Characterization Of Leaf Rust Resistance And The Causal Gene/QTL Mapping In Wheat-thinopyrum Amphiploid-derived Lines

Bread wheat（Triticum aestivum L.）is one of the most valuable food and feed crops worldwide.Among the diseases causing significant yield losses in bread wheat,leaf rust,caused by Puccinia triticina Eriks.（Pt）,is one of the most widespread and dangerous fungus.Resistance breeding achieved by incorporation of leaf rust resistance（Lr）genes into cultivars through breeding programs is the most cost-effective,economical,and environmentally sound method of controlling this disease.To date,over 80 Lr genes/alleles controlling seedling or adult plant resistance（APR）have been catalogued in wheat.However,most of the rust resistance genes,although initially effective,were often short lived due to the constant evolution and mutation of Pt races.Hence,breeding for new sources for wheat rust resistance,discovering new resistance gene and its molecular mapping are especially essential and critical to control the occurrence and prevalence of leaf rust,thereby providing continuous resistance protection for wheat production.Long-term breeding practice has been proven that perennial wheatgrasses（Thinopyrum spp.）,the relatives of wheat,are immune or highly resistant to various fungal diseases,including leaf rust and can be exploited as sources of resistance for use in wheat breeding.Such resistance is usually broad-spectrum and effective over a long period of time because most pathogens cannot infect and cause disease in species that differ from their normal hosts.In order to combat the threats of fungal diseases to wheat production,a program aimed to transfer resistance to rusts,powdery mildew,and fusarium head blight into wheat from Thinopyrum.intermedium and Th.ponticum was initiated in the 1990s at our laboratory,and a panel of wheat-Thinopyrum amphiploid-derived hexaploid wheat germplasm lines conferring multiple resistance have been developed by using chromosome engineering technology.This study aimed to:ⅰ)assess the response of 170 Tritipyrum derived lines derived from wheat-Th.ponticum and wheat-Th.intermedium amphiploids to the native Pt races,to identify the known seedling and APR genes,and to determine if any potentially new leaf rust resistance genes are present;ⅱ)characterize genetic mode and fine map the Lr gene carried in the seedling resistant line CH1539 discovered in the present resistance evaluation using single spike descendant-derived recombinant inbred lines（RIL）and secondary mapping populations developed from the cross of the susceptible line with the resistance line in RIL,and investigate its presence or not in Chinese wheat mini-core collections;iii)detect a major QTL for reducing leaf rust severity in the adult resistant line CH1357 and identify linked DNA marker,and test the applicability of a DNA marker to marker-based selection for QLr.sxau-6BL.Main results showed that:1.Identification of new sources of resistance to leaf rust.The seedling responses to leaf rust with eight Chinese Pt races were investigated at the greenhouse in a total of 170Tritipyrum derived lines,which were derived from wheat-Th.ponticum or wheat-Th.intermedium partial amphiploids and have similar morphology with wheat.Multi-race tests combined with marker genotyping identified 28 lines that were resistant against either all or seven of the eight Pt races tested at the seedling stage,but contained no known seedling Lr gene（s）except Lr26.This suggests that additional unidentified leaf rust resistance gene（s）may be present in these lines.In the case of APR,we found that 18 lines were resistant to the mixed races at the adult plant stage with the average maximum disease severity（MDS）being below 20%,and of them,11 APR lines that displayed the average MDS below 15%may carry unknown APR genes.The lines with potentially new genes can be used in resistance breeding to increase the genetic diversity of bread wheat.2.The fine mapping of Lr CH1539.The present resistance evaluation showed CH1539 conferring a high level of seedling resistance to leaf rust.A mapping population consisted of 184 RILs from a cross between CH1539 and SY95-71（a susceptible cultivar）,was developed to map Lr gene present in CH1539.The result from Pt races tested indicated that the RILs had diverse infection responses to the Pt race THK at the seedling stage.Genetic analysis revealed that leaf rust resistance in CH1539 was controlled by a monogenic gene,and temporarily named Lr CH1539.BSA using a 35K DAr Tseq array located Lr CH1539 on the short arm of chromosome 2B.Subsequently,a genetic linkage map of Lr CH1539 was constructed using the developed 2BS chromosome-specific markers,and its flanking markers were sxau-2BS136 and sxau-2BS81.An F_2:3 secondary mapping population having 3619 lines was developed by crossing the resistant to susceptible lines selected from the RIL population.The results from inoculation identification on this subpopulation demonstrated that Lr CH1539 was recessively inherited and fine-mapped to a 779.4-kb region between markers sxau-2BS47 and sxau-2BS255 at the end of 2BS.Lr CH1539 has the almost same position as Lr16 on the linkage marker map,but the two genes displayed diverse response profiles to the Pt races tested,suggesting that they might be different causal genes.Lr CH1539 and its co-segregation marker should be useful in diversifying the Lr genes deployed in modern wheat breeding programs and marker-assisted selection for pyramiding leaf rust resistance genes.3.The mapping of a major QTL for APR.The results from field phenotypic responses showed that the lines CH1357,03W262 and 07C102 all showed high-level adult resistance to leaf rust.A F_4:5 RIL population derived from CH1357×TC29 was used to identify quantitative trait loci（QTLs）controlling leaf rust resistance,and to validate the major QTL in two different genetic populations,with one being 03W262×TC29-derived F_5:6 RIL,another being 07C102×Chang 4738-derived F_2:3 lines.Genome-wide genotyping of parental,resistant and susceptible pools were carried out on these populations using the wheat i Select 90K SNP chip technology combined with BSA.All of three populations have the same resistance locus at the end of chromosome 6BL,with a contributing 28.8%of the phenotypic variance.A linkage map consisting of 32 markers with a length of 77.0 c M was constructed using the known and the developed polymorphic SSR markers on 6BL.A major QTL,temporarily named QLr.sxau-6BL,was identified by inclusive composite interval mapping（Ici Mapping）and preliminarily mapped to a 0.6 c M interval flanked by SSR markers sxau-6BL120 and sxau-6BL14,and this locus verified in different genetic backgrounds.Through the analysis of physical map and integrated genetic map,this QTL is different from other known Lr genes on 6BL and should be a new APR locus,indicating a new source for leaf rust resistance.QLr.sxau-6BL,together with the identified closely linked markers,could be used for Lr gene pyramiding and marker-assisted selection breeding for adult resistance.