Sturtevant's discovery led to the golden age of chromosome transmission genetics, with an emphasis on identifying genes through alleles with visible phenotypes , and using them as markers for determining their position on the linkage map. Since then the emphasis in genetics has shifted to understanding the functions of genes. Linkage and gene mapping studies have progressed to being a critical tool in cloning genes and providing more description of their roles in the organism. These approaches include: Using map locations to distinguish different genes with similar sequences, mutant phenotypes, or functions. Examples are the cell division cycle mutants of the yeast Saccharomyces cercvisiae or the uncoordinated mutants of the roundworm C. elegans. In some cases mutants with different phenotypes have been shown to be done to different mutations in the same gene, as is the case with the Drosophila circadian rhythm period mutants termed short, long, and none (per[S], per[L] and per[0]). Using map locations to track down genes to clone their deoxyribonucleic acid (DNA) by chromosome position. Examples are the human cystic fibrosis transmembrane regulator gene mutated in cystic fibrosis, or the polyglutamine repeat gene that is mutated in Huntington's disease. With genome sequences available on databases, mapping mutant phenotypes points to candidate loci for the gene at the chromosome position. New classes of markers in linkage analysis are based on naturally occurring DNA variation in the genome , and have many advantages. These variations are usually harmless and don't interrupt a gene, so there is no selection against them, meaning they persist over many generations. They are quite numerous and are distinguished throughout in the genome. Individuals are likely to be heterozygous from many of them and therefore the markers are informative for linkage. If the DNA variant is present heterozygously, can be detected, and shows Mendelian segregation, it is as good a linkage marker as yellow bodies or white eyes. The disadvantage is that analysis to detect the variant is sometimes more laborious and requires the techniques of molecular biology.

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