Dataset Information

The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet.

ABSTRACT:

Background

Multi-parent populations (MPPs) are important resources for studying plant genetic architecture and detecting quantitative trait loci (QTLs). In MPPs, the QTL effects can show various levels of allelic diversity, which can be an important factor influencing the detection of QTLs. In MPPs, the allelic effects can be more or less specific. They can depend on an ancestor, a parent or the combination of parents in a cross. In this paper, we evaluated the effect of QTL allelic diversity on the QTL detection power in MPPs.

Results

We simulated: a) cross-specific QTLs; b) parental and ancestral QTLs; and c) bi-allelic QTLs. Inspired by a real application in sugar beet, we tested different MPP designs (diallel, chessboard, factorial, and NAM) derived from five or nine parents to explore the ability to sample genetic diversity and detect QTLs. Using a fixed total population size, the QTL detection power was larger in MPPs with fewer but larger crosses derived from a reduced number of parents. The use of a larger set of parents was useful to detect rare alleles with a large phenotypic effect. The benefit of using a larger set of parents was however conditioned on an increase of the total population size. We also determined empirical confidence intervals for QTL location to compare the resolution of different designs. For QTLs representing 6% of the phenotypic variation, using 1600 F₂ offspring individuals, we found average 95% confidence intervals over different designs of 49 and 25 cM for cross-specific and bi-allelic QTLs, respectively.

Conclusions

MPPs derived from less parents with few but large crosses generally increased the QTL detection power. Using a larger set of parents to cover a wider genetic diversity can be useful to detect QTLs with a reduced minor allele frequency when the QTL effect is large and when the total population size is increased.

SUBMITTER: Garin V

PROVIDER: S-EPMC7860181 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Publications

The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet.

Garin Vincent V Wimmer Valentin V Borchardt Dietrich D Malosetti Marcos M van Eeuwijk Fred F

BMC genomic data 20210203 1

<h4>Background</h4>Multi-parent populations (MPPs) are important resources for studying plant genetic architecture and detecting quantitative trait loci (QTLs). In MPPs, the QTL effects can show various levels of allelic diversity, which can be an important factor influencing the detection of QTLs. In MPPs, the allelic effects can be more or less specific. They can depend on an ancestor, a parent or the combination of parents in a cross. In this paper, we evaluated the effect of QTL allelic dive ...[more]

PMID: 33568071

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Project description:Productivity of sugar beet and brassica vegetable crops is constrained by the nematode Heterodera schachtii worldwide. In sugar beet cropping areas of Central Europe and North America, H. schachtii is managed by crop rotation, and cultivation of resistant brassica cover crops. The recently released nematode-tolerant sugar beet cultivars suffer less damage than susceptible cultivars at high initial population densities of H. schachtii. Many tolerant cultivars allow for less nematode reproduction than susceptible cultivars. Monoculture of susceptible hosts can facilitate the evolution of suppressive soil. Objectives of this study were to determine if susceptible hosts are required for this process, and if monoculture with sugar beet genotypes of different host status (susceptible, resistant, tolerant) impact this capacity. Additionally, we tested if amending soil with the cyst nematode pathogens Pasteuria nishizawae or Hyalorbilia sp. strain DoUCR50 favored the establishment of soil suppressiveness. In 4-year microplot studies with H. schachtii Schach0 or Schach1, one susceptible, one Schach0-resistant, and one tolerant sugar beet genotype were monocultured. In 2010, plots were amended with P. nishizawae or DoUCR50, the last being introduced into non-treated soil for Schach0, and into previously biocide-treated soil for Schach1. In 2011, respective Schach0 plots received a second amendment with DoUCR50. Nematode population densities and growth and yield parameters were determined annually. Effects of P. nishizawae and DoUCR50 on populations of H. schachtii were limited and not consistent. Starting in the second year of the monoculture, eggs of both H. schachtii pathotypes became diseased. Up to 90% of the total eggs were encumbered by the third cropping cycle, under the susceptible, resistant, and tolerant cultivar. In all years, the tolerant genotype produced the highest and most stable white sugar yields while yields of the other cultivars slowly improved during the monoculture. Results of this study suggested the presence of egg-infecting factors in this sugar beet monoculture that dramatically increased the proportions of diseased eggs. The tolerant cultivar allowed establishment of soil suppressiveness without the initial yield decline observed when susceptible sugar beet genotypes are grown in monoculture.

Project description:BackgroundCharacterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore the patterns of population structure in the pollen parent heterotic pool using different methods, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in elite sugar beet germplasm.ResultsA total of 264 and 238 inbred lines from the yield type and sugar type inbreds of the pollen parent heterotic gene pools, respectively, which had been genotyped with 328 SNP markers, were used in this study. Two distinct subgroups were detected based on different statistical methods within the elite sugar beet germplasm set, which was in accordance with its breeding history. MCLUST based on principal components, principal coordinates, or lapvectors had high correspondence with the germplasm type information as well as the assignment by STRUCTURE, which indicated that these methods might be alternatives to STRUCTURE for population structure analysis. Gene diversity and modified Roger's distance between the examined germplasm types varied considerably across the genome, which might be due to artificial selection. This observation indicates that population genetic approaches could be used to identify candidate genes for the traits under selection. Due to the fact that r2 >0.8 is required to detect marker-phenotype association explaining less than 1% of the phenotypic variance, our observation of a low proportion of SNP loci pairs showing such levels of LD suggests that the number of markers has to be dramatically increased for powerful genome-wide association mapping.ConclusionsWe provided a genome-wide distribution map of genetic diversity and linkage disequilibrium for the elite sugar beet germplasm, which is useful for the application of genome-wide association mapping in sugar beet as well as the efficient organization of germplasm.

Dataset Information

The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet.

Background

Results

Conclusions

Publications

The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet.

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