Temporal genetic structure patterns in tropical maize populations under reciprocal recurrent selection.

In order to investigate the effect of long term recurrent selection on the pattern of gene diversity, thirty randomly-selected individuals from the progenitors (p) and four selection cycles (C0, C3, C6 and C11) were sampled for DNA analysis from the tropical maize (Zea mays L.) breeding populations, Atherton 1 (AT1) and Atherton 2 (AT2). Fifteen polymorphic Simple Sequence Repeat markers amplified a total of 284 and 257 alleles in AT1 and AT2 populations, respectively. Reductions in the number of alleles were observed at advanced selection cycles. About 11 and 12% of the alleles in AT1 and AT2 populations respectively, were near to fixation. However, a higher number of alleles (37% in AT1 and 33% in AT2) were close to extinction. Fisher's exact test and analysis of molecular variance (AMOVA) showed significant population differentiations. Gene diversity estimates and AMOVA revealed increased genetic differentiations at the expense of loss of heterozygosity. Population differentiations were mainly due to fixation of complementary alleles at a locus in the two breeding populations. The estimates of effective population at an advanced selection cycle were close to the population size predicted by the breeding method.

DAQ00141 Recurrent Selection Program in Hexaploid Wheat

Joint project with the University of Queensland that will use the recurrent selection breeding method to produce adapted, high-yielding and disease resistant wheat parents to breeders.

Crop and environmental attributes underpinning genotype by environment interaction in synthetic-derived bread wheat evaluated in Mexico and Australia

Synthetic backcrossed-derived bread wheats (SBWs) from CIMMYT were grown in the north-west of Mexico (CIANO) and sites across Australia during 3 seasons. A different set of lines was evaluated each season, as new materials became available from the CIMMYT crop enhancement program. Previously, we have evaluated both the performance of genotypes across environments and the genotype x environment interaction (G x E). The objective of this study was to interpret the G x E for yield in terms of crop attributes measured at individual sites and to identify the potential environmental drivers of this interaction. Groups of SBWs with consistent yield performance were identified, often comprising closely related lines. However, contrasting performance was also relatively common among sister lines or between a recurrent parent and its SBWs. Early flowering was a common feature among lines with broad adaptation and/or high yield in the northern Australian wheatbelt, while yields in the southern region did not show any association with the maturity type. Lines with high yields in the southern and northern regions had cooler canopies during flowering and early grain filling. Among the SBWs with Australian genetic backgrounds, lines best adapted to CIANO were tall (>100 cm), with a slightly higher ground cover. These lines also displayed a higher concentration of water-soluble carbohydrates in the stem at flowering, which was negatively correlated with stem number per unit area when evaluated in southern Australia (Horsham). Possible reasons for these patterns are discussed. Selection for yield at CIANO did not specifically identify the lines best adapted to northern Australia, although they were not the most poorly adapted either. In addition, groups of lines with specific adaptation to the south would not have been selected by choosing the highest yielding lines at CIANO. These findings suggest that selection at CIMMYT for Australian environments may be improved by either trait based selection or yield data combined with trait information. Flowering date, canopy temperature around flowering, tiller density, and water-soluble carbohydrate concentration in the stem at flowering seem likely candidates.

Genetic variation within two sympatric spotted gum eucalypts exceeds between taxa variation

Population substructure and hybridization, among other factors, have the potential to cause erroneous associations in linkage disequilibrium (LD) mapping. Two closely related spotted gum eucalypts, Corymbia variegata and C. henryi (Myrtaceae) occur in sympatry in the east coast of Australia and potentially interbreed. They are morphologically similar but are distinguished as separate species based on capsule and foliage size. To determine whether they hybridize in nature and its implications for LD mapping, we investigated the level of molecular divergence between the two species at two sympatric locations separated by 300 kilometres. Very few individuals of intermediate morphology were identified, despite the two species occurring only metres apart. Analysis of genetic structure using 12 microsatellite loci showed that genetic differentiation between populations of the same species at different locations (FST = 0.07 for both species; p = 0.0001) was significantly higher than that observed between species at each location (mean FST = 0.02 and 0.04 for Cherry tree and Bunyaville respectively; p = 0.0001; all Mann-Whitney U-test p ≤ 0.01). No species-specific alleles or significant allele frequency differences were detected within a site, suggesting recurrent local gene flow between the two species. The lack of significant allele frequency differences implies no population stratification along taxonomic lines. This suggested that there is little concern for cryptic hybridization when sampling from sites of sympatry for LD mapping.

DNA markers linked to yield, yield components, and morphological traits in autotetraploid lucerne (Medicago sativa L.)

We have mapped and identified DNA markers linked to morphology, yield, and yield components of lucerne, using a backcross population derived from winter-active parents. The high-yielding and recurrent parent, D, produced individual markers that accounted for up to 18% of total yield over 6 harvests, at Gatton, south-eastern Queensland. The same marker, AC/TT8, was consistently identified at each individual harvest, and in individual harvests accounted for up to 26% of the phenotypic variation for yield. This marker was located in linkage group 2 of the D map, and several other markers positively associated with yield were consistently identified in this linkage group. Similarly, markers negatively associated with yield were consistently identified in the W116 map, W116 being the low-yielding parent. Highly significant positive correlations were observed between total yield and yield for harvests 1-6, and between total yield and stem length, tiller number, leaf yield/plant, leaf yield/5 stems, stem yield/plant, and stem yield/5 stems. Highly significant QTL were located for all these characters as well as for leaf shape and pubescence.

A marker-assisted backcross approach for developing submergence-tolerant rice cultivars

Submergence stress regularly affects 15 million hectares or more of rainfed lowland rice areas in South and Southeast Asia. A major QTL on chromosome 9, Sub1, has provided the opportunity to apply marker assisted backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. In the present study, molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used to apply foreground, recombinant, and background selection, respectively, in backcrosses between a submergence-tolerant donor and the widely grown recurrent parent Swarna. By the BC2F2 generation a submergence tolerant plant was identified that possessed Swarna type simple sequence repeat (SSR) alleles on all fragments analyzed except the tip segment of rice chromosome 9 that possessed the Sub1 locus. A BC3F2 double recombinant plant was identified that was homozygous for all Swarna type alleles except for an approximately 2.3-3.4 Mb region surrounding the Sub1 locus. The results showed that the mega variety Swarna could be efficiently converted to a submergence tolerant variety in three backcross generations, involving a time of two to three years. Polymorphic markers for foreground and recombinant selection were identified for four other mega varieties to develop a wider range of submergence tolerant varieties to meet the needs of farmers in the flood-prone regions. This approach demonstrates the effective use of marker assisted selection for a major QTL in a molecular breeding program.

Identification of intersectional Corymbia hybrids based on seedling morphology improves with parental divergence

Differences in morphology have provided a basis for detecting natural interspecific hybridisation in forest trees for decades but have come to prominence again more recently as a means for directly measuring gene flow from planted forests. Here we examined the utility of seedling morphology for hybrid discrimination in three hybrid groups relevant to the monitoring of gene flow from plantings of Corymbia (L.D. Pryor & L.A.S. Johnson ex Brooker) taxa in subtropical Australia. Thirty leaf and stem characters were assessed on 907 8-month old seedlings from four parental and six hybrid taxa grown in a common garden. Outbred F1 hybrids between spotted gums (Corymbia citriodora subspecies variegata, C. citriodora subspecies citriodora and Corymbia henryi) tended to more closely resemble their maternal Corymbia torelliana parent and the most discriminating characters were the ratio of blade length to maximum perpendicular width, the presence or absence of a lignotuber, and specific leaf weight. Assignment of individuals into genealogical classes based on a multivariate model limited to a set of the more discriminating and independent characters was highest in the hybrid group, where parental taxa were genetically most divergent. Overall power to resolve among outbred F1 hybrids from both parental taxa was low to moderate, but this may not be a limitation to its likely major application of identifying hybrids in seedlots from native spotted gum stands. Advanced generation hybrids (outbred F2 and outbred backcrosses) were more difficult to resolve reliably due to the higher variances of hybrid taxa and the tendency of backcrosses to resemble their recurrent parents. Visual assessments of seedling morphology may provide a filter allowing screening of the large numbers needed to monitor gene flow, but will need to be combined with other hybrid detection methods to ensure hybrids are detected.

High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H

Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designated dense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC7F3 nearly isogenic line (NIL) of cv. Bowman as potentially containing the dense spike mutant locus dsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808 (Hv_SPL14)-CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum and Brachypodium, Classical map-based isolation of the gene dsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

Drought adaptation of stay-green sorghum is associated with canopy development, leaf anatomy, root growth, and water uptake

Stay-green sorghum plants exhibit greener leaves and stems during the grain-filling period under water-limited conditions compared with their senescent counterparts, resulting in increased grain yield, grain mass, and lodging resistance. Stay-green has been mapped to a number of key chromosomal regions, including Stg1, Stg2, Stg3, and Stg4, but the functions of these individual quantitative trait loci (QTLs) remain unclear. The objective of this study was to show how positive effects of Stg QTLs on grain yield under drought can be explained as emergent consequences of their effects on temporal and spatial water-use patterns that result from changes in leaf-area dynamics. A set of four Stg near-isogenic lines (NILs) and their recurrent parent were grown in a range of field and semicontrolled experiments in southeast Queensland, Australia. These studies showed that the four Stg QTLs regulate canopy size by: (1) reducing tillering via increased size of lower leaves, (2) constraining the size of the upper leaves; and (3) in some cases, decreasing the number of leaves per culm. In addition, they variously affect leaf anatomy and root growth. The multiple pathways by which Stg QTLs modulate canopy development can result in considerable developmental plasticity. The reduction in canopy size associated with Stg QTLs reduced pre-flowering water demand, thereby increasing water availability during grain filling and, ultimately, grain yield. The generic physiological mechanisms underlying the stay-green trait suggest that similar Stg QTLs could enhance post-anthesis drought adaptation in other major cereals such as maize, wheat, and rice.

Resistance to Fusarium oxysporum f. sp fragariae and Predicted Breeding Values in Strawberry

Fusarium wilt of strawberry, incited by Fusarium oxysporum f. sp. fragariae (Fof), is a major disease of the cultivated strawberry (Fragaria xananassa) worldwide. An increase in disease outbreaks of the pathogen in Western Australia and Queensland plus the search for alternative disease management strategies place emphasis on the development of resistant cultivars. In response, a partial incomplete diallel cross involving four parents was performed for use in glasshouse resistance screenings. The resulting progeny were evaluated for their susceptibility to Fof. Best-performing progeny and suitability of progenies as parents were determined using data from disease severity ratings and analyzed using a linear mixed model incorporating a pedigree to produce best linear unbiased predictions of breeding values. Variation in disease response, ranging from highly susceptible to resistant, indicates a quantitative effect. The estimate of the narrow-sense heritability was 0.49 +/- 0.04 (SE), suggesting the population should be responsive to phenotypic recurrent selection. Several progeny genotypes have predicted breeding values higher than any of the parents. Knowledge of Fof resistance derived from this study can help select best parents for future crosses for the development of new strawberry cultivars with Fof resistance.

Crusted scabies is associated with increased IL-17 secretion by skin T cells

Scabies is an ectoparasitic infestation by the mite Sarcoptes scabiei. Although commonly self-limiting, a fraction of patients develop severely debilitating crusted scabies. The immune mechanisms underlying the development of crusted scabies are unclear, and undertaking longitudinal infection studies in humans is difficult. We utilized a porcine model to compare cellular immune responses in peripheral blood and skin of pigs with different clinical manifestations of scabies (n = 12), and in uninfected controls (n = 6). Although clinical symptoms were not evident until at least 4 weeks post-infestation, the numbers of peripheral IFNγ-secreting CD4+ T cells and γδ T cells increased in infected pigs from week 1 post-infestation. γδ T cells remained increased in the blood at week 15 post-infestation. At week 15, skin cell infiltrates from pigs with crusted scabies had significantly higher CD8+ T cell, γδ T cell and IL-17+ cell numbers than those with ordinary scabies. Peripheral IL-17 levels were not increased, suggesting that localized skin IL-17-secreting T cells may play a critical role in the pathogenesis of crusted scabies development. Given the potential of anti-IL-17 immunotherapy demonstrated for other inflammatory skin diseases, this study may provide a novel therapeutic avenue for patients with recurrent crusted scabies.

Gene flow from Corymbia hybrids in northern New South Wales

Some of the most productive taxa for forestry are interspecific F1 hybrids grown as exotics in the tropics and subtropics. Attributes of resilience, adaptability and vigour which engender the hybrids for wood production, may also exacerbate the risk they present from gene flow to native species gene pools or to local ecologies as weeds. To determine the biological and genetic factors that influence the extent of hybridisation, we examine the distribution and genealogy of wildlings surrounding plantings of locally-exotic Corymbia torelliana (Section Cadageria) near native C. henryi (Section Maculatae) in northern New South Wales. Our study showed pre-mating and pre- and post-zygotic barriers were incomplete, with in situ generation and natural establishment of both F1 hybrids (n = 3) and advanced generation hybrids under the disturbed conditions bordering native forest. As hybrids were located on alluvial flats exposed to frost, they also likely have an extended ecological range relative to native C. henryi. Despite the likely generation of large viable seed crops on F1 trees at the site over many years, establishment success and survival of advanced generation hybrids may be low, as only 5 immature and no mature advanced generation hybrids were identified. Propagation and genetic analysis of a seed crop from one F1 wildling showed early survival and vigour of seedlings in cultivation was high, and that at least for some F1 in some seasons, backcrossing to the recurrent native C. henryi parent is favoured (60%), whereas selfing (10%) and crossing with other F1 (30%) was less frequent. Transport of seed by stingless bees probably accounted for long distance dispersal from C. torelliana, but this mechanism does not appear to supplement gravity-dispersal of seed from the F1. Coupled with other evidence from studies of bee behaviour, controlled pollination in Corymbia sp., and long-term fitness in second generation eucalypt hybrids, we anticipate gene flow via pollen rather than seed will be the greater challenge for managing the risk of introgression of C. torelliana ancestry into native species from the planted F1 hybrid. If large sources of F1 pollen become available to compete with native pollen, gene flow will probably be frequent and hybrids may establish in disturbed conditions and in habitats beyond the ecological range of their native parent. Further study is needed to determine the degree to which outbreeding depression and poor survival inhibits on-going gene flow.