Theoretical and Applied Genetics

, Volume 127, Issue 11, pp 2293–2311 | Cite as

QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.)

  • Amy L. Burton
  • James M. Johnson
  • Jillian M. Foerster
  • Candice N. Hirsch
  • C. R. Buell
  • Meredith T. Hanlon
  • Shawn M. Kaeppler
  • Kathleen M. Brown
  • Jonathan P. Lynch
Original Paper

Abstract

Key message

QTL were identified for root architectural traits in maize.

Abstract

Root architectural traits, including the number, length, orientation, and branching of the principal root classes, influence plant function by determining the spatial and temporal domains of soil exploration. To characterize phenotypic patterns and their genetic control, three recombinant inbred populations of maize were grown for 28 days in solid media in a greenhouse and evaluated for 21 root architectural traits, including length, number, diameter, and branching of seminal, primary and nodal roots, dry weight of embryonic and nodal systems, and diameter of the nodal root system. Significant phenotypic variation was observed for all traits. Strong correlations were observed among traits in the same root class, particularly for the length of the main root axis and the length of lateral roots. In a principal component analysis, relationships among traits differed slightly for the three families, though vectors grouped together for traits within a given root class, indicating opportunities for more efficient phenotyping. Allometric analysis showed that trajectories of growth for specific traits differ in the three populations. In total, 15 quantitative trait loci (QTL) were identified. QTL are reported for length in multiple root classes, diameter and number of seminal roots, and dry weight of the embryonic and nodal root systems. Phenotypic variation explained by individual QTL ranged from 0.44 % (number of seminal roots, NyH population) to 13.5 % (shoot dry weight, OhW population). Identification of QTL for root architectural traits may be useful for developing genotypes that are better suited to specific soil environments.

Supplementary material

122_2014_2353_MOESM1_ESM.xlsx (13 kb)
Map summaries IBM OhW NyH: marker number, map length, average and maximum spacing statistics of the genetic maps created for the IBM, NyH and OhW populations separated by chromosome (XLSX 13 kb)
122_2014_2353_MOESM2_ESM.xlsx (380 kb)
IBM bin map physicial positions: this file contains the chromosome, genetic position and physical position for each recombination bin marker in the IBM population. This information can be utilized to identify the physical location of QTL identified in mapping and narrow in on gene models that fall within the LOD support interval (XLSX 381 kb)
122_2014_2353_MOESM3_ESM.xlsx (6.2 mb)
IBM bin map rqtl: this file contains the genotypes for 8,224 recombination bins in the IBM population created using SEG-map and formatted for R/qtl. The chromosome and genetic position for each recombination bin is contained in row 2 and 3. Column 2 contains a dummy trait variable that would be replaced with trait data prior to being used in R/qtl. Additional traits may be added by inserting additional columns. B73 alleles are coded as “A” and Mo17 alleles are coded as “B” (XLSX 6310 kb)
122_2014_2353_MOESM4_ESM.tiff (1.3 mb)
IBM genetic map: B73 × Mo17 (IBM) mapping population genetic map constructed using SEG-Map with GBS marker data (TIFF 1330 kb)
122_2014_2353_MOESM5_ESM.pdf (26 kb)
IBM Marker pull directions: detailed instructions on how to use Marker_pull.pl for creating a subset of the raw data for a specified region of interest (PDF 26 kb)
122_2014_2353_MOESM6_ESM.pl (1 kb)
IBM Marker pull: this Perl script can be utilized to easily create a subset of the raw marker information that was used in the bin map construction when one is only interested in a specified region (PL 2 kb)
122_2014_2353_MOESM7_ESM.txt (91.5 mb)
IBM raw marker data: this file contains all of the raw marker information for 68,246 SNPs identified via genotyping-by-sequencing as well as 1,721 publically available SSR markers. The first six columns contain the marker name, chromosome, start position, end position, B73 consensus base and Mo17 consensus base respectively. This is followed by the marker information for each of the RILs. If the marker is a SNP, the start and end position are synonymous. Genotypes are coded A,C,G,T for homozygous, 2 bases for heterozygous and NN for missing (TXT 93684 kb)
122_2014_2353_MOESM8_ESM.tiff (2.9 mb)
IBM individual similarity plot: histogram of the proportion of markers with identical genotypes for each pair of individuals in the B73 × Mo17 (IBM) mapping population (TIFF 2930 kb)
122_2014_2353_MOESM9_ESM.tiff (2.9 mb)
IBM indivudal genotype frequency plot: genotype frequencies across all individuals in the B73 × Mo17 (IBM) mapping population (TIFF 2930 kb)
122_2014_2353_MOESM10_ESM.tiff (4.1 mb)
IBM RF plot: estimated recombination fractions (upper-left triangle) and LOD scores (lower-right triangle) for all pairs of bin markers in the B73 × Mo17 (IBM) mapping population. Red indicates linked (large LOD score or small recombination fraction) and blue indicates not linked (small LOD score or large recombination fraction) (XLSX 4219 kb)
122_2014_2353_MOESM11_ESM.xlsx (208 kb)
NyH bin map physicial positions: this file contains the chromosome, genetic position and physical position for each recombination bin marker in the NyH population. This information can be utilized to identify the physical location of QTL identified in mapping and narrow in on gene models that fall within the LOD support interval (XLSX 209 kb)
122_2014_2353_MOESM12_ESM.xlsx (3.7 mb)
NyH bin map rqtl: this file contains the genotypes for 5,320 recombination bins in the NyH population created using SEG-map and formatted for R/qtl. The chromosome and genetic position for each recombination bin is contained in row 2 and 3. Column 2 contains a dummy trait variable that would be replaced with trait data prior to being used in R/qtl. Additional traits may be added by inserting additional columns. H99 alleles are coded as “A” and Ny821 alleles are coded as “B” (XLSX 3761 kb)
122_2014_2353_MOESM13_ESM.tiff (2.9 mb)
NyH genetic map: Ny821 × H99 (NyH) mapping population genetic map constructed using SEG-Map with GBS marker data (TIFF 2930 kb)
122_2014_2353_MOESM14_ESM.pdf (26 kb)
NyH Marker pull directions: detailed instructions on how to use Marker_pull.pl for creating a subset of the raw data for a specified region of interest (PDF 26 kb)
122_2014_2353_MOESM15_ESM.pl (1 kb)
NyH Marker pull: this Perl script can be utilized to easily create a subset of the raw marker information that was used in the bin map construction when one is only interested in a specified region (PL 2 kb)
122_2014_2353_MOESM16_ESM.txt (22.9 mb)
NyH raw marker data: This file contains all of the raw marker information for 19,970 SNPs identified via genotyping-by-sequencing. The first six columns contain the marker name, chromosome, start position, end position, H99 consensus base and Ny821 consensus base respectively. This is followed by the marker information for each of the RILs. If the marker is a SNP, the start and end position are synonymous. Genotypes are coded A,C,G,T for homozygous, 2 bases for heterozygous and NN for missing (TXT 23493 kb)
122_2014_2353_MOESM17_ESM.tiff (2.9 mb)
NyH individual similarity plot: histogram of the proportion of markers with identical genotypes for each pair of individuals in the Ny821 × H99 (NyH) mapping population (TIFF 2930 kb)
122_2014_2353_MOESM18_ESM.tiff (2.9 mb)
NyH indivudal genotype frequency_plot: Genotype frequencies across all individuals in the Ny821 × H99 (NyH) mapping population (TIFF 2930 kb)
122_2014_2353_MOESM19_ESM.tiff (4.1 mb)
NyH RF plot: estimated recombination fractions (upper-left triangle) and LOD scores (lower-right triangle) for all pairs of bin markers in the Ny821 x H99 (NyH) mapping population. Red indicates linked (large LOD score or small recombination fraction) and blue indicates not linked (small LOD score or large recombination fraction) (TIFF 4219 kb)
122_2014_2353_MOESM20_ESM.xlsx (195 kb)
OhW bin map physicial positions: this file contains the chromosome, genetic position and physical position for each recombination bin marker in the OHW population. This information can be utilized to identify the physical location of QTL identified in mapping and narrow in on gene models that fall within the LOD support interval (XLSX 195 kb)
122_2014_2353_MOESM21_ESM.xlsx (4.3 mb)
OhW bin map rqtl: this file contains the genotypes for 5,683 recombination bins in the OhW population created using SEG-map and formatted for R/qtl. The chromosome and genetic position for each recombination bin is contained in row 2 and 3. Column 2 contains a dummy trait variable that would be replaced with trait data prior to being used in R/qtl. Additional traits may be added by inserting additional columns. Oh43 alleles are coded as “A” and W64a alleles are coded as “B” (XLSX 4383 kb)
122_2014_2353_MOESM22_ESM.tiff (2.9 mb)
OhW_genetic map: Oh43 × W64a (OhW) mapping population genetic map constructed using SEG-Map with GBS marker data (TIFF 2930 kb)
122_2014_2353_MOESM23_ESM.pdf (26 kb)
OhW Marker pull directions: detailed instructions on how to use Marker_pull.pl for creating a subset of the raw data for a specified region of interest (PDF 26 kb)
122_2014_2353_MOESM24_ESM.pl (1 kb)
OhW Marker pull: this Perl script can be utilized to easily create a subset of the raw marker information that was used in the bin map construction when one is only interested in a specified region (PL 2 kb)
122_2014_2353_MOESM25_ESM.txt (51.1 mb)
OhW raw marker data: This file contains all of the raw marker information for 40,959 SNPs identified via genotyping-by-sequencing. The first six columns contain the marker name, chromosome, start position, end position, Oh43 consensus base and W64a consensus base respectively. This is followed by the marker information for each of the RILs. If the marker is a SNP, the start and end position are synonymous. Genotypes are coded A,C,G,T for homozygous, 2 bases for heterozygous and NN for missing (TXT 52287 kb)
122_2014_2353_MOESM26_ESM.tiff (2.9 mb)
OhW individual similarity plot: histogram of the proportion of markers with identical genotypes for each pair of individuals in the Oh43 × W64a (OhW) mapping population (TIFF 2930 kb)
122_2014_2353_MOESM27_ESM.tiff (2.9 mb)
OhW indivudal genotype frequency plot: genotype frequencies across all individuals in the Oh43 × W64a (OhW) mapping population (TIFF 2930 kb)
122_2014_2353_MOESM28_ESM.tiff (4.1 mb)
OhW RF plot: estimated recombination fractions (upper-left triangle) and LOD scores (lower-right triangle) for all pairs of bin markers in the Oh43 × W64a (OhW) mapping population. Red indicates linked (large LOD score or small recombination fraction) and blue indicates not linked (small LOD score or large recombination fraction) (TIFF 4219 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Amy L. Burton
    • 1
  • James M. Johnson
    • 2
  • Jillian M. Foerster
    • 2
  • Candice N. Hirsch
    • 3
    • 4
  • C. R. Buell
    • 3
    • 4
  • Meredith T. Hanlon
    • 1
  • Shawn M. Kaeppler
    • 2
  • Kathleen M. Brown
    • 1
  • Jonathan P. Lynch
    • 1
  1. 1.Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkUSA
  2. 2.Department of AgronomyUniversity of WisconsinMadisonUSA
  3. 3.Department of Plant BiologyMichigan State UniversityEast LansingUSA
  4. 4.DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingUSA

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