Structure of linkage disequilibrium in plants.

Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome. LD, the nonrandom association of alleles at different loci, plays an integral role in association mapping, and determines the resolution of an association study. Recently, association mapping has been exploited to dissect quantitative trait loci (QTL). With the exception of maize and Arabidopsis, little research has been conducted on LD in plants. The mating system of the species (selfing versus outcrossing), and phenomena such as population structure and recombination hot spots, can strongly influence patterns of LD. The basic patterns of LD in plants will be better understood as more species are analyzed.

Plant molecular diversity and applications to genomics.

Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping.

Biochemical and molecular characterization of photosystem I deficiency in the NCS6 mitochondrial mutant of maize.

Interorganellar signaling interactions are poorly understood. The maize non-chromosomal stripe (NCS) mutants provide models to study the requirement of mitochondrial function for chloroplast biogenesis and photosynthesis. Previous work suggested that the NCS6 mitochondrial mutation, a cytochrome oxidase subunit 2 (cox2) deletion, is associated with a malfunction of Photosystem I (PSI) in defective chloroplasts of mutant leaf sectors (Gu et al., 1993). We have now quantified the reductions of photosynthetic rates and PSI activity in the NCS6 defective stripes. Major reductions of the plastid-coded PsaC and nucleus-coded PsaD and PsaE PSI subunits and of their corresponding mRNAs are seen in mutant sectors; however, although the psaA/B mRNA is greatly reduced, levels of PsaA and PsaB (the core proteins of PSI) are only slightly decreased. Levels of the PsaL subunit and its mRNA appear to be unchanged. Tested subunits of other thylakoid membrane complexes--PSII, Cyt b6/f, and ATP synthase, have minor (or no) reductions within mutant sectors. The results suggest that specific signaling pathways sense the dysfunction of the mitochondrial electron transport chain and respond to down-regulate particular PSI mRNAs, leading to decreased PSI accumulation in the chloroplast. The reductions of both nucleus and plastid encoded components indicate that complex interorganellar signaling pathways may be involved.