TY - JOUR
T1 - A multivalent three-point linkage analysis model of autotetraploids
AU - Lu, Yafei
AU - Yang, Xiaoxia
AU - Tong, Chunfa
AU - Li, Xin
AU - Feng, Sisi
AU - Wang, Zhong
AU - Pang, Xiaoming
AU - Wang, Yaqun
AU - Wang, Ningtao
AU - Tobias, Christian M.
AU - Wu, Rongling
PY - 2013/7
Y1 - 2013/7
N2 - Because of its widespread occurrence and role in shaping evolutionary processes in the biological kingdom, especially in plants, polyploidy has been increasingly studied from cytological to molecular levels. By inferring gene order, gene distances and gene homology, linkage mapping with molecular markers has proven powerful for investigating genome structure and organization. Here we review and assess a general statistical model for three-point linkage analysis in autotetraploids by integrating double reduction, a phenomenon that commonly occurs in autopolyploids whose chromosomes are derived from a single ancestral species. This model does not require any assumption on the distribution of the occurrence of double reduction and can handle the complexity of multilocus linkage in terms of crossover interference. Implemented with the expectation-maximization (EM) algorithms, the model can estimate and test the recombination fractions between less informative dominant markers, thus facilitating its practical implications for any autopolyploids in most of which inexpensive dominant markers are still used for their genetic and evolutionary studies. The model was applied to reanalyze a published data in tetraploid switchgrass, validating its practical usefulness and utilization.
AB - Because of its widespread occurrence and role in shaping evolutionary processes in the biological kingdom, especially in plants, polyploidy has been increasingly studied from cytological to molecular levels. By inferring gene order, gene distances and gene homology, linkage mapping with molecular markers has proven powerful for investigating genome structure and organization. Here we review and assess a general statistical model for three-point linkage analysis in autotetraploids by integrating double reduction, a phenomenon that commonly occurs in autopolyploids whose chromosomes are derived from a single ancestral species. This model does not require any assumption on the distribution of the occurrence of double reduction and can handle the complexity of multilocus linkage in terms of crossover interference. Implemented with the expectation-maximization (EM) algorithms, the model can estimate and test the recombination fractions between less informative dominant markers, thus facilitating its practical implications for any autopolyploids in most of which inexpensive dominant markers are still used for their genetic and evolutionary studies. The model was applied to reanalyze a published data in tetraploid switchgrass, validating its practical usefulness and utilization.
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U2 - 10.1093/bib/bbs051
DO - 10.1093/bib/bbs051
M3 - Article
C2 - 22988254
AN - SCOPUS:84889077322
SN - 1467-5463
VL - 14
SP - 460
EP - 468
JO - Briefings in bioinformatics
JF - Briefings in bioinformatics
IS - 4
M1 - bbs051
ER -