Increase in coleoptile length and establishment by Lcol-A1, a genetic locus with major effect in wheat

Abstract

Background: Good establishment is important for rapid leaf area development in wheat crops. Poor establishment results in fewer, later-emerging plants, reduced leaf area and tiller number. In addition, poorly established crops suffer from increased soil moisture loss through evaporation and greater competition from weeds while fewer spikes are produced which can reduce grain yield. By protecting the emerging first leaf, the coleoptile is critical for achieving good establishment, and its length and interaction with soil physical properties determine the ability of a cultivar to emerge from depth.

Results: Here we characterise a locus on chromosome 1AS, that increases coleoptile length in wheat, which we designate as Lcol-A1. We identified Lcol-A1 by bulked-segregant analysis and used a Halberd-derived population to fine map the gene to a 2 cM region, equivalent to 7 Mb on the IWGSC genome reference sequence of Chinese Spring (RefSeqv1.0). By sowing recently released cultivars and near-isogenic lines in the field at both conventional and deep sowing depths, we confirmed that Locl-A1 was associated with increased emergence from depth in the presence and absence of conventional dwarfing genes. Flanking markers IWB58229 and IWA710 were developed to assist breeders to select for long coleoptile wheats.

Conclusions: Increased coleoptile length is sought in many global wheat production areas to improve crop emergence. The identification of the gene Lcol-A1, together with tools to allow wheat breeders to track the gene, will enable improvements to be made for this important trait.

Keywords: Coleoptile; Emergence; Molecular marker; SNP; Triticum aestivum; Wheat.

Fig. 1

Phenotypic distribution of coleoptile length in 188 BC₁F₂ lines from each of the Halberd*2/CM18 population (a) and the Uruguay386*2/CM18 populations (b). Parental means are indicated by filled (CM18) and unfilled (Halberd and Uruguay) arrows

Fig. 2

Association between genotype at marker IWA164 and coleoptile length of BC₁F₃ seedlings from the Young*2/H125M. AA, homozygous negative; AB, heterozygous; BB homozygous positive. The lower and upper edges of the box represent 25th and 75th percentiles, interior solid lines denote the median and dashed lines denote the mean. Potential outliers are plotted as black dots, and identified according to the 1.5× interquartile range criterion

Fig. 3

Genetic and physical maps of 1AS region carrying Lcol-A1. a: Low resolution genetic map based on 54 BC₁F₂:F₃ lines of Young*2/H125M population, b: High resolution genetic map based on 900 BC₂F₂ equivalents of Young*3/H125M population, and c: corresponding physical map from Chinese Spring (CS; IWGSC RefSeqv1.0 genome sequence assembly)

Fig. 4

Association between genotype at marker IWA164 and coleoptile length of BC₃F₃ seedlings from the Espada*4/H125M population. AA, homozygous negative; AB, heterozygous; BB homozygous positive. The lower and upper edges of the box represent 25th and 75th percentiles, interior solid lines denote the median and dashed lines denote the mean. Potential outliers are plotted as black dots, and identified according to the 1.5× interquartile range criterion

Fig. 5

Coleoptile length of isolines (iso) and cultivars with long (BB) and short (AA) Lcol-A1 alleles under controlled conditions. Data are means (n = 5 for each isoline class; 6 for the short [AA] cultivar class; and 5 for the long [BB] cultivar class, obtained by averaging values from varieties within the relevant [isoline vs cultivar] genotype class) ± standard error; differences within genotype class are significant (p = 0.011 for cultivars, p < 0.01 for tall isolines)

Fig. 6

Emergence (plants per linear meter) of isolines and cultivars with long (BB) and short (AA) Lcol-A1 alleles under normal (25 mm) and deep (70 mm) sowing in the field at Yanco in 2016 and 2017. Data are haplotype by depth by genotype class (Isolines vs Cultivars) means (obtained by averaging lines within a genotype class) ± standard error

Fig. 7

Frequency of the long Lcol-A1 allele in an Australian diversity panel. The number of cultivars genotyped from each time period is indicated above the bars