Saturation and comparative mapping of a major Fusarium head blight resistance QTL in tetraploid wheat

Fusarium head blight (FHB) is a devastating disease of cultivated wheat worldwide. Partial resistance to FHB has been identified in common wheat (Triticum aestivum L.). However, sources of effective FHB resistance have not been found in durum wheat (T. turgidum L. var. durum). A major FHB resistance quantitative trait loci (QTL), Qfhs.ndsu-3AS, was identified on chromosome 3A of T. dicoccoides, a wild relative of durum wheat. Here, we saturated the genomic region containing the QTL using EST-derived target region amplified polymorphism (TRAP), sequence tagged site (STS), and simple sequence repeat (SSR) markers. A total of 45 new molecular marker loci were detected on chromosome 3A and the resulting linkage map consisted of 55 markers spanning a genetic distance of 277.2 cM. Qfhs.ndsu-3AS was positioned within a chromosomal interval of 11.5 cM and is flanked by the TRAP marker loci, Xfcp401 and Xfcp397.2. The average map distance between the marker loci within this QTL region was reduced from 4.9 cM in the previous study to 3.5 cM in the present study. Comparative mapping indicated that Qfhs.ndsu-3AS is not homoeologous to Qfhs.ndsu-3BS, a major FHB QTL derived from the common wheat cultivar Sumai 3. These results facilitate our efforts toward map-based cloning of Qfhs.ndsu-3AS and utilization of this QTL in durum wheat breeding via marker-assisted selection.     

Complex microcolinearity among wheat, rice, and barley revealed by fine mapping of the genomic region harboring a major QTL for resistance to Fusarium head blight in wheat

A major quantitative trait locus (QTL), Qfhs.ndsu-3BS, for resistance to Fusarium head blight (FHB) in wheat has been identified and verified by several research groups. The objectives of this study were to construct a fine genetic map of this QTL region and to examine microcolinearity in the QTL region among wheat, rice, and barley. Two simple sequence repeat (SSR) markers (Xgwm533 and Xgwm493) flanking this QTL were used to screen for recombinants in a population of 3,156 plants derived from a single F₇ plant heterozygous for the Qfhs.ndsu-3BS region. A total of 382 recombinants were identified, and they were genotyped with two more SSR markers and eight sequence-tagged site (STS) markers. A fine genetic map of the Qfhs.ndsu-3BS region was constructed and spanned 6.3 cM. Based on replicated evaluations of homozygous recombinant lines for Type II FHB resistance, Qfhs.ndsu-3BS, redesignated as Fhb1, was placed into a 1.2-cM marker interval flanked by STS3B-189 and STS3B-206. Primers of STS markers were designed from wheat expressed sequence tags homologous to each of six barley genes expected to be located near this QTL region. A comparison of the wheat fine genetic map and physical maps of rice and barley revealed inversions and insertions/deletions. This suggests a complex microcolinearity among wheat, rice, and barley in this QTL region.     

Revealing the genetic architecture of FHB resistance in hexaploid wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) by QTL meta-analysis

Fusarium head blight (FHB) in wheat results in reduced yield and quality and in accumulation of mycotoxins. The objective of this study was to identify genomic regions in wheat involved in the control of FHB resistance applying a QTL meta-analysis approach by combining QTL of 30 mapping populations to propose independent meta-QTL (MQTL). A consensus map was created on which initial QTL were projected. Nineteen MQTL comprising 2–13 initial QTL with widely varying confidence intervals were found on 12 chromosomes. Some of them coincided with genomic regions previously identified (e.g. chromosomes 3BS, 6B), however, some MQTL were newly detected by this study. Separate analysis of populations with the same resistant parent showed a rather high consistency for the Chinese spring wheat donor ‘Sumai 3’, but little consistency for the Chinese donor ‘Wangshuibai’ and the Swiss donor ‘Arina’. According to our results breeders can in future (1) choose parents for crossing not comprising the same resistance loci or QTL intervals, (2) exploit new MQTL, and (3) select markers of some of these MQTL to be used in marker-assisted selection. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Location of a gene regulating drought-induced abscisic acid production on the long arm of chromosome 5A of wheat

The accumulation of abscisic acid (ABA) by detached and partially dehydrated wheat leaves is known to be inherited in a quantitative manner. The location of genes having a major effect on drought-induced ABA accumulation in wheat was determined using a set of single chromosome substitution lines and populations derived from a cross between a high-ABA- and a low-ABA-producing genotype. Examination of a series of chromosome substitution lines of the high-ABA genotype Ciano 67 into the low-ABA recipient Chinese Spring showed that chromosome 5A carries gene(s) that have a major influence on ABA accumulation in a drought test with detached and partially dehydrated leaves (DLT). A similar DLT was used to examine ABA accumulation in a population of F₂ plants and doubled haploid (DH) lines derived from the cross between Chinese Spring (low-ABA) and SQ1 (high-ABA) in which the F₂ population (139 plants) and DH lines (96 lines) were also mapped partially with molecular markers. Analysis of variance of ABA accumulation between and within marker allele classes in the F₂ confirmed the location of a gene(s) regulating ABA accumulation on the long arm of chromosome 5A. MAPMAKERQTL showed the most likely position for the ABA quantitative trait locus (QTL) to be between the loci Xpsr575 and Xpsr426, about 8 cM from Xpsr426. A similar trend for high ABA accumulation was found in DH lines having the SQ1 allele at marker loci in the same region of chromosome 5AL, but the QTL effect was not significant. The function of the QTL is discussed.     

Microsatellite analysis of wheat chromosome 2D allows the reconstruction of chromosomal inheritance in pedigrees of breeding programmes

Fusarium head blight (FHB, scab) is a fungal disease of wheat and other small cereals that is found in both temperate and semi-tropical regions. FHB causes severe yield and quality losses, but the most-serious concern is the possible mycotoxin contamination of cereal food and feed. Breeding for FHB resistance by conventional selection is feasible, but tedious and expensive. This study was conducted to identify and map DNA markers associated with FHB resistance genes in wheat. A population of 364 F₁-derived doubled-haploid (DH) lines from the cross ’CM-82036’ (resistant)/’Remus’ (susceptible) was evaluated for Type II resistance (spread within the spike) during 2 years under field conditions. Marker analysis was performed on 239 randomly chosen DH lines. Different marker types were applied, with an emphasis on AFLP and SSR markers. Analysis of variance, as well as simple and composite interval mapping, were applied. Three genomic regions were found significantly associated with FHB resistance. The most-prominent effect was detected on the short arm of chromosome 3B, explaining up to 60% of the phenotypic variance for Type II FHB resistance. A further QTL was located on chromosome 5A and a third one on 1B. The QTL regions on 3B and 5A were tagged with flanking SSR markers, the 1B QTL was found associated with the high-molecular-weight glutenin locus. These results indicate that FHB resistance is under control of a few major QTLs operating together with unknown numbers of minor genes. Marker-assisted selection for these major QTLs involved in FHB resistance appears feasible and should accelerate the development of resistant and agronomically improved wheat cultivars. Received: 25 January 2001 / Accepted: 18 February 2001     

Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing

Background

One of the reasons hard red winter wheat cultivar ‘Duster’ (PI 644016) is widely grown in the southern Great Plains is that it confers a consistently high level of resistance to biotype GP of Hessian fly (Hf). However, little is known about the genetic mechanism underlying Hf resistance in Duster. This study aimed to unravel complex structures of the Hf region on chromosome 1AS in wheat by using genotyping-by-sequencing (GBS) markers and single nucleotide polymorphism (SNP) markers.

Results

Doubled haploid (DH) lines generated from a cross between two winter wheat cultivars, ‘Duster’ and ‘Billings’ , were used to identify genes in Duster responsible for effective and consistent resistance to Hf. Segregation in reaction of the 282 DH lines to Hf biotype GP fit a one-gene model. The DH population was genotyped using 2,358 markers developed using the GBS approach. A major QTL, explaining 88% of the total phenotypic variation, was mapped to a chromosome region that spanned 178 cM and contained 205 GBS markers plus 1 SSR marker and 1 gene marker, with 0.86 cM per marker in genetic distance. The analyses of GBS marker sequences and further mapping of SSR and gene markers enabled location of the QTL-containing linkage group on the short arm of chromosome 1A. Comparative mapping of the common markers for the gene for QHf.osu-1A^d in Duster and the Hf-resistance gene for QHf.osu-1A⁷⁴ in cultivar ‘2174’ showed that the two Hf resistance genes are located on the same chromosome arm 1AS, only 11.2 cM apart in genetic distance. The gene at QHf.osu-1A^d in Duster has been delimited within a 2.7 cM region.

Conclusion

Two distinct resistance genes exist on the short arm of chromosome 1A as found in the two hard red winter cultivars, 2174 and Duster. Whereas the Hf resistance gene in 2174 is likely allelic to one or more of the previously mapped resistance genes (H9, H10, H11, H16, or H17) in wheat, the gene in Duster is novel and confers a more consistent phenotype than 2174 in response to biotype GP infestation in controlled-environment assays.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1297-7) contains supplementary material, which is available to authorized users.     

A microsatellite marker associated with a QTL for grain protein content on chromosome arm 2DL of bread wheat

 This study was undertaken with a view to tag gene(s) controlling grain protein content (GPC) using molecular markers in bread wheat. For this purpose, the genotype PH132 with high protein content (13.5%) was crossed with genotype WL711 with significantly lower protein content (9.7%), and 100 RILs were derived. These RILs showed normal distribution for protein content. The parental genotypes were analysed with 232 STMS primer pairs for detection of polymorphism. Of these, 167 primer pairs gave scorable amplification products, and 57 detected polymorphism between the parents. Using each of these 57 primer pairs, we carried out bulked segregant analysis on RILs representing the two extremes of the distribution. One primer pair for the locus wmc41 showed association with protein content. This was further confirmed through selective genotyping. The co-segregation data on the molecular marker (wmc41) and protein content on 100 RILs was analysed by means of a single-marker linear regression approach. Significant regression suggested linkage between wmc41 and a QTL (designated as QGpc.ccsu-2D.) for protein content. The results showed that this marker-linked QTL accounted for 18.73% of the variation for protein content between the parents. The marker has been located on chromosome arm 2DL using nulli-tetrasomic lines and two ditelocentric stocks for chromosome 2D. Received: 25 August 1998 / Accepted: 5 January 1999     

High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa‐5A

The Qfhs.ifa‐5A allele, contributing to enhanced Fusarium head blight resistance in wheat, resides in a low‐recombinogenic region of chromosome 5A close to the centromere. A near‐isogenic RIL population segregating for the Qfhs.ifa‐5A resistance allele was developed and among 3650 lines as few as four recombined within the pericentromeric C‐5AS1‐0.40 bin, yielding only a single recombination point. Genetic mapping of the pericentromeric region using a recombination‐dependent approach was thus not successful. To facilitate fine‐mapping the physically large Qfhs.ifa‐5A interval, two gamma‐irradiated deletion panels were generated: (i) seeds of line NIL3 carrying the Qfhs.ifa‐5A resistance allele in an otherwise susceptible background were irradiated and plants thereof were selfed to obtain deletions in homozygous state and (ii) a radiation hybrid panel was produced using irradiated pollen of the wheat line Chinese Spring (CS) for pollinating the CS‐nullisomic5Atetrasomic5B. In total, 5157 radiation selfing and 276 radiation hybrid plants were screened for deletions on 5AS and plants containing deletions were analysed using 102 5AS‐specific markers. Combining genotypic information of both panels yielded an 817‐fold map improvement (cR/cM) for the centromeric bin and was 389‐fold increased across the Qfhs.ifa‐5A interval compared to the genetic map, with an average map resolution of 0.77 Mb/cR. We successfully proved that the RH mapping technique can effectively resolve marker order in low‐recombining regions, including pericentromeric intervals, and simultaneously allow developing an in vivo panel of sister lines differing for induced deletions across the Qfhs.ifa‐5A interval that can be used for phenotyping.     

Mapping of Fhb2 on chromosome 6BS: a gene controlling Fusarium head blight field resistance in bread wheat (Triticum aestivum L.)

Fusarium head blight (FHB) is one of the most important fungal wheat diseases worldwide. Understanding the genetics of FHB resistance is key to facilitate the introgression of different FHB resistance genes into adapted wheat. The objective of this project was to study the FHB resistance QTL on chromosome 6B, quantify the phenotypic variation, and qualitatively map the resistance gene as a Mendelian factor. The FHB resistant parent BW278 (AC Domain*2/Sumai 3) was used as the source of the resistance allele. A large recombinant inbred line (RIL) mapping population was developed from the cross BW278/AC Foremost. The population segregated for three known FHB resistance QTL located on chromosomes 3BSc, 5A, and 6B. Molecular markers on chromosome 6B (WMC104, WMC397, GWM219), 5A (GWM154, GWM304, WMC415), and 3BS (WMC78, GWM566, WMC527) were amplified on approximately 1,440 F_2:7 RILs. The marker information was used to select 89 RILs that were fixed homozygous susceptible for the 3BSc and 5A FHB QTLs and were recombinant in the 6B interval. Disease response was evaluated on 89 RILs and parental checks in the greenhouse and field nurseries. Dual floret injection (DFI) was used in greenhouse trials to evaluate disease severity (DS). Macroconidial spray inoculations were used in field nurseries conducted at two locations in southern Manitoba (Carman and Glenlea) over two years 2003 and 2004, to evaluate disease incidence, disease severity, visual rating index, and Fusarium-damaged kernels. The phenotypic distribution for all five-disease infection measurements was bimodal, with lines resembling either the resistant or susceptible checks and parents. All of the four field traits for FHB resistance mapped qualitatively to a coincident position on chromosome 6BS, flanked by GWM133 and GWM644, and is named Fhb2. The greenhouse-DS trait mapped 2 cM distal to Fhb2. Qualitative mapping of Fhb2 in wheat provides tightly linked markers that can reduce linkage drag associated with marker assisted selection of Fhb2 and aid the pyramiding of different resistance loci for wheat improvement.     

Genetic analysis of the dwarfing gene (Rht8) in wheat. Part I. Molecular mapping of Rht8 on the short arm of chromosome 2D of bread wheat (Triticum aestivum L.)

 Two sets of single chromosome recombinant lines comparing 2D chromosomes from the wheat varieties ‘Ciano 67’ and ‘Mara’ with the common 2D chromosome of ‘Cappelle-Desprez’ in a ‘Cappelle-Desprez’ background were used to detect a diagnostic wheat microsatellite marker for the dwarfing gene Rht8. The genetic linkage maps place the wheat microsatellite marker WMS 261 0.6 cM distal to Rht8 on the short arm of chromosome 2D. By PCR analysis the WMS 261 alleles of ‘Mara’, ‘Cappelle-Desprez’ and ‘Ciano 67’ could be distinguished by different fragment sizes of 192 bp, 174 bp and 165 bp, respectively. A screen of over 100 international varieties of wheat showed that the three allelic variants were all widespread. It also demonstrated that a limited number of varieties carried novel WMS 261 variants of over 200 bp. Following classification of the individual recombinant lines for allelic variants at the WMS 261 locus it was possible to attribute a 7- to 8-cm reduction in plant height with the WMS 261-192-bp allele compared to the WMS 261-174-bp allele in the set of recombinant lines comparing 2D chromosomes of ‘Mara’ and ‘Cappelle-Desprez’. A height reduction of around 3 cm was detected between the WMS 261-174-bp allele and the WMS 261-165-bp allele in the recombinant lines comparing 2D chromosomes of ‘Cappelle-Desprez’ and ‘Ciano 67’. Received: 17 October 1997 / Accepted: 12 November 1997     

Identification and validation of SSR markers linked to the stem rust resistance gene Sr6 on the short arm of chromosome 2D in wheat

The wheat stem rust resistance gene Sr6, present in several wheat cultivars, confers a high level of resistance against a wide range of races of Puccinia graminis f. sp. tritici. Resistance conferred by Sr6 is influenced by temperature, light intensity, and genetic background of the recipient genotype. Here, we report the identification and validation of molecular markers linked to Sr6 that can be used for the detection of this gene in wheat breeding programs. A mapping population of 136 F₂ plants and their F_2:3 families derived from a cross between near-isogenic lines, ‘Chinese Spring’ and ISr6-Ra, were screened for stem rust reaction in the seedling stage. Bulked segregant analysis (BSA) based on seedling tests was used to screen 418 SSR markers that covered the entire genome of wheat. Four markers, Xwmc453, Xcfd43, Xcfd77, and Xgwm484, were mapped within a chromosome region that spanned 9.7 cM from Sr6. The closest markers, Xwmc453 and Xcfd43, were linked to Sr6 at a distance of 1.1 and 1.5 cM, respectively. The markers Xwmc453 and Xcfd43 amplified Sr6-specific marker alleles that were diagnostic for Sr6 in a diverse set of 46 wheat accessions and breeding lines developed and/or collected in Australia, Canada, China, Egypt, Ethiopia, Kenya, Mexico, South Africa, and USA. These markers can now be used for marker-assisted selection of Sr6 and for pyramiding it with other stem rust resistance genes.     

A 3-Mbp fragment on rat chromosome 1 affects susceptibility both to stroke and kidney injury under salt loading in the stroke-prone spontaneously hypertensive rat: a genetic approach using multiple congenic strains

We have previously reported that a major quantitative trait locus (QTL) responsible for susceptibility to salt-induced stroke in the stroke-prone spontaneously hypertensive rat (SHRSP) is located in a 3-Mbp region on chromosome 1 covered by SHRSP.SHR-(D1Rat23-D1Rat213)/Izm (termed Pr1.31), a congenic strain with segments from SHRSP/Izm introduced into the stroke-resistant SHR/Izm. Here, we attempted to narrow down the candidate region on chromosome 1 further through analyses of subcongenic strains constructed for the target region. Simultaneously, salt-induced kidney injury was evaluated through the measurement of urinary albumin and the gene expression of renal tubular injury markers (Kim-1 and Clu) to explore a possible mechanism leading to the onset of stroke. All subcongenic strains examined in this study showed lower susceptibility to salt-induced stroke than SHRSP. Interestingly, Pr1.31 had the lowest stroke susceptibility when compared with newly constructed subcongenic strains harboring fragments of the congenic sequence in Pr1.31. Although Kim-1 and Clu expression after 1 week of salt loading in Pr1.31 did not differ significantly from those in SHRSP, the urinary albumin level of Pr1.31 was significantly lower than those of the other subcongenic strains and that of SHRSP. The present results indicated that, although the congenic fragment in Pr1.31 harbored the gene(s) related to salt-induced organ damages, further genetic dissection of the candidate region was difficult due to multiple QTLs suggested in this region. Further analysis using Pr1.31 will unveil genetic and pathophysiological mechanisms underlying salt-induced end organ damages in SHRSP.     

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1–8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.     

A mutation at the Ala122 position of acetohydroxyacid synthase (AHAS) located on chromosome 6D of wheat: improved resistance to imidazolinone and a faster assay for marker assisted selection

A new mutation at the acetohydroxyacid synthase (AHAS) locus on chromosome 6D of wheat was analyzed in detail because it conferred an improved resistance to the imidazolinone group of herbicides. Sequence analysis showed that the mutation was at the Ala122 position (A122T), a position in AHAS which has not to date been identified in imidazolinone resistant wheat lines even though the position has been identified in other plants and is associated with resistance. An allele-specific assay for the mutation (in the wheat line Brookton-8) was developed and used in a genetic analysis. Two mapping populations were analysed and the doubled haploid progeny from the cross Brookton-8 × Clearfield STL proved to be most informative. The AHAS^Ala122 mutation (A122T) was allelic to the AHAS^Ser653 mutation (S653N) in Clearfield STL (Imi1, on chromosome 6D) and hence was assigned to the chromosome 6D locus. The analysis of the doubled haploid lines in the mapping population demonstrated the greater resistance conferred by the A122T mutation because lines from the same cross and carrying either the A122T or S653N mutations could be directly compared. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.