Multi-Parental Populations Suitable for Identifying Sources of Resistance to Powdery Mildew in Winter Wheat

Wheat (Triticum aestivum L.) is one of the world's staple food crops and one of the most devastating foliar diseases attacking wheat is powdery mildew (PM). In Denmark only a few specific fungicides are available for controlling PM and the use of resistant cultivars is often recommended. In this study, two Chinese wheat landraces and two synthetic hexaploid wheat lines were used as donors for creating four multi-parental populations with a total of 717 individual lines to identify new PM resistance genetic variants. These lines and the nine parental lines (including the elite cultivars used to create the populations) were genotyped using a 20 K Illumina SNP chip, which resulted in 8,902 segregating single nucleotide polymorphisms for assessment of the population structure and whole genome association study. The largest genetic difference among the lines was between the donors and the elite cultivars, the second largest genetic difference was between the different donors; a difference that was also reflected in differences between the four multi-parental populations. The 726 lines were phenotyped for PM resistance in 2017 and 2018. A high PM disease pressure was observed in both seasons, with severities ranging from 0 to >50%. Whole genome association studies for genetic variation in PM resistance in the populations revealed significant markers mapped to either chromosome 2A, B, or D in each of the four populations. However, linkage disequilibrium between these putative quantitative trait loci (QTL) were all above 0.80, probably representing a single QTL. A combined analysis of all the populations confirmed this result and the most associated marker explained 42% of the variation in PM resistance. This study gives both knowledge about the resistance as well as molecular tools and plant material that can be utilised in marker-assisted selection. Additionally, the four populations produced in this study are highly suitable for association studies of other traits than PM resistance.

A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.

Genetic mapping of QTL for resistance to Fusarium head blight spread (type 2 resistance) in a Triticum dicoccoides × Triticum durum backcross-derived population

Improvement of resistance to Fusarium head blight (FHB) is a continuous challenge for durum wheat breeders, particularly due to the limited genetic variation within this crop species. We accordingly generated a backcross-derived mapping population using the type 2 FHB resistant Triticum dicoccoides line Mt. Gerizim #36 as donor and the modern Austrian T. durum cultivar Helidur as recipient; 103 BC1F6:7 lines were phenotyped for type 2 FHB resistance using single-spikelet inoculations and genotyped with 421 DNA markers (SSR and AFLP). QTL mapping revealed two highly significant QTL, mapping to chromosomes 3A and 6B, respectively. For both QTL the T. dicoccoides allele improved type 2 FHB resistance. Recombinant lines with both favorable alleles fixed conferred high resistance to FHB similar to that observed in the T. dicoccoides parent. The results appear directly applicable for durum wheat resistance breeding.

Mapping of QTL for Fusarium head blight resistance and morphological and developmental traits in three backcross populations derived from Triticum dicoccum × Triticum durum

Breeding for resistance to Fusarium head blight (FHB) in durum wheat continues to be hindered by the lack of effective resistance sources. Only limited information is available on resistance QTL for FHB in tetraploid wheat. In this study, resistance to FHB of a Triticum dicoccum line in the background of three Austrian T. durum cultivars was genetically characterized. Three populations of BC(1)F(4)-derived RILs were developed from crosses between the resistant donor line T. dicoccum-161 and the Austrian T. durum recipient varieties DS-131621, Floradur and Helidur. About 130 BC(1)F(4)-derived lines per population were evaluated for FHB response using artificial spray inoculation in four field experiments during two seasons. Lines were genetically fingerprinted using SSR and AFLP markers. Genomic regions on chromosomes 3B, 4B, 6A, 6B and 7B were significantly associated with FHB severity. FHB resistance QTL on 6B and 7B were identified in two populations and a resistance QTL on 4B appeared in three populations. The alleles that enhanced FHB resistance were derived from the T. dicoccum parent, except for the QTL on chromosome 3B. All QTL except the QTL on 6A mapped to genomic regions where QTL for FHB have previously been reported in hexaploid wheat. QTL on 3B and 6B coincided with Fhb1 and Fhb2, respectively. This implies that tetraploid and hexaploid wheat share common genomic regions associated with FHB resistance. QTL for FHB resistance on 4B co-located with a major QTL for plant height and mapped at the position of the Rht-B1 gene, while QTL on 7B overlapped with QTL for flowering time.

Identification and comparative mapping of a powdery mildew resistance gene derived from wild emmer (Triticum turgidum var. dicoccoides) on chromosome 2BS

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is an important foliar disease of wheat worldwide. Wild emmer (Triticum turgidum var. dicoccoides) is a valuable genetic resource for improving disease resistance in common wheat. A powdery mildew resistance gene conferring resistance to B. graminis f. sp. tritici isolate E09 at the seedling and adult stages was identified in wild emmer accession IW170 introduced from Israel. An incomplete dominant gene, temporarily designated MlIW170, was responsible for the resistance. Through molecular marker and bulked segregant analyses of an F(2) population and F(3) families derived from a cross between susceptible durum wheat line 81086A and IW170, MlIW170 was located in the distal chromosome bin 2BS3-0.84-1.00 and flanked by SSR markers Xcfd238 and Xwmc243. MlIW170 co-segregated with Xcau516, an STS marker developed from RFLP marker Xwg516 that co-segregated with powdery mildew resistance gene Pm26 on 2BS. Four EST-STS markers, BE498358, BF201235, BQ160080, and BF146221, were integrated into the genetic linkage map of MlIW170. Three AFLP markers, XPaacMcac, XPagcMcta, XPaacMcag, and seven AFLP-derived SCAR markers, XcauG2, XcauG3, XcauG6, XcauG8, XcauG10, XcauG20, and XcauG25, were linked to MlIW170. XcauG3, a resistance gene analog (RGA)-like sequence, co-segregated with MlIW170. The non-glaucousness locus Iw1 was 18.77 cM distal to MlIW170. By comparative genomics of wheat-Brachypodium-rice genomic co-linearity, four EST-STS markers, CJ658408, CJ945509, BQ169830, CJ945085, and one STS marker XP2430, were developed and MlIW170 was mapped in an 2.69 cM interval that is co-linear with a 131 kb genomic region in Brachypodium and a 105 kb genomic region in rice. Four RGA-like sequences annotated in the orthologous Brachypodium genomic region could serve as chromosome landing target regions for map-based cloning of MlIW170.

Association of AFLP and SCAR markers with common leafspot resistance in autotetraploid alfalfa (Medicago sativa)

To identify amplified fragment length polymorphism (AFLP) markers associated with resistance or susceptibility of alfalfa to common leafspot (CLS) caused by the fungus Pseudopeziza medicaginis (Dermateaceae), bulked segregant analysis was conducted based on an F(1(M × M)) population of 93 plants and a BC(1)S population of 91 plants. Three AFLP markers, ACTCAA(R206), TAGCAC(R185), and GGACTA(S264), were found to be associated with CLS resistance or susceptibility. All three markers were found at significantly different frequencies (71.9, 80.3 and 91.8%) compared to resistant or susceptible plants in the original population. Subsequently, these three AFLP markers were converted into three SCAR markers, ACTCAA(R136), TAGCAC(R128) and GGACTA(S254), which are easier to employ in breeding programs. The three SCAR markers were used in a randomly selected population with 50% resistance; the probability of finding one resistant plant was increased to 67.3, 66.7 and 90.0% with markers ACTCAA(R136), TAGCAC(R128) and GGACTA(S254), independently. If two of the SCAR markers were used simultaneously, the probability would be higher than 89%. The three SCAR markers identified in this study would be applicable for selection for CLS resistance in alfalfa breeding programs. Moreover, the genetic analysis indicated that CLS resistance in alfalfa is conferred by a single dominant gene.

Advanced backcross QTL mapping of resistance to Fusarium head blight and plant morphological traits in a Triticum macha × T. aestivum population

While many reports on genetic analysis of Fusarium head blight (FHB) resistance in bread wheat have been published during the past decade, only limited information is available on FHB resistance derived from wheat relatives. In this contribution, we report on the genetic analysis of FHB resistance derived from Triticum macha (Georgian spelt wheat). As the origin of T. macha is in the Caucasian region, it is supposed that its FHB resistance differs from other well-investigated resistance sources. To introduce valuable alleles from the landrace T. macha into a modern genetic background, we adopted an advanced backcross QTL mapping scheme. A backcross-derived recombinant-inbred line population of 321 BC(2)F(3) lines was developed from a cross of T. macha with the Austrian winter wheat cultivar Furore. The population was evaluated for Fusarium resistance in seven field experiments during four seasons using artificial inoculations. A total of 300 lines of the population were genetically fingerprinted using SSR and AFLP markers. The resulting linkage map covered 33 linkage groups with 560 markers. Five novel FHB-resistance QTL, all descending from T. macha, were found on four chromosomes (2A, 2B, 5A, 5B). Several QTL for morphological and developmental traits were mapped in the same population, which partly overlapped with FHB-resistance QTL. Only the 2BL FHB-resistance QTL co-located with a plant height QTL. The largest-effect FHB-resistance QTL in this population mapped at the spelt-type locus on chromosome 5A and was associated with the wild-type allele q, but it is unclear whether q has a pleiotropic effect on FHB resistance or is closely linked to a nearby resistance QTL.

Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L

Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Olkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety "Lady Godiva" (O5) and the Italian crookneck variety "Bianco Friulano" (CN), which are the parents of our previous F(2) mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%.

Molecular mapping of resistance to Fusarium head blight in the spring wheat cultivar Frontana

Fusarium head blight (FHB) is a destructive disease of wheat. The objective of this study was to characterise the FHB resistance of the Brazilian spring wheat cultivar Frontana through molecular mapping. A population of 210 doubled-haploid lines from a cross of Frontana (partially resistant) and Remus (susceptible) was evaluated for FHB resistance during three seasons. Spray and single-spikelet inoculations were applied. The severity, incidence and spread of the disease were assessed by visual scoring. The population was genotyped with 566 DNA markers. The major QTL effect associated with FHB resistance mapped to chromosome 3A near the centromere, explaining 16% of the phenotypic variation for disease severity over 3 years. The most likely position is in the Xgwm720-Xdupw227 interval. The genomic region on 3A was significantly associated with FHB severity and incidence in all years evaluated, but not with FHB spread, indicating the prominent contribution of this QTL to resistance against initial infection. The map interval Xgwm129-Xbarc197 on chromosome 5A also showed consistent association with FHB severity and accounted for 9% of the phenotypic variation. In addition, smaller effects for FHB severity were identified on chromosomes 1B, 2A, 2B, 4B, 5A and 6B in single years. Individual QTLs for resistance to FHB spread accounted for less than 10% of the variation in trait expression. The present study indicates that FHB resistance of Frontana primarily inhibits fungal penetration (type I resistance), but has a minor effect on fungal spread after infection (type II resistance).

QTL mapping for resistance against non-parasitic leaf spots in a spring barley doubled haploid population

Phenotypic variability for resistance against non-parasitic leaf spots (NPLS) has been observed between varieties. For the genetic characterization of NPLS resistance, a population with 430 doubled haploid (DH) lines was developed from the cross between the NPLS-resistant Hordeum vulgare breeding line IPZ24727 and the NPLS-sensitive barley cultivar Barke. A molecular map was constructed based on 164 AFLPs, 30 SSRs and one STS marker derived from the mlo gene. Field trials were performed over four environments in which NPLS and other agronomic traits were assessed. Estimates of genotypic variance were highly significant for NPLS. Moreover, no transgression was found for the trait. Quantitative trait loci (QTLs) for NPLS resistance were mapped in the DH population on chromosomes 1H, 4H, and 7H, with the most important effect on chromosome 4H. The QTLs for NPLS explained together 39% of the phenotypic and 49% of the genotypic variance, thereby showing additive gene action. Consequently, marker-assisted selection for improving NPLS resistance is possible.

Powdery mildew resistance gene Pm22 in cultivar Virest is a member of the complex Pm1 locus in common wheat ( Triticum aestivum L. em Thell.)

The powdery mildew resistance gene Pm22, identified in the Italian wheat cultivar Virest and originally assigned to wheat chromosome 1D, was mapped to chromosome 7A with the aid of molecular markers. Mapping of common AFLP and SSR markers in two wheat crosses segregating for Pm22 and Pm1c, respectively, indicated that Pm22 is a member of the complex Pm1 locus. Pm22 also showed a pattern of resistance reaction to a differential set of Blumeria graminis f. sp. tritici isolates that was distinguishable from those from other Pm1 alleles in lines Axminster/8*Cc ( Pm1a), MocZlatka ( Pm1b), Weihenstephan Stamm M1N ( Pm1c) and Triticum spelta var. duhamelianum TRI 2258 ( Pm1d). Based on these results, the gene symbol Pm1e is proposed for the powdery mildew resistance gene in cv. Virest.