Association Mapping of Germination Traits inArabidopsis thalianaUnder Light and Nutrient Treatments: Searching for G×E Effects

Abstract

In the natural world, genotype expression is influenced by an organism’s environment. Identifying and understanding the genes underlying phenotypes in different environments is important for making advances in fields ranging from evolution to medicine to agriculture. With the availability of genome-wide genetic-marker datasets, it is possible to look for genes that interact with the environment. Using the model organism, Arabidopsis thaliana, we looked for genes underlying phenotypes as well as genotype-by-environment interactions in four germination traits under two light and two nutrient conditions. We then performed genome-wide association tests to identify candidate genes underlying the observed phenotypes and genotype-by-environment interactions. Of the four germination traits examined, only two showed significant genotype-by-environment interactions. While genome-wide association analyses did not identify any markers or genes explicitly linked to genotype-by-environment interactions, we did identify a total of 55 markers and 71 genes associated with germination differences. Of the 71 genes, four—ZIGA4, PS1, TOR, and TT12—appear to be strong candidates for further study of germination variation under different environments.

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

“…To date, such studies were only reported in Arabidopsis thaliana (Li et al , 2010; Morrison and Linder, 2014; El-Soda et al , 2015; Sasaki et al , 2015), and maize (Saïdou et al , 2014). Explicitly accounting for ‘QTL by environment interactions’ in QTL studies can help to discover novel genes that act synergistically with the environment, potentially leading to the identification of superior genotypes according to the environments (Des Marais et al , 2013).…”

Lineage‐specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana

“…This could suggest, in these cases, that an adaptive signature has been partially masked by disproportionate synonymous substitutions at the edges of exons. Of note is that AT1G08680 (ARF GAP-like zinc finger-containing protein ZIGA4) has been linked to adaptive germination phenotypes (Morrison & Linder 2014) and that AT1G60930 (RECQ helicase L4B) appears to be a duplicate gene that has undergone a degree of functional divergence (Singh et al 2010). As duplicated genes undergo asymmetric sequence divergence relative to each other (Conant & Wagner 2003), an adaptive interpretation is in this case plausible.…”

An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time

“…Seeds obtained from these plants were then stored 12 for approximately 30 days before sowing (e.g. (Morrison and Linder, 2014)), in a dark chamber kept 13 at 15°C and 15% relative humidity. To check the quality of seed collected and stored for ~30 days in 14 these conditions, we performed stratification experiments for a subset of MAGIC lines (32 lines, 15 including the most highly variable lines), by putting imbibed seeds at 4°C in the dark for 4 days prior 16 to sowing.…”