Genome‐wide association analysis of chilling‐tolerant germination in a new maize association mapping panel

Abstract

Maize is a crop that is highly susceptible to the negative effects of low temperature. Low temperature can delay seed germination and cause a decrease in seed vigor, which seriously affects seedling emergence and yield. In this study, 190 maize accessions (inbred lines) with strong germination potential at normal temperature (25℃) were selected from more than 500 accessions to construct a new association mapping panel to further investigate germination under chilling stress (5℃). We re-sequenced the genomes of the 190 diverse accessions and obtained 4,886,919 high quality SNPs. We then used this data to analyze population structure, perform principal components analysis, and construct a phylogenetic tree of the new maize panel. The relative germination rate (RGR) and relative germination index (RGI) are two traits that are signi cantly related to chilling-tolerant germination. Genome-wide association analysis showed that RGR and RGI shared a major QTL, and they also shared the top SNP.There were a total of 26 signi cant SNPs in common. These SNPs hit directly or indirectly within 37 candidate genes. Among these 37 gene candidates are homologs of eight genes previously reported to be related to both germination and low temperature stress, and another 12 genes related to low temperature stress or other abiotic stresses such as drought, salinity, oxidative, and high light stress. In addition, RGR and RGI had another 15 and 26 signi cant SNPs, respectively, which were associated with 17 and 92 candidate genes, respectively. Further qRT-PCR analysis using 26 chilling-tolerant and 22 chilling-sensitive accessions implied that Zm00001eb272370, Zm00001eb272390, and Zm00001eb272400 associated with the top SNP, may play different roles during cold-germination. Thus, our study not only established a new association mapping panel suitable for investigation of germination at low temperature, but also provided valuable genetic resources for future studies to improve chilling-tolerant maize varieties.

Sweet corn association panel and genome-wide association analysis reveal loci for chilling-tolerant germination

“…1 ). This was much lower than the germination rate of ordinary corn at low temperatures 3 , 46 . 19hi135 (DY084) and M688 (DY002) exhibited high germination rate under normal and low temperature.…”

Diversity in the genome ofAegilops tauschii, a wild wheat relative, to generate Fe-biofortified and Fe-deficiency-tolerant wheat

“…Fe solubility differs with soil pH: it is high in acidic soils and low in alkaline soils. TauL3 is found only in Georgia, while TauL2 and TauL1 are found over larger areas (Mahjoob et al, 2021). TauL2 is found mainly along the Caspian Sea in Azerbaijan and Iran.…”

“…Although natural variations in Ae. tauschii are separated into three lineages (TauL1, 2, 3) by molecular phylogenetic analysis (Sohail et al, 2012;Matsuoka et al, 2013;Mahjoob et al, 2021), the phenotypic traits were not associated with any specific group. Fe solubility differs with soil pH: it is high in acidic soils and low in alkaline soils.…”

“…tauschii into three groups in two main lineages (TauL1 and TauL2) and one minor lineage (TauL3), suggesting diversity among Ae. tauschii accessions (Matsuoka et al, 2013;Mahjoob et al, 2021). Since wild Ae.…”

Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize

“…Chilling stress has also been a focus of GWAS, with the authors of [118] identifying 19 genes highly associated with early growth and chlorophyll fluorescence traits under chilling stress in field conditions. A recent study [119] highlighted three genes associated with chilling tolerance during maize germination. While GWAS have proven valuable in uncovering genetic factors related to stress tolerance, it is important to note that environmental factors play a significant role in gene expression.…”