Chromosome engineering in wheat to restore male fertility in the msH1 CMS system

Pollen fertility restoration of the CMS phenotype caused by H. chilense cytoplasm in wheat was associated with the addition of chromosome 6H^chS from H. chilense accession H1. In order to develop an euploid restored line, different genomic combinations substituting the 6H^chS arm for another homoeologous chromosome in wheat were evaluated, with the conclusion that the optimal combination was the translocation T6H^chS·6DL. The double translocation T6H^chS·6DL in H. chilense cytoplasm was obtained. This line is fertile and stable under different environmental conditions. However, a single dose of the T6H^chS·6DL translocation is insufficient for fertility restoration when chromosome 6D is also present. Restoration in the msH1 system is promoted by interaction between two or more genes, and in addition to the restorer of fertility (Rf) located on chromosome 6H^chS, one or more inhibitor of fertility (Fi) genes may be present in chromosome 6DL.     

Molecular and cytological characterization of an extra acrocentric chromosome that restores male fertility of wheat in the msH1 CMS system

A new CMS system designated as ‘msH1’ has been reported in bread wheat using the cytoplasm of H. chilense. While testing this system in different wheat backgrounds, a highly fertile line with chromosome number 42 plus an extra acrocentric chromosome was obtained. The extra chromosome did not pair with any wheat chromosome at meiosis, and progeny from this line which lack the acrocentric chromosome showed pollen abortion and male sterility. In order to establish the origin of this chromosome, FISH using H. chilense genomic DNA as probe was used and showed that it had originated from H. chilense chromosome(s). The novel chromosome did not possess sequences similar to wheat rDNA; however, the probe pSc119.2 from S. cereale containing the 120 bp family was found to occur at the end of its long arm. Data obtained from FISH and EST molecular markers confirm that the long arm of the acrocentric chromosome is indeed, the short arm of chromosome 1H^ch from H. chilense. We suggest that the novel chromosome originated from a deletion of the distal part of the long arm of chromosome 1H^ch. Neither the 1H^chS short arm, nor the whole chromosome 1H^ch restores pollen fertility of the alloplasmic wheat. Therefore, the restorer gene on the acrocentric chromosome must be located on the retained segment from the hypothetical 1H^chL, while some pollen fertility inhibitor could be present on the deleted 1H^chL distal segment. Disomic addition of the acrocentric chromosome was obtained and this line resulted fully stable and fertile.     

Molecular mapping of QTL for Fusarium head blight resistance introgressed into durum wheat

Key message

The major QTL for FHB resistance from hexaploid wheat line PI 277012 was successfully introgressed into durum wheat and minor FHB resistance QTL were detected in local durum wheat cultivars. A combination of these QTL will enhance FHB resistance of durum wheat.

Abstract

Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating disease of durum wheat. To combat the disease, great efforts have been devoted to introgress FHB resistance from its related tetraploid and hexaploid wheat species into adapted durum cultivars. However, most of the quantitative trait loci (QTL) for FHB resistance existing in the introgression lines are not well characterized or validated. In this study, we aimed to identify and map FHB resistance QTL in a population consisting of 205 recombinant inbred lines from the cross between Joppa (a durum wheat cultivar) and 10Ae564 (a durum wheat introgression line with FHB resistance derived from the hexaploid wheat line PI 277012). One QTL (Qfhb.ndwp-2A) from Joppa and two QTL (Qfhb.ndwp-5A and Qfhb.ndwp-7A) from 10Ae564 were identified through phenotyping of the mapping population for FHB severity and DON content in greenhouse and field and genotyping with 90K wheat Infinium iSelect SNP arrays. Qfhb.ndwp-2A explained 14, 15, and 9% of the phenotypic variation, respectively, for FHB severity in two greenhouse experiments and for mean DON content across the two greenhouse environments. Qfhb.ndwp-5A explained 19, 10, and 7% of phenotypic variation, respectively, for FHB severity in one greenhouse experiment, mean FHB severity across two field experiments, and mean DON content across the two greenhouse experiments. Qfhb.ndwp-7A was only detected for FHB severity in the two greenhouse experiments, explaining 9 and 11% of the phenotypic variation, respectively. This study confirms the existence of minor QTL in North Dakota durum cultivars and the successful transfer of the major QTL from PI 277012 into durum wheat.

     

Detection of alien genetic introgressions in bread wheat using dot-blot genomic hybridisation

Simple, reliable methods for the identification of alien genetic introgressions are required in plant breeding programmes. The use of genomic dot-blot hybridisation allows the detection of small Hordeum chilense genomic introgressions in the descendants of genetic crosses between wheat and H. chilense addition or substitution lines in wheat when molecular markers are difficult to use. Based on genomic in situ hybridisation, DNA samples from wheat lines carrying putatively H. chilense introgressions were immobilised on a membrane, blocked with wheat genomic DNA and hybridised with biotin-labelled H. chilense genomic DNA as a probe. This dot-blot screening reduced the number of plants necessary to be analysed by molecular markers or in situ hybridisation, saving time and money. The technique was sensitive enough to detect a minimum of 5 ng of total genomic DNA immobilised on the membrane or about 1/420 dilution of H. chilense genomic DNA in the wheat background. The robustness of the technique was verified by in situ hybridisation. In addition, the detection of other wheat relative species such as Hordeum vulgare, Secale cereale and Agropyron cristatum in the wheat background was also reported.     

Mapping gibberellin-sensitive dwarfing locus <Emphasis Type="Italic">Rht18</Emphasis> in durum wheat and development of SSR and SNP markers for selection in breeding

Gibberellin-sensitive dwarfing gene Rht18 was mapped in two durum wheat recombinant inbred lines (RIL) populations developed from crosses, Bijaga Yellow/Icaro and HI 8498/Icaro. Rht18 was mapped within genetic interval of 1.8 cM on chromosome 6A. Simple sequence repeat (SSR) markers S470865SSR4, barc37 and TdGA2ox-A9 specific marker showed co-segregation with Rht18 in Bijaga Yellow/Icaro population consisting 256 RILs. Effect of Rht18 on plant height was validated in HI 8498/Icaro RIL population which segregated for Rht18 and Rht-B1b. Rht-B1b from HI 8498 showed pleiotropic effect on plant height and coleoptile length, on the other hand, Rht18 did not show effect on coleoptile length. The SSR and SNP markers linked to Rht18 were also validated by assessing their allelic frequency in 89 diverse durum and bread wheat accessions. It was observed that 204 bp allele of S470865SSR4 could differentiate Icaro from rest of the wheat accessions except HI 8498, suggesting its utility for selection of Rht18 in wheat improvement programs. Rht18 associated alleles of TdGA2ox-A9, IAW4371 and IAW7940 were absent in most of the tall Indian local durum wheat and bread wheat, hence could be used to transfer Rht18 to bread wheat and local durum wheat. SSR marker barc3 showed high recombination frequency with Rht18, though it showed allele unique to Icaro. Since semidwarf wheat with GA-sensitive dwarfing genes are useful in dry environments owing to their longer coleoptile, better emergence and seedling vigor, Rht18 may provide a useful alternative to widely used GA-insensitive dwarfing genes under dry environments.     

Identification and mapping of <Emphasis Type="Italic">MLIW30</Emphasis>, a novel powdery mildew resistance gene derived from wild emmer wheat

Powdery mildew, caused by Blumeria graminis f.sp. tritici (Bgt), is a destructive foliar disease of common wheat in areas with cool or maritime climates. Wild emmer wheat, Triticum turgidum ssp. dicoccoides, the progenitor of both domesticated tetraploid durum wheat and hexaploid bread wheat, harbors abundant genetic diversity related to resistance to powdery mildew that can be utilized for wheat improvement. An F₂ segregating population was obtained from a cross between resistant bread wheat line 2L6 and susceptible cultivar Liaochun 10, after which genetic analysis of F₂ and F₂-derived F₃ families was performed by inoculating plants with isolate Bgt E09. The results of this experiment demonstrated that powdery mildew resistance in 2L6, which was derived from wild emmer wheat accession IW30, was controlled by a single dominant gene, temporarily designated MLIW30. Nineteen SSR markers and two STS markers linked with MLIW30 were acquired by applying bulked segregant analysis. Finally, MLIW30 was located to the long arm of chromosome 4A and found to be flanked by simple sequence repeat markers XB1g2000.2 and XB1g2020.2 at 0.1 cM. Because no powdery mildew resistance gene in or derived from wild emmer wheat has been reported in wheat chromosome 4A, MLIW30 might be a novel Pm gene.     

Mapping stripe rust resistance gene <Emphasis Type="Italic">YrZH22</Emphasis> in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses

Key message

A stripe rust resistance gene YrZH22 was mapped by combined BSR-Seq and comparative genomics analyses to a 5.92 centimorgan (cM) genetic interval spanning a 4 Mb physical genomic region on wheat chromosome 4BL1.

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases of wheat and severely threatens wheat production worldwide. The widely grown Chinese wheat cultivar Zhoumai 22 is highly resistant to the current prevailing PST race CYR34 (V26). Genetic analysis of F_5:6 and F_6:7 recombinant inbred line (RIL) populations indicated that adult-plant stripe rust resistance in Zhoumai 22 is controlled by a single gene, temporarily designated YrZH22. By applying bulked segregant RNA-Seq (BSR-Seq), 7 SNP markers were developed and SNP mapping showed that YrZH22 is located between markers WGGB105 and WGGB112 on chromosome arm 4BL. The corresponding genomic regions of the Chinese Spring 4BL genome assembly and physical map of Aegilops tauschii 4DL were selected for comparative genomics analyses to develop nine new polymorphic markers that were used to construct a high-resolution genetic linkage map of YrZH22. YrZH22 was delimited in a 5.92 cM genetic interval between markers WGGB133 and WGGB146, corresponding to 4.1 Mb genomic interval in Chinese Spring 4BL and a 2.2 Mb orthologous genomic region in Ae. tauschii 4DL. The genetic linkage map of YrZH22 will be valuable for fine mapping and positional cloning of YrZH22, and can be used for marker-assisted selection in wheat breeding.

     

Morphological and genetic characterization of a new cytoplasmic male sterility system (<Emphasis Type="Italic">oxa</Emphasis> CMS) in stem mustard (<Emphasis Type="Italic">Brassica juncea</Emphasis>)

Key message

oxa CMS is a new cytoplasmic male sterility type in Brassica juncea.

Abstract

oxa CMS is a cytoplasmic male sterility (CMS) line that has been widely used in the production and cultivation of stem mustard in the southwestern China. In this study, different CMS-type specific mitochondrial markers were used to confirm that oxa CMS is distinct from the pol CMS, ogu CMS, nap CMS, hau CMS, tour CMS, Moricandia arvensis CMS, orf220-type CMS, etc., that have been previously reported in Brassica crops. Pollen grains of the oxa CMS line are sterile with a self-fertility rate of almost 0% and the sterility strain rate and sterility degree of oxa CMS is 100% due to a specific flower structure and flowering habit. Scanning electron microscopy revealed that most pollen grains in mature anthers of the oxa CMS line are empty, flat and deflated. Semi-thin section further showed that the abortive stage of anther development in oxa CMS is initiated at the late uninucleate stage. Abnormally vacuolated microspores caused male sterility in the oxa CMS line. This cytological study combined with marker-assisted selection showed that oxa CMS is a novel CMS type in stem mustard (Brassica juncea). Interestingly, the abortive stage of oxa CMS is later than those in other CMS types reported in Brassica crops, and there is no negative effect on the oxa CMS line growth period. This study demonstrated that this novel oxa CMS has a unique flower structure with sterile pollen grains at the late uninucleate stage. Our results may help to uncover the mechanism of oxa CMS in Brassica juncea.

     

Novel Bread Wheat Lines Enriched in Carotenoids Carrying Hordeum chilense Chromosome Arms in the ph1b Background

The use of crop wild relative species to improve major crops performance is well established. Hordeum chilense has a high potential as a genetic donor to increase the carotenoid content of wheat. Crosses between the 7H^ch H. chilense substitution lines in wheat and the wheat pairing homoeologous1b (ph1b) mutant allowed the development of wheat-H. chilense translocation lines for both 7H^chα and 7H^chβ chromosome arms in the wheat background. These translocation lines were characterized by in situ hybridization and using molecular markers. In addition, reverse phase chromatography (HPLC) analysis was carried out to evaluate the carotenoid content and both 7H^chα∙7AL and 7AS∙7H^chβ disomic translocation lines. The carotenoid content in 7H^chα∙7AL and 7AS∙7H^chβ disomic translocation lines was higher than the wheat-7H^ch addition line and double amount of carotenoids than the wheat itself. A proteomic analysis confirmed that the presence of chromosome 7H^ch introgressions in wheat scarcely altered the proteomic profile of the wheat flour. The Psy1 (Phytoene Synthase1) gene, which is the first committed step in the carotenoid biosynthetic pathway, was also cytogenetically mapped on the 7H^chα chromosome arm. These new wheat-H. chilense translocation lines can be used as a powerful tool in wheat breeding programs to enrich the diet in bioactive compounds.     

Cereal cyst nematode resistance gene <Emphasis Type="Italic">CreV</Emphasis> effective against <Emphasis Type="Italic">Heterodera filipjevi</Emphasis> transferred from chromosome 6VL of <Emphasis Type="Italic">Dasypyrum villosum</Emphasis> to bread wheat

Cereal cyst nematodes (CCN) are a global economic problem for cereal production. Heterodera filipjevi is one of the most commonly identified and widespread CCN species found in many wheat production regions of the world. Transferring novel genes for resistance to H. filipjevi from wild relatives of wheat is a promising strategy for protection of wheat crops. A set of wheat–Dasypyrum villosum chromosome addition lines, T6V#4S·6AL translocation lines and their donor parental lines were tested for their response to the nematode. D. villosum and wheat–D. villosum disomic addition line DA6V#4 were resistant. As T6V#4S·6AL translocation lines were susceptible, resistance was presumed to be located on chromosome 6V#4L. The objective of this study was to produce and characterize wheat–6V#4L translocations and confirm the chromosome location of the resistance. Introgression lines T6V#4L·6AS, T6V#4L-4BL·4BS and DT6V#4L were developed and subjected to molecular cytogenetic analysis. These and four additional wheat–6V#4 introgression lines were tested for response to H. filipjevi in the greenhouse. The results indicated that introgression lines DA6V#4, T6V#4L·6AS, T6V#4L-4BL·4BS, T6V#4L·6V#4S-7BS and DT6VL#4 had higher levels of H. filipjevi resistance than their recurrent parent. However, Del6V#4L-1 and translocation line T6V#4S·6AL were equally susceptible to wheat cv. Chinese Spring. The CCN resistance gene, temporarily named CreV, was therefore physically mapped to chromosome arm 6V#4L FL 0.80–1.00. Translocation chromosomes T6V#4L·6AS transferred to a modern wheat cv. Aikang 58 with its co-dominant molecular markers could be utilized as a novel germplasm for CCN resistance breeding in wheat.     

QTL mapping of Fusarium head blight resistance in three related durum wheat populations

Key message

The QTL Fhb1 was successfully introgressed and validated in three durum wheat populations. The novel germplasm and the QTL detected will support improvement of Fusarium resistance in durum wheat.

Abstract

Durum wheat (Triticum durum Desf.) is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is hampered by limited genetic variation within this species. To date, resistant sources are mainly available in a few wild relative tetraploid wheat accessions. In this study, the effect of the well-known hexaploid wheat (Triticum aestivum L.) quantitative trait locus (QTL) Fhb1 was assessed for the first time in durum wheat. Three F7-RIL mapping populations of about 100 lines were developed from crosses between the durum wheat experimental line DBC-480, which carries an Fhb1 introgression from Sumai-3, and the European T. durum cultivars Karur, Durobonus and SZD1029K. The RILs were evaluated in field experiments for FHB resistance in three seasons using spray inoculation and genotyped with SSR as well as genotyping-by-sequencing markers. QTL associated with FHB resistance were identified on chromosome arms 2BL, 3BS, 4AL, 4BS, 5AL and 6AS at which the resistant parent DBC-480 contributed the positive alleles. The QTL on 3BS was detected in all three populations centered at the Fhb1 interval. The Rht-B1 locus governing plant height was found to have a strong effect in modulating FHB severity in all populations. The negative effect of the semi-dwarf allele Rht-B1b on FHB resistance was compensated by combining with Fhb1 and additional resistance QTL. The successful deployment of Fhb1 in T. durum was further substantiated by assessing type 2 resistance in one population. The efficient introgression of Fhb1 represents a significant step forward for enhancing FHB resistance in durum wheat.

     

A new leaf rust resistance gene <Emphasis Type="Italic">Lr79</Emphasis> mapped in chromosome 3BL from the durum wheat landrace Aus26582

Key message

A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection.

Abstract

Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3. LrAW2 was located in chromosome 6BS and this study focused on characterisation of LrAW3 using RILs lacking LrAW2. LrAW3 was incorporated into the DArTseq map of Aus26582/Bansi and was located in chromosome 3BL. Markers linked with LrAW3 were developed from the chromosome survey sequence contig 3B_10474240 in which closely-linked DArTseq markers 1128708 and 3948563 were located. Although bulk segregant analysis (BSA) with the 90 K Infinium array identified 51 SNPs associated with LrAW3, only one SNP-derived KASP marker mapped close to the locus. Deletion bin mapping of LrAW3-linked markers located LrAW3 between bins 3BL11-0.85-0.90 and 3BL7-0.63. Since no other all stage leaf rust resistance gene is located in chromosome 3BL, LrAW3 represented a new locus and was designated Lr79. Marker sun786 mapped 1.8 cM distal to Lr79 and Aus26582 was null for this locus. However, the marker can be reliably scored as it also amplifies a monomorphic fragment that serves as an internal control to differentiate the null status of Aus26582 from reaction failure. This marker was validated among a set of durum and common wheat cultivars and was shown to be useful for marker-assisted selection of Lr79 at both ploidy levels.

     

Mapping of novel salt tolerance QTL in an Excalibur × Kukri doubled haploid wheat population

Key message

Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields.

Abstract

Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur?×?Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity (QG_(1–5).asl-7A), one for leaf Na⁺ exclusion (QNa.asl-7A) and four for leaf K⁺ accumulation (QK.asl-2B.1, QK.asl-2B.2, QK.asl-5A and QK:Na.asl-6A). The beneficial allele for QG_(1–5).asl-7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na⁺ exclusion and/or K⁺ maintenance at three QTL (QNa.asl-7A, QK.asl-2B.2 and QK:Na.asl-6A) excluded more Na⁺ or accumulated more K⁺ compared to lines without these alleles. Importantly, the QK.asl-2B.2 allele for higher K⁺ accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.

     

Cloning of <Emphasis Type="Italic">TaTPP-6AL1</Emphasis> associated with grain weight in bread wheat and development of functional marker

Trehalose 6-phosphate phosphatase (TPP) dephosphorylates trehalose 6-phosphate to trehalose, an important growth regulator, and is involved in starch accumulation and grain yield. In this study, wheat TPP homologs were isolated from chromosomes 6AL, 6BL, and 6DL, designated as TaTPP-6AL1, TaTPP-6BL1, and TaTPP-6DL1, respectively. Sequence alignment showed a single-nucleotide polymorphism (SNP) at TaTPP-6AL1 locus between cultivars with contrasting thousand grain weight (TGW), forming alleles TaTPP-6AL1a and TaTPP-6AL1b, respectively. A cleaved amplified polymorphic sequence (CAPS) marker, TaTPP-6AL1-CAPS, was developed to differentiate the two alleles. TaTPP-6AL1 was mapped within the interval of IWB65749 and IWB60449 in a recombinant inbred line (RIL) population derived from Zhou8425B/Chinese Spring using the wheat 90K SNP assay. A QTL for TGW identified in the interval explained 12.1–19.1% of the phenotypic variance across five environments. Association analysis on 141 Chinese wheat cultivars also indicated a significant correlation of TaTPP-6AL1 with TGW. In conclusion, TaTPP-6AL1 and its functional marker are valuable to improve grain yield in wheat breeding.     

Identification,mapping, and marker development of stem rust resistance genes in durum wheat ‘Lebsock’

Wheat production in many wheat-growing regions is vulnerable to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt). Several previous studies showed that most of the durum cultivars adapted to the upper Great Plains in the USA have good resistance to the major Pgt pathotypes, including the Ug99 race group. To identify the stem rust resistance (Sr) genes in the durum cultivar ‘Lebsock’, a tetraploid doubled haploid (DH) population derived from a cross between Lebsock and Triticum turgidum ssp. carthlicum PI 94749 was screened with the Pgt races TTKSK, TRTTF, and TTTTF. The stem rust data and the genotypic data previously developed were used to identify quantitative trait loci (QTL) associated with resistance. We identified one QTL each on chromosome arms 4AL, 6AS, 6AL, and 2BL. Based on marker and race-specification analysis, we postulated that the QTL on 4AL, 6AS, 6AL, and 2BL correspond to Sr7a, Sr8155B1, Sr13, and likely Sr9e, respectively. The results indicated that most of the US durum germplasm adapted to the upper Great Plains likely harbors the four major Sr genes characterized in this study. Among these genes, Sr8155B1 was recently identified and shown to be unique in that it conferred susceptibility to TTKSK but resistance to variant race TTKST. Two, three, and one thermal asymmetric reverse PCR (STARP) markers were developed for Sr7a, Sr8155-B1, and Sr13, respectively. Knowledge of the Sr genes in durum germplasm and the new STARP markers will be useful to pyramid and deploy multiple Sr genes in future durum and wheat cultivars.     

Chromosomal location of structural genes controlling isozymes in Hordeum chilense

Summary A study of 6-phosphogluconate dehydrogenase and malate dehydrogenase isozyme expression in Triticum turgidum conv. durum /Hordeum chilense monosomic addition lines has revealed the location of two structural genes, 6-pgd-H ^ch 2 and Mdh-H ^ch 1, on chromosome 1H^ch of H. chilense. The homoeology between 1H^ch and other chromosome of Triticeae related species is discussed on the basis of isozyme gene analysis.     

IRAP,REMAP and ISSR Fingerprinting in Newly Formed Hexaploid Tritordeum (X Tritordeum Ascherson et Graebner) and Respective Parental Species

Retrotransposon (RTN)-based markers, such as the inter-retrotransposon amplified polymorphism (IRAP) and the retrotransposon-microsatellite amplified polymorphism (REMAP), are highly informative, multilocus, and reveal insertion polymorphisms among individuals. These markers have been used for evolutionary studies, genetic diversity assessment, DNA fingerprinting, and detection of genetic rearrangements induced by allopolyploidization. The hexaploid tritordeum (H^chH^chAABB; 2n?=?6x?=?42) is an allopolyploid produced from crosses between wild barley (Hordeum chilense Roem. et Schultz.) (H^chH^ch; 2n?=?2x?=?14) and durum wheat (Triticum turgidum L. conv. durum) (AABB; 2n?=?4x?=?28). With this study, we carried out the DNA fingerprinting of two newly formed hexaploid tritordeum lines (HT22 and HT27) and their respective parents, line H1 of H. chilense and line T81 of durum wheat, based on IRAPs, REMAPs and inter-simple sequence repeats (ISSRs), in order to detect potential rearrangements in tritordeum derived from polyploidization. The amphiploid nature of the HT22 and HT27 individuals was successfully confirmed after fluorescence in situ hybridization (FISH), which was performed on their mitotic chromosome spreads with genomic DNA from H. chilense and 45S ribosomal DNA (rDNA), simultaneously, as probes. Six combinations of LTR (long terminal repeat) primers and seven combinations of one LTR and one SSR (simple sequence repeat) primers successfully produced IRAPs and REMAPs, respectively, in both tritordeum lines, and their respective parents. ISSRs were produced with three SSR primers (8081, 8082, and 8564). The analysis of the presence/absence of bands among the tritordeum lines and the respective parents allowed the detection of polymorphic bands: (1) shared by tritordeum and one of the parents; (2) exclusively amplified in tritordeum; and (3) exclusively present in one of the parents. Once no polymorphism was detected among the individuals of each parental species, the polymorphic bands that fit into the second and third cases probably constituted rearrangements in the newly formed tritordeums that arose in response to allopolyploidization, which resulted from the loss of parental bands or, conversely, from the appearance of novel bands not seen in the parental species. Most of the polymorphic IRAPs in tritordeum were shared with the female parent (H. chilense), while most of the polymorphic REMAPs and ISSRs were common to the male parent (durum wheat), but globally, most of the bands inherited by tritordeum had a wheat origin. In conclusion, these dominant markers were successful for DNA fingerprinting and detection of rearrangements in newly formed tritordeum derived from responses to allopolyploidization.     

Genetic analysis and mapping of adult plant resistance loci to leaf rust in durum wheat cultivar Bairds

Key message

New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds.

Abstract

CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP. The RIL population and its parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. A genetic map comprising 1150 markers was used to map the resistance loci. Four significant quantitative trait loci (QTLs) were detected on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTLs, named Lr46, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, respectively, explained 13.5–60.8%, 9.0–14.3%, 2.8–13.9%, and 11.6–29.4%, respectively, of leaf rust severity variation by the inclusive composite interval mapping method. All of these resistance loci were contributed by the resistant parent Bairds, except for QLr.cim-2BC, which came from susceptible parent Atred#1. Among these, the QTL on chromosome 1BL was the known pleiotropic APR gene Lr46, whereas QLr.cim-6BL, a consistently detected locus, should be a new leaf rust resistance locus in durum wheat. The mean leaf rust severity of RILs carrying all four QTLs ranged from 8.0 to 17.5%, whereas it ranged from 10.9 to 38.5% for three QTLs (Lr46 + 5BL + 6BL) derived from the resistant parent Bairds. Two RILs with four QTLs combinations can be used as sources of complex APR in durum wheat breeding.

     

Novel sources of resistance to Septoria nodorum blotch in the Vavilov wheat collection identified by genome-wide association studies

Key message

The fungus Parastagonospora nodorum causes Septoria nodorum blotch (SNB) of wheat. A genetically diverse wheat panel was used to dissect the complexity of SNB and identify novel sources of resistance.

Abstract

The fungus Parastagonospora nodorum is the causal agent of Septoria nodorum blotch (SNB) of wheat. The pathosystem is mediated by multiple fungal necrotrophic effector–host sensitivity gene interactions that include SnToxA–Tsn1, SnTox1–Snn1, and SnTox3–Snn3. A P. nodorum strain lacking SnToxA, SnTox1, and SnTox3 (toxa13) retained wild-type-like ability to infect some modern wheat cultivars, suggesting evidence of other effector-mediated susceptibility gene interactions or the lack of host resistance genes. To identify genomic regions harbouring such loci, we examined a panel of 295 historic wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources in Russia, which is comprised of genetically diverse landraces and breeding lines registered from 1920 to 1990. The wheat panel was subjected to effector bioassays, infection with P. nodorum wild type (SN15) and toxa13. In general, SN15 was more virulent than toxa13. Insensitivity to all three effectors contributed significantly to resistance against SN15, but not toxa13. Genome-wide association studies using phenotypes from SN15 infection detected quantitative trait loci (QTL) on chromosomes 1BS (Snn1), 2DS, 5AS, 5BS (Snn3), 3AL, 4AL, 4BS, and 7AS. For toxa13 infection, a QTL was detected on 5AS (similar to SN15), plus two additional QTL on 2DL and 7DL. Analysis of resistance phenotypes indicated that plant breeders may have inadvertently selected for effector insensitivity from 1940 onwards. We identify accessions that can be used to develop bi-parental mapping populations to characterise resistance-associated alleles for subsequent introgression into modern bread wheat to minimise the impact of SNB.