The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping

Abstract

Association mapping focused on 36 genes involved in branch development was used to identify candidate genes for variation in shoot branching in Arabidopsis thaliana. The associations between four branching traits and moderate-frequency haplogroups at the studied genes were tested in a panel of 96 accessions from a restricted geographic range in Central Europe. Using a mixed-model association-mapping method, we identified three loci--MORE AXILLARY GROWTH 2 (MAX2), MORE AXILLARY GROWTH 3 (MAX3), and SUPERSHOOT 1 (SPS1)--that were significantly associated with branching variation. On the basis of a more extensive examination of the MAX2 and MAX3 genomic regions, we find that linkage disequilibrium in these regions decays within approximately 10 kb and trait associations localize to the candidate genes in these regions. When the significant associations are compared to relevant quantitative trait loci (QTL) from previous Ler x Col and Cvi x Ler recombinant inbred line (RIL) mapping studies, no additive QTL overlapping these candidate genes are observed, although epistatic QTL for branching, including one that spans the SPS1, are found. These results suggest that epistasis is prevalent in determining branching variation in A. thaliana and may need to be considered in linkage disequilibrium mapping studies of genetically diverse accessions.

Figure 1.—

Maximum-parsimony gene genealogies of the 36 candidate genes, corresponding to (A) ABI3, (B) AMP1, (C) ANT, (D) AP1, (E) ARGOS, (F) AXR1, (G) AXR2, (H) AXR3, (I) AXR6, (J) BP, (K) BUD1, (L) CAL, (M) CKI1, (N) CRE1, (O) EMF1, (P) ER, (Q) ERA1, (R) LAS, (S) LFY, (T) MAX1, (U) MAX2, (V) MAX3, (W) MAX4, (X) MP, (Y) PID, (Z) PIN1, (AA) PNH, (AB) RAX1, (AC) RAX2, (AD) RAX3, (AE) REV, (AF) SEU, (AG) SPS1, (AH) STM, (AI) TFL1, and (AJ) TIR1. The shaded circles represent branches along which a SNP was genotyped. All genealogies are presented at the same scale.

Figure 2.—

Trait distributions for the 96 accessions used for association mapping. Aa-0 and Li-6, which have the highest and lowest number of lateral branches in long day, respectively, are shown as reference accessions across all environment–trait combinations. (A) Lateral branches in long day; (B) lateral branches in short day; (C) basal branches in long day; (D) basal branches in short day; (E) total branches in long day; (F) total branches in short day; (G) lateral branch nodes in long day; (H) lateral branch nodes in short day. LD, long day; SD, short day.

Figure 3.—

Linkage disequilibrium (LD) across the MAX2 and MAX3 regions. The MAX2 (A) and MAX3 (B) regions are shown according to scale. Fragments that were not polymorphic or were without common polymorphisms do not have lines connecting the LD plots to the physical maps. The At2g prefixes for all numbered genes are omitted in this and subsequent figures. Gene annotations are presented below the gene numbers. “Exp Prot,” expressed protein.

Figure 4.—

Decay of LD in MAX2 and MAX3 regions. Median r² is plotted by the midpoint of each pairwise marker distance bin.

Figure 5.—

Trait associations across the MAX2 (A) and MAX3 (B) regions. P-values are plotted as −log(P). Genes with no polymorphisms at ≥10% frequency are not included. The horizontal line with light shading denotes P = 0.05, while the horizontal line with dark shading represents P = 0.005. LB, lateral branches; TB, total branches; LBN, lateral branch nodes; LD, long day; SD, short day.

Figure 6.—

Genomic map of candidate gene associations and QTL in the Ler × Col (A) and Cvi × Ler (B) RILs. Environment–trait combinations are colored as red, green, blue, and purple for lateral branches in long day, lateral branch nodes in long day, lateral branches in short day, and lateral branch nodes in short day, respectively. Each epistatic QTL is referenced to the table of epistatic QTL by number. Additive QTL are included on the map as colored rectangles at the marker location reported in Ungerer et al. (2002, 2003), using the same color scheme as for the epistatic QTL.