Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia.

Daniel Matsusaka,Daniele Filiault,Javier F Botto,Diego H Sanchez

doi:10.3389/fpls.2021.677728

Abstract

Arabidopsis thaliana shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, Arabidopsis has a high potential for the identification of genes underlying ecologically important complex traits, thus providing new insights on genome evolution. Previous research suggested that distinct light responses were crucial for Arabidopsis establishment in a peculiar ecological niche of southern Patagonia. The aim of this study was to explore the genetic basis of contrasting light-associated physiological traits that may have mediated the rapid adaptation to this new environment. From a biparental cross between the photomorphogenic contrasting accessions Patagonia (Pat) and Columbia (Col-0), we generated a novel recombinant inbred line (RIL) population, which was entirely next-generation sequenced to achieve ultra-high-density saturating molecular markers resulting in supreme mapping sensitivity. We validated the quality of the RIL population by quantitative trait loci (QTL) mapping for seedling de-etiolation, finding seven QTLs for hypocotyl length in the dark and continuous blue light (Bc), continuous red light (Rc), and continuous far-red light (FRc). The most relevant QTLs, Rc1 and Bc1, were mapped close together to chromosome V; the former for Rc and Rc/dark, and the latter for Bc, FRc, and dark treatments. The additive effects of both QTLs were confirmed by independent heterogeneous inbred families (HIFs), and we explored TZP and ABA1 as potential candidate genes for Rc1 and Bc1QTLs, respectively. We conclude that the Pat × Col-0 RIL population is a valuable novel genetic resource to explore other adaptive traits in Arabidopsis.

Highlights

Physical cues of the surrounding environment represent primary agents by which evolution proceeds, imposing selective sieves, which lead to the buildup of adaptive mechanisms that enable organismal survival
We first confirmed that seedling de-etiolation was reduced in Pat compared with Col-0, a light responsive accession (Figure 1)
We focused on TANDEM ZINC KNUCLE PROTEIN (TZP), since it has been implicated in de-etiolation and photoperiodic responses (Loudet et al, 2008; Kaiserli et al, 2015; Zhang et al, 2018), and TZP-Pat presented a high number of missense variants (#6), with an additional stop codon gained at the end portion of the protein (Supplementary Table 10)

Summary

Introduction

Physical cues of the surrounding environment represent primary agents by which evolution proceeds, imposing selective sieves, which lead to the buildup of adaptive mechanisms that enable organismal survival. Arabidopsis is a plant model for plant breeding due to its small and simple genome, ample distribution in different environments, and diverse ecological conditions It is a cosmopolitan species found mostly in the Northern Hemisphere, native to Eurasia and North Africa, it has been introduced recently to the Americas (Koornneef et al, 2004; Krämer, 2015; Kasulin et al, 2017). The plants conspicuously thrive below Neneo (Mulinum spinosum) and Coliguaya (Colliguaya integerrima) shrubs, protected from sheep and cow foraging This suggests that Pat may be adapted to shade as an escape strategy to combined drought, stressful irradiance, and grazing. The ecology environment of its distribution, its phenotypic characteristics, and the very recent colonization of a narrow Patagonian niche under seemly novel abiotic/biotic interactions, suggest that Pat represents an excellent resource for exploring the genetic and molecular basis of adaptive traits explaining complex developmental responses to light (Kasulin et al, 2017; Legris et al, 2019; Takou et al, 2019)

Objectives

Methods

Results