Spontaneous Mutational Effects on Reproductive Traits of Arabidopsis thaliana

Abstract

A study of spontaneous mutation in Arabidopsis thaliana was initiated from a single inbred Columbia founder; 120 lines were established and advanced 17 generations by single-seed descent. Here, we report an assay of reproductive traits in a random set of 40 lines from generations 8 and 17, grown together at the same time with plants representing generation 0. For three reproductive traits, mean number of seeds per fruit, number of fruits, and dry mass of the infructescence, the means did not differ significantly among generations. Nevertheless, by generation 17, significant divergence among lines was detected for each trait, indicating accumulation of mutations in some lines. Standardized measures of mutational variance accord with those obtained for other organisms. These findings suggest that the distribution of mutational effects for these traits is approximately symmetric, in contrast to the usual assumption that mutations have predominantly negative effects on traits directly related to fitness. Because distinct generations were grown contemporaneously, each line was represented by three sublines, and seeds were equal in age, these estimates are free of potentially substantial sources of bias. The finding of an approximately symmetric distribution of mutational effects invalidates the standard approach for inferring properties of spontaneous mutation and necessitates further development of more general approaches that avoid restrictions on the distribution of mutational effects.

Shifts in mutation spectra enhance access to beneficial mutations

“…Further, they do not estimate the number of underlying mutations to account for epistasis. Our direct, genome-wide estimates of the DFE of single, randomly-sampled new mutations support the idea (45, 46) that new beneficial mutations may be more common than generally believed.…”

Are mutations usually deleterious? A perspective on the fitness effects of mutation accumulation

“…It is among plants that the most notable cases of MA studies without significant fitness decline can be found. Indeed, a debate around the notion that mutations are predominantly deleterious was ignited by a study in the model plant Arabidopsis thaliana (Shaw et al 2000(Shaw et al , 2002Keightley and Lynch 2003) examined at three life history traits: number of seeds per fruit, fruit number, and reproductive mass after 17 generations of MA. No significant decline was noted for any of the traits despite a significant increase in among-line variance for all traits.…”

“…A prior study in the same organism (Schultz et al 1999) with more lines but fewer generations of MA detected a decline in fitness of about the same magnitude as in this later study, but it was found to be statistically significant although variance was not reported. From their data, Shaw et al (2000) concluded that about half of all mutations that occurred in their study were beneficial. Later studies of these lines extended MA to further generations (Rutter et al 2010(Rutter et al , 2012 and in a variety of environmental conditions ranging from field plantings across geographic ranges to greenhouse studies and over different seasons (Roles et al 2016;Rutter et al 2018).…”

“…First, it is important to consider the limitations and assumptions underlying MA studies in general and how those factors may come into play depending on the biological realities of the study organism. After the first studies suggested that fitness does not necessarily decline after MA (Vassilieva and Lynch 1999;Shaw et al 2000Shaw et al , 2002 some suggested that this could be due to the traits measured being under stabilizing selection rather than directional selection (Keightley and Lynch 2003;Shaw et al 2003). In such a case, any deviation from the mean, regardless of sign, would actually correspond to a reduction in fitness.…”

Single-Plant Selection at Ultra-Low Density Enhances Buffering Capacity of Barley Varieties and Landraces to Unpredictable Environments and Improves Their Agronomic Performance

“…Residual heterozygosity, due to segregation of parental loci during the breeding process is presumably one source of genetic variation (Haun et al, 2011;Tokatlidis, 2015). On the other hand, additional heterogeneity might stem from de novo generated variation, resulting from spontaneous mutations (Shaw et al, 2000;Ossowski et al, 2010) or via genetic and epigenetic mechanisms, such as intragenic recombination, unequal crossing over, gene duplications, or deletions, DNA methylation, excision or insertion of transposable elements, chromatin alterations, and others (Rasmusson and Phillips, 1997;Sani et al, 2013;Cavrak et al, 2014;Kim and Zilberman, 2014).…”