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Efficient construction of a linkage map and haplotypes for Mentha suaveolens using sequence capture
Helen Tsai1, Nestor Kippes1, Alana Firl1
1Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.
G3 (Bethesda, Md.)
|September 20, 2021
Summary
This study introduces a fast method for creating genetic linkage maps in plants, crucial for improving crop breeding. The new technique successfully mapped the genome of Mentha suaveolens, aiding reference genome validation.
Area of Science:
- Genomics
- Plant Breeding
- Molecular Genetics
Background:
- Crop sustainability is limited by insufficient genomic resources and understanding of genetic diversity.
- Modern crop improvement necessitates high-density linkage maps integrated with contiguous reference genomes.
Purpose of the Study:
- To present a rapid method for haplotype derivation and linkage map development.
- To apply this method to Mentha suaveolens, a key progenitor of cultivated mints.
- To validate the utility of the generated linkage map for reference genome improvement.
Main Methods:
- Utilized sequence-capture hybridization to genotype single nucleotide polymorphisms (SNPs) in over 400 individuals from a self-cross.
- Applied stringent quality control and identified 1919 informative SNPs for linkage analysis.
- Constructed a genetic linkage map covering 942.17 cM across 12 linkage groups.
Main Results:
- Developed a high-density genetic linkage map for Mentha suaveolens.
- The map comprises 1919 informative SNPs distributed across 12 linkage groups.
- The linkage map showed good congruence with preliminary genome assembly pseudomolecules.
Conclusions:
- The presented method offers a rapid and effective approach for generating plant genetic linkage maps.
- The linkage map serves as a valuable resource for correcting and validating the Mentha suaveolens reference genome.
- This work facilitates advancements in genomic resource development for crop improvement.
