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Updated: May 31, 2026

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Published on: September 2, 2019

Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum.

James C Nelson¹, Shichen Wang, Yuye Wu

¹Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA. jcn@ksu.edu

|July 9, 2011

Summary

This study optimized sorghum (Sorghum bicolor L. Moench) genome sequencing by using specific DNA libraries, improving single-nucleotide polymorphism (SNP) discovery and data imputation for future genetic research.

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Published on: June 23, 2012

Area of Science:

Plant Genomics
Molecular Biology
Bioinformatics

Background:

Investigated single-nucleotide polymorphism (SNP) distribution in diverse sorghum accessions.
Evaluated two DNA library preparation strategies for genome sequencing.
Assessed the impact of library type and genomic diversity on SNP discovery and imputation.

Purpose of the Study:

To characterize single-nucleotide polymorphism (SNP) distribution in sorghum.
To compare the efficacy of different DNA library preparation methods for SNP genotyping.
To determine optimal strategies for SNP imputation in sorghum genomes.

Main Methods:

Performed short-read genome sequencing on eight diverse sorghum accessions.
Utilized two DNA library preparation strategies: restriction site-based and semirandom.
Imputed missing SNP genotype data using local haplotype comparison.

Main Results:

Sequencing using restriction site-based libraries yielded 10-fold more SNPs and 11% more accurate imputation than semirandom libraries.
Reduced-representation sequencing showed a lower SNP yield advantage than expected due to noncanonical restriction site usage.
Genomic similarity within the germplasm panel was more critical for imputation accuracy than panel size or sequencing depth.

Conclusions:

A BsrFI library with 3 million 50-base reads per accession can reliably genotype approximately 96,000 sorghum SNPs.
For accurate SNP imputation in shallowly sequenced genomes, germplasm panels should comprise genomically similar accessions.
Findings provide a framework for designing cost-effective genotyping-by-sequencing strategies for large plant collections.