Abstract
The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present “Parental Allele Tracing, Recombination Identification, and Optimal predicTion” (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity-by-descent relationships, PATRIOT showed an improvement in GP accuracy by 16.6% relative to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs.
Highlights
Crop domestication has caused extreme genetic bottleneck, with a reduction in genetic diversity in domesticated crops compared to wild ancestors including in soybean
Released Cultivars and Isolines We identified 868 accessions within the National Plant Germplasm System (NPGS) soybean collection wherein both parent and progeny were genotyped with the SoySNP50k Single-nucleotide polymorphism (SNP) set, including near-isogenic lines derived from backcrossing schema
Using the soybean nested association mapping (SoyNAM) panel marker data after “Parental Allele Tracing (PATRIOT) IBD tracing and imputation, we examined the rates of recombination throughout the genome
Summary
Crop domestication has caused extreme genetic bottleneck, with a reduction in genetic diversity in domesticated crops compared to wild ancestors including in soybean 17 founding lines contributed 75% of the genes in modern US soybean cultivars, and 95% of genes could be traced to 35 ancestral lines, demonstrating an extremely narrow genetic variation challenging breeding progress. This is not confined to soybean alone, as other crops have similar challenges (Smith, 2007; Bennett et al, 2012). Tracking identity-by-descent (IBD) presents unique advantages that can benefit ongoing plant breeding efforts in utilizing the narrow genetic germplasm pool within modern varieties effectively, as the limited number of founder sources increases the occurrence rate of each chromosomal segment from each founder. Each founder’s chromosomal segment is expected to be replicated sufficiently within breeding materials to obtain accurate predictions of the segment effect
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