Exploring natural diversity of Medicago truncatula reveals physiotypes and loci associated with the response of seedling performance to nitrate supply

Abstract

Seedling pre‐emergence is a critical phase of development for successful crop establishment because of its susceptibility to environmental conditions. In a context of reduced use of inorganic fertilizers, the genetic bases of the response of seedlings to nitrate supply received little attention. This issue is important even in legumes where nitrate absorption starts early after germination, before nodule development. Natural variation of traits characterizing seedling growth in the absence or presence of nitrate was investigated in a core collection of 192 accessions of Medicago truncatula. Plasticity indexes to the absence of nitrate were calculated. The genetic determinism of the traits was dissected by genome‐wide association study (GWAS). The absence of nitrate affected seed biomass mobilization and root/shoot length ratio. However, the large range of genetic variability revealed different seedling performances within natural diversity. A principal component analysis (PCA) carried out with plasticity indexes highlighted four physiotypes of accessions differing in relationships between seedling elongation and seed biomass partitioning traits in response to the absence of nitrate. Finally, GWAS revealed 45 associations with single or combined traits corresponding to coordinates of accessions on PCA, as well as two clusters of genes encoding sugar transporters and glutathione transferases surrounding loci associated with seedling elongation traits.

Experimental Evidence for Seed Metabolic Allometry in Barrel Medic (Medicago truncatula Gaertn.)

“…Despite having different extreme values in seed weight, the eight accessions examined here did not exhibit significant differences in seed weight overall, as found previously in [ 16 ]. Seed weight varied within a 1–9 mg window, which is quite wide.…”

“…Since all accessions fell on the same metabolic response curve to seed weight ( Figure 3 b), selecting seeds of a given weight class (e.g., median 4–5 mg) is probably desirable in physiological assays assessing seed quality. This is even more important for seedling properties, since total available N influences growth rate and emergence [ 15 , 16 ], and we show here that total N does not scale proportionally with seed weight but increases disproportionally ( Figure 1 b). It is also illustrated in Figure S4 , where we conducted multivariate analyses using only seeds with a weight comprised between 3.5 and 5.5 mg. As expected, the discrimination of samples by seed weight is much less efficient, and natural grouping by accessions appears in both unsupervised (PCA) and supervised (OPLS) analyses.…”

“…In Legumes, a positive correlation has been found between seed weight and seed vigour, germination performance and seedling heterotrophic growth [ 11 , 12 , 13 , 14 , 15 ]. In addition, genome-wide association studies (GWAS) carried out with barrel medic accessions (from the core collection) have suggested a link between seed size, N content and seedling establishment [ 15 , 16 ].…”

“…In Legumes, a positive correlation has been found between seed weight and seed vigour, germination performance and seedling heterotrophic growth [ 11 , 12 , 13 , 14 , 15 ]. In addition, genome-wide association studies (GWAS) carried out with barrel medic accessions (from the core collection) have suggested a link between seed size, N content and seedling establishment [ 15 , 16 ]. Additionally, a recent GWAS analysis with barrel medic accessions has suggested the involvement of a U12-type spliceosome component in determining seed size, showing a link with mRNA synthesis and maturation [ 17 ].…”