Arron H. Carter

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.

Genome-wide association mapping for stripe rust (Puccinia striiformis F. sp. tritici) in US Pacific Northwest winter wheat (Triticum aestivum L.)

Key messagePotential novel and known QTL for race-specific all-stage and adult plant resistance to stripe rust were identified by genome-wide association mapping in the US PNW winter wheat accessions.AbstractStripe rust (Puccinia striiformis F. sp. tritici; also known as yellow rust) is a globally devastating disease of wheat (Triticum aestivum L.) and a major threat to wheat production in the US Pacific Northwest (PNW), therefore both adult plant and all-stage resistance have been introduced into the winter wheat breeding programs in the PNW. The goal of this study was to identify quantitative trait loci (QTL) and molecular markers for these resistances through genome-wide association (GWAS) mapping in winter wheat accessions adapted to the PNW. Stripe rust response for adult plants was evaluated in naturally occurring epidemics in a total of nine environments in Washington State, USA. Seedling response was evaluated with three races under artificial inoculation in the greenhouse. The panel was genotyped with the 9K Illumina Wheat single nucleotide polymorphism (SNP) array and additional markers linked to previously reported genes and QTL for stripe rust resistance. The population was grouped into three sub-populations. Markers linked to Yr17 and previously reported QTL for stripe rust resistance were identified on chromosomes 1B, 2A, and 2B. Potentially novel QTL associated with race-specific seedling response were identified on chromosomes 1B and 1D. Potentially novel QTL associated with adult plant response were located on chromosomes 2A, 2B, 3B, 4A, and 4B. Stripe rust was reduced when multiple alleles for resistance were present. The resistant allele frequencies were different among sub-populations in the panel. This information provides breeders with germplasm and closely linked markers for stripe rust resistance to facilitate the transfer of multiple loci for durable stripe rust resistance into wheat breeding lines and cultivars.

Field-based crop phenotyping

High-resolution multispectral aerial imaging was used to estimate winter wheat growth parameters.Visual ratings of emergence and spring stand were compared with data extracted from aerial images.A high correlation (r=0.86) between the ground-truth and aerial image data was observed.UAV-based sensing can be an alternative to standard methods for rapid field-based crop phenotyping. The physical growing environment of winter wheat can critically be affected by micro-climatic and seasonal changes in a given agroclimatic zone. Therefore, winter wheat breeding efforts across the globe focus heavily on emergence and winter survival, as these traits must first be accomplished before yield potential can be evaluated. In this study, multispectral imaging using unmanned aerial vehicle was investigated for evaluation of seedling emergence and spring stand (an estimate of winter survival) of three winter wheat market classes in Washington State. The studied market classes were soft white club, hard red, and soft white winter wheat varieties. Strong correlation between the ground-truth and aerial image-based emergence (Pearson correlation coefficient, r=0.87) and spring stand (r=0.86) estimates was established. Overall, aerial sensing technique can be a useful tool to evaluate emergence and spring stand phenotypic traits. Also, the image database can serve as a virtual record during winter wheat variety development and may be used to evaluate the variety performance over the study years.

Mapping Stripe Rust Resistance in a BrundageXCoda Winter Wheat Recombinant Inbred Line Population

A recombinant inbred line (RIL) mapping population developed from a cross between winter wheat (Triticum aestivum L.) cultivars Coda and Brundage was evaluated for reaction to stripe rust (caused by Puccinia striiformis f. sp. tritici). Two hundred and sixty eight RIL from the population were evaluated in replicated field trials in a total of nine site-year locations in the U.S. Pacific Northwest. Seedling reaction to stripe rust races PST-100, PST-114 and PST-127 was also examined. A linkage map consisting of 2,391 polymorphic DNA markers was developed covering all chromosomes of wheat with the exception of 1D. Two QTL on chromosome 1B were associated with adult plant and seedling reaction and were the most significant QTL detected. Together these QTL reduced adult plant infection type from a score of seven to a score of two reduced disease severity by an average of 25% and provided protection against race PST-100, PST-114 and PST-127 in the seedling stage. The location of these QTL and the race specificity provided by them suggest that observed effects at this locus are due to a complementation of the previously known but defeated resistances of the cultivar Tres combining with that of Madsen (the two parent cultivars of Coda). Two additional QTL on chromosome 3B and one on 5B were associated with adult plant reaction only, and a single QTL on chromosome 5D was associated with seedling reaction to PST-114. Coda has been resistant to stripe rust since its release in 2000, indicating that combining multiple resistance genes for stripe rust provides durable resistance, especially when all-stage resistance genes are combined in a fashion to maximize the number of races they protect against. Identified molecular markers will allow for an efficient transfer of these genes into other cultivars, thereby continuing to provide excellent resistance to stripe rust.

UAS imaging-based decision tools for arid winter wheat and irrigated potato production management

ABSTRACT Small unmanned aerial systems (UAS) are gaining global attention for rapid image-based decision making in agricultural production. In this study, the aim was to evaluate UAS-based imagery for rapid assessment of wheat winter survival and spring stand in winter wheat production and crop necrosis in potato production. Both are critical aspects of field (arid) and row (irrigated) crop farming practices. Aerial images from 97 hard and 352 soft single nucleotide polymorphism winter wheat plots, and 32 potato field plots (with 1 and 2 years of green manure applications) were acquired using a multi-band imaging sensor integrated with UAS. The UAS-based imagery was useful in evaluating winter wheat plant winter survival and spring stand, with Pearson correlation coefficient (r) in the range 0.60–0.82 between imagery and ground reference data. Similarly, the image-based potato field necrosis assessment showed a strong relationship with ground reference data (r = 0.93 and 0.88 for 1 and 2 years of green manure application, respectively). Overall, UAS imagery provided quantifiable, timely, and unbiased field data with high spatial resolution (about 2.3 cm/pixel for images acquired at 100 m altitude) that can aid in field and row crop production decision making.

Genetic relationships between race-nonspecific and race-specific interactions in the wheat-Pyrenophora tritici-repentis pathosystem.

Key messageWe identified a major QTL conferring race-nonspecific resistance and revealed its relationships with race-specific interactions in the wheat–Pyrenophora tritici-repentispathosystem.AbstractTan spot, caused by the fungus Pyrenophora tritici-repentis (Ptr), is a destructive disease of wheat worldwide. The disease system is known to include inverse gene-for-gene, race-specific interactions involving the recognition of fungal-produced necrotrophic effectors (NEs) by corresponding host sensitivity genes. However, quantitative trait loci (QTLs) conferring race-nonspecific resistance have also been identified. In this work, we identified a major race-nonspecific resistance QTL and characterized its genetic relationships with the NE-host gene interactions Ptr ToxA-Tsn1 and Ptr ToxC-Tsc1 in a recombinant inbred wheat population derived from the cross between ‘Louise’ and ‘Penawawa.’ Both parental lines were sensitive to Ptr ToxA, but Penawawa and Louise were highly resistant and susceptible, respectively, to conidial inoculations of all races. Resistance was predominantly governed by a major race-nonspecific QTL on chromosome arm 3BL for resistance to all races. Another significant QTL was detected at the distal end of chromosome arm 1AS for resistance to the Ptr ToxC-producing isolates, which corresponded to the known location of the Tsc1 locus. The effects of the 3B and 1A QTLs were largely additive, and the 3B resistance QTL was epistatic to the Ptr ToxA-Tsn1 interaction. Resistance to race 2 in F1 plants was completely dominant; however, race 3-inoculated F1 plants were only moderately resistant because they developed chlorosis presumably due to the Ptr ToxC-Tsc1 interaction. This work provides further understanding of genetic resistance in the wheat-tan spot system as well as important guidance for tan spot resistance breeding.

Karyotype and Ideogram Analyses of Four Wheatgrass Cultivars for Use in Perennial Wheat Breeding

ABSTRACT The development of perennial wheat cultivars in the Pacific Northwest (PNW) region of the U.S. addresses the need for alternative cropping systems that reduce soil erosion and degradation from mechanical tillage. Selection of parental lines will be especially important for breeding perennial wheat. Here we describe the karyotypes of three cultivars of bluebunch wheatgrass, Pseudoroegnaria spicata [Pursh] A. Love, and one cultivar of Snake River wheatgrass, Elymus wawawaiensis. These four cultivars are wild relatives of wheat that are adapted to the low rainfall regions of the PNW and can be crossed with bread wheat (Triticum aestivum L.) using traditional breeding methods. Chromosome number, arm ratio, relative length and centromere index are given for Ps. spicata cultivars ‘Whitmar’ (ssp. inermis), ‘Goldar’ (ssp. spicata), and ‘Anatone’ (ssp. spicata), and the E. wawawaiensis cultivar ‘Secar’.

Tolerance of Wheat (Poales: Poaceae) Seedlings to Wireworm (Coleoptera: Elateridae)

ABSTRACT Wireworms (Coleoptera: Elateridae), the subterranean larval stage of the click beetle, are becoming more prevalent in many cropping systems and posing an increasing economic threat to wheat growers in the Pacific Northwest following the cancellation of the insecticide lindane in 2006. Current insecticide seed treatments alone are not adequate for wireworm control. The objective of this study was to evaluate a diverse set of 163 wheat genotypes for tolerance to wireworm feeding. Entries were planted in replicated field trials over 3 yr and evaluated for their performance when grown in the presence of wireworms. Entries were rated based on survival and given a tolerance score. Results indicated that differences exist among wheat genotypes in their level of tolerance to wireworm feeding. In particular, consistently high-ranking genotypes of interest may be ‘BR 18’, ‘Sonalika’, ‘Safed Lerma’, and ‘Hollis’. These genotypes, used in conjunction with other cultural or chemical control methods, may help provide an economic means of controlling wireworms.

The Effect of Imazamox Application Timing and Rate on Imazamox Resistant Wheat Cultivars in The Pacific Northwest

Grass weeds are a major problem in winter wheat fields in the Pacific Northwest (PNW). Control of these weeds is now enhanced with the use of imazamox resistant winter wheat cultivars, which have been rapidly adopted by wheat growers. However, the effect of spray rate and timing on crop injury and agronomic traits of wheat cultivars with different genetic backgrounds has not been adequately evaluated. Thus, experiments were conducted near Moscow and Genesee, ID in the 2003–2004 and 2004–2005 growing seasons to evaluate the effect of imazamox on four resistant cultivars and seven resistant breeding lines. Wheat plants were treated at the 3- to 5-leaf stage and the 3- to 7-tiller stage with 45 and 90 g ai/ha of imazamox. Visible crop injury was evaluated from 14 to 35 d after treatment (DAT). Heading date, plant height, grain yield and test weight, and end-use grain quality also were measured. The cultivar by treatment interaction was significant at 21 DAT, caused by a differential response of wheat lines to imazamox treatment. This interaction also was significant for plant height and grain yield. Although cultivars and breeding lines responded differently to imazamox treatment, two lines consistently showed the least levels (3 to 8%) of crop injury, with no reductions in plant height or grain yield following imazamox application. Orthogonal contrasts of visible crop injury at 21 DAT showed that the 2× imazamox rate caused more crop injury (12%) than the 1× rate (7%). The 2× rate of imazamox reduced plant height 1%, grain yield 8%, test weight 1%, and percent flour yield 1%. All other traits were not affected by application of imazamox. Application timing only minimally affected crop injury, and had no effect on agronomic or end-use quality traits. Nomenclature: Imazamox; wheat, Triticum aestivum L. ‘FS4’; ‘Brundage’; ‘Brundage 96’; ‘Lambert’; ‘87-52814A’.

Characterizing and Validating Stripe Rust Resistance Loci in US Pacific Northwest Winter Wheat Accessions ( Triticum aestivum L.) by Genome-wide Association and Linkage Mapping

Stripe rust resistance QTL were detected in PNW wheat panels. QTL mapping and haplotyping confirmed QYr.wac‐1B.1 and QYr.wac‐2A, and validated GWAS. SNP markers for QYr.wac‐1B.1 and for Yr17 and linked loci enable marker‐assisted selection.