Fr-B2 is a complex locus on chromosome 5B that affects frost tolerance, days to heading, grain yield and probably other traits of commercial importance in wheat (Triticum aestivum L.). It interacts epistatically with other major genes, especially VRN1. There are two known alleles of Fr-B2: an intact, wild-type allele, and an allele with a large deletion. Published methods for identifying these alleles are slow and expensive, making the development of a high-throughput, co-dominant SNP (single-nucleotide polymorphism) marker highly desirable, especially for commercial wheat breeding.

A diverse panel of cultivars and breeding lines was characterised for SNPs and alleles of Fr-B2. Four SNP markers co-segregated as a haplotype block with Fr-B2 across unrelated cultivars and related backcrosses differing for alleles of Fr-B2. A robust KASP (Kompetitive allele-specific PCR) assay was developed for one of the SNPs, KASP_IWB26333, which should facilitate the inclusion of Fr-B2 on genotyping platforms for breeding and research.

Resistance to pre-harvest sprouting (PHS) in wheat (Triticum aestivum L.) is one of the most valuable traits in many breeding programs. However, the quantitative nature of inheritance of PHS resistance challenges the study of this trait. Near-isogenic lines (NILs) can turn a complicated quantitative trait into a Mendelian factor (qualitative) and are, therefore, valuable materials for identification of the gene(s) responsible for a specific phenotypic trait and for functional studies of specific loci. Five pairs of NILs were developed and confirmed for a major quantitative trait locus (QTL) located on the long arm of chromosome 3A contributing to PHS resistance in wheat. These NILs were generated by using the heterogeneous inbred family method and a fast generation-cycling system. Significant differences in PHS resistance between the isolines were detected in the NILs. The presence of the PHS-resistance allele from the resistant parent increased resistance to sprouting on spikes by 26.7–96.8%, with an average of 73.8%, and increased seed dormancy by 36.9–87.2%, with an average of 59.9% across the NILs. These NILs are being used for the identification of candidate genes responsible for this major PHS-resistance locus on wheat chromosome arm 3AL.

High-molecular-weight glutenin subunits (HMW-GS) in bread wheat are major determinants of dough viscoelastic properties and the end-use quality of wheat flour. Cysteine residues, which form intermolecular disulphide bonds in HMW-GS, could improve the strength of gluten. To our knowledge, the number and position of cysteine residues in HMW-GS are conserved between wheat (Triticum aestivum) and Aegilops markgrafii. In the present study, we modified a gene (1Cx1.1) from Ae. markgrafii for an HMW-GS that possessed the typical structure and conserved number of cysteines. Site-directed mutagenesis was carried out in 1Cx1.1 to investigate how the position of cysteine residues in HMW-GS affects the mixing properties of dough. Six HMW-GS containing an extra cysteine residue were expressed in Escherichia coli, and the proteins were purified at sufficient scale for incorporation into flour to test dough quality. There were large differences in dough property among samples containing different modified subunits. Cysteine substituting in the N-terminal or repetitive-domain of HMW-GS could significantly improve dough quality. The results showed that the strategy was useful for providing genetic resources for gene engineering, and hence could be valuable for improving the processing quality of wheat.

Combining morphological and molecular data to identify genetic variation and marker–trait association is one of the most important prerequisites for genomics-assisted selection in crop improvement. To this end, a total of 138 finger millet (Eleusine coracana subsp. coracana) accessions including five improved varieties were evaluated to assess the genetic variation and population structure and undertake association mapping. These accessions were basically collected from Ethiopia (96), Eritrea (8), Kenya (7), Zambia (9) and Zimbabwe (13). Finger millet accessions were evaluated in the field for 10 important agronomic traits and also characterised using a set of 20 microsatellite markers. Mean polymorphism information content of 0.61 was observed from a total of 222 alleles with an average of 11.1 alleles per microsatellite locus. About 61% of alleles detected were rare (<5%) and specific allele amplification was observed in 34 accessions. Both weighted neighbour-joining based clustering using molecular data and hierarchical clustering using phenotypic trait data grouped the 138 accessions into four major clusters that were not entirely based on their geographical origins. Genome-wide association studies depicted 16 significant (P < 0.01) associations between 13 microsatellite markers and six agronomic traits. Our results reveal a unique abundance of rare alleles in finger millet and highlight the need for more careful selection of genome-wide association studies in the future in order to capture the contribution of rare alleles to important agronomic traits.

Development of food products from legume flours is increasing. Seed and flour characteristics must be analysed for selection of the best screening quality traits. With this purpose, germplasm collections of faba bean (Vicia faba), chickpea (Cicer arietinum), lentil (Lens culinaris) and grass pea (Lathyrus sativus) were evaluated for their physico-chemical, pasting and cooking characteristics. The accessions were grouped accordingly to several seed traits (size, shape, colour, variety and surface) that affected final viscosity, cooking time, hydration capacity and seed weight. In general, seed weight was correlated with hydration capacity. Among species, faba bean revealed higher values of pasting parameters. Cooking time was significantly negatively correlated with final viscosity (–0.298) and positively correlated with seed weight (0.601). The general variance was analysed by using principal component analysis, which allowed identification of specific accessions with important traits such as higher protein or fibre content, hydration capacity or seed weight.

Narbon vetch (Vicia narbonensis L.) is a promising forage legume with good resistance to cold and drought. The assessment of genetic diversity of Narbon vetch is an essential component in germplasm management. In this study, we analysed the genetic diversity of 13 local and introduced Narbon vetch accessions from three continents using 27 morphological traits and 13 simple sequence repeat (SSR) markers. Significant differences among accessions for morphological and phenological traits were observed. The SSR markers showed a total of 126 alleles with a mean number of two alleles per locus. Polymorphic information content values were in the range of 0.772–0.915 with an average of 0.858. A high level of diversity (Nei’s genetic differentiation index of 59) was observed among accessions. Analysis of genetic distances separated the studied accessions into three groups based on both morphological and SSR markers. Cluster analysis of the SSR markers separated the accessions into three groups according to geographical origin. The Tunisian populations shared the same morphological traits but differed genetically from each other and were similar to those from Lebanon. A significant correlation was detected between morphological traits and SSR markers. The results suggested that SSR markers can be used to efficiently distinguish Narbon vetch accessions and estimate their genetic diversity.

Early-season leaf loss due to damage by thrips (Thysanoptera: Thripidae) is considered an important issue by Australian cotton growers. To understand the potential impact of early-season leaf loss in the southern region of New South Wales, we investigated the effects of artificial defoliation on cotton growth, maturity timing and lint yield over four seasons (2013–14 to 2016–17) in commercial cotton crops in the Riverina district. Four defoliation scenarios were investigated: (i) complete defoliation, 100% removal of all true leaves from all plants; (ii) partial defoliation by plant, 100% removal of all true leaves from 75% of plants; (iii) partial defoliation by leaf, removal of 75% of leaf area from all individual true leaves on all plants; and (iv) no defoliation. Defoliation was done by hand at the onset of the 2-, 4-, and 6-node growth stages. Defoliated plants were initially shorter than undefoliated (control) plants, but by ∼100-days post seedling emergence, height differences were no longer statistically significant in two of the four seasons. Defoliation did not affect the total number of bolls shortly before harvest. However, complete defoliation delayed crop maturity by up to 18 days and partial defoliation by plant delayed crop maturity by up to 8 days. Because of the delays, fully defoliated plants often had fewer open bolls shortly before harvest and yielded significantly less than undefoliated plants in three of the four seasons. A laboratory experiment with caged cotton seedlings showed that weekly introductions of up to10 thrips per seedling (predominantly onion thrips (Thrips tabaci), the most abundant species on cotton in the region) caused significant clubbing in true leaves, but the total leaf area was not significantly reduced at the 6-node stage. Implications of the results for southern cotton integrated pest management are discussed.

In Australia, Sonchus oleraceus has been emerging as a major weed in conservation agricultural systems. The effect of environmental factors on germination and emergence of S. oleraceus was assessed on populations collected from Gatton (SOG) and St. George (SOS) regions of Australia, which are high and low rainfall regions respectively. Germination of both populations responded similarly to various environmental factors studied. Although S. oleraceus seeds germinated under a broad range of temperatures (15/5, 20/10, 25/15 and 30/20°C day/night), germination was lower at 15/5°C. There was only 47–53% germination under dark conditions compared with 62–87% under alternating light–dark. Germination was only 2 and 3% at –0.8 MPa osmotic potential for SOG and SOS populations respectively, and no germination occurred at –1 MPa. Germination was 6 and 8% at 200 mM NaCl for SOG and SOS populations respectively. Although S. oleraceus seed germination exceeded 80% for pH 6–7, germination was reduced at pH outside this range. Germination was 83 and 87% for SOG and SOS populations respectively at the soil surface; and emergence decreased with increasing depth, with none from seeds buried at 6 cm depth. Wheat residue amount within the range of 0–2000 kg ha^–1 did not alter germination; however, germination was significantly reduced when the crop residue amount increased to 4000 kg ha^–1 and the lowest germination was at 6000 kg ha^–1. The potential to germinate under diverse environmental conditions correlates with the widespread occurrence of this weed in the northern region of Australia. High residue amounts and occasional tillage leading to deep burial of seeds may reduce its emergence and incidence.

Spring black stem and leaf spot of lucerne (alfalfa, Medicago sativa L.), caused by Phoma medicaginis, is an important disease in temperate regions of the world. It is now a serious disease threatening global lucerne production. This experiment was designed to test the combined effects of the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae and the rhizobium Sinorhizobium medicae on growth, nutrient uptake and disease severity in lucerne. The results showed that F. mosseae increased plant phosphorus and nitrogen uptake and plant dry weight, and this beneficial effect was enhanced when in association with S. medicae. Rhizobial and AM fungal effects were mutually promoting; inoculation with AM fungus significantly increased the formation of root nodules, and inoculation with rhizobium increased the percentage of root length colonised by AM fungus (P < 0.05). After infection with P. medicaginis, typical leaf spot symptoms with the lowest disease incidence and disease index occurred on plants that were host to both F. mosseae and S. medicae. Plants with both symbiotic microorganisms had higher activities (concentrations) of phenylalanine ammonia-lyase, chitinase, β-1,3-glucanase, lignin, hydroxyproline-rich glycoprotein and jasmonic acid. Therefore, the tested AM fungus (F. mosseae) and rhizobium (S. medicae) have the potential to reduce damage and yield loss in lucerne from spring black stem and leaf spot caused by P. medicaginis.

Based on biomass composition of plants collected from saline habitats, Phragmites karka (Retz.) Trin. ex Steud. has emerged as a suitable feedstock for biofuel. In the present study, plant growth, eco-physiological responses and bioenergy characteristics of P. karka grown under conditions ranging from non-saline to ∼80% seawater salinity are reported. Moderate salinity (NaCl at 100 mol m^–3) increased plant fresh weight (20%), number of leaves (25%) and specific plant length, which were directly linked with increased net photosynthetic rate (25%) and stomatal conductance (25%) compared with the non-saline control. Higher photosynthetic efficiency was achieved by increasing electron transport rate (ETR, 20%), effective quantum yield (YII, 21%) and maximum efficiency of photosystem II (Fv/Fm, 20%). Decreased non-photochemical quenching (Y(NPQ)) and malondialdehyde content (18%) indicated an oxidative balance, which was also reflected in total carotenoids and chlorophylls. These eco-physiological parameters worked together to increase cellulose (34%) and hemicellulose (70%) at NaCl concentrations up to 200 mol m^–3. Decreased growth under higher salinity could be linked with photosynthesis inhibition, due to stomatal closure and co-occurring reduction in CO₂ uptake. Lower stomatal conductance increased water-use efficiency but led to over-production of reactive oxygen species, which disturbed oxidative stability (increasing ETR/P_N) and imposed membrane leakage. Consequently, plants accumulated more carotenoids and soluble carbohydrates to stabilise PSII machinery (Fv/Fm, YII and Y(NPQ)), and to survive under high salinity. Such adaptations, however, led to growth penalty and reduced quality of lignocellulosic biomass. The above findings suggest that P. karka qualifies as a suitable raw material for biofuel under moderate salinity.