Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development

Abstract

Growth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes.

Genetic architecture of variation in Arabidopsis thaliana rosettes

“…Thus, rosette shape variation is visible and genetically controlled within some range as predicted by the ‘continuum and process morphology’ [ 140 – 142 ]. Our results on shape descriptors heritability are consistent with these observations and build up on the concept that morphological traits act as functional ones [ 63 , 143 ]. The QTLs found here agree with the theory that finely tuned genetic regulatory networks, linking and integrating environmental clues during ontogenetic development, are among the major contributions to plant local adaptations [ 144 – 147 ].…”

“…Imaging techniques are readily scalable and have been widely used to measure growth rate [ 3 , 54 , 55 ], leaf number and size [ 56 ], leaf hyponasty [ 57 ] and hypocotyl angle [ 58 ], and can be used to estimate morphological parameters. We have previously characterized rosette morphology in 19 Arabidopsis ecotypes using image based approaches during growth and development [ 22 ] and other studies have used similar descriptors for screening large Arabidopsis populations and mutants, tracking morphological changes over time and allowing a more precise dissection of developmental timing of plant growth and development [ 59 – 63 ]. Image analysis can quantify size and shape variation due to defined genetic lesions in rosette plants [ 64 ] and used to identify QTL for variation in rosette area, revealing a number of candidate genes for growth and size traits [ 3 , 4 , 62 , 63 , 65 – 67 ].…”

“…We have previously characterized rosette morphology in 19 Arabidopsis ecotypes using image based approaches during growth and development [ 22 ] and other studies have used similar descriptors for screening large Arabidopsis populations and mutants, tracking morphological changes over time and allowing a more precise dissection of developmental timing of plant growth and development [ 59 – 63 ]. Image analysis can quantify size and shape variation due to defined genetic lesions in rosette plants [ 64 ] and used to identify QTL for variation in rosette area, revealing a number of candidate genes for growth and size traits [ 3 , 4 , 62 , 63 , 65 – 67 ]. More recently, a multi-scale approach was used with the purpose of linking genes to plant shape at several scales, from the whole plant to cells and tissues attending to quantitative measurements extracted from digital images and models [ 50 ].…”

Coffea arabica L. Resistant to Coffee Berry Borer (Hypothenemus hampei) Mediated by Expression of the Bacillus thuringiensis Cry10Aa Protein

“…MCM4 has a role in the mitotic cycle, consequently in cell proliferation, which is key for plant growth. Mutations induce different degrees of reduction in rosette size (González et al, 2020). ETG1 mutants are macroscopically normal, but an increase in cell size and endoreduplication occurs.…”

QTL analysis of vegetative phase change in natural accessions ofArabidopsis thaliana

“…In particular, the genetic basis for intra-and interspecies variation in the timing of vegetative phase change, as well its relationship to the reproductive phase transition is unknown (Goebel 1900; Wiltshire et al 1991; Hudson et al 2014; Foerster et al 2015). Studies of natural variation in A. thaliana have been vital for understanding the mechanism of flowering time (Alonso-Blanco et al 1998; Lempe et al 2005; Shindo et al 2005; Rosas et al 2014), germination (Chiang et al 2009; Martínez-Berdeja et al 2020), senescence (Lyu et al 2018; He et al 2018b) and many other phenomena (Bergelson and Roux 2010; Yuan and Kessler 2019; Rubin et al 2019; Sasaki et al 2019; Nakano et al 2020; González et al 2020). However, the extent to which the timing of vegetative phase change varies within this species, and the genetic basis for this variation remain to be investigated.…”