Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population

Abstract

Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.

Keywords: Association mapping; Diversity arrays technology; Quantitative trait locus; Single nucleotide polymorphism; Triticum aestivum L.; Water deficit stress.

Graphical abstract

Fig. 1

Distribution of 146 spring wheat (Triticum aestivum L.) genotypes on 28 different countries all over the world (a), Daily Temperature (T) during drought treatment experiment (b), humidity in % (H) during the experiment (c), visual scoring of leaf wilting (1−9) and leaf rolling (1−5) (d).

Fig. 2

Density diagram for all genotype in each morphological trait; (a) RW (root width), RL (root length), NOR (number of roots), LR (leaf rolling), LA(leaf area), DTW (days to wilting), (b) RTA (root tip angle), SLW (sum of leaf wilting), SHL (shoot length), REA (root emergence angle).

Fig. 3

(a) Analysis result of population structure of 111 spring wheat genotypes, (b) Principal component analysis (PCA) based on the population structure result into two sub-populations, (c) Principal component analysis (PCA) for genotypes based on their continent.

Fig. 4

The percentage of significant markers on each genome (a), Number of QTLs of leaf traits on each chromosome (b), Number of QTLs of root traits on each chromosome (c).

Fig. 5

Physical position of the pleiotropic markers on each chromosome.

Fig. 6

Markers associated with root traits(RT) and leaf traits(LT) detected by GWAS(a), and shared genes and encoding protein (EG) between RT and LR) (b), gene expression of the common gene associated with RT and LT; TPM(transcript per million).

Fig. 7

The candidate genes expression of leaf traits in leaves/shoots tissue at the seedling stage under different conditions (control, drought and PEG) (a), The candidate genes expression of root traits in leaves/shoots tissue at the seedling stage under different conditions ( control, drought and PEG) (b). Golden star refers to the genes which association with more than one trait.