Genome‐wide association study dissects the genetic bases of salt tolerance in maize seedlings

Abstract

Excess salinity is a natural stress that causes crop yield losses worldwide. The genetic bases of maize salt tolerance remain largely unknown. Here we investigated the survival rates of 445 maize natural accessions after salt treatments. A skewed distribution of the salt‐tolerant phenotypes was observed in this population. Genome‐wide association studies (GWAS) revealed 57 loci significantly associated with salt tolerance. Forty‐nine candidate genes were detected from these loci. About 10% of these genes were co‐localized with loci from QTL mapping. Forty four percent of the candidate genes were involved in stress responses, ABA signaling, stomata division, DNA binding/transcription regulation and auxin signaling, suggesting that they are key genetic mechanisms of maize salt tolerance. Transgenic studies showed that two genes, the salt‐tolerance‐associated‐gene 4 (SAG4, GRMZM2G077295) and SAG6 (GRMZM2G106056), which encode a protein transport protein and the double‐strand break repair protein MRE11, respectively, had positive roles in plant salt tolerance, and their salt‐tolerant haplotypes were revealed. The genes we identified in this study provide a list of candidate targets for further study of maize salt tolerance, and of genetic markers and materials that may be used for breeding salt‐tolerance in maize.

Genome‐wide association studies and QTL mapping uncover the genetic architecture of ear tip‐barrenness in maize

“…A polymorphism site at a stringent threshold of P ‐value ≤0.05/n was considered to have a significant association with ETB. Haplotypes were calculated using the Haploview software (Luo et al ) and the haplotypes with shorter ETB were regarded as superior haplotypes. anova of the ETB length among haplotypes was performed using SPSS version 21.0 (IBM, USA, 2012).…”

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (Hordeum vulgare L.)

“…Nayyeripasand et al (2019) reported a positive correlation among stress tolerance indices, including STI, SSI, and TOL, but not in the subgroups. Yu et al (2018) reported that salttolerance levels in rice (O. sativa) were not strongly correlated with rice subgroups, which was confirmed in a maize population the following year (Luo et al, 2019). Tolerance indices do not accurately distinguish cultivars under severe stress (Mardeh et al, 2006;Mohammadi, 2019), but can be used as indicators for high-yielding, salt-tolerant lines in stress, and non-stress environments or for traits like germination (Nayyeripasand et al, 2019;Sedri et al, 2019).…”

Natural variation of an EF-hand Ca2+-binding-protein coding gene confers saline-alkaline tolerance in maize

“…mays) is a glycophytic specie that is sensitive to saline-alkaline stress 29 . Previous studies have shown that natural maize inbred lines show large variations of sensitivity to saline and saline-alkaline stress, and which is substantially attributed to the variations of shoot Na + contents 30,31 . Here, we show that a calcium-binding EF-hand protein ZmNSA1 underlies the natural variations of shoot-Na + contents under NaHCO 3 condition by a GWAS analysis.…”