Genome-wide association study of coleoptile length with Shanxi wheat

Abstract

In arid and semi-arid regions, coleoptile length is a vital agronomic trait for wheat breeding. The coleoptile length determines the maximum depth that seeds can be sown, and it is critical for establishment of the crop. Therefore, identifying loci associated with coleoptile length in wheat is essential. In the present study, 282 accessions from Shanxi Province representing wheat breeding for the Loess Plateau were grown under three experimental conditions to study coleoptile length. The results of phenotypic variation indicated that drought stress and light stress could lead to shortening of coleoptile length. Under drought stress the growth rate of environmentally sensitive cultivars decreased more than insensitive cultivars. The broad-sense heritability (H2) of BLUP (best linear unbiased prediction) under various conditions showed G × E interaction for coleoptile length but was mainly influenced by heredity. Correlation analysis showed that correlation between plant height-related traits and coleoptile length was significant in modern cultivars whereas it was not significant in landraces. A total of 45 significant marker-trait associations (MTAs) for coleoptile length in the three conditions were identified using the 3VmrMLM (3 Variance-component multi-locus random-SNP-effect Mixed Linear Model) and MLM (mixed linear model). In total, nine stable genetic loci were identified via 3VmrMLM under the three conditions, explaining 2.94–7.79% of phenotypic variation. Five loci on chromosome 2B, 3A, 3B, and 5B have not been reported previously. Six loci had additive effects toward increasing coleoptile length, three of which are novel. Molecular markers for the loci with additive effects on coleoptile length can be used to breed cultivars with long coleoptiles.

Identification of a novel and plant height-independent QTL for coleoptile length in barley and validation of its effect using near isogenic lines

“…Short coleoptiles pose challenges in many cereals often leading to issues such as poor establishment, late emergence, and slow early leaf area development particularly in water-limited growing regions. Previous studies also indicated that strong correlations between CL and drought resistance index (Wang and Zou 1997 ; Hu et al 2007 ) and suggested that CL can be used as a surrogate trait to screen for drought tolerant genotypes at seedling stage (Khadka et al 2020 ; Wei et al 2022 ). Thus, identification of genomic regions contributing to CL is highly valuable to breeding programs.…”

Genome-Wide Association Study Uncovers Genomic Regions Associated with Coleoptile Length in a Worldwide Collection of Oat

“…For example, wheat landraces in the Northern Spring Wheat Zone (NS) and the Northwestern Spring Wheat Zone (NWS) in China displayed longer coleoptile lengths compared to landraces from other agro-ecological zones [11]. Another study in wheat also showed that irrigated wheat cultivars have shorter coleoptile lengths compared to dryland cultivars [16]. Additionally, previous studies in wheat [15] revealed that the modern cultivars exhibited significantly shorter coleoptile lengths compared to the landraces.…”

“…Considerable studies have been carried out to evaluate the coleoptile length in major cereal crops, such as rice [14], wheat [11,15,16], and barley [17,18], revealing a wide range of variation in these crops. In contrast, there is limited information available on the coleoptile length of oat cultivars.…”

Unravelling the Genetic Basis of Moisture Deficit Stress Tolerance in Wheat for Seedling Vigour-Related Traits and Root Traits Using Genome-Wide Association Study

“…This gene is involved in seed germination, plant growth and development, organ senescence, immunity, and stress response [59]. Among the seedling vigour traits, CL was found to be associated with drought tolerance in wheat due to determining the maximum depth that seeds can be sown, and it is critical for the establishment of the crop [60]. The SNP markers AX-94583923, AX-95017965, and AX-94773224 were associated with CL across the year.…”