An Integrated Genotyping-by-Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes

Area of Science:

• Agricultural Science
• Genomics
• Plant Breeding

Background:

• Large-scale single nucleotide polymorphism (SNP) datasets in sorghum are crucial for genetic research but hampered by reference genome coordinate inconsistencies.
• Genotyping-by-sequencing of reduced representation libraries has generated substantial sorghum SNP data.

Purpose of the Study:

• To construct and characterize an integrated SNP dataset for 10,323 sorghum genotypes on the version 3.1 reference genome.
• To facilitate the reuse of existing sorghum genomic data for advanced genetic studies and molecular breeding.

Main Methods:

• Integrated 459,304 SNPs from multiple datasets onto the sorghum version 3.1 reference genome.
• Analyzed SNP distribution, genetic structure, and linkage disequilibrium decay.
• Validated the dataset using genome-wide association studies (GWAS) with genebank and population-specific phenotype data.

Main Results:

• Developed an integrated SNP dataset of 459,304 markers for 10,323 sorghum genotypes.
• Observed high SNP enrichment in subtelomeric and genic regions, correlating with restriction site distribution.
• Genetic structure analysis revealed population and familial differences; linkage disequilibrium decay varied between diversity and RIL panels.
• GWAS successfully mapped known genes and identified novel associations for traits like plant height and flowering time, including epistatic interactions.

Conclusions:

• The integrated SNP dataset is a high-quality genomics resource for sorghum.
• This resource significantly enhances the potential for genetic research and molecular breeding in sorghum.
• Facilitates precise genetic mapping and discovery of trait-associated loci and interactions.