Association mapping for yield, yield components and drought tolerance-related traits in spring wheat grown under rainfed and irrigated conditions

2013 Summer.Includes bibliographical references.Genome-wide association mapping shows promise for identifying quantitative trait loci (QTL) for many traits including drought stress tolerance. Candidate gene analysis also has been used to identify functional single nucleotide polymorphisms (SNPs) that can be associated with important traits. In 2010 and 2011, we evaluated an International maize and wheat improvement center (CIMMYT) spring wheat association mapping panel under rainfed and full irrigation conditions in Greeley, CO, and Melkassa, Ethiopia (total of five environments) for grain yield and its components, canopy spectral reflectance, and several other phenological or drought-related traits. A total of 287 lines were genotyped with Diversity Array Technology (DArT) markers to identify associations with measured traits under different moisture regimes. Significant differences among lines were observed for most traits within each environment and across environments. Best linear unbiased predictors (BLUPs) of each line were used to calculate marker-trait associations using 1863 markers with a mixed linear model with population structure and a kinship-matrix included as covariates. Three drought responsive candidate genes (Dehydration-Responsive Element Binding 1A, DREB1A; Enhanced Response to abscisic acid (ABA), ERA1; and Fructan 1-exohydrolase, 1-FEH), were amplified using genome-specific primers and sequenced from 126 lines to identify single nucleotide polymorphisms (SNPs) within the candidate genes and determine their association with measured traits. For genome wide association mapping, the highest number of stable associations was obtained for kernel hardness followed by grain volume weight (test weight), an important trait under drought stress conditions. The most stable marker-trait association was obtained for grain yield on chromosome 2DS. All marker-trait associations for above-ground biomass were environment-specific. Multi-trait marker-trait association for grain yield and other traits such as harvest index, final biomass, thousand kernel weight, plant height and flag leaf length were detected on chromosome 5B. A grain yield QTL was again co-localized with harvest index QTL on chromosome 1BS. Normalized difference vegetation index (NDVI) shared QTL region with a harvest index QTL on chromosome 1AL, while green leaf area shared a QTL with harvest index on chromosomes 5A. For drought tolerance candidate genes, SNPs within DREB1A gene were associated with final biomass, spikelets per spike, days to heading and NDVI. The 1-FEH gene amplified from the A genome showed associations with grain yield, final biomass, NDVI, green leaf area, kernel number per spike and spike length. However, 1-FEH from the B genome was associated with traits such as days to heading, days to maturity, thousand kernel weight and test weight. The ERA1 gene from the B genome was associated with spike m-2, harvest index, grain filling duration, leaf senescence, flag leaf width, plant height and spike length, whereas ERA1 from the D genome was associated with kernel weight per spike, flag leaf width, leaf senescence, kernel number per spike and harvest index. In general, each candidate gene had effects on multiple traits under both rainfed and irrigated conditions. Both genome wide and candidate gene approaches showed that most of the measured traits are controlled by several QTL/genes with minor effects. QTL/genes with pleotropic effects were also detected. Therefore, the information generated by this study might be used in marker-assisted selection to improve drought tolerance of wheat

Kortsiktige aksjekurseffekter ved rapporterte innsidehandler på Oslo Børs : en empirisk studie av norske innsidehandler

Denne utredningen har ved hjelp av eventstudiemetoden studert de kortsiktige effektene av 467 rapporterte innsidehandler ved Oslo Børs i tidsperioden 01.09.2008 til 31.08.2010. Disse effektene er analysert med utgangspunkt i fem ulike faktorer i et forsøk på å avdekke trender og forskjeller mellom de ulike innsidehandlene. I samsvar med majoritetsandelen av tidligere forskning finner vi at innsidere oppnår akkumulert gjennomsnittlig anormal avkastning (CAR) signifikant forskjellig fra null. For kjøpstransaksjoner oppnår innsidere CAR på 2,02% i løpet av de første to dagene etter handelen, og tilsvarende -1,64% for salgstransaksjoner. Når det gjelder effektene av innsidekjøp, viser analysene flere faktorer som signifikant påvirker anormal avkastning. Vi finner at store kjøpssummer, handler i selskaper med markedsverdi mellom 1 og 3 milliarder og handler i selskaper som har falt mye 14 dager før handelen, genererer størst signifikant CAR for periode (0,2) på henholdsvis 3,96%, 3,41% og 3,16%. Studien viser også at innsiders stilling vil ha påvirking på den anormale avkastningen. Videre finner vi at innsidekjøp har signifikant høyere anormal avkastning i nedgangstider enn oppgangstider. For salgstransaksjoner gir salg i små selskaper signifikant CAR på -6,79%. Resultatene viser også at innsidesalg har signifikant høyere negativ anormal avkastning i oppgangstider enn nedgangstider. I tillegg er innsidere gode til å “time” markedet ved at de kjøper aksjer etter at verdien har falt mye og omvendt selger aksjer etter at verdien har steget mye. Tilslutt slår utredningen fast at utsidere kan replikere innsidere og oppnå anormal avkastning

Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing

Background: One of the reasons hard red winter wheat cultivar 'Duster' (PI 644016) is widely grown in the southern Great Plains is that it confers a consistently high level of resistance to biotype GP of Hessian fly (Hf). However, little is known about the genetic mechanism underlying Hf resistance in Duster. This study aimed to unravel complex structures of the Hf region on chromosome 1AS in wheat by using genotyping-by-sequencing (GBS) markers and single nucleotide polymorphism (SNP) markers.Results: Doubled haploid (DH) lines generated from a cross between two winter wheat cultivars, 'Duster' and 'Billings', were used to identify genes in Duster responsible for effective and consistent resistance to Hf. Segregation in reaction of the 282 DH lines to Hf biotype GP fit a one-gene model. The DH population was genotyped using 2,358 markers developed using the GBS approach. A major QTL, explaining 88% of the total phenotypic variation, was mapped to a chromosome region that spanned 178 cM and contained 205 GBS markers plus 1 SSR marker and 1 gene marker, with 0.86 cM per marker in genetic distance. The analyses of GBS marker sequences and further mapping of SSR and gene markers enabled location of the QTL-containing linkage group on the short arm of chromosome 1A. Comparative mapping of the common markers for the gene for QHf.osu-1A d in Duster and the Hf-resistance gene for QHf.osu-1A 74 in cultivar '2174' showed that the two Hf resistance genes are located on the same chromosome arm 1AS, only 11.2 cM apart in genetic distance. The gene at QHf.osu-1A d in Duster has been delimited within a 2.7 cM region.Conclusion: Two distinct resistance genes exist on the short arm of chromosome 1A as found in the two hard red winter cultivars, 2174 and Duster. Whereas the Hf resistance gene in 2174 is likely allelic to one or more of the previously mapped resistance genes (H9, H10, H11, H16, or H17) in wheat, the gene in Duster is novel and confers a more consistent phenotype than 2174 in response to biotype GP infestation in controlled-environment assays.Peer reviewedPlant and Soil Science

A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat

Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a, and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, and Sr57. Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat

Bulked segregant analysis RNA-seq (BSR-Seq) validated a stem resistance locus in Aegilops umbellulata, a wild relative of wheat.

Many disease resistance genes that have been transferred from wild relatives to cultivated wheat have played a significant role in wheat production worldwide. Ae. umbellulata is one of the species within the genus Aegilops that have been successfully used as sources of resistance genes to leaf rust, stem rust and powdery mildew. The objectives of the current work was to validate the map position of a major QTL that confers resistance to the stem rust pathogen races Ug99 (TTKSK) and TTTTF with an independent bi-parental mapping population and to refine the QTL region with a bulk segregant analysis approach. Two F2 bi-parental mapping populations were developed from stem rust resistant Ae. umbellulata accessions (PI 298905 and PI 5422375) and stem rust susceptible accessions (PI 542369 and PI 554395). Firstly, one of the two populations was used to map the chromosome location of the resistance gene. Later on, the 2nd population was used to validate the chromosome location in combination with a bulk segregant analysis approach. For the bulk segregant analysis, RNA was extracted from a bulk of leaf tissues of 12 homozygous resistant F3 families, and a separate bulk of 11 susceptible homozygous F3 families derived from the PI 5422375 and PI 554395 cross. The RNA samples of the two bulks and the two parents were sequenced for SNPs identification. Stem rust resistance QTL was validated on chromosome 2U of Ae. umbellulata in the same region in both populations. With bulk segregant analysis, the QTL position was delimited within 3.2 Mbp. Although there were a large number of genes in the orthologous region of the detected QTL on chromosome 2D of Ae. tauschii, we detected only two Ae. umbellulata NLR genes which can be considered as a potential candidate genes

Genotyping-by-Sequencing Facilitates a High-Density Consensus Linkage Map for Aegilops umbellulata, a Wild Relative of Cultivated Wheat

High-density genetic maps are useful to precisely localize QTL or genes that might be used to improve traits of nutritional and/or economical importance in crops. However, high-density genetic maps are lacking for most wild relatives of crop species, including wheat. Aegilops umbellulata is a wild relative of wheat known for its potential as a source of biotic and abiotic stress resistance genes. In this work, we have developed a framework consensus genetic map using two biparental populations derived from accessions PI 298905, PI 542369, PI 5422375, and PI 554395. The framework map comprised 3009 genotype-by-sequence SNPs with a total map size of 948.72 cM. On average, there were three SNPs per centimorgan for each chromosome. Chromosome 1U was the shortest (66.5 cM), with only 81 SNPs, whereas the remaining chromosomes had between 391 and 591 SNP markers. A total of 2395 unmapped SNPs were added to the linkage maps through a recombination frequency approach, and increased the number of SNPs placed on the consensus map to a total of 5404 markers. Segregation distortion was disproportionally high for chromosome 1U for both populations used to construct component linkage maps, and thus segregation distortion could be one of the probable reasons for the exceptionally reduced linkage size for chromosome 1U. From comparative analysis, Ae. umbellulata chromosomes except 4U showed moderate to strong collinearity with corresponding homeologous chromosomes of hexaploid wheat and barley. The present consensus map may serve as a reference map in QTL mapping and validation projects, and also in genome assembly to develop a reference genome sequence for Ae. umbellulata

Additional file 2: Table S2. of Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat

QTL detected by Single QTL mapping methods. (XLSX 17 kb

The genetics of Ug99 stem rust resistance in spring wheat variety ‘Linkert‘

Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in ‘Linkert’, a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with ‘Linkert’ as a stem rust resistant parent. Hard red spring wheat variety ‘Forefront’ and genetic stock ‘LMPG’ were used as stem rust susceptible parents of the DH populations. Breeding line ‘MN07098-6’ was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs

Characterization of Ethiopian Wheat Germplasm for Resistance to Four Puccinia graminis f. sp. tritici Races Facilitated by Single-Race Nurseries

In Ethiopia, breeding rust resistant wheat cultivars is a priority for wheat production. A stem rust epidemic during 2013 to 2014 on previously resistant cultivar Digalu highlighted the need to determine the effectiveness of wheat lines to multiple races of Puccinia graminis f. sp. tritici in Ethiopia. During 2014 and 2015, we evaluated a total of 97 bread wheat and 14 durum wheat genotypes against four P. graminis f. sp. tritici races at the seedling stage and in single-race field nurseries. Resistance genes were postulated using molecular marker assays. Bread wheat lines were resistant to race JRCQC, the race most virulent to durum wheat. Lines with stem rust resistance gene Sr24 possessed the most effective resistance to the four races. Only three lines with adult plant resistance possessed resistance effective to the four races comparable with cultivars with Sr24. Although responses of the wheat lines across races were positively correlated, wheat lines were identified that possessed adult plant resistance to race TTKSK but were relatively susceptible to race TKTTF. This study demonstrated the importance of testing wheat lines for response to multiple races of the stem rust pathogen to determine if lines possessed non-race-specific resistance