Genome-wide association study reveals novel SNPs and genes in Gossypium hirsutum underlying Aphis gossypii resistance

Linear mixed models have attracted considerable recent attention as a powerful and effective tool for accounting for population stratification and relatedness in genetic association tests. However, existing methods for exact computation of standard test statistics are computationally impractical for even moderate-sized genome-wide association studies. To deal with this several approximate methods have been proposed. Here, we present an efficient exact method that makes these approximations unnecessary in many settings. This method is roughly n times faster than the widely-used exact method EMMA, where n is the sample size, making exact genome-wide association analysis computationally practical for large numbers of individuals.

The incidence of phloem sap feeding by animals appears paradoxical. Although phloem sap is nutrient-rich compared with many other plant products and generally lacking in toxins and feeding deterrents, it is consumed as the dominant or sole diet by a very restricted range of animals, exclusively insects of the order Hemiptera. These insects display two sets of adaptations. First, linked to the high ratio of non-essential:essential amino acids in phloem sap, these insects contain symbiotic micro-organisms which provide them with essential amino acids. For example, bacteria of the genus Buchnera contribute up to 90% of the essential amino acids required by the pea aphid Acyrthosiphon pisum feeding on Vicia faba. Second, the insect tolerance of the very high sugar content and osmotic pressure of phloem sap is promoted by their possession in the gut of sucrase-transglucosidase activity, which transforms excess ingested sugar into long-chain oligosaccharides voided via honeydew. Various other animals consume phloem sap by proxy, through feeding on the honeydew of phloem-feeding hemipterans. Honeydew is physiologically less extreme than phloem sap, with a higher essential:non-essential amino acid ratio and lower osmotic pressure. Even so, ant species strongly dependent on honeydew as food may benefit from nutrients derived from their symbiotic bacteria Blochmannia.