Haplotype-resolved genetic mapping using selfed progeny enables simultaneous genome assembly validation and trait dissection in a heterozygous plant

Abstract

Genetic linkage maps are essential for genome analysis and molecular breeding, but developing suitable mapping populations remains challenging in many plant species. Approaches requiring inbred parental lines are particularly difficult to implement in plants with long generation times or severe inbreeding depression. We developed haplotype-resolved genetic mapping (HRGM) to construct linkage maps from a single heterozygous individual and its selfed progeny without requiring inbred parental lines. HRGM combines haplotype-resolved unitig assemblies from the S0 parent with genotype data from its S1 progeny, using sequence differences between the two haplotypes to define phased SNP markers. Application to Cynanchum wilfordii generated a high-density genetic map comprising 8,147 SNP markers consolidated into 464 bins across 11 linkage groups, spanning 786.4 cM. The map enabled the detection of two loci associated with root development. Recombination patterns derived from the S1 population showed strong concordance with the chromosome-scale genome assembly and exhibited recombination suppression in putative centromeric regions. HRGM integrates recombination-based genome assembly validation and trait mapping within a single framework. By using one generation of selfed progeny and obtaining linkage-phase information directly from phased assemblies, it simplifies mapping population development and extends the utility of genomic resources for genetic analysis and molecular breeding, particularly in species where selfed progeny can be obtained but conventional mapping populations are difficult to establish.