Saturation Mapping of a Major Effect QTL for Stripe Rust Resistance on Wheat Chromosome 2B in Cultivar Napo 63 Using SNP Genotyping Arrays

Abstract

Stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.). Widespread deployment of resistant cultivars is the best means of achieving durable disease control. The red grain, spring wheat cultivar Napo 63 produced by CIMMYT in the 1960s shows a high level of adult-plant resistance to stripe rust in the field. To elucidate the genetic basis of resistance in this cultivar we evaluated 224 F2:3 lines and 175 F2:6 recombinant inbred lines (RILs) derived from a cross between Napo 63 and the Pst-susceptible line Avocet S. The maximum disease severity (MDS) data of F2:3 lines and the relative area under the disease progress curve (rAUDPC) data of RILs were collected during the 2014–2015 and 2015–2016 wheat growing seasons, respectively. Combined bulked segregant analysis and 90K single nucleotide polymorphism (SNP) arrays placed 275 of 511 polymorphic SNPs on chromosome 2B. Sixty four KASP markers selected from the 275 SNPs and 76 SSR markers on 2B were used to identify a chromosome region associated with rust response. A major effect QTL, named Qyrnap.nwafu-2BS, was identified by inclusive composite interval mapping and was preliminarily mapped to a 5.46 cM interval flanked by KASP markers 90K-AN34 and 90K-AN36 in chromosome 2BS. Fourteen KASP markers more closely linked to the locus were developed following a 660K SNP array analysis. The QTL region was finally narrowed to a 0.9 cM interval flanked by KASP markers 660K-AN21 and 660K-AN57 in bin region 2BS-1-0.53. The resistance of Napo 63 was stable across all environments, and as a QTL, explained an average 66.1% of the phenotypic variance in MDS of F2:3 lines and 55.7% of the phenotypic variance in rAUDPC of F5:6 RILs. The short genetic interval and flanking KASP markers developed in the study will facilitate marker-assisted selection, gene pyramiding, and eventual positional cloning of Qyrnap.nwafu-2BS.

Mapping QTL for Resistance to New Virulent Races of Wheat Stripe Rust from Two Argentinean Wheat Cultivars

“…4). The same haplotype was also detected in Kariega, Opata85, Luke, and Louise (Wu et al, 2017), suggesting that these five lines might carry the YrKK resistance gene. 4).…”

“…Allelism tests will be required to determine if QYr.ucw-2BS is different from the overlapping YrF (from Francolin#1; Lan et al, 2014) and YrH9014 (from Psathyrotachys huashanica translocation line H9014-14-4-6-1; Ma et al, 2013) (Fig. cau-2BS2 from 'Luke' (Guo et al, 2008), QYrlo.wpg-2BS from 'Louise' (Carter et al, 2009), QYr.ucw-2BS from UC 1110(Lowe et al, 2011, and Qyrnap.nwafu-2BS from 'Napo 63' (Wu et al, 2017). In addition to the named Yr genes, multiple QTL for Pst resistance have been mapped on chromosome 2BS (Fig.…”

“…Several named Pst resistance genes, including Yr27, Yr31, Yr41, YrC51-YrP81, YrF, YrH9014, and YrKK, have been mapped on the short arm of chromosome 2B Lan et al, 2014;Maccaferri et al, 2015;Wu et al, 2017). Most of these genes confer all-stage, race-specific resistance and have been defeated by Chinese Pst races (Wu et al, 2017). However, YrKK (derived from cultivar 'Kenya Kudu') conferred near immunity to adult plants in field trials in Toluca, Mexico, in 2010 and 2011 and showed limited effect on seedling resistance to three Mexican Pst isolates .…”

“…These include QYr.sgi-2B.1 from 'Kariega' (Agenbag et al, 2014), QYr3 from 'Opata85' (Boukhatem et al, 2002), QYr.caas-2BS from Pingyuan 50 , QYrlu. cau-2BS2 from 'Luke' (Guo et al, 2008), QYrlo.wpg-2BS from 'Louise' (Carter et al, 2009), QYr.ucw-2BS from UC 1110(Lowe et al, 2011, and Qyrnap.nwafu-2BS from 'Napo 63' (Wu et al, 2017). Napo 63 is related to Kenya Kudu through the common parent 'Florence' and shares the same haplotype at four Kompetitive allele-specific polymerase chain reaction (KASP) markers in the YrKK region.…”

Advances in understanding obligate biotrophy in rust fungi

“…Three M. lini avirulence genes (AvrL567, AvrP4 and Avr123) were found under positive selection at the intraspecific and/or interspecific levels (Dodds et al, 2004;Barrett et al, 2009). A genome-wide search for single nucleotide polymorphisms or insertion/deletion in rust fungal isolates has enabled the detection of avirulence candidates among secreted protein genes (Cantu et al, 2013;Bruce et al, 2014;Persoons et al, 2014;Upadhyaya et al, 2014;Bueno-Sancho et al, 2017;Cuomo et al, 2017;Wu et al, 2017). Sequencing large volumes of isolates is now possible for relatively low cost, and highdensity genetic maps can be constructed through the resequencing of progenies or by restriction site detection sequencing (RAD-seq) in rust fungi (Pernaci et al, 2014;Anderson et al, 2016;Yuan et al, 2018).…”