title: Genome-wide association mapping of soybean chlorophyll traits based on canopy spectral reflectance and leaf extracts.
abstract: Chlorophyll is a major component of chloroplasts and a better understanding of the genetic basis of chlorophyll in soybean [Glycine max (L.) Merr.] might contribute to improving photosynthetic capacity and yield in regions with adverse environmental conditions. A collection of 332 diverse soybean genotypes were grown in 2 years (2009 and 2010) and chlorophyll a (eChl_A), chlorophyll b (eChl_B), and total chlorophyll (eChl_T) content as well as chlorophyll a/b ratio (eChl_R) in leaf tissues were determined by extraction and spectrometric determination. Total chlorophyll was also derived from canopy spectral reflectance measurements using a model of wavelet transformed spectra (tChl_T) as well as with a spectral reflectance index (iChl_T).
  
  
  
  A genome-wide associating mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify loci associated with the extract based eChl_A, eChl_B, eChl_R and eChl_T measurements and the two canopy spectral reflectance-based methods (tChl_T and iChl_T). A total of 23 (14 loci), 15 (7 loci) and 14 SNPs (10 loci) showed significant association with eChl_A, eChl_B and eChl_R respectively. A total of 52 unique SNPs were significantly associated with total chlorophyll content based on at least one of the three approaches (eChl_T, tChl_T and iChl_T) and likely tagged 27 putative loci for total chlorophyll content, four of which were indicated by all three approaches.
  
  
  
  Results presented here show that markers for chlorophyll traits can be identified in soybean using both extract-based and canopy spectral reflectance-based phenotypes, and confirm that high-throughput phenotyping-amenable canopy spectral reflectance measurements can be used for association mapping.
authors.affiliation: Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Arun Prabhu
authors.initials: AP
authors.lastname: Dhanapal
authors.affiliation: Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA.
authors.forename: Jeffery D
authors.initials: JD
authors.lastname: Ray
authors.affiliation: Crop Systems and Global Change Lab, USDA-ARS, Beltsville, MD, 20705, USA.
authors.forename: Shardendu K
authors.initials: SK
authors.lastname: Singh
authors.affiliation: Forage Improvement Group, Lincoln Science Centre, Christchurch, 8140, New Zealand.
authors.forename: Valerio
authors.initials: V
authors.lastname: Hoyos-Villegas
authors.affiliation: Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, Stoneville, MS, 38776, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Smith
authors.affiliation: Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA.
authors.forename: Larry C
authors.initials: LC
authors.lastname: Purcell
authors.affiliation: Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. fritschif@missouri.edu.
authors.forename: Felix B
authors.initials: FB
authors.lastname: Fritschi
mesh_terms: D002734:Chlorophyll / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055106:Genome-Wide Association Study; D005838:Genotype; D010936:Plant Extracts / Q000737:chemistry* / Q000378:metabolism; D018515:Plant Leaves / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D013025:Glycine max / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D010936:Plant Extracts; D010940:Plant Proteins; D002734:Chlorophyll
keywords: Abiotic stress tolerance; Chlorophyll a; Chlorophyll a/b ratio; Chlorophyll b; Genome-wide association mapping; High-throughput phenotyping; Single nucleotide polymorphisms; Total chlorophyll