Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching

Abstract

BackgroundShoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines.ResultsDetailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations.ConclusionsIn sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most promising target for future functional analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0458-9) contains supplementary material, which is available to authorized users.

Vigour/tolerance trade‐off in cultivated sunflower (Helianthus annuus) response to salinity stress is linked to leaf elemental composition

“…Twenty inbred genotypes (Table S1), including elite varieties and landraces, of cultivated sunflower (Helianthus annuus L.) were selected from a diversity panel, sunflower association mapping (SAM) population of 288 genotypes (Mandel, Dechaine, Marek, & Burke, 2011;Nambeesan et al, 2015). Genotypes were selected based on their differential responses in previous abiotic stress studies (Bowsher et al, 2017;Masalia, Temme, Torralba, & Burke, 2018).…”

Sustaining the Future of Plant Breeding: The Critical Role of the USDA‐ARS National Plant Germplasm System

“…This screening identified 10 wheat accessions, mostly from Central Asia, that were highly resistant to the new biotype (Collins et al, 2005) (Seiler et al, 2017). In addition, NPGS genebank materials were used to better understand plant architecture and its influences on aspects of plant growth and development, including the genetic basis of variation of branching and its role in crop domestication (Nambeesan et al, 2015). As a result of the study, an association mapping population of 288 lines is now available for research, together with rich genomic data resources (Mandel et al, 2011(Mandel et al, , 2013.…”

Genetic Characterization of Maximilian Sunflower for the Development of a Locally Adapted Perennial Grain Oilseed

“…The rapid linkage decay we observed is in line with previous estimates from wild Helianthus species (Liu and Burke, 2006;Mandel et al, 2011) and is largely a function of the obligate outcrossing nature of the genus. Recent efforts using association mapping and genome-wide association approaches in sunflower have employed marker densities ranging from ?5300 to ?450,000 SNPs (Mandel et al, 2013;Nambeesan et al, 2015;Badouin et al, 2017) with linkage decays within ?1100 bp (Liu and Burke, 2006). The rate of linkage decay based on marker order in the cultivated H. annuus reference genome (?93 bp) and the large genome size of diploid Helianthus species (?3.6 Gb) suggests that similar to other wild Helianthus species, marker density for genome wide association studies or genomic selection in Maximilian sunflower would need to be high to capture historic recombination events in wild collected germplasm.…”

“…Further research is needed to confirm marker order and chromosomal structure in this species and other perennial Helianthus. Recent efforts using association mapping and genome-wide association approaches in sunflower have employed marker densities ranging from ?5300 to ?450,000 SNPs (Mandel et al, 2013;Nambeesan et al, 2015;Badouin et al, 2017) with linkage decays within ?1100 bp (Liu and Burke, 2006). Given the rapid linkage decay, approaches in which linkage blocks are maintained to a greater degree through consanguinity such as through family-based association mapping approaches (Guo et al, 2013) or pseudo-testcross approaches such as those used in other outcrossing species (Zhang et al, 2016;Covarrubias-Pazaran et al, 2016) may be appropriate in Maximilian sunflower.…”