Person: Anderson, J.
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Anderson
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Anderson, J.
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0000-0003-4655-6517 11 results
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- The genetics of Ug99 stem rust resistance in spring wheat variety ‘Linkert‘(Frontiers Media S.A., 2024) Edae, E.A.; Kosgey, Z.C.; Bajgain, P.; Ndung'u, N.C.; Gemechu, A.; Bhavani, S.; Anderson, J.; Rouse, M.N.
Publication - Quantitative trait loci mapping reveals the complexity of adult plant resistance to leaf rust in spring wheat ‘Copio’(Wiley, 2022) Rauf, Y.; Lan, C.; Randhawa, M.S.; Singh, R.P.; Huerta-Espino, J.; Anderson, J.
Publication - Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes(BioMed Central, 2010) Akhunov, E.; Akhunova, A.; Anderson, O.; Anderson, J.; Blake, N.K.; Clegg, M.T.; Coleman-Derr, D.; Conley, E.J.; Crossman, C.C.; Deal, K.R.; Dubcovsky, J.; Gill, B.S.; Yong Qiang Gu; Hadam, J.; Hwayoung Heo; Naxin Huo; Lazo, G.R.; Ming-Cheng Luo; Yaqin Q Ma; Matthews, D.; McGuire, P.E.; Morrell, P.L.; Qualset, C.; Renfro, J.; Tabanao, D.; Talbert, L.E.; Chao Tian; Toleno, D.M.; Warburton, M.; You, F.M.; Wenjun Zhang; Dvorak, J.
Publication - Erratum to: Association mapping of North American spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other African stem rust races(BioMed Central, 2016) Bajgain, P.; Rouse, M.N.; Bulli, P.; Bhavani, S.; Gordon, T.; Wanyera, R.; Njau, P.N.; Wolde, L.; Anderson, J.; Pumphrey, M.
Publication - The performance of early-generation perennial winter cereals at 21 sites across four continents(MDPI, 2018) Hayes, R.; Wang, S.; Newell, M.T.; Turner, K.; Larsen, J.; Gazza, L.; Anderson, J.; Bell, L.; Cattani, D.J.; Frels, K.; Galassi, E.; Morgounov, A.; Revell, C.K.; Thapa, D.B.; Sacks, E.J.; Sameri, M.; Wade, L.J.; Westerbergh, A.; Shamanin, V.; Amanov, A.; Li, G.D.A network of 21 experiments was established across nine countries on four continents and spanning both hemispheres, to evaluate the relative performance of early generation perennial cereal material derived from wheat, rye, and barley and to inform future breeding strategies. The experimental lines were grown in replicated single rows, and first year production and phenology characteristics as well as yield and persistence for up to three years were monitored. The study showed that the existing experimental material is all relatively short-lived (?3 years), with environments that are milder in summer and winter generally conferring greater longevity. No pedigree was superior across this diverse network of sites although better performing lines at the higher latitude sites were generally derived from Thinopyrum intermedium. By contrast, at lower latitudes the superior lines were generally derived from Th. ponticum and Th. elongatum parentage. The study observed a poor relationship between year 1 performance and productivity in later years, highlighting the need for perennial cereal material with greater longevity to underpin future experimental evaluation, and the importance for breeding programs to emphasize post-year 1 performance in their selections. Hybrid lines derived from the tetraploid durum wheat generally showed greater longevity than derivatives of hexaploid wheat, highlighting potential for greater use of Triticum turgidum in perennial wheat breeding. We advocate a model in future breeding initiatives that develops perennial cereal genotypes for specific target environments rather than a generic product for one global market. These products may include a diversity of cultivars derived from locally adapted annual and perennial parents. In this scenario the breeding program may have access to only a limited range of adapted perennial grass parents. In other situations, such as at very high latitude environments, perennial crops derived from barley or rye may have a better chance of success than those derived from wheat. In either case, development and selection of the perennial parent for adaptation to local environments would seem fundamental to success.A network of 21 experiments was established across nine countries on four continents and spanning both hemispheres, to evaluate the relative performance of early generation perennial cereal material derived from wheat, rye, and barley and to inform future breeding strategies. The experimental lines were grown in replicated single rows, and first year production and phenology characteristics as well as yield and persistence for up to three years were monitored. The study showed that the existing experimental material is all relatively short-lived (?3 years), with environments that are milder in summer and winter generally conferring greater longevity. No pedigree was superior across this diverse network of sites although better performing lines at the higher latitude sites were generally derived from Thinopyrum intermedium. By contrast, at lower latitudes the superior lines were generally derived from Th. ponticum and Th. elongatum parentage. The study observed a poor relationship between year 1 performance and productivity in later years, highlighting the need for perennial cereal material with greater longevity to underpin future experimental evaluation, and the importance for breeding programs to emphasize post-year 1 performance in their selections. Hybrid lines derived from the tetraploid durum wheat generally showed greater longevity than derivatives of hexaploid wheat, highlighting potential for greater use of Triticum turgidum in perennial wheat breeding. We advocate a model in future breeding initiatives that develops perennial cereal genotypes for specific target environments rather than a generic product for one global market. These products may include a diversity of cultivars derived from locally adapted annual and perennial parents. In this scenario the breeding program may have access to only a limited range of adapted perennial grass parents. In other situations, such as at very high latitude environments, perennial crops derived from barley or rye may have a better chance of success than those derived from wheat. In either case, development and selection of the perennial parent for adaptation to local environments would seem fundamental to success.
Publication - Nested association mapping of stem rust resistance in wheat using genotyping by sequencing(Public Library of Science, 2016) Bajgain, P.; Rouse, M.N.; Tsilo, T.J.; Macharia, G.; Bhavani, S.; Yue Jin; Anderson, J.We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% – 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar markertrait association studies in other plant species.
Publication - Genome-wide association mapping of leaf rust response in a durum wheat worldwide germplasm collection(Crop Science Society of America, 2016) Aoun, M.; Breiland, M.; Turner, K.; Loladze, A.; Shiaoman Chao; Xu, S.; Ammar, K.; Anderson, J.; Kolmer, J.; Acevedo, M.Leaf rust (caused by Puccinia triticina Erikss. [Pt]) is increasingly impacting durum wheat (Triticum turgidum L. var. durum) production with the recent appearance of races with virulence to widely grown cultivars in many durum producing areas worldwide. A highly virulent P. triticina race on durum wheat was recently detected in Kansas. This race may spread to the northern Great Plains, where most of the US durum wheat is produced. The objective of this study was to identify sources of resistance to several races from the United States and Mexico at seedling stage in the greenhouse and at adult stage in field experiments. Genome-wide association study (GWAS) was used to identify single-nucleotide polymorphism (SNP) markers associated with leaf rust response in a worldwide durum wheat collection of 496 accessions. Thirteen accessions were resistant across all experiments. Association mapping revealed 88 significant SNPs associated with leaf rust response. Of these, 33 SNPs were located on chromosomes 2A and 2B, and 55 SNPs were distributed across all other chromosomes except for 1B and 7B. Twenty markers were associated with leaf rust response at seedling stage, while 68 markers were associated with leaf rust response at adult plant stage. The current study identified a total of 14 previously uncharacterized loci associated with leaf rust response in durum wheat. The discovery of these loci through association mapping (AM) is a significant step in identifying useful sources of resistance that can be used to broaden the relatively narrow leaf rust resistance spectrum in durum wheat germplasm.
Publication - Association mapping of North American spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other African stem rust races(BioMed Central, 2015) Bajgain, P.; Rouse, M.N.; Bulli, P.; Bhavani, S.; Gordon, T.; Wanyera, R.; Njau, P.N.; Wolde, L.; Anderson, J.; Pumphrey, M.Background: The recently identified Puccinia graminis f. sp. tritici (Pgt) race TTKSK (Ug99) poses a severe threat to global wheat production because of its broad virulence on several widely deployed resistance genes. Additional virulences have been detected in the Ug99 group of races, and the spread of this race group has been documented across wheat growing regions in Africa, the Middle East (Yemen), and West Asia (Iran). Other broadly virulent Pgt races, such as TRTTF and TKTTF, present further difficulties in maintaining abundant genetic resistance for their effective use in wheat breeding against this destructive fungal disease of wheat. In an effort to identify loci conferring resistance to these races, a genome-wide association study was carried out on a panel of 250 spring wheat breeding lines from the International Maize and Wheat Improvement Center (CIMMYT), six wheat breeding programs in the United States and three wheat breeding programs in Canada. Results The lines included in this study were grouped into two major clusters, based on the results of principal component analysis using 23,976 SNP markers. Upon screening for adult plant resistance (APR) to Ug99 during 2013 and 2014 in artificial stem rust screening nurseries at Njoro, Kenya and at Debre Zeit, Ethiopia, several wheat lines were found to exhibit APR. The lines were also screened for resistance at the seedling stage against races TTKSK, TRTTF, and TKTTF at USDA-ARS Cereal Disease Laboratory in St. Paul, Minnesota; and only 9 of the 250 lines displayed seedling resistance to all the races. Using a mixed linear model, 27 SNP markers associated with APR against Ug99 were detected, including markers linked with the known APR gene Sr2. Using the same model, 23, 86, and 111 SNP markers associated with seedling resistance against races TTKSK, TRTTF, and TKTTF were identified, respectively. These included markers linked to the genes Sr8a and Sr11 providing seedling resistance to races TRTTF and TKTTF, respectively. We also identified putatively novel Sr resistance genes on chromosomes 3B, 4D, 5A, 5B, 6A, 7A, and 7B. Conclusion Our results demonstrate that the North American wheat breeding lines have several resistance loci that provide APR and seedling resistance to highly virulent Pgt races. Using the resistant lines and the SNP markers identified in this study, marker-assisted resistance breeding can assist in development of varieties with elevated levels of resistance to virulent stem rust races including TTKSK.
Publication - Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars(National Academy of Sciences, 2013) Cavanagh, C.R.; Shiaoman Chao; Shichen Wang; Huang, B.E.; Stephen, S.; Kiani, S.; Forrest, K.L.; Saintenac, C.; Brown-Guedira, G.; Akhunova, A.; See, D.; Guihua Bai; Pumphrey, M.; Tomar, L.; Wong, D.; Kong, S.; Reynolds, M.P.; Lopes, M.; Bockelman, H.; Talbert, L.E.; Anderson, J.; Dreisigacker, S.; Baenziger, P.S.; Carter, A.; Korzun, V.; Morrell, P.L.; Dubcovsky, J.; Morell, M.K.; Sorrells, M.E.; Hayden, M.; Akhunov, E.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.
Publication - Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)(BioMed Central, 2010) Shiaoman Chao; Dubcovsky, J.; Dvorak, J.; Ming-Cheng Luo; Baenziger, P.S.; Matnyazov, R.; Clark, D.R.; Talbert, L.E.; Anderson, J.; Dreisigacker, S.; Glover, K.; Jianli Chen; Campbell, K.; Bruckner, P.; Rudd, J.C.; Haley, S.D.; Carver, B.F.; Perry, S.; Sorrells, M.E.; Akhunov, E.Background: Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. Results: Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the predefined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). Conclusions: Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.
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