Association Mapping and the Genomic Consequences of Selection in Sunflower

Abstract

The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) association mapping population that captures nearly 90% of the allelic diversity present within the cultivated sunflower germplasm collection. We used these data to characterize overall patterns of genomic diversity and to perform association analyses on plant architecture (i.e., branching) and flowering time, successfully identifying numerous associations underlying these agronomically and evolutionarily important traits. Overall, we found variable levels of linkage disequilibrium (LD) across the genome. In general, islands of elevated LD correspond to genomic regions underlying traits that are known to have been targeted by selection during the evolution of cultivated sunflower. In many cases, these regions also showed significantly elevated levels of differentiation between the two major sunflower breeding groups, consistent with the occurrence of divergence due to strong selection. One of these regions, which harbors a major branching locus, spans a surprisingly long genetic interval (ca. 25 cM), indicating the occurrence of an extended selective sweep in an otherwise recombinogenic interval.

Genome-Wide Association Studies Identifies Seven Major Regions Responsible for Iron Deficiency Chlorosis in Soybean (Glycine max)

“…One method of generating a high frequency of SNPs is next generation sequencing [41], [42]. Using GBS, we identified ∼35,000 polymorphic markers with a minor allele frequency>0.05.…”

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

“…However, GWA is not restricted to model species and is becoming increasingly widespread in nonmodel ones such as sunflower (Helianthus annuus; Mandel et al, 2013) and tomato (Solanum lycopersicum; Xu et al, 2013), where numerous associations have been successfully identified for traits related to plant architecture (branching in the case of sunflower) and fruit quality (e.g. fresh weight in tomato).…”

Turning heads: The biology of solar tracking in sunflower

“…Recent advances facilitating reverse genetics through targeted induced lesions and germline transformation will allow targeted alteration of candidate genes [19]. In addition, recently generated germplasm resources -including advanced generation recombinant inbred lines and association mapping panels [18,20] -will provide powerful tools for connecting natural allelic variation to phenotypic variation in solar tracking.…”

“…Consequently, many aspects of the physiology, development, and ecological function of solar tracking remain unexplained. Recent genetic and genomic advances [e.g., [18][19][20] poise sunflower to be a strong, tractable model system for revealing the basic mechanisms underlying growth-mediated heliotropism. Here, we review the state of our knowledge regarding solar tracking in sunflower with the purpose of highlighting open questions and raising hypotheses to be addressed by future efforts that take advantage of these new experimental resources.…”