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PubMed · 11258199

Notes from the SNP vs. haplotype front.

R Judson·J C Stephens
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Abstract

Single nucleotide polymorphisms (SNPs) and haplotypes are commonly used genetic markers in clinical studies. We provide some broad guidelines for deciding which of the two is most appropriate in particular circumstances. Molecular haplotyping techniques are also briefly reviewed and contrasted with electronic approaches.

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Genetic MarkersGenetic VariationGenome, HumanHaplotypesHeteroduplex AnalysisHumansLinkage DisequilibriumPharmacogeneticsPolymorphism, Single NucleotideSequence Analysis, DNAJournal Article

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R Judson, J C Stephens. 2001. Notes from the SNP vs. haplotype front.. https://doi.org/10.1517/14622416.2.1.7

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Forage quality of maize is influenced by both the content and structure of lignin in the cell wall. Phenylalanine Ammonia-Lyase (PAL) catalyzes the first step in lignin biosynthesis in plants; the deamination of L-phenylalanine to cinnamic acid. Successive enzymatic steps lead to the formation of three monolignols, constituting the complex structure of lignin. We have cloned and sequenced a PAL genomic sequence from 32 maize inbred lines currently employed in forage maize breeding programs in Europe. Low nucleotide diversity and excessive linkage disequilibrium (LD) was identified at this PAL locus, possibly reflecting selective constrains resulting from PAL being the first enzyme in the monolignol, and other, pathways. While the association analysis was affected by extended LD and population structure, several individual polymorphisms were associated with neutral detergent fiber (not considering population structure) and a single polymorphism was associated with in vitro digestibility of organic matter (considering population structure).

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