Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines

Chromosome diversity in Dasypyrum villosum, an important genetic and trait resource for hexaploid wheat engineering

BACKGROUND AND AIMS

Dasypyrum villosum (2n = 2x = 14) harbours potentially beneficial genes for hexaploid and tetraploid wheat improvement. Highly diversified chromosome variation exists among and within accessions due to its open-pollination nature. The wheat-D. villosum T6VS·6AL translocation was widely used in breeding mainly because gene Pm21 in the 6VS segment conferred high and lasting powdery mildew resistance. However, the widespread use of this translocation may narrow the genetic base of wheat. A better solution is to utilize diversified D. villosum accessions as the genetic source for wheat breeding. Analysis of cytological and genetic polymorphisms among D. villosum accessions also provides genetic evolution information on the species. Using cytogenetic and molecular tools we analysed genetic polymorphisms among D. villosum accessions and developed consensus karyotypes to assist the introgression of beneficial genes from D. villosum into wheat.

METHODS

A multiplex probe of repeats for FISH, GISH and molecular markers were used to detect chromosome polymorphisms among D. villosum accessions. Polymorphic signal block types, chromosome heterogeneity and heterozygosity, and chromosome polymorphic information content were used in genetic diversity analysis.

KEY RESULTS

Consensus karyotypes of D. villosum were developed, and the homoeologous statuses of individual D. villosum chromosomes relative to wheat were determined. Tandem repeat probes of pSc119.2, (GAA)10 and the AFA family produced high-resolution signals and not only showed different signal patterns in D. villosum chromosomes but also revealed the varied distribution of tandem repeats among chromosomes and accessions. A total of 106 polymorphic chromosomes were identified from 13 D. villosum accessions and high levels of chromosomal heterozygosity and heterogeneity were observed. A subset of 56 polymorphic chromosomes was transferred into durum wheat through wide crosses, and seven polymorphic chromosomes are described in two newly developed durum-D. villosum amphidiploids.

CONCLUSIONS

Consensus karyotypes of D. villosum and oligonucleotide FISH facilitated identification of polymorphic signal blocks and a high level of chromosomal heterozygosity and heterogeneity among D. villosum accessions, seen in newly developed amphiploids. The abundant genetic diversity of D. villosum and range of alleles, exploitable through interploid crosses, backcrosses and recombination (chromosome engineering), allow introduction of biotic and abiotic stress resistances into wheat, translating into increasing yield, end-use quality and crop sustainability.

Cytogenetic identification and molecular marker development of a novel wheat-Leymus mollis 4Ns(4D) alien disomic substitution line with resistance to stripe rust and Fusarium head blight

Leymus mollis (Trin.) Pilg. (2n = 4x = 28, NsNsXmXm) potentially harbours useful genes that might contribute to the improvement of wheat. We describe M862 as a novel wheat-L. mollis alien disomic substitution line from a cross between wheat cv. 7182 and octoploid Tritileymus M47. Cytological observations indicate that M862 has a chromosome constitution of 2n = 42 = 21II. Two 4D chromosomes of wheat substituted by two L. mollis Ns chromosomes were observed, using the GISH and ND-FISH analyses. Molecular marker, 55K SNP array and wheat-P. huashanica liquid array (GenoBaits^®WheatplusPh) analyses further indicate that the alien chromosomes are L. mollis 4Ns. Therefore, it was deduced that M862 was a wheat-L. mollis 4Ns(4D) alien disomic substitution line. There were also changes in chromosomes 1A, 1D, 2B and 5A detected by ND-FISH analysis. Transcriptome sequencing showed that the structural variation of 1D, 1A and 5A may have smaller impact on gene expression than that for 2B. In addition, a total of 16 markers derived from Lm#4Ns were developed from transcriptome sequences, and these proved to be highly effective for tracking the introduced chromosome. M862 showed reduced height, larger grains (weight and width), and was highly resistance to CYR32 and CYR34 stripe rust races at the seedling stage and mixed stripe rust races (CYR32, CYR33 and CYR34) at the adult stage. It was also resistance to Fusarium head blight (FHB). This alien disomic substitution line M862 may be exploited as an important genetic material in the domestication of stipe rust and FHB resistance wheat varieties.

Development of wheat-Dasypyrum villosum T6V#4S·6AL translocation lines with enhanced inheritance for powdery mildew resistance

New translocation lines with T6V#4S·6AL in the Ph1 and ph1b backgrounds were developed with improved inheritance of powdery mildew resistance. The wheat-Dasypyrum villosum T6V#4S·6DL translocation line Pm97033, which exhibits strong powdery mildew (PM) resistance, was developed many years ago, but has limited application in wheat breeding. One of the major reasons for this is that the translocation chromosome has low transmission rate, which makes it difficult to obtain ideal genotype through recombination with other elite agronomic traits in a limited segregating population. Further modifications are thus needed to make better use of this genetic resource. In this study, Pm97033 and the T6V#2S·6AL translocation line NY-W were hybridized with the CS ph1b mutant, and two F₁ hybrids were hybridized with each other. Then, plants homozygous for the ph1b deletion carrying the alien chromosome arm(s) 6V#2S and 6V#4S were identified from the segregating populations using molecular markers. New T6V#4S·6AL and T6V#2-6V#4S·6AL translocations were identified by molecular markers and confirmed by genomic in situ hybridization (GISH). Individuals that were heterozygous or homozygous for the translocation chromosome in Ph1 and ph1b backgrounds were obtained. The ratio of PM resistance vs. susceptibility in the self-pollinated heterozygous plants was 3:1, and the phenotype was completely consistent with the KASP genotyping. Thus, the new translocation chromosomes had higher transmission rate than the original T6V#4S·6DL, and so can be effectively applied in breeding programs.

Molecular Cytogenetic Identification of the Wheat–Dasypyrum villosum T3DL·3V#3S Translocation Line with Resistance against Stripe Rust

The annual species Dasypyrum villosum possesses several potentially valuable genes for the improvement of common wheat. Previously, we identified a new stripe rust-resistant line, the Chinese Spring (CS)–D. villosum 3V#3 (3D) substitution line (named CD-3), and mapped its potential rust resistance gene (designated as YrCD-3) on the 3V#3 chromosome originating from D. villosum. The objective of the present study was to further narrow down the YrCD-3 locus to a physical region and develop wheat-3V#3 introgression lines with strong stripe rust resistance. By treating CD-3 seeds with 60Co γ-irradiation, two CS-3V#3 translocation lines, T3V#3S.3DL and T3DS.3V#3L (termed 22-12 and 24-20, respectively), were identified from the M4 generation through a combination of non-denaturing fluorescence in situ hybridization (ND-FISH) and functional molecular markers. Stripe rust resistance tests showed that the line 22-12 exhibited strong stripe rust resistance similarly to CD-3, whereas 24-20 was susceptible to stripe rust similarly to CS, indicating that YrCD-3 is located on the short arm of 3V#3. The line 22-12 can potentially be used for further wheat improvement. Additionally, to trace 3V#3 in the wheat genetic background, we produced 30 3V#3-specific sequence tag (EST) markers, among which, 11 markers could identify 3V#3S. These markers could be valuable in fine-mapping YrCD-3.

Diagnostic Kompetitive Allele-Specific PCR Markers of Wheat Broad-Spectrum Powdery Mildew Resistance Genes Pm21, PmV, and Pm12 Developed for High-Throughput Marker-Assisted Selection

Wheat powdery mildew is a devastating disease that seriously threatens yield worldwide. Utilization of host resistance is considered an effective strategy to minimize powdery mildew damage. Pm21, PmV, and Pm12 confer broad-spectrum resistance to wheat powdery mildew in China, of which Pm21 and PmV are allelic genes derived from the 6VS chromosome of Dasypyrum villosum, and Pm12 is derived from the 6SS chromosome of Aegilops speltoides and most likely orthologous to the former two genes. To accurately and efficiently transfer and pyramid these genes using marker-assisted selection (MAS), distinctive single-nucleotide polymorphisms (SNPs) among the exon sequences of Pm21, PmV, and Pm12 and their homologous sequences in the common wheat genome were identified and then used for developing diagnostic Kompetitive Allele-Specific PCR (KASP) markers. The markers were validated in different genotypes including transgenic vectors, transgenic lines, translocation lines, resistance stocks with documented Pm genes, and in multiple susceptible cultivars without Pm genes. As a result, we initially developed a KASP marker that can simultaneously diagnose Pm21, Pm12, and PmV. Subsequently, we obtained a highly diagnostic KASP marker for each of the three genes that could distinguish among the three genes and also accurately distinguish them from other resistant stocks with documented Pm genes and from multiple susceptible genotypes. Compared with previously reported markers, the highly diagnostic KASP markers developed in this study have the advantages of low cost, easy assay, accuracy, and potentially high throughput for MAS.

Screening and functional characterization of candidate resistance genes to powdery mildew from Dasypyrum villosum#4 in a wheat line Pm97033

KEY MESSAGE

Three genes designated DvLox, Pm21#4, and Pm21#4-H identified in a wheat-Dasypyrum villosum#4 T6V#4S·6DL translocation line Pm97033 conferred wheat for powdery mildew resistance. Powdery mildew (PM) caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most devastating diseases in wheat. To date, only a few genes conferring resistance to wheat PM are cloned. Dasypyrum villosum is a wild relative of wheat, which provides Pm21 conferring wheat immunity to PM. In this study, we obtained many differentially expressed genes (DEGs) from a wheat-D. villosum#4 T6V#4S·6DL translocation line Pm97033 using RNA-sequencing. Among them, 7 DEGs associated with pathogen resistance were up-regulated in front of Bgt infection. Virus-induced gene silencing and transformation assays demonstrated that two of them, DvLox and Pm21#4 encoding a lipoxygenase and a encoding coiled-coil/nucleotide-binding site/leucine-rich repeat resistance protein, conferred wheat PM resistance. The transgenic wheat plants expressing DvLox enhanced PM resistance, and the transgenic wheat plants expressing Pm21#4 showed PM immunity. The Pm21#4-silenced Pm97033 plants by the cluster regularly interspaced short palindromic repeats-associated endonuclease (CRISPR/Cas9) system were susceptible to PM. Thus, Pm21#4 is a key gene contributing PM immune resistance in Pm97033. Constitutively expression of Pm21#4-H, which is silenced in Pm97033 and D. villosum#4, endowed a PM-susceptible wheat variety Fielder with PM immune resistance.

Molecular Characterization of the Dwarf53 Gene Homolog in Dasypyrum villosum

The Dwarf53 (D53) gene, first studied in rice, encodes a protein that acts as a repressor of the physiological response of plants to strigolactones—substances that regulate the activity of axillary buds, stem growth, branching of roots and other physiological processes. In this work, we isolated and sequenced the homolog of the D53 gene in several accessions of the wild grass Dasypyrum villosum of different geographical origins, resulting in the discovery of large allelic variety. A molecular marker was also created that allows us to differentiate the D. villosum D53 gene from common wheat genes. Using this marker and monosomic addition, substitution and translocation wheat lines carrying the known D. villosum chromosomes, the D53 gene was localized on the long arm of the 5V chromosome.

Pairing and Exchanging between Daypyrum villosum Chromosomes 6V#2 and 6V#4 in the Hybrids of Two Different Wheat Alien Substitution Lines

Normal pairing and exchanging is an important basis to evaluate the genetic relationship between homologous chromosomes in a wheat background. The pairing behavior between 6V#2 and 6V#4, two chromosomes from different Dasypyrum villosum accessions, is still not clear. In this study, two wheat alien substitution lines, 6V#2 (6A) and 6V#4 (6D), were crossed to obtain the F₁ hybrids and F₂ segregating populations, and the testcross populations were obtained by using the F₁ as a parent crossed with wheat variety Wan7107. The chromosomal behavior at meiosis in pollen mother cells (PMCs) of the F₁ hybrids was observed using a genomic in situ hybridization (GISH) technique. Exchange events of two alien chromosomes were investigated in the F₂ populations using nine polymerase chain reaction (PCR) markers located on the 6V short arm. The results showed that the two alien chromosomes could pair with each other to form ring- or rod-shaped bivalent chromosomes in 79.76% of the total PMCs, and most were pulled to two poles evenly at anaphase I. Investigation of the F₂ populations showed that the segregation ratios of seven markers were consistent with the theoretical values 3:1 or 1:2:1, and recombinants among markers were detected. A genetic linkage map of nine PCR markers for 6VS was accordingly constructed based on the exchange frequencies and compared with the physical maps of wheat and barley based on homologous sequences of the markers, which showed that conservation of sequence order compared to 6V was 6H and 6B > 6A > 6D. In the testcross populations with 482 plants, seven showed susceptibility to powdery mildew (PM) and lacked amplification of alien chromosomal bands. Six other plants had amplification of specific bands of both the alien chromosomes at multiple sites, which suggested that the alien chromosomes had abnormal separation behavior in about 1.5% of the PMCs in F₁, which resulted in some gametes containing two alien chromosomes. In addition, three new types of chromosome substitution were developed. This study lays a foundation for alien allelism tests and further assessment of the genetic relationship among 6V#2, 6V#4, and their wheat homoeologous chromosomes.

Discovery of powdery mildew resistance gene candidates from Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing

Powdery mildew is one of the most widespread diseases of wheat. The development and deployment of resistant varieties are one of the most economical and effective methods to manage this disease. Our previous study showed that the gene(s) at 2Mb in Chinese Spring (CS)-Aegilops biuncialis 2Mb disomic addition line TA7733 conferred a high level of resistance to powdery mildew of wheat. In this study, resistance spectrum of TA7733 was assayed by using 15 Blumeria graminis f. sp. tritici (Bgt) isolates prevalent in different regions of China. The result indicated that TA7733 was highly resistant to all tested Bgt isolates and the gene(s) on chromosome 2Mb conferred broad-spectrum resistance to powdery mildew. In order to characterize mechanism of powdery mildew resistance by identifying candidates R-genes derived from Ae. biuncialis chromosome 2Mb and develop 2Mb-specific molecular markers, we performed RNA-seq analysis on TA7733 and CS. In total we identified 7,278 unigenes that showed specific expression in TA7733 pre and post Bgt-infection when compared to CS. Of these 7,278 unigenes, 295 were annotated as putative resistance (R) genes. Comparatively analysis of R-gene sequences from TA7733 and CS and integration CS Ref Seq v1.0 were used to develop R-gene specific primers. Of 295 R-genes we identified 53 R-genes were specific to 2Mb and could be involved in powdery mildew resistance. Functional annotation of majority of the 53 R-genes encoded nucleotide binding leucine rich repeat (NLR) protein. The broad-spectrum resistance to powdery mildew in TA7733 and availability of 2Mb-derived putative candidate R-gene specific molecular markers identified in this study will lay foundations for transferring powdery mildew resistance from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination. Our study also provides useful candidates for further isolation and cloning of powdery mildew resistance gene(s) from Ae. biuncialis chromosome 2Mb.