Artificial selection for determinate growth habit in soybean

Abstract

Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit, whereas Glycine soja, the wild progenitor of soybean, is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes, when mated, produce progeny that segregate in a monogenic pattern. Here, we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1), a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene, each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype, but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However, the GmTfl1 homeolog, despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1, appears to be sub- or neo-functionalized, as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.

Fig. 1.

Anchoring genetic markers to the genomic sequence to define the candidate Dt1 gene. Vertical bar between Sat_099 and Satt006 on the genetic map and vertical bar on LG and chromosome sequence indicate the candidate Dt1 gene, Glyma19g37890.1. Gene model was predicted and is depicted by the cartoon underneath the “chromosome.”

Fig. 2.

Inferring the candidate gene by association analysis. (A) Distribution and association of four independent Gmtfl1 mutations with determinacy in four wild and cultivated soybean populations. The genetic structure of the populations was depicted by the vertical bars along the horizontal axis, in which the proportions of ancestry that can be attributed to each cluster were indicated by the length of each colored segment. The GmTfl1/GmTfl1 or Gmtfl1/Gmtfl1 genotypes of individual cultivars were marked by thin vertical bars above the plot of population structure, and their phenotypes, i.e., indeterminacy (I), semideterminacy (S), and determinacy (D), were indicated by up triangles, diamonds and down triangles, respectively. (B) Alignment of the amino acid sequences encoded by the GmTfl1 and Gmtfl1 alleles showing four single amino acid substitutions caused by four corresponding point mutations.

Fig. 3.

Functional analysis of GmTfl1 and Gmtfl1 alleles in the Arabidopsis tfl1 mutants. (A) Wild-type Arabidopsis (TFL1/TFL1), (B) tfl1-1 mutant, (C) tfl1-1 mutant with transgene GmTfl1. (D) tfl1-1 mutant with transgene Gmtfl1-ab. (E–H) Cartoons of growths of the wild-type (TFL1), tfl1 mutant, the GmTfl1 transgenic line, and Gmtfl1-ab transgenic line, as shown in A, B, C, and D, respectively. Curves and letters beneath the cartoons illustrate a single nucleotide difference (G and A) between Arabidopsis TFL1 and tfl1-1 alleles detected in the three lines by sequencing. (I and J) Confirmation of presence of soybean GmTfl1 and Gmtfl1-ab alleles, marked by a single nucleotide (A and T), respectively, in the transgenic Arabidopsis tfl1 lines by PCR and sequencing of PCR fragments.

Fig. 4.

Allelic mutations at the GmTfl1 locus in the context of genetic diversity and eco-geographic distribution of a core collection of soybean landraces. (A) Phylogenetic relationship of the landraces assessed by 59 SSR markers and the types of alleles (GmTfl1 or Gmtfl1) detected in individual landraces. (B) Geographical distribution of the landraces in the soybean growing eco-regions or subregions in China.