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(Rhynchosporium Commune) in the Barley Nested Büttner et al. BMC Genomics (2020) 21:837 https://doi.org/10.1186/s12864-020-07258-7 RESEARCH ARTICLE Open Access Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25 Bianca Büttner1, Vera Draba2, Klaus Pillen2, Günther Schweizer1 and Andreas Maurer2* Abstract Background: Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC1S3 generation, derived from crosses of 25 wild barley accessions with cv. Barke. Results: In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected. Conclusions: To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars. Keywords: HEB-25, Hordeum vulgare, Hordeum vulgare ssp. spontaneum, Rrs, Wild barley, Scald resistance, Rhynchosporium commune, Nested association mapping (NAM), Greenhouse trials Background occurs in all barley growing areas around the world, espe- Rhynchosporium commune, a haploid fungus, is the causal cially in cool, humid climates [1]. The typical disease agent of scald or barley leaf blotch, an important foliar dis- symptoms are tan necrotic lesions with dark brown mar- ease of barley (Hordeum vulgare ssp. vulgare L.). R. com- gins, which occur after a latent period [2]. Besides barley mune has been classified as a hemibiotroph fungus which the genus Rhynchosporium is able to infect further species, e. g. rye [1]andLolium species [3]. Scald can cause yield losses of up to 40%, decreases grain quality [2, 4]andis * Correspondence: [email protected] considered a major economic barley disease, especially in 2Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany the UK, Australia and Tunisia [5–7]. Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Büttner et al. BMC Genomics (2020) 21:837 Page 2 of 12 In practice the pathogen is mainly controlled by growing different loci conferring resistance were both named resistant cultivars or chemical protection, while phytosani- Rrs15 whereby one is located on 2H and the other on 7H tary techniques, e. g. ploughing or crop rotation can also [2]. The single dominant gene on the long arm of chromo- help to protect the crop [1, 2]. In general, winter barley some 7H is derived from an Israeli accession of wild barley cultivars show a higher partial resistance to scald than [16]. The locus on 2H originated from Hordeum vulgare spring barley cultivars [2]. Because the pathogen itself is and is named Rrs15CI8288 according to the resistance highly diverse [1, 2, 8] scald is able to overcome crop pro- donor CIho8288 [36]. To avoid confusion Zhan et al. [2] tection methods like fungicides or specific cultivation suggested to rename the locus on 2H as Rrs17. The first methods as well as resistance genes within a few growing resistance gene against scald from the secondary gene- seasons, especially when extensively used [2]. In addition, pool of barley is Rrs16Hb on chromosome 4HS. It is de- the high genetic variation may enable the pathogen to rived from a recombinant hybrid between H. vulgare and cope with climate warming [9]. H. bulbosum [17]. A recently identified resistance locus on Since decades breeders and scientists deal with the com- chromosome 6H is called Rrs18 and was mapped distal plex interaction of barley and R. commune, which is only from Rrs13 on chromosome 6H [37, 38]. partly understood. Up to now, nine major resistance genes Possibly some QTLs are alleles of known resistance (R genes) and many quantitative trait loci (QTLs) have genes [39]. Furthermore, some QTLs independently iden- been identified and have been mapped on a consensus tified in different studies may be allelic or even identical bin-map [2]. Björnstad et al. [10]suggestedanomencla- [2]. Schweizer and Stein [40] integrated 166 QTLs from ture to classify R genes against Rhynchosporium using the 28 studies to identify meta-QTLs mediating resistance to Rrs/rrs terminology considering that some described several fungal pathogens. Twenty meta-QTLs were de- resistance genes are alleles of the same gene. Part of the R tected over all chromosomes including ten regions associ- gene suite identified thus far are derived from wild Hor- ated with scald resistance on all chromosomes except deum species, e. g. Rrs13, Rrs14 and Rrs15 from Hordeum chromosome 5H. Looseley et al. [19]identifiedaltogether vulgare ssp. spontaneum [11–16]orRrs16 from Hordeum 17 QTLs by means of genome-wide association study bulbosum [17]. Most of them are mapped and markers for (GWAS) in two different data sets (European spring barley marker-assisted selection (MAS) are developed, but except and old list trials). The QTLs are in the region of Rrs1, Rrs2 [18] none of them are diagnostic. So far, none of the Rrs3, Rrs13, Rrs15b and Rrs16, but are probably not the scald resistance genes has been cloned [1, 19]. resistance genes. Wang et al. [41] combined in total 43 The Rrs1 locus was the first resistance locus described QTLs and seven genes conferring quantitative and qualita- in barley, which is a powerful and still effective resistance tive resistance, which had been located on individual locus against scald in barley [20], although the fungus is maps, in a consensus map. Again they found QTLs/genes able to overcome Rrs1 by losing the avirulence gene NIP1 on all chromosomes except 5H. (necrosis-inducing peptide 1, [21]). Rrs1 represents a com- The majority of genetic studies on scald resistance has plex locus with either many tightly linked genes or mul- been conducted at the seedling stage focusing on major tiple alleles at a single gene allocated to the centromeric gene resistance presumably based on problems with the region of chromosome 3HL [2, 22]. Although Rrs1 is a field tests [2, 42]. Normally there is a good correlation be- major resistance gene sometimes even in resistant plants tween seedling and adult plant resistance with some excep- the fungus is able to complete its life cycle and sporulate tions [2, 33]. Disease escape may be one reason why plants [23–25]. Additionally, Patil et al. [26] mapped a second re- seem to be more resistant in the field than in the green- sistance locus, named Rrs4CI11549 22 cM distal to Rrs1 on house [2]. Disease escape is mainly based on unfavourable chromosome 3HL. For Rrs2,locatedon7HS[27], eight growing conditions for the fungi like drought and diagnostic markers are described [18]. The genomic re- temperature as well as plant height, maturity and canopy gion near Rrs2 was re-sequenced in a diverse set of wild structure limiting the spreading of the pathogen [2]. There- and cultivated barley. The nucleotide diversity was higher fore, the resistance QTLs on 3H [32, 33, 43, 44] in the re- in wild than cultivated barley and the domestication signal gion of sdw1 possibly are pleiotropic effects of the semi- in this region was weak [28]. Pectin esterase inhibitor dwarfing gene [2]. Adult plant resistance (APR) is based on (PEI) genes were analysed as possible candidate genes for many minor genes with small effects [41, 45]. Accordingly, Rrs2, but this could not be confirmed [29]. Rrs13 is de- several QTLs for APR were detected on chromosome 2H, rived from a wild barley accession and located on the 3H, 4H, 6H and 7H [31–33, 41–43, 46, 47]. short arm of chromosome 6H [12, 30].
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