Genetic architecture of NaCl tolerance in Arabidopsis

Abstract

The little success of breeding approaches toward the improvement of salt tolerance in crop species is thought to be attributable to the quantitative nature of most, if not all the processes implicated. Hence, the identification of some of the quantitative trait loci (QTL) that contribute to natural variation in salt tolerance should be instrumental in eventually manipulating the perception of salinity and the corresponding responses. A good choice to reach this goal is the plant model system Arabidopsis, whose complete genome sequence is now available. Aiming to analyze natural variability in salt tolerance, we have compared the ability of 102 wild-type races (named ecotypes or accessions) of Arabidopsis to germinate on 250 mM NaCl, finding a wide range of variation among them. Accessions displaying extremely different responses to NaCl were intercrossed, and the phenotypes found in their F(2) progenies suggested that natural variation in NaCl tolerance during germination was under polygenic controls. Genetic distances calculated on the basis of variations in repeat number at 22 microsatellites, were analyzed in a group of either extremely salt-tolerant or extremely salt-sensitive accessions. We found that most but not all accessions with similar responses to NaCl are phylogenetically related. NaCl tolerance was also studied in 100 recombinant inbred lines derived from a cross between the Columbia-4 and Landsberg erecta accessions. We detected 11 QTL harboring naturally occurring alleles that contribute to natural variation in NaCl tolerance in Arabidopsis, six at the germination and five at the vegetative growth stages, respectively. At least five of these QTL are likely to represent loci not yet described by their relationship with salt stress.

Figure 1

Germination rates of different Arabidopsis accessions sown on growth media supplemented with 250 mm NaCl, determined 14 d after sowing.

Figure 2

Phylogenetic tree of accessions displaying extremely different responses to NaCl. Extremely salt-sensitive and -tolerant accessions are indicated as SS and ST, respectively. The phylogram was constructed using the NEIGHBOR program included in the PHYLIP 3.5c package, from a distance matrix calculated by the Microsat 1.5d program on the basis of the number of repeats found in 22 polymorphic microsatellites, using the neighbor-joining algorithm and the absolute distance (D_AD) parameter.

Figure 3

Frequency distribution of the germination rates of the RILs 15 d after sowing (A), their angular (arcsin) transformation (B), and their variation with time estimated from the T₅₀ values (C), on media supplemented with 250 mm NaCl. Frequency distributions are also shown for the variation with time of the fresh (D) and dry weight (E), of plants grown on 50 mm NaCl. Arrows indicate the values corresponding to the parental accessions and the horizontal bars their standard variation.

Figure 4

QTL contributing to NaCl tolerance at the germination stage of Arabidopsis, as determined with the MapQTL 4.0 program. One hundred RILs were analyzed by determining on growth media supplemented with 250 mm NaCl the angular (arcsin) transformation of the germination rate, 15 d after sowing (A) and the variation with time of the germination rate (B; T₅₀). LOD threshold levels for major (2.4) and minor (1.5) QTL are indicated by dotted lines.

Figure 5

QTL contributing to NaCl tolerance during vegetative growth in Arabidopsis. One hundred RILs derived from a cross between the Col-4 and Ler-0 accessions were analyzed by determining for each of them the ratio between the fresh weight of the aerial part of the plants grown on media supplemented with 50 mm NaCl and the fresh weight obtained on non-supplemented media, 21 d after sowing. The analysis of the data was performed as described in Figure 4.