Methods and compositions for preparation of nucleic acids

A method for isolating genomic DNA (gDNA) from a biological material. In some embodiments, the method includes (a) contacting a sample that contains gDNA with a solution of hydroxide and a detergent under conditions and for a time sufficient to degrade a cell wall, a cell membrane, a nuclear membrane, a nucleoprotein, or combinations thereof and/or to denature the gDNA; (b) mixing into the solution resulting from step (a) a solution characterized by high salt and sufficient buffering capacity to reduce the pH of the solution to less than 10, thereby producing a neutralized solution; (c) centrifuging the sample at a speed and length of time sufficient to clarify the preparation; and (d) removing insoluble material from the neutralized and clarified preparation, whereby a solution of gDNA is produced. Also provided are method for performing a quantitative polymerase chain reaction (qPCR) of a gDNA sample, methods for performing genotyping or other molecular marker analysis of a gDNA sample, and methods for determining a haplotype of a cell.