Characterization and mapping of leaf rust resistance in four durum wheat cultivars

<div><p>Widening the genetic basis of leaf rust resistance is a primary objective of the global durum wheat breeding effort at the International Wheat and Maize Improvement Center (CIMMYT). Breeding programs in North America are following suit, especially after the emergence of new races of <i>Puccinia triticina</i> such as BBG/BP and BBBQD in Mexico and the United States, respectively. This study was conducted to characterize and map previously undescribed genes for leaf rust resistance in durum wheat and to develop reliable molecular markers for marker-assisted breeding. Four recombinant inbred line (RIL) mapping populations derived from the resistance sources Amria, Byblos, Geromtel_3 and Tunsyr_2, which were crossed to the susceptible line ATRED #2, were evaluated for their reaction to the Mexican race BBG/BP of <i>P</i>. <i>triticina</i>. Genetic analyses of host reactions indicated that leaf rust resistance in these genotypes was based on major seedling resistance genes. Allelism tests among resistant parents supported that Amria and Byblos carried allelic or closely linked genes. The resistance in Geromtel_3 and Tunsyr_2 also appeared to be allelic. Bulked segregant analysis using the Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified two genomic regions for leaf rust resistance; one on chromosome 6BS for Geromtel_3 and Tunsyr_2 and the other on chromosome 7BL for Amria and Byblos. Polymorphic SNPs identified within these regions were converted to kompetitive allele-specific PCR (KASP) assays and used to genotype the RIL populations. KASP markers <i>usw215</i> and <i>usw218</i> were the closest to the resistance genes in Geromtel_3 and Tunsyr_2, while <i>usw260</i> was closely linked to the resistance genes in Amria and Byblos. DNA sequences associated with these SNP markers were anchored to the wild emmer wheat (WEW) reference sequence, which identified several candidate resistance genes. The molecular markers reported herein will be useful to effectively pyramid these resistance genes with other previously marked genes into adapted, elite durum wheat genotypes.</p></div

Frequency distributions of the disease severity (DS) scores in the F₆ generation of four RIL populations.

<p>(A) Frequency distribution of DS for the Byblos/ATRED #2 population. (B) Frequency distribution of DS for the Tunsyr_2/ATRED #2 population. (C) Frequency distribution of DS for the Amria/ATRED #2 population. (D) Frequency distribution of DS for the Geromtel_3/ATRED #2 population.</p

Linkage groups of KASP markers associated with the leaf rust resistance genes <i>Lr_Amria</i> and <i>Lr_Byblos</i> and their positions on the consensus map.

<p>(A) Markers associated with resistance in Amria. (B) Markers associated with resistance in Byblos. (C) High-density tetraploid consensus map for chromosome 7B [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197317#pone.0197317.ref048" target="_blank">48</a>]. Markers highlighted in blue are linked to the resistance in both Amria and Byblos. Genetic distances are displayed in cM.</p

Map positions of the SNP markers linked to leaf rust resistance in Geromtel_3 and Tunsyr_2 and their corresponding physical intervals in the WEW sequence of chromosome 6B.

<p>Map positions of the SNP markers linked to leaf rust resistance in Geromtel_3 and Tunsyr_2 and their corresponding physical intervals in the WEW sequence of chromosome 6B.</p

Classification of field reactions to the race BBG/BP of <i>P</i>. <i>triticina</i> of F₃, F₆ and F₈ progenies from four crosses involving four sources of resistance crossed to the susceptible genotype ATRED #2.

<p>Classification of field reactions to the race BBG/BP of <i>P</i>. <i>triticina</i> of F₃, F₆ and F₈ progenies from four crosses involving four sources of resistance crossed to the susceptible genotype ATRED #2.</p

Linkage groups of KASP markers associated with the leaf rust resistance genes <i>Lr_Geromtel_3</i> and <i>Lr_Tunsyr_2</i> and their positions on the consensus map.

<p>(A) Markers associated with resistance in Geromtel_3. (B) Markers associated with resistance in Tunsyr_2. (C) High-density tetraploid consensus map for chromosome 6B [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197317#pone.0197317.ref048" target="_blank">48</a>]. Markers highlighted in blue are linked to the resistance in both Geromtel_3 and Tunsyr_2. Markers highlighted in red are linked only to the resistance in Geromtel_3. Genetic distances are displayed in cM.</p

Number of resistant and susceptible F₂ plants from crosses between different sources of resistance to leaf rust used for allelism testing.

<p>Number of resistant and susceptible F₂ plants from crosses between different sources of resistance to leaf rust used for allelism testing.</p

Map positions of the SNP markers linked to leaf rust resistance in Amria and Byblos and their corresponding physical intervals in the WEW sequence of chromosome 7B.

<p>Map positions of the SNP markers linked to leaf rust resistance in Amria and Byblos and their corresponding physical intervals in the WEW sequence of chromosome 7B.</p

High density mapping and haplotype analysis of the major stem-solidness locus <i>SSt1</i> in durum and common wheat

<div><p>Breeding for solid-stemmed durum <i>(Triticum turgidum</i> L. var <i>durum</i>) and common wheat (<i>Triticum aestivum</i> L.) cultivars is one strategy to minimize yield losses caused by the wheat stem sawfly (<i>Cephus cinctus</i> Norton). Major stem-solidness QTL have been localized to the long arm of chromosome 3B in both wheat species, but it is unclear if these QTL span a common genetic interval. In this study, we have improved the resolution of the QTL on chromosome 3B in a durum (Kofa/W9262-260D3) and common wheat (Lillian/Vesper) mapping population. Coincident QTL (LOD = 94–127, <i>R</i>^<i>2</i> = 78–92%) were localized near the telomere of chromosome 3BL in both mapping populations, which we designate <i>SSt1</i>. We further examined the <i>SSt1</i> interval by using available consensus maps for durum and common wheat and compared genetic to physical intervals by anchoring markers to the current version of the wild emmer wheat (WEW) reference sequence. These results suggest that the <i>SSt1</i> interval spans a physical distance of 1.6 Mb in WEW (positions 833.4–835.0 Mb). In addition, minor QTL were identified on chromosomes 2A, 2D, 4A, and 5A that were found to synergistically enhance expression of <i>SSt1</i> to increase stem-solidness. These results suggest that developing new wheat cultivars with improved stem-solidness is possible by combining <i>SSt1</i> with favorable alleles at minor loci within both wheat species.</p></div

Synergistic two-way interactions between <i>SSt1</i> and minor QTL identified in the Kofa/W9262-260D3 (durum) and Lillian/Vesper (common wheat) mapping populations.

<p>Synergistic two-way interactions between <i>SSt1</i> and minor QTL identified in the Kofa/W9262-260D3 (durum) and Lillian/Vesper (common wheat) mapping populations.</p