Impaired nodule function in Medicago polymorpha L. infected with alfalfa mosaic virus

The effects of alfalfa mosaic virus (AMV) on growth, nodule formation and nodule function in the annual burr medic, Medicago polymorpha cv. Circle Valley, were investigated in glasshouse pot experiments. Systemically‐infected plants from AMV‐infected seed produced 21% less shoot dry weight and accumulated 24% less fixed nitrogen in shoots than healthy plants when harvested 53 d after germination. At day 75, infected plants showed similar shoot dry weight losses (22%), but the quantity of nitrogen fixed fell by only 15%. At day 53, soluble sugar, starch and bacteroid concentrations in nodules were unaffected by AMV infection, but nitrogenase specific activity was decreased by 25% and soluble amino acids by 20%. Although AMV infection resulted in no differences in the number of nodules formed in the first 11 d after germination or at any harvest thereafter, nodule mass was decreased by 23% for virus‐infected plants at day 53. However this difference disappeared by day 75. Growth of AMV‐infected plants was decreased probably because of impaired N2 fixation with nodule function affected rather than nodulation. Increased nodule mass relative to plant weight in virus‐infected plants, seen at day 75, implied some degree of compensation for the limitation in N2‐fixing capacity. ELISAs for AMV antigen indicated that nodules were active sites of virus multiplication

Comparisons between sequenced and re-sequenced genomes of historical subterranean clover mottle virus isolates

We report comparisons between the complete genomic sequences of five historical Western Australian isolates of subterranean clover mottle virus (SCMoV) from 1989–2000, and an infectious clone of its 1989 isolate. Sanger Sequencing (SS) and High Throughput Sequencing (HTS), or both, were used to obtain these genomes. Four of the SCMoV isolates were sequenced by SS in 1999–2002, but re-sequenced again by HTS in 2020. The pairs of sequences obtained from these four isolates differed by only 18–59 nucleotides. This small difference resulted from the different sequencing methods, the < 1–5 years each isolate was host passaged before freeze-drying prior to HTS sequencing, or a combination of both. Since SCMoV has not been reported outside Australia, this similarity suggests the population sequenced represents the progeny of either an indigenous virus that spread from a native legume to subterranean clover after its introduction or a recent seed-borne incursion from elsewhere. The ORF1 was the most variable, and the phylogenetic tree constructed with ORF1s showed the isolates grouped according to their symptom severity in subterranean clover, indicating the probability that ORF1-encoded P1 protein is a symptom determinant. A satellite RNA was associated with all SCMoV genomes obtained by HTS but none derived by SS

A genetic association study of glutamine-encoding DNA sequence structures, somatic CAG expansion, and DNA repair gene variants, with Huntington disease clinical outcomes

Background: Huntington disease (HD) is caused by an unstable CAG/CAA repeat expansion encoding a toxic polyglutamine tract. Here, we tested the hypotheses that HD outcomes are impacted by somatic expansion of, and polymorphisms within, the HTT CAG/CAA glutamine-encoding repeat, and DNA repair genes. Methods: The sequence of the glutamine-encoding repeat and the proportion of somatic CAG expansions in blood DNA from participants inheriting 40 to 50 CAG repeats within the TRACK-HD and Enroll-HD cohorts were determined using high-throughput ultra-deep-sequencing. Candidate gene polymorphisms were genotyped using kompetitive allele-specific PCR (KASP). Genotypic associations were assessed using time-to-event and regression analyses. Findings: Using data from 203 TRACK-HD and 531 Enroll-HD participants, we show that individuals with higher blood DNA somatic CAG repeat expansion scores have worse HD outcomes: a one-unit increase in somatic expansion score was associated with a Cox hazard ratio for motor onset of 3·05 (95% CI = 1·94 to 4·80, p = 1·3 × 10−6). We also show that individual-specific somatic expansion scores are associated with variants in FAN1 (pFDR = 4·8 × 10-6), MLH3 (pFDR = 8·0 × 10−4), MLH1 (pFDR = 0·004) and MSH3 (pFDR = 0·009). We also show that HD outcomes are best predicted by the number of pure CAGs rather than total encoded-glutamines. Interpretation: These data establish pure CAG length, rather than encoded-glutamine, as the key inherited determinant of downstream pathophysiology. These findings have implications for HD diagnostics, and support somatic expansion as a mechanistic link for genetic modifiers of clinical outcomes, a driver of disease, and potential therapeutic target in HD and related repeat expansion disorders

First report of Bean common mosaic virus in Western Australia

No abstract availabl

Phylogenetic analysis of Bean yellow mosaic virus isolates from four continents: Relationship between the seven groups found and their hosts and origins

Genetic diversity of Bean yellow mosaic virus (BYMV) was studied by comparing sequences from the coat protein (CP) and genome-linked viral protein (VPg) genes of isolates from four continents. CP sequences compared were those of 17 new isolates and 47 others already on the database, while the VPg sequences used were from four new isolates and 10 from the database. Phylogenetic analysis of the CP sequences revealed seven distinct groups, six polytypic and one monotypic. The largest and most genetically diverse polytypic group, which had intragroup diversity of 0.061 nucleotide substitutions per site, contained isolates from natural infections in eight host species. These original isolation hosts included both wild (four) and domesticated (four) species and were from monocotyledonous and dicotyledonous plant families, indicating a generalized natural host range strategy. Only one of the other five polytypic groups spanned both monocotyledons and dicotyledons, and all contained isolates from fewer species (one to four), all of which were domesticated and had lower intragroup diversity (0.019 to 0.045 nucleotide substitutions per site), indicating host specialization. Phylogenetic analysis of the fewer VPg sequences revealed three polytypic and two monotypic groupings. These groups also correlated with original natural isolation hosts, but the branch topologies were sometimes incongruous with those formed by CPs. Also, intragroup diversity was generally higher for VPgs than for CPs. A plausible explanation for the groups found when the 64 different CP sequences were compared is that the generalized group represents the original ancestral type from which the specialist host groups evolved in response to domestication of plants after the advent of agriculture. Data on the geographical origins of the isolates within each group did not reveal whether the specialized groups might have coevolved with their principal natural hosts where these were first domesticated, but this seems plausible

Responses of alternative annual pasture and forage legumes to challenge with infectious subterranean clover mottle virus

The most economically important virus infecting subterranean clover within pastures in Australia is subterranean clover mottle virus (SCMoV) which is transmitted by trampling and grazing of stock, on mower blades, on the wheels of vehicles and through seed. SCMoV was originally discovered in 1979 in plots of subterranean clover at Karridale in south-west Australia. Subsequently, infection was shown to be common in high rainfall pastures in Western Australia, Tasmania, South Australia, New South Wales and Victoria. It was also found naturally infecting some other cultivated annual clovers, and wild annual clovers, such as cluster clover. Diseased clover plants show obvious symptoms consisting of leaf mottling, leaf distortion, decreased leaf size and plant stunting. The incidence of infection often reaches high levels within old pastures. Infection decreases herbage and seed production, diminishing feed for stock and ability of pastures to regenerate annually from seed. The virus contributes to the decline of the subterranean clover component within pastures. Although the reactions of subterranean clover and annual medics to infection with SCMoV are known, there is incomplete information on whether infection with SCMoV might pose a threat to the productivity of pastures sown with the alternative annual pasture and forage legumes currently under evaluation for their commercial potential or already being sown commercially

Occurrence of barley yellow dwarf virus serotypes MAV and RMV in over-summering grasses

Over-summering grasses were collected in the south-west of Western Australia in 1991 and 1992 and tested by ELISA using serotype specific polyclonal antibodies for presence of barley yellow dwarf virus (BYDV) serotypes MAV, PAV and RPV (1991) or MAV, PAV, RPV and RMV (1992). In 1991, 33 samples from 33 sites were tested and MAV was detected in four of 12 samples of Pennisetum clandestinum found infected with BYDV. Presence of MAV was confirmed by retesting these samples using MAV specific monoclonal antibodies. In 1992, 802 samples from 16 grass species were collected from 579 sites in six regions. BYDV was detected in 214 (27%) samples at 178 (31%) sites. MAV was found in 50% and RMV in 38% of infected samples. Both were found either alone or in mixed infections with each other or with PAV and/or RPV; all four serotypes were found in 18 (8%) infected samples. The most important hosts were four perennials: Cynodon dactylon, Eragrostis curvula, Paspalum dilatatum and P. clandestinum. Eight other perennial and five annual grass species were also infected. MAV was most commonly found in C. dactylon and P. clandestinum and RMV in P. dilatatum. All four serotypes were present in the six regions sampled, but the relative proportions of the serotypes found varied from region to region. This paper represents the first extensive survey of MAV and RMV serotypes of BYDV in over-summering grasses in Australia. Aphid species found during this survey infesting over-summering grasses were Rhopalosiphum padi, R. maidis and Hysteroneura setariae. In the Mediterranean type climate of the south-west of Western Australia, BYDV and aphids on over-summering perennial grasses constitute the main reservoir of infection and means of spread to cereal crops. Factors favouring grass survival over summer result in increased cereal crop infection

Occurrence of alfalfa mosaic and subterranean clover red leaf viruses in legume pastures in Western Australia

When leaf samples were collected from 94 Trifolium subterraneum (subterranean clover) pastures from six districts in spring 1993 in the south-west of Western Australia and tested by enzyme-linked immunosorbent assay, no alfalfa mosaic virus (AMV) or subterranean clover red leaf virus (SCRLV) was detected. In contrast, when 21 irrigated T. repens (white clover) pastures from one district (Bunbury) were sampled and tested in January (summer) 1994, AMV was detected in 16, with eight having infection levels >86%, while SCRLV was found in seven at infection levels of <12%. When a further five T. repens pastures were tested for AMV in October (spring) 1994, the virus was found in all with incidences up to 100%. None of the T. repens pastures with high levels of AMV infection had been resown with T. repens within the last 20 years, whereas those resown within the last five years had little or no infection. AMV was detected in 9/91 annual medic (Medicago spp.) pastures from seven wheatbelt districts sampled in spring 1991 or 1993; a single pasture of M. polymorpha (burr medic) cv. Serena was 21% infected, but the other eight infected ones had <3%. AMV seed transmission was detected in 1/19 commercial seed stocks of M. polymorpha harvested in 1991-93. AMV infection was followed over a 12-year period in M. murex (murex medic) cv. Zodiac seed stocks. It persisted readily through successive seed harvests during this period. It is concluded that infection with AMV and SCRLV is currently not a threat to T. subterraneum pastures in the south-west of Western Australia and that AMV seems not to be one in wheatbelt annual medic pastures provided these are sown with healthy medic seed. In contrast, AMV poses a potential threat to the productivity of irrigated T. repens pastures. SCRLV is also sometimes present in T. repens pastures, but was not found at serious levels