Population Genetics of the Highly Polymorphic RPP8 Gene Family

Area of Science:

• Plant genetics
• Evolutionary biology
• Genomics

Background:

• Nucleotide-binding domain and leucine-rich repeat containing (NLR) genes exhibit significant polymorphism, comparable to vertebrate MHC.
• Arabidopsis thaliana, a selfing species, surprisingly displays high NLR gene heterozygosity.

Purpose of the Study:

• Investigate the roles of gene duplication and intergenic exchange in generating extraordinary NLR gene variation.
• Analyze the RPP8 gene system in Arabidopsis thaliana and Arabidopsis lyrata to understand polymorphism patterns.

Main Methods:

• Sequencing of 48 RPP8 alleles from 37 Arabidopsis thaliana accessions and 12 alleles from Arabidopsis lyrata.
• Analysis of interlocus shared variation patterns within the RPP8 gene system.
• Forward-in-time simulations incorporating neutral evolution and balancing selection.

Main Results:

• The RPP8 three-locus system exists as tandem duplicates or a single copy plus a distant locus.
• Tandem duplicates show fixed differences; shared variation occurs between distant paralogs.
• High shared polymorphism suggests involvement of crossing over and gene conversion.

Conclusions:

• Genetic architecture, gene function, and balancing selection interact to create high NLR gene diversity.
• Neutral simulations fail to replicate observed nucleotide diversity; balancing selection is necessary.
• The RPP8 gene triad exemplifies complex evolutionary mechanisms driving plant immune receptor diversity.