Natural Allelic Variations in Highly Polyploidy Saccharum Complex

Area of Science:

• Plant genetics and genomics.
• Crop science and breeding.

Background:

• Sugarcane (Saccharum spp.) is a vital polyploid crop for sugar and biofuel production.
• The Saccharum complex harbors significant genetic diversity crucial for breeding, but allelic variation is challenging to study.

Purpose of the Study:

• To characterize natural allelic variations within the Saccharum complex.
• To establish an effective method for discovering genetic variations in complex polyploid genomes.

Main Methods:

• Target enrichment sequencing of 12 representative sugarcane germplasm accessions.
• Development of a specialized pipeline for polyploid variant and genotype calling.
• Utilized sorghum genome as a reference for probe design and sequence alignment.

Main Results:

• Detected over 1.1 million SNPs, 150K InDels, and thousands of copy number and presence/absence variations.
• Achieved nearly 90% SNP validation rate using multiple callers.
• Identified nearly 1 million single dosage SNPs and inferred haplotype blocks, revealing divergence times up to 1.2 million years ago.

Conclusions:

• Target enrichment sequencing is an effective strategy for cataloging natural allelic variation in complex polyploid genomes.
• The identified variations provide valuable genetic resources for sugarcane breeding and trait discovery.