doi:10.1534/genetics.106.064311

Cited by 67 publications

(75 citation statements)

References 73 publications

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“…Many of these studies have identified QTL or significant associations between markers on Omy5 and life-history traits such as spawn timing [47,65,68], smoltification [42,46] and development rate or early maturation [17,66,67,70]. Thus, this study supports previous suggestions that the LD block on chromosome Omy5 represents a 'master control region' influencing residency and anadromy in O. mykiss [46,72] and is a parallel selected region [21] that has experienced repeated selection in multiple populations.…”

Section: Discussionsupporting

confidence: 87%

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

et al. 2014

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Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) lifehistory strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

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Section: Discussionsupporting

confidence: 87%

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

et al. 2014

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“…In rainbow trout, studies have variously identified QTL of major and minor effect for hatch timing. Nichols et al (2007) identified six minor QTL for hatch timing, one of which was located on rainbow trout linkage group RT14 (termed OC-14 in Nichols et al, 2007). In this study the QTL for hatch timing was associated with marker Omm1241 that has been mapped to OKI14, the coho linkage group homologous to RT14 (McClelland and Naish, 2008).…”

Section: Ek Mcclelland and Ka Naishmentioning

confidence: 65%

Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon, Oncorhynchus kisutch

McClelland

Naish

2010

Heredity

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In quantitative genetics, multivariate statistical approaches are increasingly used to describe genetic correlations in natural populations, yet the exact genetic relationship between phenotype and genotype is often unknown. Quantitative trait locus (QTL) analyses can be used to describe the molecular basis of this relationship. In salmonids, growth and development are important fitness traits that are phenotypically correlated with each other and with other life-history traits, and an understanding of the molecular basis of these relationships is valuable for future evolutionary studies. Here, a QTL analysis using an outbred cross was initiated to determine the molecular basis of phenotypic correlations between such growth traits in coho salmon (Oncorhynchus kisutch), an important fish species distributed throughout the North Pacific Ocean. Fifty-three QTL for growth rate, length and weight at eight time periods were located on seven linkage groups (OKI03, OKI06, OKI18, OKI19, OKI23, OKI24 and an unnamed linkage group) or associated with five unlinked markers (Omm1159, Omm1367/ i, Omy325UoG, OmyRGT55TUF and OtsG422UCD). One QTL for hatch timing was associated with the marker, Omm1241. All QTL were of minor effect, explaining no more than 20% of the observed variation in phenotypic value. Several instances of colocalization of QTL weight, length and growth rate were observed, suggesting a genetic basis for phenotypic correlations observed between these traits. This study lays the foundation for future QTL mapping efforts, for detailed examinations of the genetic basis of phenotypic correlations between growth traits, and for exploring the adaptive significance of growth traits in natural populations.

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“…Second, randomization in permutation tests removes the main effect of the QTL, as well as its interaction with the environment, and so assumes that the probability distribution for G 3 E interactions is the same in the absence as in the presence of a QTL (cf. Nichols et al 2007), which may not be the case.…”

Section: Methodsmentioning

confidence: 96%

Quantitative Trait Locus Mapping of Genes Under Selection Across Multiple Years and Sites inAvena barbata: Epistasis, Pleiotropy, and Genotype-by-Environment Interactions

Latta

Gardner²,

Staples³

2010

Genetics

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The genetic architecture of variation in evolutionary fitness determines the trajectory of adaptive change. We identified quantitative trait loci (QTL) affecting fitness in a mapping population of recombinant inbred lines (RILs) derived from a cross between moist-and dry-associated ecotypes of Avena barbata. We estimated fitness in 179 RILs in each of two natural environments in each of 4 years. Two loci account for over half of the variation in geometric mean fitness across environments. These loci are associated in repulsion phase in the wild ecotypes, suggesting the potential for strong transgressive segregation, but also show significant epistasis giving hybrid breakdown. This epistasis is the result of sharply lower fitness in only one of the recombinant genotypes, suggesting that the loci may contain synergistically acting mutations. Within each trial (year/site combination), we can explain less of the variation than for geometric mean fitness, but the two major loci are associated with variation in fitness in most environments. Tests for pleiotropic effects of QTL on fitness in different environments reveal that the same loci are under selection in all trials. Genotype-by-environment interactions are significant for some loci, but this reflects variation in the strength, not the direction of selection.

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Quantitative Trait Loci × Maternal Cytoplasmic Environment Interaction for Development Rate in Oncorhynchus mykiss

Cited by 67 publications

References 73 publications

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon, Oncorhynchus kisutch

Quantitative Trait Locus Mapping of Genes Under Selection Across Multiple Years and Sites inAvena barbata: Epistasis, Pleiotropy, and Genotype-by-Environment Interactions

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