Selective Genotyping and Phenotyping Strategies in a Complex Trait Context

Sen, Sáunak; Johannes, Frank; Broman, Karl W.

doi:10.1534/genetics.108.094607

Cited by 33 publications

(22 citation statements)

References 21 publications

(28 reference statements)

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“…Thus the power and accuracy of QTL analysis improves when the selection is more finely targeted using prior knowledge. Sen et al [34] confirmed this but the efficiency of SP decreased as the number of unlinked loci considered increased. According to the authors, when only a small sample can be phenotyped, the efficiency of the SP is still higher compared to random sampling, even when more than ten loci are used for the selection.…”

Section: Effect Of Sampling Strategy On the Detection And Mapping Of mentioning

confidence: 87%

Assessment of a new strategy for selective phenotyping applied to complex traits in Brassica napus

Jestin¹,

Vallée²,

Domin³

et al. 2012

OJGen

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The accurate mapping of quantitative trait loci (QTL) depends notably on the number of recombination events occurring in the segregating population. The cost of phenotyping often limits the sample size used in QTL mapping. To get round this problem, we assessed a selective phenotyping method, called qtlRec sampling. In order to improve the accuracy of QTL mapping, a subset of individuals was selected to maximize the number of recombination events at putative QTL positions; the usefulness of this subset was compared to a selected sample built to maximize the recombination rate over the whole genome. We assessed this method on the quantitative oil content trait in Brassica napus. We showed that the qtlRec strategy could allow increasing accuracy (both support interval and position) of QTL location while it maintained a similar power of detection. We then applied this approach to the B. napus—Leptosphaeria maculans pathosystem for which resistance QTL with minor effect were previously identified. This allowed the validation of the QTL in six genomic regions. The qtlRec method is an attractive strategy for validating QTL in multiple year and/or location trials for a trait which requires costly and time-consuming phenotyping.

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Section: Effect Of Sampling Strategy On the Detection And Mapping Of mentioning

confidence: 87%

Assessment of a new strategy for selective phenotyping applied to complex traits in Brassica napus

Jestin¹,

Vallée²,

Domin³

et al. 2012

OJGen

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show abstract

“…Studies of response to selection (Gallais et al 2009;) and selective genotyping, i.e., genotyping only individuals from the high and low tails of the phenotypic distribution (Lebowitz et al 1987;Navabi et al 2009;Sen et al 2009), were reported to be effective even for the detection of quantitative trait loci (QTL). However, the identification of QTL for the selected trait (DG) and estimation of their effects was beyond the scope of this study.…”

Section: Genetic Structure Of the Selected Linesmentioning

confidence: 99%

Cold tolerance in field conditions, its inheritance, agronomic performance and genetic structure of maize lines divergently selected for germination at low temperature

Frascaroli

Landi

2016

Euphytica

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Given the importance of early cold tolerance in maize (Zea mays L.), we previously conducted a divergent selection for low (L) and high (H) cold tolerance at germination. The source population was the F 2 of B73 9 IABO78 single cross. Selection was first conducted as recurrent selection (four cycles) and then in inbreeding (three generations). Ten lines were finally selected for L and ten for H; these lines were then evaluated to investigate: (i) their field cold tolerance in the early autotrophic phase and the relationship with the cold tolerance expressed at emergence and in the heterotrophic phase; (ii) the inheritance of these cold tolerance traits; (iii) their agronomic performance as lines per se and as crosses; (iv) their SNP-based genetic characterization. For all cold tolerance traits, the H group of lines was superior to the L group; selection responses were often symmetric, suggesting the prevalence of additive effects. The relationship among cold tolerance traits was appreciable, suggesting a common genetic basis. Differences among testcrosses were largely due to general combining ability effects and the relationship between line per se and testcross performance was high, confirming the prevalence of additive effects. Correlated responses were also obtained for agronomic traits, the H lines being superior to L lines both per se and as crosses. For SNP-marker loci, the B73 allelic frequency was greater in the H group (61.7 %) than in L group (39.7 %). Across field trials, an H line excelled for all traits, thus proving to deserve further investigations.

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“…However, with large numbers of selection candidates in the female population, a preselection of genotyped animals is needed to optimize genotyping costs (Blonk et al, 2010). Selective genotyping of the most informative individuals might increase genotyping efficiency (Spangler et al, 2008;Sen et al, 2009). However, there has been very limited research as to which animals are most informative in terms of single-nucleotide polymorphism (SNP) effects and genomic predictions when females are used in the reference population.…”

Section: Introductionmentioning

confidence: 99%

Genotyping strategies for genomic selection in small dairy cattle populations

Jiménez-Montero

González-Recio²,

Alenda

2012

Animal

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This study evaluated different female-selective genotyping strategies to increase the predictive accuracy of genomic breeding values (GBVs) in populations that have a limited number of sires with a large number of progeny. A simulated dairy population was utilized to address the aims of the study. The following selection strategies were used: random selection, two-tailed selection by yield deviations, two-tailed selection by breeding value, top yield deviation selection and top breeding value selection. For comparison, two other strategies, genotyping of sires and pedigree indexes from traditional genetic evaluation, were included in the analysis. Two scenarios were simulated, low heritability (h 2 5 0.10) and medium heritability (h 2 5 0.30). GBVs were estimated using the Bayesian Lasso. The accuracy of predicted GBVs using the two-tailed strategies was better than the accuracy obtained using other strategies (0.50 and 0.63 for the two-tailed selection by yield deviations strategy and 0.48 and 0.63 for the two-tailed selection by breeding values strategy in low-and medium-heritability scenarios, respectively, using 1000 genotyped cows). When 996 genotyped bulls were used as the training population, the sire' strategy led to accuracies of 0.48 and 0.55 for low-and medium-heritability traits, respectively. The Random strategies required larger training populations to outperform the accuracies of the pedigree index; however, selecting females from the top of the yield deviations or breeding values of the population did not improve accuracy relative to that of the pedigree index. Bias was found for all genotyping strategies considered, although the Top strategies produced the most biased predictions. Strategies that involve genotyping cows can be implemented in breeding programs that have a limited number of sires with a reliable progeny test. The results of this study showed that females that exhibited upper and lower extreme values within the distribution of yield deviations may be included as training population to increase reliability in small reference populations. The strategies that selected only the females that had high estimated breeding values or yield deviations produced suboptimal results.

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Selective Genotyping and Phenotyping Strategies in a Complex Trait Context

Cited by 33 publications

References 21 publications

Assessment of a new strategy for selective phenotyping applied to complex traits in <i>Brassica napus</i>

Assessment of a new strategy for selective phenotyping applied to complex traits in <i>Brassica napus</i>

Cold tolerance in field conditions, its inheritance, agronomic performance and genetic structure of maize lines divergently selected for germination at low temperature

Genotyping strategies for genomic selection in small dairy cattle populations

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Selective Genotyping and Phenotyping Strategies in a Complex Trait Context

Cited by 33 publications

References 21 publications

Assessment of a new strategy for selective phenotyping applied to complex traits in &lt;i&gt;Brassica napus&lt;/i&gt;

Assessment of a new strategy for selective phenotyping applied to complex traits in &lt;i&gt;Brassica napus&lt;/i&gt;

Cold tolerance in field conditions, its inheritance, agronomic performance and genetic structure of maize lines divergently selected for germination at low temperature

Genotyping strategies for genomic selection in small dairy cattle populations

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Assessment of a new strategy for selective phenotyping applied to complex traits in <i>Brassica napus</i>

Assessment of a new strategy for selective phenotyping applied to complex traits in <i>Brassica napus</i>