title: Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean.
abstract: BACKGROUND
  Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.
  
  
  RESULTS
  Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type cyclin and auxin efflux carrier protein) with insertion/deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second G. soja accession, three genes (slow anion channel associated 1 like, Auxin responsive NEDD8-activating complex and peroxidase), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition, Apoptosis inhibitor 5-like on chromosome 7 and slow anion channel associated 1-like on chromosome 15 had epistatic interactions for taproot length QTLs in soybean.
  
  
  CONCLUSIONS
  Rare alleles from a G. soja accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. princesj@missouri.edu.
authors.forename: Silvas J
authors.initials: SJ
authors.lastname: Prince
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. songli@missouri.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Song
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. qiud@missouri.edu.
authors.forename: Dan
authors.initials: D
authors.lastname: Qiu
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. maldonadodossantosj@missouri.edu.|Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. maldonadodossantosj@missouri.edu.
authors.forename: Joao V
authors.initials: JV
authors.lastname: Maldonado Dos Santos
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. chaic@missouri.edu.
authors.forename: Chenglin
authors.initials: C
authors.lastname: Chai
authors.affiliation: Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. joshitr@missouri.edu.|Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA. joshitr@missouri.edu.
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. patilg@missouri.edu.
authors.forename: Gunvant
authors.initials: G
authors.lastname: Patil
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. valliyodanb@missouri.edu.
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. vuongt@missouri.edu.
authors.forename: Tri D
authors.initials: TD
authors.lastname: Vuong
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. murphymc@missouri.edu.
authors.forename: Mackensie
authors.initials: M
authors.lastname: Murphy
authors.affiliation: Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA. agbiotec@gmail.com.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Krampis
authors.affiliation: Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA. dotucke2@vt.edu.
authors.forename: Dominic M
authors.initials: DM
authors.lastname: Tucker
authors.affiliation: Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA. rbiyashe@vt.edu.
authors.forename: Ruslan
authors.initials: R
authors.lastname: Biyashev
authors.affiliation: Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, 44691, USA. dorrance.1@osu.edu.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Dorrance
authors.affiliation: Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA. smaroof@vt.edu.
authors.forename: M A Saghai
authors.initials: MA
authors.lastname: Maroof
authors.affiliation: Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. xudong@missouri.edu.|Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA. xudong@missouri.edu.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. ShannonG@missouri.edu.
authors.forename: J Grover
authors.initials: JG
authors.lastname: Shannon
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA. nguyenhenry@missouri.edu.|Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. nguyenhenry@missouri.edu.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D018745:Genome, Plant; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development