The New Is Old: Novel Germination Strategy Evolved From Standing Genetic Variation in Weedy Rice

Abstract

Feralization of crop plants has aroused an increasing interest in recent years, not only for the reduced yield and quality of crop production caused by feral plants but also for the rapid evolution of novel traits that facilitate the evolution and persistence of weedy forms. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, with separate and independent origins. The weedy rice distributed in eastern and northeastern China did not diverge from their cultivated ancestors by reverting to the pre-domestication trait of seed dormancy during feralization. Instead, they developed a temperature-sensing mechanism to control the timing of seed germination. Subsequent divergence in the minimum critical temperature for germination has been detected between northeastern and eastern populations. An integrative analysis was conducted using combinations of phenotypic, genomic and transcriptomic data to investigate the genetic mechanism underlying local adaptation and feralization. A dozen genes were identified, which showed extreme allele frequency differences between eastern and northeastern populations, and high correlations between allele-specific gene expression and feral phenotypes. Trancing the origin of potential adaptive alleles based on genomic sequences revealed the presence of most selected alleles in wild and cultivated rice genomes, indicating that weedy rice drew upon pre-existing, “conditionally neutral” alleles to respond to the feral selection regimes. The cryptic phenotype was exposed by activating formerly silent alleles to facilitate the transition from cultivation to wild existence, promoting the evolution and persistence of weedy forms.

Genetic Diversity of Transcription Factor Genes in Triticum and Mining for Promising Haplotypes for Beneficial Agronomic Traits

“…The haplotype diversity of wild subpopulations was higher than that of cultivated populations, consistent with a previous study in rice (He et al, 2021). Crop domestication is a complex evolutionary process driven by strong artificial selection (reviewed in Zhou et al, 2021), and wheat epitomizes the effectiveness of artificial selection and improvement in shaping a crop to meet human demands and economic incentives (Gegas et al, 2010). Thus, the increased frequency of some haplotypes during domestication and improvement suggests that these haplotypes were selected for and played important roles to humans, especially in yield-related traits.…”

Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds

“…In response to agricultural environments, feral weeds have developed mechanisms that regulate seed germination, for example, endoferal Tibetan wheat, 44 exoferal weedy sunflower, 45 and temperaturesensing mechanisms (instead of seed dormancy) in weedy rice from eastern and northeastern China. 46,47 Shoot branching (hereafter referred to as "branching"), understood as the formation of side shoots (tillers and branches) from axillary meristems on the shoots of a plant, plays a key role in weed performance in agroecosystems. It is a major determinant of plant architecture and size, so it influences the ability of weed plants to acquire resources (for example, light) and to compete with neighboring plants.…”

Bray‐Curtis (AFD) differentiation in molecular ecology: Forecasting, an adjustment (AA), and comparative performance in selection detection

“…Candidate adaptive loci are identified because they depart from neutral forecasts, as is commonly done with , , and other measures (Bierne et al, 2013; Lotterhos & Whitlock, 2014; Narum & Hess, 2011; Schneider et al, 2021; Xiang‐Yu et al, 2016). Similar searches for adaptive loci are now using BCAFD (Bharti et al, 2021; Boyle et al, 2021; Haenel, Guerard, et al, 2021; Haenel, Oke, et al, 2021; Price et al, 2020; Yin et al, 2021; Zhou et al, 2021). These searches are expected to benefit from using A A instead of BCAFD , because as shown in the results above, the limitation of BCAFD truncates the high values of differentiation, which are the very values used to identify the potentially adaptive loci.…”

“…Similar searches for adaptive loci are now using BCAFD (Bharti et al, 2021;Boyle et al, 2021;Haenel, Guerard, et al, 2021;Haenel, Oke, et al, 2021;Price et al, 2020;Yin et al, 2021;Zhou et al, 2021).…”

“…In the molecular ecology literature, BCAFD has been used or mentioned many times since Berner's publications (Berner, 2019a , 2019b ), including for assessment of population differentiation in time or space, with implications for likely genetic connectivity (Amos, 2021 ; Lou et al, 2021 ; Popovic et al, 2021 ; Subramanian, 2021 ; Taylor et al, 2021 ; Weldekidan et al, 2022 ; Wolf et al, 2021 ), as well as identifying candidate adaptive loci by their strong differentiation relative to other presumably neutral loci (Bharti et al, 2021 ; Boyle et al, 2021 ; Haenel, Guerard, et al, 2021 ; Haenel, Oke, et al, 2021 ; Price et al, 2020 ; Yin et al, 2021 ; Zhou et al, 2021 ).…”