Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus

Key message

The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect.

Abstract

Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using visual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars.

     

Development of PCR markers linked to resistance to wheat streak mosaic virus in wheat

Wheat streak mosaic virus (WSMV), vectored by the wheat curl mite (Acer tulipae), is an important disease of wheat (Triticum aestivum L.) in the North American Great Plains. Resistant varieties have not been developed for two primary reasons. First, useful sources of resistance have not been available, and second, field screening for virus resistance is laborious and beyond the scope of most breeding programs. The first problem may have been overcome by the development of resistance to both the mite and the virus by the introgression of resistance genes from wild relatives of wheat. To help address the second problem, we have developed polymerase chain reaction (PCR) markers linked to the WSMV resistance gene Wsm1. Wsm1 is contained on a translocated segment from Agropyron intermedium. One sequence-tagged-site (STS) primer set (WG232) and one RAPD marker were found to be linked to the translocation containing Wsm1. The diagnostic RAPD band was cloned and sequenced to allow the design of specific PCR primers. The PCR primers should be useful for transferring Wsm1 into locally adapted cultivars.This is Journal Series No. J-4041 of the Montana Agricultural Experiment Station     

Molecular cytogenetic characterization of Thinopyrum intermedium-derived wheat germplasm specifying resistance to wheat streak mosaic virus

Thinopyrum intermedium is a promising source of resistance to wheat streak mosaic virus (WSMV), a devastating disease of wheat. Three wheat germplasm lines possessing resistance to WSMV, derived from Triticum aestivum×Th. intermedium crosses, are analyzed by C-banding and genomic in situ hybridization (GISH) to determine the amount and location of alien chromatin in the transfer lines. Line CI15092 was confirmed as a disomic substitution line in which wheat chromosome 4A was replaced by Th. intermedium chromosome 4Ai?2. The other two lines, CI17766 and A29-13-3, carry an identical Robertsonian translocation chromosome in which the complete short arm of chromosome 4Ai?2 was transferred to the long arm of wheat chromosome 4A. Fluorescence in situ hybridization (FISH) using ABD genomic DNA from wheat as a probe and S genomic DNA from Pseudoroegneria stipifolia as the blocker, and vice versa, revealed that the entire short arm of the translocation was derived from the short arm of chromosome 4Ai?2 and the breakpoint was located at the centromere. Chromosomal arm ratios (L/S) of 2.12 in CI17766 and 2.15 in A29-13-3 showed that the translocated chromosome is submetacentric. This translocated chromosome is designated as T4AL?? 4Ai?2S as suggested by Friebe et al. (1991).     

Molecular cytogenetic analysis of Agropyron elongatum chromatin in wheat germplasm specifying resistance to wheat streak mosaic virus

Summary Three lines derived from wheat (6x) x Agropyron elongatum (10x) that are resistant to wheat streak mosaic virus (WSMV) were analyzed by chromosome pairing, banding, and in situ hybridization. Line CI15321 was identified as a disomic substitution line where wheat chromosome 1D is replaced by Ag. elongatum chromosome 1Ae-1. Line 87-94-1 is a wheat-Ag. elongatum ditelosomic addition 1Ae-1L. Line CI15322 contains an Ag. elongatum chromosome, 1Ae-2, that substitutes for chromosome 1D. The short arm of 1Ae-2 paired with the short arm of 1Ae-1 at metaphase I (MI) in 82% of the pollen mother cells (PMCs). However, the long arms of these two chromosomes did not pair with each other. In CI15322, the long arm of chromosome 4D has an Agropyron chromosome segment which was derived from the distal part of 1Ae-1L. This translocation chromosome is designated as T4DS·4DL-1L. T4DS·4DL-1Ae-1L has a 0.73 m distal part of the long arm of 4D replaced by a 1.31 m distal segment from 1Ae-1L. The major WSMV resistance gene(s) in these lines is located on the distal part of 1Ae-1L.Contribution No. 92-599-J from the Kansas Agricutural Experiment Station, Kansas State University, Manhattan, Kansas, USA     

Wheat curl mite resistance: interactions of mite feeding with wheat streak mosaic virus infection

The majority of plant viruses are dependent on arthropod vectors for spread between plants. Wheat streak mosaic virus (family Potyviridae, genus Tritimovirus, WSMV) is transmitted by the wheat curl mite, Aceria tosichella Keifer, and this virus and vector cause extensive yield losses in most major wheat (Triticum aestivum L.)-growing regions of the world. Many cultivars in use are susceptible to this vector-virus complex, and yield losses of 10-99% have been documented. wheat curl mite resistance genes have been identified in goat grass, Aegilops tauschii (Coss) Schmal., and transferred to hexaploid wheat, but very few varieties contain effectively wheat curl mite resistance, due to virulent wheat curl mite populations. However, wheat curl mite resistance remains an effective strategy to reduce losses due to WSMV. The goal of our project was to identify the most effective, reproducible, and rapid method for assessing wheat curl mite resistance. We also wanted to determine whether mite resistance is affected by WSMV infection, because the pathogen and pest commonly occur together. Single and group wheat curl mite infestations produced similar amounts of leaf rolling and folding on wheat curl mite-susceptible wheat varieties that were independent of initial wheat curl mite infestation. This finding will allow accurate, efficient, large-scale screening of wheat germplasm for wheat curl mite resistance by infesting plants with sections of wheat leaf tissue containing mixed stages of wheat curl mite. The wheat curl mite-resistant breeding line 'OK05312' displayed antibiosis (reduced wheat curl mite population development). The effect of WSMV infection on wheat curl mite reproduction was genotype-dependent. Mite populations increased on infected wheat curl mite- and WSMV-susceptible plants compared with uninfected plants, but WSMV infection had no significant effect on wheat curl mite populations on resistant plants. OK05312 is a strong source of wheat curl mite resistance for wheat breeding programs.     

Resistance to wheat streak mosaic virus in transgenic wheat engineered with the viral coat protein gene

Wheat (Triticum aestivum) plants were stably transformed with the coat protein (CP) gene of wheat streak mosaic virus (WSMV) by the biolistic method. Eleven independently transformed plant lines were obtained and five were analyzed for gene expression and resistance to WSMV. One line showed high resistance to inoculations of two WSMV strains. This line had milder symptoms and lower virus titer than control plants after inoculation. After infection, new growth did not show symptoms. The observed resistance was similar to the recovery type resistance described previously using WSMV NIb transgene and in other systems. This line looked morphologically normal but had an unusually high transgene copy number (approximately 90 copies per 2C homozygous genome). Northern hybridization analysis indicated a high level of degraded CP mRNA expression. However, no coat protein expression was detected.     

Resistance to wheat streak mosaic virus in transgenic wheat expressing the viral replicase (NIb) gene

Wheat (Triticum aestivum L. cv. Hi-Line) immature embryos were transformed with the replicase gene (NIb) of wheat streak mosaic virus (WSMV) by the biolistic method. Six independent transgenic plant lines were analyzed for transgene expression and for resistance to mechanical inoculation of WSMV at R3 or R4 generation. Four out of the six lines showed various degree of resistance to WSMV. These lines had initially milder symptoms than controls, and the new growth ranged from milder symptoms, a substantial delay in symptom development, or asymptomatic. Two lines displayed higher resistance with very mild virus symptoms after inoculation and the new growth of 72% and 32% plants from these lines were asymptomatic and had no detectable virus through the plant life cycle. Interestingly, five out of the six transgenic lines had no detectable transgene mRNA expression by RNA gel blot hybridization. The only line that had detectable transgene mRNA did not show delay in the symptom development but had overall milder symptom to the virus.     

Structure and temporal dynamics of populations within wheat streak mosaic virus isolates

Variation within the Type and Sidney 81 strains of wheat streak mosaic virus was assessed by single-strand conformation polymorphism (SSCP) analysis and confirmed by nucleotide sequencing. Limiting-dilution subisolates (LDSIs) of each strain were evaluated for polymorphism in the P1, P3, NIa, and CP cistrons. Different SSCP patterns among LDSIs of a strain were associated with single-nucleotide substitutions. Sidney 81 LDSI-S10 was used as founding inoculum to establish three lineages each in wheat, corn, and barley. The P1, HC-Pro, P3, CI, NIa, NIb, and CP cistrons of LDSI-S10 and each lineage at passages 1, 3, 6, and 9 were evaluated for polymorphism. By passage 9, each lineage differed in consensus sequence from LDSI-S10. The majority of substitutions occurred within NIa and CP, although at least one change occurred in each cistron except HC-Pro and P3. Most consensus sequence changes among lineages were independent, with substitutions accumulating over time. However, LDSI-S10 bore a variant nucleotide (G(6016)) in NIa that was restored to A(6016) in eight of nine lineages by passage 6. This near-global reversion is most easily explained by selection. Examination of nonconsensus variation revealed a pool of unique substitutions (singletons) that remained constant in frequency during passage, regardless of the host species examined. These results suggest that mutations arising by viral polymerase error are generated at a constant rate but that most newly generated mutants are sequestered in virions and do not serve as replication templates. Thus, a substantial fraction of variation generated is static and has yet to be tested for relative fitness. In contrast, nonsingleton variation increased upon passage, suggesting that some mutants do serve as replication templates and may become established in a population. Replicated mutants may or may not rise to prominence to become the consensus sequence in a lineage, with the fate of any particular mutant subject to selection and stochastic processes such as genetic drift and population growth factors.     

Hairpin RNA derived from viral NIa gene confers immunity to wheat streak mosaic virus infection in transgenic wheat plants

Wheat streak mosaic virus (WSMV), vectored by Wheat curl mite, has been of great economic importance in the Great Plains of the United States and Canada. Recently, the virus has been identified in Australia, where it has spread quickly to all major wheat growing areas. The difficulties in finding adequate natural resistance in wheat prompted us to develop transgenic resistance based on RNA interference (RNAi). An RNAi construct was designed to target the nuclear inclusion protein ‘a’ (NIa) gene of WSMV. Wheat was stably cotransformed with two plasmids: pStargate‐NIa expressing hairpin RNA (hpRNA) including WSMV sequence and pCMneoSTLS2 with the nptII selectable marker. When T₁ progeny were assayed against WSMV, ten of sixteen families showed complete resistance in transgenic segregants. The resistance was classified as immunity by four criteria: no disease symptoms were produced; ELISA readings were as in uninoculated plants; viral sequences could not be detected by RT‐PCR from leaf extracts; and leaf extracts failed to give infections in susceptible plants when used in test‐inoculation experiments. Southern blot hybridization analysis indicated hpRNA transgene integrated into the wheat genome. Moreover, accumulation of small RNAs derived from the hpRNA transgene sequence positively correlated with immunity. We also showed that the selectable marker gene nptII segregated independently of the hpRNA transgene in some transgenics, and therefore demonstrated that it is possible using these techniques, to produce marker‐free WSMV immune transgenic plants. This is the first report of immunity in wheat to WSMV using a spliceable intron hpRNA strategy.     

Resistance to Wheat streak mosaic virus generated by expression of an artificial polycistronic microRNA in wheat

Wheat streak mosaic virus (WSMV) is a persistent threat to wheat production, necessitating novel approaches for protection. We developed an artificial miRNA strategy against WSMV, incorporating five amiRNAs within one polycistronic amiRNA precursor. Using miRNA sequence and folding rules, we chose five amiRNAs targeting conserved regions of WSMV but avoiding off-targets in wheat. These replaced the natural miRNA in each of five arms of the polycistronic rice miR395, producing amiRNA precursor, FanGuard (FGmiR395), which was transformed into wheat behind a constitutive promoter. Splinted ligation detected all five amiRNAs being processed in transgenic leaves. Resistance was assessed over two generations. Three types of response were observed in T(1) plants of different transgenic families: completely immune; initially resistant with resistance breaking down over time; and initially susceptible followed by plant recovery. Deep sequencing of small RNAs from inoculated leaves allowed the virus sequence to be assembled from an immune transgenic, susceptible transgenic, and susceptible non-transgenic plant; the amiRNA targets were fully conserved in all three isolates, indicating virus replication on some transgenics was not a result of mutational escape by the virus. For resistant families, the resistance segregated with the transgene. Analysis in the T(2) generation confirmed the inheritance of immunity and gave further insights into the other phenotypes. Stable resistant lines developed no symptoms and no virus by ELISA; this resistance was classified as immunity when extracts failed to transmit from inoculated leaves to test plants. This study demonstrates the utility of a polycistronic amiRNA strategy in wheat against WSMV.     

Durable field resistance to wheat yellow mosaic virus in transgenic wheat containing the antisense virus polymerase gene

Wheat yellow mosaic virus (WYMV) has spread rapidly and causes serious yield losses in the major wheat‐growing areas in China. Because it is vectored by the fungus‐like organism Polymyxa graminis that survives for long periods in soil, it is difficult to eliminate by conventional crop management or fungicides. There is also only limited resistance in commercial cultivars. In this research, fourteen independent transgenic events were obtained by co‐transformation with the antisense NIb8 gene (the NIb replicase of WYMV) and a selectable gene bar. Four original transgenic lines (N12, N13, N14 and N15) and an offspring line (N12‐1) showed high and durable resistance to WYMV in the field. Four resistant lines were shown to have segregated and only contain NIb8 (without bar) by PCR and herbicide resistance testing in the later generations. Line N12‐1 showed broad‐spectrum resistance to WYMV isolates from different sites in China. After growing in the infested soil, WYMV could not be detected by tissue printing and Western blot assays of transgenic wheat. The grain yield of transgenic wheat was about 10% greater than the wild‐type susceptible control. Northern blot and small RNA deep sequencing analyses showed that there was no accumulation of small interfering RNAs targeting the NIb8 gene in transgenic wheat plants, suggesting that transgene RNA silencing, a common mechanism of virus‐derived disease resistance, is not involved in the process of WYMV resistance. This durable and broad‐spectrum resistance to WYMV in transgenic wheat will be useful for alleviating the damage caused by WYMV.     

Identification of RFLP markers for resistance to wheat spindle streak mosaic bymovirus (WSSMV) disease.

Wheat spindle streak mosaic bymovirus (WSSMV) causes an economically important disease of winter wheat in Europe and North America. Artificial inoculation with this virus to identify resistant wheat genotypes is difficult. This study was conducted to identify restriction fragment length polymorphism (RFLP) markers associated with resistance to this disease. A population, consisting of 104 F5 recombinant inbred lines from a cross between hexaploid Triticum aestivum cultivars 'Geneva' (resistant) and 'Augusta' (susceptible), was evaluated for WSSMV symptoms under field conditions for four years. Two linked markers on the long arm of chromosome 2D, Xbcd1095 and Xcdo373, were determined to be associated with WSSMV resistance by bulked segregant analysis of the 10 most resistant and 10 most susceptible lines. Marker Xcdo373 accounted for 79% and Xbcd1095 for 73% of the phenotypic variation. Our results suggest that resistance to WSSMV in this population is qualitative in nature and is controlled by few genes. These markers should be useful in the development of wheat cultivars resistant to WSSMV and perhaps also to wheat yellow mosaic bymovirus (WYMV).     

Soilborne wheat mosaic virus movement protein and RNA and wheat spindle streak mosaic virus coat protein accumulate inside resting spores of their vector, Polymyxa graminis

To study virus-vector interactions between Soilborne wheat mosaic virus (SBWMV) or Wheat spindle streak mosaic virus (WSSMV) and Polymyxa graminis Ledingham, P. graminis was propagated in plants grown hydroponically. P. graminis accumulated to high levels in several barley cultivars tested. Multiple developmental stages of P. graminis could be identified in infected barley roots. Accumulation of SBWMV and WSSMV inside P. graminis sporosori in the roots of soil-grown winter wheat and hydroponically grown barley was compared to determine if data obtained from plants naturally infected plants and plants infected by manual inoculation were similar. WSSMV coat protein (CP), SBWMV RNAs, SBWMV movement protein but not SBWMV CP were detected in both soil-grown winter wheat and hydroponically grown barley roots. These data are the first direct evidence that SBWMV and WSSMV are internalized by P. graminis.     

Identification of alien chromatin specifying resistance to wheat streak mosaic and greenbug in wheat germ plasm by C-banding and in situ hybridization

Summary The chromosome constitutions of eight wheat streak mosaic virus (WSMV)-resistant lines, three of which are also greenbug resistant, derived from wheat/ Agropyron intermedium/Aegilops speltoides crosses were analyzed by C-banding and in situ hybridization. All lines could be traced back to CI15092 in which chromosome 4A is substituted for by an Ag. intermedium chromosome designated 4Ai-2, and the derived lines carry either 4Ai-2 or a part of it. Two (CI17881, CI17886) were 4Ai-2 addition lines. CI17882 and CI17885 were 4Ai-2-(4D) substitution lines. CI17883 was a translocation substitution line with a pair of 6AL.4Ai-2S and a pair of 6AS.4Ai-2L chromosomes substituting for chromosome pairs 4D and 6A of wheat. CI17884 carried a 4DL.4Ai-2S translocation which substituted for chromosome 4D. CI17766 carried a 4AL.4Ai-2S translocation substituting for chromosome 4A. The results show that the 4Ai-2 chromosome is related to homoeologous group 4 and that the resistance gene(s) against WSMV is located on the short arm of 4Ai-2. In addition, CI17882, CI17884, and CI17885 contained Ae. speltoides chromosome 7S substituting for chromosome 7A of wheat. The greenbug resistance gene Gb5 was located on chromosome 7S.Contribution No. 90-515-J from the Kansas Agricultural Experiment Station, Kansas State University, Manhattan, Kan., USA     

The distribution of wheat curl mite (Aceria tosichella) lineages in Australia and their potential to transmit wheat streak mosaic virus

The wheat curl mite (WCM), Aceria tosichella , is an eriophyid pest of cereals, and the vector responsible for the transmission of wheat streak mosaic virus (WSMV). In a previous study, the taxonomic status of A. tosichella in Australia was assessed using molecular markers. A. tosichella was shown to consist of two genetically distinct lineages likely to represent different species. Here we show that both lineages occupy similar distributions, occurring throughout the entire Australian wheat belt, and that the lineages are often found in sympatry. CLIMEX analysis suggests that tolerance to heat and desiccation limit the distribution of A. tosichella . In the laboratory, only one WCM lineage transmitted WSMV virus under controlled conditions. These results have implications for the management of WCM and WSMV within Australia.     

Molecular cytogenetic discrimination and reaction to wheat streak mosaic virus and the wheat curl mite in Zhong series of wheat--Thinopyrum intermedium partial amphiploids.

Thinopyrum intermedium (2n = 6x = 42, JJJsJsSS) is potentially a useful source of resistance to wheat streak mosaic virus (WSMV) and its vector, the wheat curl mite (WCM). Five partial amphiploids, namely Zhong 1, Zhong 2, Zhong 3, Zhong 4, and Zhong 5, derived from Triticum aestivum x Thinopyrum intermedium crosses produced in China, were screened for WSMV and WCM resistance. Zhong 1 and Zhong 2 had high levels of resistance to WSMV and WCM. The other three partial amphiploids, Zhong 3, 4, and 5, were resistant to WSMV, but were susceptible to WCM. Genomic in situ hybridization (GISH) using a genomic DNA probe from Pseudoroegneria strigosa (SS, 2n = 14) demonstrated that two partial amphiploids, Zhong 1 and Zhong 2, have almost the identical 10 Th. intermedium chromosomes, including four Js, four J, and two S genome chromosomes. Both of them carry two pairs of J and a pair of Js genome chromosomes and two different translocations that were not observed in the other three Zhong lines. The partial amphiploids Zhong 3, 4, and 5 have another type of basic genomic composition, which is similar to a reconstituted alien genome consisting of four S and four Js genome chromosomes of Th. intermedium (Zhong 5 has two Js chromosomes plus two Js-W translocations) with six translocated chromosomes between S and Js or J genomes. All three lines carry a specific S-S-Js translocated chromosome, which might confer resistance to barley yellow dwarf virus (BYDV-PAV). The present study identified a specific Js2 chromosome present in all five of the Zhong lines, confirming that a Js chromosome carries WSMV resistance. Resistance to WCM may be linked with J or Js chromosomes. The discovery of high levels of resistance to both WSMV and WCM in Zhong 1 and Zhong 2 offers a useful source of resistance to both the virus and its vector for wheat breeding programs.