Genome-wide association analysis identifies the genetic basis of coleoptile length and its relationship with green revolution dwarfing genes in bread wheat

Abstract

Understanding the genetic basis of coleoptile length in bread wheat is essential due to its association with drought adaptability for developing more resilient and high-yielding wheat varieties. This study aimed to investigate the coleoptile length in a diversity panel of 150 bread wheat (Triticum aestivum L.) genotypes and identify the genetic factors influencing the trait, including the role of dwarfing genes. A blotter-paper germination protocol was conducted to evaluate coleoptile lengths, and SNP and Silico-DArT markers were used to perform a genome-wide association study (GWAS) for coleoptile length. Additionally, allele-specific markers were used to detect the presence of Rht-B1b and Rht-D1b dwarfing alleles in the population. The coleoptile length ranged from 4.79 to 10.94 cm (two-trial mean 6.89 cm), with high broad-sense heritability (H2 = 0.95) and low coefficients of variation (5.56-6.12%), confirming the reliability of the phenotypic data. GWAS conducted without dwarfing-gene covariates revealed a significant marker-trait association on chromosome 4B, represented by the Silico-DArT marker DArT4991238 at 40.30 Mb. The wild-type Rht-B1a and Rht-D1a alleles were generally associated with longer coleoptile lengths. DArT4991238 was strongly associated with Rht-B1b status. However, when FarmCPU analysis was conducted using the two-trial mean with Rht-B1b and Rht-D1b as fixed covariates, DArT4991238 was no longer statistically significant. The present data do not establish DArT4991238 as a coleoptile-length locus independent of the assayed dwarfing genes; therefore, candidate-gene inference from this 4BS marker interval was not retained in the present study. These findings highlight the importance of further investigation into the genetic determinants influencing coleoptile length, especially in breeding efforts aimed at developing wheat varieties with improved seedling establishment under dry conditions.