The genetic architecture of flowering time changes in pea from wild to crop

Abstract

Change in phenology has been an important component in crop evolution, and selection for earlier flowering through a reduction in environmental sensitivity has helped broaden adaptation in many species. Natural variation for flowering in domesticated pea (Pisum sativum L.) has been noted and studied for decades, but there has been no clear account of change relative to its wild progenitor. Here we examined the genetic control of differences in flowering time between wild P. sativum ssp. humile and a typical late-flowering photoperiodic P. s. sativum accession in a recombinant inbred population under long and short photoperiods. Our results confirm the importance of the major photoperiod sensitivity locus Hr/PsELF3a and identify two other loci on chromosomes 1 (DTF1) and 3 (DTF3) that contribute to earlier flowering in the domesticated line under both photoperiods. The domesticated allele at a fourth locus on chromosome 6 (DTF6) delays flowering under long days only. Map positions, inheritance patterns, and expression analyses in near-isogenic comparisons imply that DTF1, DTF3, and DTF6 represent gain-of-function alleles of the florigen/antiflorigen genes FTa3, FTa1, and TFL1c/LF, respectively. This echoes similar variation in chickpea and lentil, and suggests a conserved route to reduced photoperiod sensitivity and early phenology in temperate pulses.

Keywords: FT genes; Pisum; Adaptation; QTL analysis; florigen; flowering time; genetics; legume; pea; phenology; photoperiod.

Fig. 1.

Linkage map showing QTLs detected in the JI1794×NGB5839 RIL population. QTL nomenclature follows Table 1. Scale is cM.

Fig. 2.

QTLs for flowering time detected under short or long days. Each plot shows LOD score against linkage group location for flowering time (days to flower, DTF) or the node of flower initiation (NFI) under short- (A, C, E, G) or long- (B, D, F, H) day conditions. Dashed horizontal lines represent a significance threshold of LOD score of 3.

Fig. 3.

Effects and selected interactions of flowering time QTLs in the RIL population. The RIL population was classified according to genotypes at the four flowering time QTLs detected. The data shown represent classes homozygous for wild or domesticated (Dom) alleles at all four loci together with selected classes comprised of homozygous for domesticated alleles at one or more loci as indicated. (A, B) Node of flower initiation (NFI); (C, D) days to flower (DTF); (E, F) number of reproductive nodes at apical arrest (RN) shown for plants in long-day (LD) or short-day (SD) conditions. The number of lines in each class (n) is indicated below (E) and (F). The experiment was terminated at 140 d after sowing, at which time plants in the wild and DTF6 Dom classes had not developed open flowers under SD conditions, and nominal minimum values of 140 d/60 nodes are shown in (A) and (C).

Fig. 4.

Validation of flowering time QTLs in advanced-generation segregating populations. Data represent the node of flower initiation (NFI) under long-day conditions in F₄/F₅ progenies of the JI1794×NGB5839 cross selected to segregate for the target loci (A) DTF1, (B) DTF3, and (C) DTF6. The three genotypic classes are indicated; homozygous wild (W), heterozygous (H), homozygous domesticated (D). In each panel, values not significantly different in a one-way ANOVA with Tukey’s multiple comparison test are indicated by the same letters.

Fig. 5.

Identification of candidate genes under flowering time QTLs. Markers spanning the QTL peaks for DTF1 (A), DTF3 (B), and DTF6 (C) were located in the pea genome and candidate flowering time genes in the intervals were identified. The presence of orthologous genes in the syntenic regions of Medicago and chickpea were also confirmed. In all three panels, LOD scores for DTF (SD), NFI (SD), DTF (LD), and NFI (LD) are represented by green, blue, black, and red lines, respectively. QTL peak markers are shown in green text, and candidate genes in red.

Fig. 6.

Effect of individual QTLs on expression of the corresponding candidate genes. (A, B) FTa3 expression in leaves of 4-week-old plants of F₆ near-isogenic lines (NILs) for DTF1 grown under LDs (A) and 10-week-old plants grown in SDs (B). (C, D) Expression of FTa1 in leaves of 3-week-old plants of F₅ NILs for DTF3 grown under LDs (C) and FTc in shoot apices of 4-week-old plants (D). (E) LF (TFL1c) expression in shoot apices of 4-week-old plants of F₅ NILs for DTF6 grown under LDs. W, wild allele; D, domesticated allele. In all panels, n=3–4 and t-tests indicated genotype values significantly different (P<0.01) except for (D) (P>0.1).