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. 2014 Jun;127(6):1293-304.
doi: 10.1007/s00122-014-2297-8. Epub 2014 Apr 8.

Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm

H Zhou  1 , B J Steffenson, Gary Muehlbauer, Ruth Wanyera, Peter Njau, Sylvester Ndeda
Affiliations

Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm

H Zhou et al. Theor Appl Genet. 2014 Jun.

Abstract

Loci conferring resistance to the highly virulent African stem rust race TTKSK were identified in advanced barley breeding germplasm and positioned to chromosomes 5H and 7H using an association mapping approach. African races of the stem rust pathogen (Puccinia graminis f. sp. tritici) are a serious threat to barley production worldwide because of their wide virulence. To discover and characterize resistance to African stem rust race TTKSK in US barley breeding germplasm, over 3,000 lines/cultivars were assessed for resistance at the seedling stage in the greenhouse and also the adult plant stage in the field in Kenya. Only 12 (0.3 %) and 64 (2.1 %) lines exhibited a resistance level comparable to the resistant control at the seedling and adult plant stage, respectively. To map quantitative trait loci (QTL) for resistance to race TTKSK, an association mapping approach was conducted, utilizing 3,072 single nucleotide polymorphism (SNP) markers. At the seedling stage, two neighboring SNP markers (0.8 cM apart) on chromosome 7H (11_21491 and 12_30528) were found significantly associated with resistance. The most significant one found was 12_30528; thus, the resistance QTL was named Rpg-qtl-7H-12_30528. At the adult plant stage, two SNP markers on chromosome 5H (11_11355 and 12_31427) were found significantly associated with resistance. This resistance QTL was named Rpg-qtl-5H-11_11355 for the most significant marker identified. Adult plant resistance is of paramount importance for stem rust. The marker associated with Rpg-qtl-5H-11_11355 for adult plant resistance explained only a small portion of the phenotypic variation (0.02); however, this QTL reduced disease severity up to 55.0 % under low disease pressure and up to 21.1 % under heavy disease pressure. SNP marker 11_11355 will be valuable for marker-assisted selection of adult plant stem rust resistance in barley breeding.

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Figures

Fig. 1
Fig. 1
Distribution of stem rust race TTKSK seedling and adult plant phenotypic data of US barley breeding germplasm. CAPI, CAPII, CAPIII, and CAPIV are four individual panels from 2006 to 2009 comprising both spring and winter/facultative breeding lines and CAPI-S, CAPII-S, CAPIII-S, and CAPIV-S are four individual panels from the same years comprising only spring breeding lines. CAPIII-S and CAPIV-S were evaluated in a high disease year (2009), while CAPI-S and CAPII-S were evaluated in a low disease year (2010). Five statistics (bars) are represented in each boxplot from bottom to top: the smallest observation, lower quartile, median, upper quartile, and largest observation, respectively. Data points positioned outside this range are extreme values. a Boxplots of numeric seedling disease scores by individual yearly panels. The horizontal line indicates the mean plus one standard deviation of resistant control Q21861 b Boxplots of adult plant disease severity (0–100 %) by individual yearly spring panels. The horizontal lines indicate the mean plus one standard deviation of resistant control Q21861 in 2009 and 2010
Fig. 2
Fig. 2
Genome-wide association of seedling and adult plant resistance to stem rust race TTKSK in US barley breeding germplasm. Quartile-quartile plots of naive (in blue) and corrected (in black) association p values for a seedling resistance in the complete panel (CAP) and c adult plant resistance in the complete spring panel (CAP-S). Genome-wide AM of b seedling resistance in CAP and d adult plant resistance in CAP-S. Red horizontal line indicates the threshold false discovery rate (FDR) = 0.05. The markers significantly associated with the resistance are labeled
Fig. 3
Fig. 3
Heat map of LD among SNP markers significantly associated with adult plant resistance to stem rust race TTKSK on barley chromosome 5H. The number in each square cell is the pair-wise LD calculated in D′. The most significantly associated SNP marker (11_11355) is underlined
See this image and copyright information in PMC

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