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

Abstract

This study reported the identification and validation of novel QTL conferring coleoptile length in barley and predicted candidate genes underlying the largest effect QTL based on orthologous analysis and comparison of the whole genome assemblies for both parental genotypes of the mapping population. Coleoptile length (CL) is one of the most important agronomic traits in cereal crops due to its direct influence on the optimal depth for seed sowing which facilitates better seedling establishment. Varieties with longer coleoptiles are preferred in drought-prone areas where less moisture maintains at the top layer of the soil. Compared to wheat, genetic study on coleoptile length is limited in barley. Here, we reported a study on detecting the genomic regions associated with CL in barley by assessing a population consisting of 201 recombinant inbred lines. Four putative QTL conferring CL were consistently identified on chromosomes 1H, 5H, 6H, and 7H in each of the trials conducted. Of these QTL, the two located on chromosomes 5H and 6H (designated as Qcl.caf-5H and Qcl.caf-6H) are likely novel and Qcl.caf-5H showed the most significant effect explaining up to 30.9% of phenotypic variance with a LOD value of 15.1. To further validate the effect of this putative QTL, five pairs of near isogenic lines (NILs) were then developed and assessed. Analysis of the NILs showed an average difference of 21.0% in CL between the two isolines. Notably, none of the other assessed morphological characteristics showed consistent differences between the two isolines for each pair of the NILs. Candidate genes underlying the Qcl.caf-5H locus were also predicted by employing orthologous analysis and comparing the genome assemblies for both parental genotypes of the mapping population in the present study. Taken together, these findings expand our understanding on genetic basis of CL and will be indicative for further gene cloning and functional analysis underly this locus in barley.

Fig. 1

Frequency distributions for coleoptile length obtained from the population of Morex/AWCS276 in different trials. Vertical lines indicate average coleoptile length of parents: Morex (red) and AWCS276 (blue) (Colour figure online)

Fig. 2

QTL conferring coleoptile length detected on chromosome 5H with interval mapping from the population of Morex/AWCS276. The LOD values from each centimorgan of the chromosome were plotted against the chromosome, and the vertical dotted line indicates the average significant threshold (LOD = 2.9) derived from permutation test. CL-5H indicates the marker developed close to the peak of this QTL. The short arm of the chromosome is on the left side while the long arm is on the right side

Fig. 3

Morphologies of a pair of the near isogenic lines (NIL1) showing a the difference in coleoptile length; b similar plant height and flowering time. Scale bar is 40 cm; c similar spike morphology, and d similar seed morphology. Scale bar is 1 cm. M represents lines with the Morex allele and A represents lines with the AWCS276 allele