Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome

Adult plant leaf rust resistance QTL derived from wheat line CI13227 maps to chromosomes 2AL, 4BS, and 7AL

The winter wheat (Triticum aestivum L.) line CI13227 has been characterized as having adult plant resistance to leaf rust caused by Puccinia triticina Eriks (Pt). Line CI13227 was crossed with the susceptible spring wheat 'Thatcher' (Tc) and a Tc*2/CI13227 F₆ line with adult plant leaf rust resistance designated as 411A was derived. Line 411A was crossed with Tc to develop an F₆ recombinant inbred line (RIL) population. The parents and 120 F₆ lines were assessed for leaf rust severity at the flag leaf stage in five field plot tests from 2011 through 2015 and were genotyped for single-nucleotide polymorphism (SNP) markers with the Illumina iSelect 90K wheat bead array. A total of 2,384 SNP markers segregated among the RILs. Completely linked SNPs were removed, and 474 markers that covered 2,605 centimorgans (cM) were used for linkage map construction. Quantitative trait loci (QTL) on chromosome 2AL with logarithm of odds (LOD) values 2.34-7.88, on chromosome 4BS with LOD values 1.35- 4.66, and on chromosome 7AL with LOD values 2.92-7.81 were associated with significant reduction in leaf rust severity in the field plot tests. Recombinant inbred lines that had combinations of two or three of the QTL had significantly lower leaf rust severity than RILs that lacked any resistance QTL. Kompetitive allele specific polymerase chain reaction (KASP) markers were developed for the SNPs that were closely linked with the three QTL to facilitate marker-based selection of the leaf rust resistance in breeding programs.

Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent

In wheat, exotic genotypes harbor a broad range of spike-related traits, and can be used as a source of new genes for germplasm enhancement in wheat breeding programs. In the present study, a population of 163 recombinant inbred lines was derived from a cross between an elite line (WCB414) and an exotic line (WCB617) with branched spike (supernumerary spikelet; SS) head morphology. The population was evaluated over four to six environments to identify quantitative trait loci (QTL) associated with nine spike-related traits and 10 agronomic traits. A genetic map consisting of 939 diversity arrays technology (DArT) markers was constructed. Composite interval mapping identified a total of 143 QTL located on 17 different wheat chromosomes and included 33 consistent and definitive QTL. The amount of phenotype variation explained (PVE) by individual QTL ranged from 0.61 to 91.8%. One major QTL for glume pubescence was located in a QTL-rich region on the short arm of chromosome 1A, where loci for other traits such as for kernels per spike (KS) and spike length (SL) were also identified. Similarly, a cluster of QTL associated with yield-related, agronomic and spike-related traits contributing up to 40.3% of PVE was found on the short arm of chromosome 2D, in the vicinity of a major QTL for SS-related traits. Consistent and major QTL identified in the present study may be useful in marker-assisted breeding programs to facilitate transfer of desirable alleles into other germplasm. Desirable QTL alleles were also contributed by the exotic line, suggesting the possibility of enriching the breeding germplasm with alleles from SS genotypes.

Linkage Maps of a Mediterranean × Continental Tall Fescue Population and their Comparative Analysis with Other Poaceae Species

Temperate grasses belonging to the Festuca-Lolium complex are important throughout the world in pasture and grassland agriculture. Tall fescue (Festuca arundinacea Schreb.) is the predominant species in the United States, covering approximately 15 million ha. Tall fescue has distinctive morphotypes, two of which are Continental (summer active) and Mediterranean (summer semidormant). This is the first report of a linkage map created for Mediterranean tall fescue, while updating the Continental map with additional simple sequence repeat and sequence-tagged site markers. Additionally, this is the first time that diversity arrays technology (DArT) markers were used in the construction of a tall fescue map. The male parent (Continental), R43-64, map consisted of 594 markers arranged in 22 linkage groups (LGs) and covered a total of 1577 cM. The female parent (Mediterranean), 103-2, map was shorter (1258 cM) and consisted of only 208 markers arranged in 29 LGs. Marker densities for R43-64 and 103-2 were 2.65 and 6.08 cM per marker, respectively. When compared with the other Poaceae species, meadow fescue (F. pratensis Huds.), annual ryegrass (L. multiflorum Lam.), perennial ryegrass (L. perenne L.), Brachypodium distachyon (L.) Beauv., and barley (Hordeum vulgare L.), a total of 171 and 98 orthologous or homologous sequences, identified by DArT analysis, were identified in R43-64 and 103-2, respectively. By using genomic in situ hybridization, we aimed to identify potential progenitors of both morphotypes. However, no clear conclusion on genomic constitution was reached. These maps will aid in the search for quantitative trait loci of various traits as well as help define and distinguish genetic differences between the two morphotypes.