Linkage map construction using limited parental genotypic information

Authors: Cuevas, Hugo; VERMERRIS, WILFRED - University Of Florida

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/14/2022
Publication Date: 4/15/2022
Citation: Cuevas, H.E., Vermerris, W. 2022. Linkage map construction using limited parental genotypic information. Euphytica. 218, 18. https://doi.org/10.1007/s10681-022-03005-z.
DOI: https://doi.org/10.1007/s10681-022-03005-z

Interpretive Summary: The construction of genetic linkage maps based on genetic markers [e.g. single nucleotide polymorphism (SNPs)] is necessary to associate genomic regions in chromosomes with economically important traits. To construct these linkage maps it is necessary to have two types of information: 1) adequate genotypic information of two parental lines and; 2) genotypic information of the progenies from these parental lines. A new approach was developed to construct linkage maps with or without limited genotypic information of the parental lines. The strategy was validated through the construction of a linkage map of 33,421 SNPs, 205 progenies and non-parental genotypic information. This new approach provides plant breeders and geneticists a strategy to construct linkage maps based on segregating population even though parental lines are missing or unknown and use of these linkage maps to study economically important traits.

Technical Abstract: Genetic linkage maps based on single nucleotide polymorphisms (SNPs) represent an essential tool for a variety of genomic analyses. Today, next-generation sequencing (NGS) enables rapid genotyping of different mapping populations based on thousands of SNPs and the construction of highly saturated linkage maps. Nevertheless, missing data in the genotyping of the parental lines creates a bottleneck that determines the number of SNPs that can be used for the linkage map. As a proof of concept, a highly saturated genetic linkage map was constructed using the imputed genotypic data of a recombinant inbred line (RIL) population and the limited genotypic information of its parental lines. Two ABH genotype files were created from a pseudo-parental genotypic data set that includes all the SNPs present in the RIL population. In the first ABH file pseudo-parental 1 was considered parental A, while in the second pseudo-parental 1 was considered parental B. These two duplicate ABH genotype files were merged by chromosome and subjected to linkage map analysis. Since the ABH data were duplicated, two mirrored linkage groups were generated per chromosome. The correct linkage map was identified and selected based on the partial genotypic data of the parental lines. This strategy was effective for constructing a highly saturated linkage map of 33,421 SNPs based on the genotyping of 205 RILs and a limited number of 100 SNPs present in the parental lines. Using both mirrored linkage maps, quantitative trait loci for flowering time and plant height identified previously associated genomic regions, indicating that this approach is successful in associating genomic regions to traits even when only partial genotypic data on the parental genotypes are available. This imputation strategy enables the use of all the NGS SNP data obtained from a low coverage sequencing experiment for the genomic dissection of any trait of interest in a segregating population.