Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley

Abstract

The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley.

Keywords: QTL; association mapping; barley diversity; drought tolerance; fibrous rooting; root and shoot.

FIGURE 1

Quantification of allele based trait effect of QRdw.5H. (A) Pin plot analysis based on allelic effects for Rdw across the whole population. Genotypes are ordered based on their average Rdw in 2014 and 2015. (B) Allele frequency at QTL QRdw.5H. (C) Whisker plot for 10 randomly selected genotypes per allele to quantify the trait effect of the particular allele, except heterozygous allele. Yellow: Major allele; Red: Heterozygous allele; Blue: Minor allele.

FIGURE 2

Quantification of allele based trait effect of QSdw.2H.b. (A) Pin plot analysis based on allelic effects for Sdw across the whole population. Genotypes are ordered based on their Sdw in 2014 and 2015. (B) Allele frequency at QSdw.2H.b. (C) Whisker plot for ten randomly selected genotypes per allele to quantify the trait effect of the particular allele, except heterozygous allele. Yellow: Major allele; Red: Heterozygous allele; Blue: Minor allele.

FIGURE 3

Quantification of allele based trait effect of QTil.1H. (A) Pin plot analysis based on allelic effects for Til across the whole population. Genotypes are ordered based on their average tiller number (Til) per plant in 2014 and 2015. (B) Allele frequency at QTil.1H. (C) Whisker plot for ten randomly selected genotypes per allele to quantify the trait effect of the particular allele, except the heterozygous allele. Yellow: Major allele; Red: Heterozygous allele; Blue: Minor allele.

FIGURE 4

Quantification of allele based trait effect of QRS.5H. (A) Pin plot analysis based on allelic effects for RS across the whole population. Genotypes are ordered based on their average RS ratio in 2014 and 2015. (B) Allele frequency of QRS.5H. (C) Whisker plot for ten randomly selected genotypes per allele to quantify the trait effect of the particular allele, except the heterozygous allele. Yellow: Major allele; Red: Heterozygous allele; Blue: Minor allele.

FIGURE 5

Protein alignment of WRKY29 transcription factor in cultivated barley Sloop (DQ863113, reference sequence) as well as Morex (BCC 906) and wild barley ICB180006 was made using MAFFT alignment software. The DNA-binding WRKY domain is indicated by a light gray tag. Amino acid exchanges are indicated by a dark gray tag. “+” indicates the WRKY signature motif. The solid over line indicates an anti-parallel beta-sheet. “^∗” indicates the identical amino acids in all sequences. “:” indicates conserved substitutions. “ ” indicates non-conserved substitutions.

FIGURE 6

Protein alignment of transcription factors CBF10B and CBF10A in different barley accessions using MAFFT alignment. The DNA (CRT/DRE) binding AP2/ERF domain is indicated by a light gray tag. The dark gray tag indicates amino acid exchanges. “+” indicates the CBF signature motif DSAW signature motif (Jaglo et al., 2001). The solid over line indicates an anti-parallel beta-sheet (Allen et al., 1998). The dashed over line indicates an amphipathic alpha-helix. “^∗” indicates the identical amino acids in all sequences. “:” indicates conserved substitutions. “.” indicates semi-conserved substitutions. “ :” indicates non-conserved substitutions. (A) Alignment of CBF10B in cultivated barley Optic (AAX28956, reference sequence) and Cape (HOR 4206) as well as wild barley ICB180006. (B) Alignment of CBF10A cultivated barley Nure (DQ445241, reference sequence) and Cape (HOR4206) as well as wild barley ICB180006.