Genotyping-by-sequencing and genomic selection applications in hexaploid triticale

Area of Science:

• Plant genetics and breeding
• Genomics
• Agricultural science

Background:

• Triticale, a wheat-rye hybrid, has limited genomic resources due to its complex genome.
• Understanding its genetic diversity and population structure is crucial for improvement.

Purpose of the Study:

• Generate dense marker data for triticale.
• Analyze genetic diversity, population structure, and linkage disequilibrium (LD).
• Estimate genomic selection (GS) model accuracies for forage yield.

Main Methods:

• Genotyping-by-sequencing (GBS) on 289 triticale accessions.
• De novo variant calling identified 16,378 single nucleotide polymorphism (SNP) markers.
• SNP mapping to wheat and rye genomes, LD analysis, and GS model evaluation.

Main Results:

• Identified 16,378 SNPs, with significant mapping to wheat (45%) and rye (58%) genomes.
• Observed substantial substitution of the rye genome (R) with the wheat D genome (28.9%).
• Found five distinct genetic clusters, with LD decaying rapidly within 10kb; GS accuracy reached ~0.52.

Conclusions:

• The study provides valuable genomic resources and insights into triticale genetic architecture.
• Genomic selection is a promising tool for enhancing triticale forage yield.
• Triticale's genetic makeup shows significant wheat D genome introgression.