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Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching Nambeesan, Savithri U.; Mandel, Jennifer R.; Bowers, John E.; Marek, Laura F.; Ebert, Daniel; Corbi, Jonathan; Rieseberg, Loren H.; Knapp, Steven J.; Burke, John M.

Abstract

Background: Shoot 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. Results: Detailed 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. Conclusions: In 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.

Item Metadata

Title
Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching
Creator
Nambeesan, Savithri U.; Mandel, Jennifer R.; Bowers, John E.; Marek, Laura F.; Ebert, Daniel; Corbi, Jonathan; Rieseberg, Loren H.; Knapp, Steven J.; Burke, John M.
Publisher
BioMed Central
Date Issued
2015-03-11
Description
Background: Shoot 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. Results: Detailed 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. Conclusions: In 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.
Subject
Apical dominance; Association mapping; Branching; Helianthus annuus; Linkage disequilibrium; Plant architecture; Sunflower
Genre
Article
Type
Text
Language
eng
Date Available
2016-01-13
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0223314
URI
http://hdl.handle.net/2429/56414
Affiliation
Botany, Department of; Science, Faculty of; Non UBC
Citation
BMC Plant Biology. 2015 Mar 11;15(1):84
Publisher DOI
10.1186/s12870-015-0458-9
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
Nambeesan et al.; licensee BioMed Central.
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)