Altered Expression of an FT Cluster Underlies a Major Locus Controlling Domestication-Related Changes to Chickpea Phenology and Growth Habit

Abstract

Flowering time is a key trait in breeding and crop evolution, due to its importance for adaptation to different environments and for yield. In the particular case of chickpea, selection for early phenology was essential for the successful transition of this species from a winter to a summer crop. Here, we used genetic and expression analyses in two different inbred populations to examine the genetic control of domestication-related differences in flowering time and growth habit between domesticated chickpea and its wild progenitor Cicer reticulatum. A single major quantitative trait locus for flowering time under short-day conditions [Days To Flower (DTF)3A] was mapped to a 59-gene interval on chromosome three containing a cluster of three FT genes, which collectively showed upregulated expression in domesticated relative to wild parent lines. An equally strong association with growth habit suggests a pleiotropic effect of the region on both traits. These results indicate the likely molecular explanation for the characteristic early flowering of domesticated chickpea, and the previously described growth habit locus Hg. More generally, they point to de-repression of this specific gene cluster as a conserved mechanism for achieving adaptive early phenology in temperate legumes.

Keywords: QTL; chickpea; domestication; florigen; flowering; growth habit; legume; photoperiod.

FIGURE 1

Comparative mapping of flowering time QTLs on chromosome 3. Four regions of chromosome 3 (3A to 3D, colored bars) were found to influence flowering time across three different populations. The length of the bars representing each QTL indicates the two-LOD support interval, which corresponds to a ∼95% confidence interval (Van Ooijen, 2006). Only region 3A, in the central portion of the chromosome and containing a cluster of FT genes, is consistently detected in both narrow and wide crosses. Numbers at the left of the bars represent genetic distance (in cM). Common markers were used to compare the relative position of the QTLs across populations. Markers common to all populations are shown in red, to three populations in blue and to two populations in orange. Those common to both interspecific populations are shown in green, and to both intraspecific populations, in pink.

FIGURE 2

Refinement of the DTF3A location. Marker genotypes in recombinant inbred lines from the CRIL2 population showing recombination breakpoints across a 7.14 Mb region of chromosome 3 spanning the DTF3A locus. Numbers over the markers correspond to their physical position (in Mb) in the CDC Frontier genome assembly in NCBI (ASM33114v1; Varshney et al., 2013). Alleles from the domesticated parent ICC4958 are shown in white and those from the wild parent PI489777 in gray. Flowering phenotype is shown in the column headed SD and indicates whether the indicated lines flowered (Y) or remained vegetative (N) under an 8h photoperiod. This phenotype showed no recombination between markers FTa1 and GATA9.

FIGURE 3

FT genes in the LG3 cluster are upregulated in the early parents of the crosses. Relative expression profiles of FT genes and the floral indicator PIM in the parental lines of the four chickpea populations analyzed. Expression was measured in dissected apical bud or leaves of plants grown from sowing under short (SD, gray background) and long days (LD, white background) for 2–4 weeks. Late flowering lines are shown in black and early parents in white. The average ± SE of two biological replicates (two technical replicates each) is shown, and transcripts were normalized against ACTIN. Asterisk indicates significant difference (p < 0.05) in the level of expression (t-test).

FIGURE 4

The DTF3A region is also associated with growth habit and shoot branching. Portion of the Linkage Group three from the CRIL2 genetic map showing the perfect co-location of QTLs obtained for flowering time (DTF), growth habit (GH), and branching index (BI) under short (SD) and long days (LD). Numbers at the left of the bar indicate genetic distance (in cM). Markers included in the 3A interval (95% interval confidence) are highlighted in green and the most strongly associated marker (FTa1) is shown in red.