Genetic analysis of late-maturity α-amylase in twelve wheat populations.

MAIN CONCLUSION: Genetic loci, particularly those with an effect in the independent panel, could be utilised to further reduce LMA expression when used with favourable combinations of genes known to affect LMA. Late maturity α-amylase (LMA) is a grain quality defect involving elevated α-amylase within the aleurone of wheat (Triticum aestivum L.) grains. The genes known to affect expression are the reduced height genes Rht-B1 (chromosome 4B) and Rht-D1 (chromosome 4D), and an ent-copalyl diphosphate synthase gene (LMA-1) on chromosome 7B. Other minor effect loci have been reported, but these are poorly characterised and further genetic understanding is needed. In this study, twelve F4-derived populations were created through single seed descent, genotyped and evaluated for LMA. LMA-1 haplotype C and the Rht-D1b allele substantially reduced LMA expression. The alternative dwarfing genes Rht13 and Rht18 had no significant effect on LMA expression. Additional quantitative trait loci (QTL) were mapped at 16 positions in the wheat genome. Effects on LMA expression were detected for four of these QTL in a large independent panel of Australian wheat lines. The QTL detected in mapping populations and confirmed in the large independent panel provide further opportunity for selection against LMA, especially if combined with Rht-D1b and/or favourable haplotypes of LMA-1.

Multiple loci with cumulative effects on late maturity α-amylase (LMA) in wheat.

MAIN CONCLUSION: The cumulative action of combinations of alleles at several loci on the wheat genome is associated with different levels of resistance to late maturity α-amylase in bread wheat. Resistance to late maturity α-amylase (LMA) in bread wheat (Triticum aestivum L.) involves a complex interaction between the genotype and the environment. Unfortunately, the incidence and severity of LMA expression is difficult to predict and once the trait has been triggered an unacceptably low falling number, high grain α-amylase may be the inevitable consequence. Wheat varieties with different levels of resistance to LMA have been identified but whilst some genetic loci have been reported, the mechanisms involved in resistance and the interaction between resistance loci requires further research. This investigation was focused on mapping resistance loci in populations derived by inter-crossing resistant wheat varieties or crossing resistant lines with a very susceptible line and then mapping quantitative trait loci. In addition to the previously reported locus on chromosome 7B for which a candidate gene has been proposed, loci were mapped on chromosomes 1B, 2A, 2B, 3A, 3B, 4A, 6A and 7D. These loci have limited effects on their own but have a cumulative effect in combination with each other. Further research will be required to determine the nature of the causal genes at these loci, to develop diagnostic markers and determine how the genes fit into the pathway that leads to the induction of α-AMY1 transcription in the aleurone of developing wheat grains. Depending on the target environmental conditions, different combinations of alleles may be required to achieve a low risk of LMA expression.

Analysis of Genetic Diversity and Resistance to Foliar Pathogens Based on Genotyping-by-Sequencing of a Para Rubber Diversity Panel and Progeny of an Interspecific Cross.

Para rubber trees (Hevea brasiliensis) are the largest major source of natural rubber in the world. Its major pathogens are Phytophthora spp., Corynespora cassiicola, and Colletotrichum spp. A rubber diversity panel of 116 clones using over 12,000 single nucleotide polymorphisms (SNPs) from DArTSeq genotyping revealed clear phylogenetic differences in clones that originated from different geographical regions of the world. An integrated linkage map constructed with an F1 progeny of 86 from an interspecific cross between H. brasiliensis and H. benthamiana using 23,978 markers [10,323 SNPs and 13,655 SilicoDArTs] spanned 3947.83 cM with 0.83 cM average marker-interval. The genome scaffolds that were anchored to the linkage map, covering 1.44 Gb of H. brasiliensis reference genome, revealed a high level of collinearity between the genetic map and reference genome. Association analysis identified 12 SNPs significantly associated with the resistance against Phytophthora, Corynespora, and Colletotrichum in six linkage groups: 2, 6, 12, 14, 17, and 18. Kompetitive Allele-Specific PCR marker assays were developed for those 12 SNPs, screened with 178 individuals, and detected clear separation between two genotypes. Within the proximity to those SNPs, 41 potentially key genes that have previously been reported to associate with plant disease resistance were predicted with high confidence.

Identification of Sclerotinia stem rot resistance quantitative trait loci in a chickpea (Cicer arietinum) recombinant inbred line population.

Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum , is one of the most economically devastating diseases in chickpea (Cicer arietinum L.). No complete resistance is available in chickpea to this disease, and the inheritance of partial resistance is not understood. Two hundred F7 recombinant inbred lines (RILs) derived from a cross between a partially resistant variety PBA HatTrick, and a highly susceptible variety Kyabra were characterised for their responses to SSR inoculation. Quantitative trait locus (QTL) analysis was conducted for the area under the disease progress curve (AUDPC) after RIL infection with S. sclerotiorum . Four QTLs on chromosomes, Ca4 (qSSR4-1, qSSR4-2), Ca6 (qSSR6-1) and Ca7 (qSSR7-1), individually accounted for between 4.2 and 15.8% of the total estimated phenotypic variation for the response to SSR inoculation. Candidate genes located in these QTL regions are predicted to be involved in a wide range of processes, including phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction. This is the first study investigating the inheritance of resistance to S. sclerotiorum in chickpea. Markers associated with the identified QTLs could be employed for marker-assisted selection in chickpea breeding.

Analysis of Genetic Diversity in the Traditional Chinese Medicine Plant 'Kushen' (Sophora flavescens Ait.).

Kushen root, from the woody legume Sophora flavescens, is a traditional Chinese medicine that is a key ingredient in several promising cancer treatments. This activity is attributed in part to two quinolizidine alkaloids (QAs), oxymatrine and matrine, that have a variety of therapeutic activities in vitro. Genetic selection is needed to adapt S. flavescens for cultivation and to improve productivity and product quality. Genetic diversity of S. flavescens was investigated using genotyping-by-sequencing (GBS) on 85 plants grown from seeds collected from 9 provinces of China. DArTSeq provided over 10,000 single nucleotide polymorphism (SNP) markers, 1636 of which were used in phylogenetic analysis to reveal clear regional differences for S. flavescens. One accession from each region was selected for PCR-sequencing to identify gene-specific SNPs in the first two QA pathway genes, lysine decarboxylase (LDC) and copper amine oxidase (CAO). To obtain SfCAO sequence for primer design we used a targeted transcript capture and assembly strategy using publicly available RNA sequencing data. Partial gene sequence analysis of SfCAO revealed two recently duplicated genes, SfCAO1 and SfCAO2, in contrast to the single gene found in the QA-producing legume Lupinus angustifolius. We demonstrate high efficiency converting SNPs to Kompetitive Allele Specific PCR (KASP) markers developing 27 new KASP markers, 17 from DArTSeq data, 7 for SfLDC, and 3 for SfCAO1. To complement this genetic diversity analysis a field trial site has been established in South Australia, providing access to diverse S. flavescens material for morphological, transcriptomic, and QA metabolite analysis. Analysis of dissected flower buds revealed that anthesis occurs before buds fully open suggesting a potential for S. flavescens to be an inbreeding species, however this is not supported by the relatively high level of heterozygosity observed. Two plants from the field trial site were analysed by quantitative real-time PCR and levels of matrine and oxymatrine were assessed in a variety of tissues. We are now in a strong position to select diverse plants for crosses to accelerate the process of genetic selection needed to adapt kushen to cultivation and improve productivity and product quality.

Lipoxygenase in Wheat: Genetic Control and Impact on Stability of Lutein and Lutein Esters.

Preservation of lutein concentrations in wheat-based end-products during processing is important both for product quality and nutritional value. A key constituent involved in lutein degradation is endogenous lipoxygenase. Lutein and lutein ester concentrations were compared at intervals during storage of noodle sheets prepared from flour of wheat varieties representing a range in lipoxygenase activity, as well as in different mill streams and in different grain tissues. Higher lipoxygenase concentration was associated with an increased loss of free lutein and lutein mono-esters whereas lutein diesters appeared to be more resistant to degradation. Lutein degradation was reduced in the presence of a lipoxygenase inhibitor, when noodle sheets were heated to destroy enzyme activity or when pH was increased. In addition, three populations were used to investigate the genetic control of lipoxygenase. A previously reported mutation of Lpx-B1.1 was associated with a reduction in activity from high to intermediate whilst a new locus on chromosome 4D was associated with variation between intermediate and near-zero. The gene underlying the 4D locus is a putative lipoxygenase. Stability of lutein could be improved by deployment of the mutations at the 4B and 4D loci and/or by post-harvest storage of grain under conditions that promote esterification.

Dormancy and dormancy release in white-grained wheat (Triticum aestivum L.).

MAIN CONCLUSION: Dormancy in white-grained wheat is conditioned by the cumulative effects of several QTL that delay the onset of the capacity to germinate during ripening and after-ripening. Grain dormancy at harvest-ripeness is a major component of resistance to preharvest sprouting in wheat (Triticum aestivum L.) and an important trait in regions where rain is common during the harvest period. Breeding lines developed in Australia maintained their dormancy phenotype over multiple seasons and during grain ripening, the time between anthesis and the acquisition of the capacity to germinate, dormancy release, increased in line with the strength of dormancy. Genetic dissection of two dormant lines indicated that dormancy was due to the cumulative action of between one and three major genetic loci and several minor loci. This presents a significant challenge for breeders targeting environments with a high risk of sprouting where strong dormancy is desirable. Only around half of the difference in dormancy between the dormant lines and a non-dormant variety could be attributed to the major genetic loci on chromosomes 4A and 3A. A QTL that was mapped on chromosome 5A may be an orthologue of a minor QTL for dormancy in barley. At each locus, the dormancy allele increased the time to dormancy release during ripening. In combination, these alleles had cumulative effects. Embryo sensitivity to abscisic acid was related to the dormancy phenotype of the whole caryopsis, however, changes in concentrations of abscisic acid and gibberellins in embryo sections and de-embryonated grains during ripening and after-ripening could not be linked to the timing of dormancy release.

Three-dimensional imaging reveals that positions of cyst nematode feeding sites relative to xylem vessels differ between susceptible and resistant wheat.

KEY MESSAGE: Resistance conferred by the Cre8 locus of wheat prevents cereal cyst nematode feeding sites from reaching and invading root metaxylem vessels. Cyst nematodes develop syncytial feeding sites within plant roots. The success of these sites is affected by host plant resistance. In wheat (Triticum aestivum L.), 'Cre' loci affect resistance against the cereal cyst nematode (CCN) Heterodera avenae. To investigate how one of these loci (Cre8, on chromosome 6B) confers resistance, CCN-infected root tissue from susceptible (-Cre8) and resistant (+Cre8) wheat plants was examined using confocal microscopy and laser ablation tomography. Confocal analysis of transverse sections showed that feeding sites in the roots of -Cre8 plants were always adjacent to metaxylem vessels, contained many intricate 'web-like' cell walls, and sometimes 'invaded' metaxylem vessels. In contrast, feeding sites in the roots of +Cre8 plants were usually not directly adjacent to metaxylem vessels, had few inner cell walls and did not 'invade' metaxylem vessels. Models based on data from laser ablation tomography confirmed these observations. Confocal analysis of longitudinal sections revealed that CCN-induced xylem modification that had previously been reported for susceptible (-Cre8) wheat plants is less extreme in resistant (+Cre8) plants. Application of a lignin-specific stain revealed that secondary thickening around xylem vessels in CCN-infected roots was greater in +Cre8 plants than in -Cre8 plants. Collectively, these results indicate that Cre8 resistance in wheat acts by preventing cyst nematode feeding sites from reaching and invading root metaxylem vessels.

A QTL on the Ca7 chromosome of chickpea affects resistance to the root-lesion nematode Pratylenchus thornei.

The root-lesion nematode Pratylenchus thornei Sher & Allen, 1953 is a damaging parasite of many crop plants, including the grain legume chickpea (Cicer arietinum L.). Within cultivated chickpea, there are no known sources of strong resistance to P. thornei, but some cultivars have partial resistance. In the research reported here, the genetic basis for differences in P. thornei resistance was analysed using a population derived by accelerated single seed descent from a cross between a partially resistant cultivar, PBA HatTrick, and a very susceptible cultivar, Kyabra. A genetic linkage map was constructed from genotyping-by-sequencing data. Two quantitative trait loci were mapped, one on the Ca4 chromosome and one on the Ca7 chromosome. The Ca7 locus had a greater and more consistent effect than the Ca4 locus. Marker assays designed for single nucleotide polymorphisms on Ca7 were applied to a panel of chickpea accessions. Some of these markers should be useful for marker-assisted selection in chickpea breeding. Haplotype analysis confirmed the Iranian landrace ICC14903 to be the source of the resistance allele in PBA HatTrick and indicated that other Australian cultivars inherited the same allele from other Iranian landraces. A candidate region was defined on the Ca7 pseudomolecule. Within that region, 69 genes have been predicted with high confidence. Among these, two have annotations related to biotic stress response. Three others have previously been reported to be expressed in roots of PBA HatTrick and Kyabra, including one that is more highly expressed in PBA HatTrick than in Kyabra. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01271-8.

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset.

Enset (Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied amplified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.

Infection by cyst nematodes induces rapid remodelling of developing xylem vessels in wheat roots.

Cyst nematodes induce host-plant root cells to form syncytia from which the nematodes feed. Comprehensive histological investigation of these feeding sites is complicated by their variable shape and their positions deep within root tissue. Using tissue clearing and confocal microscopy, we examined thick (up to 150 µm) sections of wheat roots infected by cereal cyst nematodes (Heterodera avenae). This approach provided clear views of feeding sites and surrounding tissues, with resolution sufficient to reveal spatial relationships among nematodes, syncytia and host vascular tissues at the cellular level. Regions of metaxylem vessels near syncytia were found to have deviated from classical developmental patterns. Xylem vessel elements in these regions had failed to elongate but had undergone radial expansion, becoming short and plump rather than long and cylindrical. Further investigation revealed that vessel elements cease to elongate shortly after infection and that they later experience delays in secondary thickening (lignification) of their outer cell walls. Some of these elements were eventually incorporated into syncytial feeding sites. By interfering with a developmental program that normally leads to programmed cell death, H. avenae may permit xylem vessel elements to remain alive for later exploitation by the parasite.

Variation among S-locus haplotypes and among stylar RNases in almond.

In many plant species, self-incompatibility systems limit self-pollination and mating among relatives. This helps maintain genetic diversity in natural populations but imposes constraints in agriculture and plant breeding. In almond [Prunus dulcis (Mill.) D.A. Webb], the specificity of self-incompatibility is mainly determined by stylar ribonuclease (S-RNase) and S-haplotype-specific F-box (SFB) proteins, both encoded within a complex locus, S. Prior to this research, a nearly complete sequence was available for one S-locus haplotype. Here, we report complete sequences for four haplotypes and partial sequences for 11 haplotypes. Haplotypes vary in sequences of genes (particularly S-RNase and SFB), distances between genes and numbers and positions of long terminal repeat transposons. Haplotype variation outside of the S-RNase and SFB genes may help maintain functionally important associations between S-RNase and SFB alleles. Fluorescence-based assays were developed to distinguish among some S-RNase alleles. With three-dimensional modelling of five S-RNase proteins, conserved active sites were identified and variation was observed in electrostatic potential and in the numbers, characteristics and positions of secondary structural elements, loop anchoring points and glycosylation sites. A hypervariable region on the protein surface and differences in the number, location and types of glycosylation sites may contribute to determining S-RNase specificity.

A GDSL Esterase/Lipase Catalyzes the Esterification of Lutein in Bread Wheat.

Xanthophylls are a class of carotenoids that are important micronutrients for humans. They are often found esterified with fatty acids in fruits, vegetables, and certain grains, including bread wheat (Triticum aestivum). Esterification promotes the sequestration and accumulation of carotenoids, thereby enhancing stability, particularly in tissues such as in harvested wheat grain. Here, we report on a plant xanthophyll acyltransferase (XAT) that is both necessary and sufficient for xanthophyll esterification in bread wheat grain. XAT contains a canonical Gly-Asp-Ser-Leu (GDSL) motif and is encoded by a member of the GDSL esterase/lipase gene family. Genetic evidence from allelic variants of wheat and transgenic rice (Oryza sativa) calli demonstrated that XAT catalyzes the formation of xanthophyll esters. XAT has broad substrate specificity and can esterify lutein, ß-cryptoxanthin, and zeaxanthin using multiple acyl donors, yet it has a preference for triacylglycerides, indicating that the enzyme acts via transesterification. A conserved amino acid, Ser-37, is required for activity. Despite xanthophylls being synthesized in plastids, XAT accumulated in the apoplast. Based on analysis of substrate preferences and xanthophyll ester formation in vitro and in vivo using xanthophyll-accumulating rice callus, we propose that disintegration of the cellular structure during wheat grain desiccation facilitates access to lutein-promoting transesterification.plantcell;31/12/3092/FX1F1fx1.

Laser ablation tomography for visualization of root colonization by edaphic organisms.

Soil biota have important effects on crop productivity, but can be difficult to study in situ. Laser ablation tomography (LAT) is a novel method that allows for rapid, three-dimensional quantitative and qualitative analysis of root anatomy, providing new opportunities to investigate interactions between roots and edaphic organisms. LAT was used for analysis of maize roots colonized by arbuscular mycorrhizal fungi, maize roots herbivorized by western corn rootworm, barley roots parasitized by cereal cyst nematode, and common bean roots damaged by Fusarium. UV excitation of root tissues affected by edaphic organisms resulted in differential autofluorescence emission, facilitating the classification of tissues and anatomical features. Samples were spatially resolved in three dimensions, enabling quantification of the volume and distribution of fungal colonization, western corn rootworm damage, nematode feeding sites, tissue compromised by Fusarium, and as well as root anatomical phenotypes. Owing to its capability for high-throughput sample imaging, LAT serves as an excellent tool to conduct large, quantitative screens to characterize genetic control of root anatomy and interactions with edaphic organisms. Additionally, this technology improves interpretation of root-organism interactions in relatively large, opaque root segments, providing opportunities for novel research investigating the effects of root anatomical phenes on associations with edaphic organisms.

Genome-wide association mapping of grain yield in a diverse collection of spring wheat (Triticum aestivum L.) evaluated in southern Australia.

Wheat landraces, wild relatives and other 'exotic' accessions are important sources of new favorable alleles. The use of those exotic alleles is facilitated by having access to information on the association of specific genomic regions with desirable traits. Here, we conducted a genome-wide association study (GWAS) using a wheat panel that includes landraces, synthetic hexaploids and other exotic wheat accessions to identify loci that contribute to increases in grain yield in southern Australia. The 568 accessions were grown in the field during the 2014 and 2015 seasons and measured for plant height, maturity, spike length, spike number, grain yield, plant biomass, HI and TGW. We used the 90K SNP array and two GWAS approaches (GAPIT and QTCAT) to identify loci associated with the different traits. We identified 17 loci with GAPIT and 25 with QTCAT. Ten of these loci were associated with known genes that are routinely employed in marker assisted selection such as Ppd-D1 for maturity and Rht-D1 for plant height and seven of those were detected with both methods. We identified one locus for yield per se in 2014 on chromosome 6B with QTCAT and three in 2015, on chromosomes 4B and 5A with GAPIT and 6B with QTCAT. The 6B loci corresponded to the same region in both years. The favorable haplotypes for yield at the 5A and 6B loci are widespread in Australian accessions with 112 out of 153 carrying the favorable haplotype at the 5A locus and 136 out of 146 carrying the favorable haplotype at the 6A locus, while the favorable haplotype at 4B is only present in 65 out of 149 Australian accessions. The low number of yield QTL in our study corroborate with other GWAS for yield in wheat, where most of the identified loci have very small effects.

Fine mapping of Rha2 in barley reveals candidate genes for resistance against cereal cyst nematode.

KEY MESSAGE: The cereal cyst nematode resistance locus Rha2 was mapped to a 978 kbp region on the long arm of barley chromosome 2H. Three candidate genes are discussed. The cereal cyst nematode (CCN) Heterodera avenae is a soil-borne obligate parasite that can cause severe damage to cereals. This research involved fine mapping of Rha2, a CCN resistance locus on chromosome 2H of barley. Rha2 was previously mapped relative to restriction fragment length polymorphisms (RFLPs) in two mapping populations. Anchoring of flanking RFLP clone sequences to the barley genome assembly defined an interval of 5077 kbp. Genotyping-by-sequencing of resistant and susceptible materials led to the discovery of potentially useful single nucleotide polymorphisms (SNPs). Assays were designed for these SNPs and applied to mapping populations. This narrowed the region of interest to 3966 kbp. Further fine mapping was pursued by crossing and backcrossing the resistant cultivar Sloop SA to its susceptible ancestor Sloop. Evaluation of F2 progeny confirmed that the resistance segregates as a single dominant gene. Genotyping of 9003 BC2F2 progeny identified recombinants. Evaluation of recombinant BC2F3 progeny narrowed the region of interest to 978 kbp. Two of the SNPs within this region proved to be diagnostic of CCN resistance across a wide range of barley germplasm. Fluorescence-based and gel-based assays were developed for these SNPs for use in marker-assisted selection. Within the candidate region of the reference genome, there are nine high-confidence predicted genes. Three of these, one that encodes RAR1 (a cysteine- and histidine-rich domain-containing protein), one that is predicted to encode an acetylglutamate kinase and one that is predicted to encode a tonoplast intrinsic protein, are discussed as candidate genes for CCN resistance.

A locus on barley chromosome 5H affects adult plant resistance to powdery mildew.

Adult plant resistance against plant pathogens is of interest as a means to achieve durable resistance. Prior to this research, the barley lines CLE210 (from Uruguay) and Denar (from the Czech Republic) had been reported to exhibit adult-plant resistance against powdery mildew. Here, populations of doubled haploid lines from crosses of these lines with the susceptible cultivar Baudin were evaluated for powdery mildew resistance in field experiments. Using linkage maps constructed from genotyping-by-sequencing (GBS) data, it was determined that differences in resistance were largely attributable to a region on the long arm of chromosome 5H (5HL). Therefore, KASP™ assays were developed based on GBS tag sequences mapped on that chromosome, providing more reliable genetic maps. In each population, a large-effect QTL was mapped on 5HL. As no sequence variation was detected between CLE210 and Denar in this region of 5HL, the two sources of resistance may be identical by descent in the QTL region and carry the same resistance gene. Marker assays from the QTL region were evaluated on a panel of barley lines, providing information that breeders could use to select assays for use in marker-assisted selection.

Mapping of novel salt tolerance QTL in an Excalibur × Kukri doubled haploid wheat population.

KEY MESSAGE: Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields. Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur × Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity (QG(1-5).asl-7A), one for leaf Na+ exclusion (QNa.asl-7A) and four for leaf K+ accumulation (QK.asl-2B.1, QK.asl-2B.2, QK.asl-5A and QK:Na.asl-6A). The beneficial allele for QG(1-5).asl-7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na+ exclusion and/or K+ maintenance at three QTL (QNa.asl-7A, QK.asl-2B.2 and QK:Na.asl-6A) excluded more Na+ or accumulated more K+ compared to lines without these alleles. Importantly, the QK.asl-2B.2 allele for higher K+ accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.

Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design.

In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars "Nonpareil" and "Lauranne." Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.

Loci on chromosomes 1A and 2A affect resistance to tan (yellow) spot in wheat populations not segregating for tsn1.

KEY MESSAGE: QTL for tan spot resistance were mapped on wheat chromosomes 1A and 2A. Lines were developed with resistance alleles at these loci and at the tsn1 locus on chromosome 5B. These lines expressed significantly higher resistance than the parent with tsn1 only. Tan spot (syn. yellow spot and yellow leaf spot) caused by Pyrenophora tritici-repentis is an important foliar disease of wheat in Australia. Few resistance genes have been mapped in Australian germplasm and only one, known as tsn1 located on chromosome 5B, is known in Australian breeding programs. This gene confers insensitivity to the fungal effector ToxA. The main aim of this study was to map novel resistance loci in two populations: Calingiri/Wyalkatchem, which is fixed for the ToxA-insensitivity allele tsn1, and IGW2574/Annuello, which is fixed for the ToxA-sensitivity allele Tsn1. A second aim was to combine new loci with tsn1 to develop lines with improved resistance. Tan spot severity was evaluated at various growth stages and in multiple environments. Symptom severity traits exhibited quantitative variation. The most significant quantitative trait loci (QTL) were detected on chromosomes 2A and 1A. The QTL on 2A explained up to 29.2% of the genotypic variation in the Calingiri/Wyalkatchem population with the resistance allele contributed by Wyalkatchem. The QTL on 1A explained up to 28.1% of the genotypic variation in the IGW2574/Annuello population with the resistance allele contributed by Annuello. The resistance alleles at both QTL were successfully combined with tsn1 to develop lines that express significantly better resistance at both seedling and adult plant stages than Calingiri which has tsn1 only.