Phenotypic variation of parents and CSSLs population
The values of RL, BL and SP of parents and CSSLs population under different salinity conditions are shown in Table 1. There is a significant difference in RL between 9311 and Nipponbare under 0 and 100 mM NaCl conditions, and the length of 9311 is significantly higher than that of Nipponbare (Fig.1); There is a significant difference in BL between 9311 and Nipponbare under 0, 100 and 400 mM NaCl conditions, and the length of 9311 is significantly lower than that of Nipponbare (Fig.1). There was no significant difference in SP under different salt conditions. RL, BL and SP of CSSLs population showed continuous frequency distribution and transgressive segregation, which were consistent with the genetic characteristics of quantitative traits (Fig.2).
Phenotypic correlation
Pearson correlation coefficients of three salt-tolerant traits RL, BL and SP under different salinity conditions are shown in Table 2. RL, BL and SP were significantly correlated at 200 and 400 mM NaCl (p<0.01), although there was no correlation between RL and SP at 200 mM NaCl. There is no significant correlation between RL, BL and SP under control and 100 mM NaCl, although there is a correlation between RL and BL under 100 mM NaCl (p<0.05).
QTL analysis
Under different salinity conditions, QTLs for three salt-tolerant traits are shown in Table 3, and the positions of these QTLs on chromosomes are shown in Fig.3.
QTLs for root length
Seven QTLs were detected for RL (Fig.3, Table 3). Under controlled condition, qRL1 and qRL10-1 were located on chromosome 1 and 10, with LOD values of 3.46 and 3.88, which explained 10.41% and 11.96% of phenotypic variation, respectively. Under the 100 mM NaCl condition, qRL10 was located on chromosome 10, with LOD value of 3.11, which explained 11.43% of phenotypic variation. Under the 200 mM NaCl condition, QTLs qRL5, qRL11, qRL11-2 were located on chromosome 5 and 10, with LOD values of 3.15, 8.52 and 4.36, which explained the phenotypic variation of 4.76%-14.34%. Under the 400 mM NaCl condition, qRL3 was located on chromosome 3, with LOD value of 5.70, which explained 19.93% of phenotypic variation.
QTLs for bud length
Five QTLs were detected for BL (Fig.3, Table 3). Under controlled condition, qBL8 and qBL11 were located on chromosome 8 and 11, with LOD values of 5.13 and 2.92, which explained 15.84% and 8.63% of phenotypic variation, respectively. Under the 100 mM NaCl condition, there was no QTL detected. Under the 200 mM NaCl condition, QTLs qBL8 and qBL11-1 were located on chromosome 8 and 11, with LOD values of 2.56 and 3.58, which explained the phenotypic variation of 7.99% and 11.41%, respectively. Under the 400 mM NaCl condition, qBL3 was located on chromosome 3, with LOD value of 3.43, which explained 12.51% of phenotypic variation.
QTLs for survival percent
Eight QTLs were detected for BL (Fig.3, Table 3). Under controlled condition, qSP2, qSP3 and qSP7-1 were located on chromosome 2, 3 and 7, with LOD values of 3.69, 4.31 and 15.31, which explained 7.07%, 8.46% and 37.59% of phenotypic variation, respectively. Under the 100 mM NaCl condition, qSP12 was located on chromosome 12, with LOD value of 6.26, which explained 19.61% of phenotypic variation. Under the 200 mM NaCl condition, QTLs qSP7 and qSP9 were located on chromosome 7 and 9, with LOD values of 6.64 and 2.54, which explained the phenotypic variation of 22.55% and 7.95%, respectively. Under the 400 mM NaCl condition, qSP3 and qSP4 was located on chromosome 3 and 4, with LOD value of 5.96 and 3.50, which explained 18.38% and 10.28% of phenotypic variation.
Candidate gene analysis
Candidate genes were analyzed for QTLs with phenotypic variation over 10%. There are 310 putative genes in qRL1, qSP3, qSP4, qSP7-1, qRL10, qRL11, qBL11-1 and qSP12. Among these candidate genes, homologous analysis showed that 16 genes were closely related to the previously cloned salt-tolerant genes (Lekklar et al. 2019) (Fig.4, Table 4), but these candidate genes need further verification.