A framework to model a web of linkage disequilibria for natural allotetraploid populations

Linkage disequilibrium (LD) is an important genetic parameter used to infer the diversity of natural populations and their evolutionary history. Traditionally, LD defined as non-random association non-alleles at different loci in gametes for diploids, but has a limited use polyploids. We formulate framework define tetraploid-specific including (a) Hardy–Weinberg disequilibria each locus, (b) composite digenic disequilibrium, (c) trigenic (d) quadrigenic loci. These four types affect population variation singly or jointly through web. implement EM algorithm estimate test its significance allotetraploid populations. perform computer simulation examine statistical properties our computational model. Through analysing data switchgrass, we chart genomic distribution on chromosomes from which history switchgrass inferred, demonstrating practical usefulness have developed model analysis allotetraploids. The can be generalized tool study evolution polyploid