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Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping.

Liu F, Schmidt RH, Reif JC, Jiang Y.

G3 (Bethesda). 2019 Oct 11. pii: g3.400451.2019. doi: 10.1534/g3.119.400451. [Epub ahead of print]


Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection.

Philipp N, Weise S, Oppermann M, Börner A, Keilwagen J, Kilian B, Arend D, Zhao Y, Graner A, Reif JC, Schulthess AW.

Sci Data. 2019 Jul 29;6(1):137. doi: 10.1038/s41597-019-0146-y.


Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding.

Mascher M, Schreiber M, Scholz U, Graner A, Reif JC, Stein N.

Nat Genet. 2019 Jul;51(7):1076-1081. doi: 10.1038/s41588-019-0443-6. Epub 2019 Jun 28. Review.


Genetic dissection of agronomic and quality traits based on association mapping and genomic selection approaches in durum wheat grown in Southern Spain.

Mérida-García R, Liu G, He S, Gonzalez-Dugo V, Dorado G, Gálvez S, Solís I, Zarco-Tejada PJ, Reif JC, Hernandez P.

PLoS One. 2019 Feb 27;14(2):e0211718. doi: 10.1371/journal.pone.0211718. eCollection 2019.


Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection.

Gonzalez MY, Weise S, Zhao Y, Philipp N, Arend D, Börner A, Oppermann M, Graner A, Reif JC, Schulthess AW.

Sci Data. 2018 Dec 4;5:180278. doi: 10.1038/sdata.2018.278.


Reciprocal recurrent genomic selection: an attractive tool to leverage hybrid wheat breeding.

Rembe M, Zhao Y, Jiang Y, Reif JC.

Theor Appl Genet. 2019 Mar;132(3):687-698. doi: 10.1007/s00122-018-3244-x. Epub 2018 Nov 28. Review.


Dissecting the genetics underlying the relationship between protein content and grain yield in a large hybrid wheat population.

Thorwarth P, Liu G, Ebmeyer E, Schacht J, Schachschneider R, Kazman E, Reif JC, Würschum T, Longin CFH.

Theor Appl Genet. 2019 Feb;132(2):489-500. doi: 10.1007/s00122-018-3236-x. Epub 2018 Nov 19.


Genebank genomics highlights the diversity of a global barley collection.

Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M, Weise S, Knüpffer H, Basterrechea M, König P, Schüler D, Sharma R, Pasam RK, Rutten T, Guo G, Xu D, Zhang J, Herren G, Müller T, Krattinger SG, Keller B, Jiang Y, González MY, Zhao Y, Habekuß A, Färber S, Ordon F, Lange M, Börner A, Graner A, Reif JC, Scholz U, Mascher M, Stein N.

Nat Genet. 2019 Feb;51(2):319-326. doi: 10.1038/s41588-018-0266-x. Epub 2018 Nov 12.


Manipulation and prediction of spike morphology traits for the improvement of grain yield in wheat.

Guo Z, Zhao Y, Röder MS, Reif JC, Ganal MW, Chen D, Schnurbusch T.

Sci Rep. 2018 Sep 26;8(1):14435. doi: 10.1038/s41598-018-31977-3.


Unlocking historical phenotypic data from an ex situ collection to enhance the informed utilization of genetic resources of barley (Hordeum sp.).

González MY, Philipp N, Schulthess AW, Weise S, Zhao Y, Börner A, Oppermann M, Graner A, Reif JC.

Theor Appl Genet. 2018 Sep;131(9):2009-2019. doi: 10.1007/s00122-018-3129-z. Epub 2018 Jun 29.


Leveraging the Use of Historical Data Gathered During Seed Regeneration of an ex Situ Genebank Collection of Wheat.

Philipp N, Weise S, Oppermann M, Börner A, Graner A, Keilwagen J, Kilian B, Zhao Y, Reif JC, Schulthess AW.

Front Plant Sci. 2018 May 8;9:609. doi: 10.3389/fpls.2018.00609. eCollection 2018.


Identification of QTL hot spots for malting quality in two elite breeding lines with distinct tolerance to abiotic stress.

Kochevenko A, Jiang Y, Seiler C, Surdonja K, Kollers S, Reif JC, Korzun V, Graner A.

BMC Plant Biol. 2018 Jun 4;18(1):106. doi: 10.1186/s12870-018-1323-4.


Genome-wide association analyses of plant growth traits during the stem elongation phase in wheat.

Guo Z, Liu G, Röder MS, Reif JC, Ganal MW, Schnurbusch T.

Plant Biotechnol J. 2018 Dec;16(12):2042-2052. doi: 10.1111/pbi.12937. Epub 2018 Aug 19.


Exploiting the Rht portfolio for hybrid wheat breeding.

Würschum T, Liu G, Boeven PHG, Longin CFH, Mirdita V, Kazman E, Zhao Y, Reif JC.

Theor Appl Genet. 2018 Jul;131(7):1433-1442. doi: 10.1007/s00122-018-3088-4. Epub 2018 Mar 19.


Haplotype-Based Genome-Wide Prediction Models Exploit Local Epistatic Interactions Among Markers.

Jiang Y, Schmidt RH, Reif JC.

G3 (Bethesda). 2018 May 4;8(5):1687-1699. doi: 10.1534/g3.117.300548.


Genome-wide association mapping of QTL underlying seed oil and protein contents of a diverse panel of soybean accessions.

Li YH, Reif JC, Hong HL, Li HH, Liu ZX, Ma YS, Li J, Tian Y, Li YF, Li WB, Qiu LJ.

Plant Sci. 2018 Jan;266:95-101. doi: 10.1016/j.plantsci.2017.04.013. Epub 2017 May 2.


Advantages and limitations of multiple-trait genomic prediction for Fusarium head blight severity in hybrid wheat (Triticum aestivum L.).

Schulthess AW, Zhao Y, Longin CFH, Reif JC.

Theor Appl Genet. 2018 Mar;131(3):685-701. doi: 10.1007/s00122-017-3029-7. Epub 2017 Dec 2.


A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat.

Jiang Y, Schmidt RH, Zhao Y, Reif JC.

Nat Genet. 2017 Dec;49(12):1741-1746. doi: 10.1038/ng.3974. Epub 2017 Oct 16.


The roles of pleiotropy and close linkage as revealed by association mapping of yield and correlated traits of wheat (Triticum aestivum L.).

Schulthess AW, Reif JC, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Ganal MW, Röder MS, Jiang Y.

J Exp Bot. 2017 Jul 10;68(15):4089-4101. doi: 10.1093/jxb/erx214.


Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments.

Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava RK, Chitikineni A, Fan G, Bajaj P, Punnuri S, Gupta SK, Wang H, Jiang Y, Couderc M, Katta MAVSK, Paudel DR, Mungra KD, Chen W, Harris-Shultz KR, Garg V, Desai N, Doddamani D, Kane NA, Conner JA, Ghatak A, Chaturvedi P, Subramaniam S, Yadav OP, Berthouly-Salazar C, Hamidou F, Wang J, Liang X, Clotault J, Upadhyaya HD, Cubry P, Rhoné B, Gueye MC, Sunkar R, Dupuy C, Sparvoli F, Cheng S, Mahala RS, Singh B, Yadav RS, Lyons E, Datta SK, Hash CT, Devos KM, Buckler E, Bennetzen JL, Paterson AH, Ozias-Akins P, Grando S, Wang J, Mohapatra T, Weckwerth W, Reif JC, Liu X, Vigouroux Y, Xu X.

Nat Biotechnol. 2017 Oct;35(10):969-976. doi: 10.1038/nbt.3943. Epub 2017 Sep 18.


Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays.

Schmidt R, Boudichevskaia A, Cao HX, He S, Meyer RC, Reif JC.

Plant Cell Rep. 2017 Dec;36(12):1871-1881. doi: 10.1007/s00299-017-2200-6. Epub 2017 Aug 30.


Genetic architecture and temporal patterns of biomass accumulation in spring barley revealed by image analysis.

Neumann K, Zhao Y, Chu J, Keilwagen J, Reif JC, Kilian B, Graner A.

BMC Plant Biol. 2017 Aug 10;17(1):137. doi: 10.1186/s12870-017-1085-4.


Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping.

Otto LG, Mondal P, Brassac J, Preiss S, Degenhardt J, He S, Reif JC, Sharbel TF.

BMC Genomics. 2017 Aug 10;18(1):599. doi: 10.1186/s12864-017-3991-0.


Hybrid Performance of an Immortalized F2 Rapeseed Population Is Driven by Additive, Dominance, and Epistatic Effects.

Liu P, Zhao Y, Liu G, Wang M, Hu D, Hu J, Meng J, Reif JC, Zou J.

Front Plant Sci. 2017 May 18;8:815. doi: 10.3389/fpls.2017.00815. eCollection 2017.


Genome-Based Identification of Heterotic Patterns in Rice.

Beukert U, Li Z, Liu G, Zhao Y, Ramachandra N, Mirdita V, Pita F, Pillen K, Reif JC.

Rice (N Y). 2017 Dec;10(1):22. doi: 10.1186/s12284-017-0163-4. Epub 2017 May 19.


Efficient strategies to assess yield stability in winter wheat.

Liu G, Zhao Y, Mirdita V, Reif JC.

Theor Appl Genet. 2017 Aug;130(8):1587-1599. doi: 10.1007/s00122-017-2912-6. Epub 2017 May 4.


Genome-Wide Prediction of the Performance of Three-Way Hybrids in Barley.

Li Z, Philipp N, Spiller M, Stiewe G, Reif JC, Zhao Y.

Plant Genome. 2017 Mar;10(1). doi: 10.3835/plantgenome2016.05.0046.


Genome-metabolite associations revealed low heritability, high genetic complexity, and causal relations for leaf metabolites in winter wheat (Triticum aestivum).

Matros A, Liu G, Hartmann A, Jiang Y, Zhao Y, Wang H, Ebmeyer E, Korzun V, Schachschneider R, Kazman E, Schacht J, Longin F, Reif JC, Mock HP.

J Exp Bot. 2017 Jan 1;68(3):415-428. doi: 10.1093/jxb/erw441.


Genome-wide mapping and prediction suggests presence of local epistasis in a vast elite winter wheat populations adapted to Central Europe.

He S, Reif JC, Korzun V, Bothe R, Ebmeyer E, Jiang Y.

Theor Appl Genet. 2017 Apr;130(4):635-647. doi: 10.1007/s00122-016-2840-x. Epub 2016 Dec 19.


Genomic Prediction of Barley Hybrid Performance.

Philipp N, Liu G, Zhao Y, He S, Spiller M, Stiewe G, Pillen K, Reif JC, Li Z.

Plant Genome. 2016 Jul;9(2). doi: 10.3835/plantgenome2016.02.0016.


Dissecting the Genetic Basis of Resistance to Soybean Cyst Nematode Combining Linkage and Association Mapping.

Li YH, Shi XH, Li HH, Reif JC, Wang JJ, Liu ZX, He S, Yu BS, Qiu LJ.

Plant Genome. 2016 Jul;9(2). doi: 10.3835/plantgenome2015.04.0020.


Seed Quality Traits Can Be Predicted with High Accuracy in Brassica napus Using Genomic Data.

Zou J, Zhao Y, Liu P, Shi L, Wang X, Wang M, Meng J, Reif JC.

PLoS One. 2016 Nov 23;11(11):e0166624. doi: 10.1371/journal.pone.0166624. eCollection 2016.


High accuracy of predicting hybrid performance of Fusarium head blight resistance by mid-parent values in wheat.

Miedaner T, Schulthess AW, Gowda M, Reif JC, Longin CF.

Theor Appl Genet. 2017 Feb;130(2):461-470. doi: 10.1007/s00122-016-2826-8. Epub 2016 Nov 19.


Validating the prediction accuracies of marker-assisted and genomic selection of Fusarium head blight resistance in wheat using an independent sample.

Jiang Y, Schulthess AW, Rodemann B, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Ganal MW, Röder MS, Reif JC.

Theor Appl Genet. 2017 Mar;130(3):471-482. doi: 10.1007/s00122-016-2827-7. Epub 2016 Nov 17.


Genetic variation of growth dynamics in maize (Zea mays L.) revealed through automated non-invasive phenotyping.

Muraya MM, Chu J, Zhao Y, Junker A, Klukas C, Reif JC, Altmann T.

Plant J. 2017 Jan;89(2):366-380. doi: 10.1111/tpj.13390. Epub 2017 Jan 7.


Potential of marker selection to increase prediction accuracy of genomic selection in soybean (Glycine max L.).

Ma Y, Reif JC, Jiang Y, Wen Z, Wang D, Liu Z, Guo Y, Wei S, Wang S, Yang C, Wang H, Yang C, Lu W, Xu R, Zhou R, Wang R, Sun Z, Chen H, Zhang W, Wu J, Hu G, Liu C, Luan X, Fu Y, Guo T, Han T, Zhang M, Sun B, Zhang L, Chen W, Wu C, Sun S, Yuan B, Zhou X, Han D, Yan H, Li W, Qiu L.

Mol Breed. 2016;36:113. Epub 2016 Jul 28.


Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat.

Liu G, Zhao Y, Gowda M, Longin CF, Reif JC, Mette MF.

PLoS One. 2016 Jul 6;11(7):e0158635. doi: 10.1371/journal.pone.0158635. eCollection 2016.


Genomic selection in a commercial winter wheat population.

He S, Schulthess AW, Mirdita V, Zhao Y, Korzun V, Bothe R, Ebmeyer E, Reif JC, Jiang Y.

Theor Appl Genet. 2016 Mar;129(3):641-51. doi: 10.1007/s00122-015-2655-1. Epub 2016 Jan 8.


Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding.

Zhao Y, Li Z, Liu G, Jiang Y, Maurer HP, Würschum T, Mock HP, Matros A, Ebmeyer E, Schachschneider R, Kazman E, Schacht J, Gowda M, Longin CF, Reif JC.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):15624-9. doi: 10.1073/pnas.1514547112. Epub 2015 Dec 9.


Multiple-trait- and selection indices-genomic predictions for grain yield and protein content in rye for feeding purposes.

Schulthess AW, Wang Y, Miedaner T, Wilde P, Reif JC, Zhao Y.

Theor Appl Genet. 2016 Feb;129(2):273-87. doi: 10.1007/s00122-015-2626-6. Epub 2015 Nov 3.


Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean.

Li YH, Reif JC, Ma YS, Hong HL, Liu ZX, Chang RZ, Qiu LJ.

BMC Genomics. 2015 Oct 23;16:841. doi: 10.1186/s12864-015-2049-4.


Potential and limits of whole genome prediction of resistance to Fusarium head blight and Septoria tritici blotch in a vast Central European elite winter wheat population.

Mirdita V, He S, Zhao Y, Korzun V, Bothe R, Ebmeyer E, Reif JC, Jiang Y.

Theor Appl Genet. 2015 Dec;128(12):2471-81. doi: 10.1007/s00122-015-2602-1. Epub 2015 Sep 8.


Modeling Epistasis in Genomic Selection.

Jiang Y, Reif JC.

Genetics. 2015 Oct;201(2):759-68. doi: 10.1534/genetics.115.177907. Epub 2015 Jul 27.


Genetic architecture is more complex for resistance to Septoria tritici blotch than to Fusarium head blight in Central European winter wheat.

Mirdita V, Liu G, Zhao Y, Miedaner T, Longin CF, Gowda M, Mette MF, Reif JC.

BMC Genomics. 2015 Jun 5;16:430. doi: 10.1186/s12864-015-1628-8.


Modelling the genetic architecture of flowering time control in barley through nested association mapping.

Maurer A, Draba V, Jiang Y, Schnaithmann F, Sharma R, Schumann E, Kilian B, Reif JC, Pillen K.

BMC Genomics. 2015 Apr 12;16:290. doi: 10.1186/s12864-015-1459-7.


Prospects and limits of marker imputation in quantitative genetic studies in European elite wheat (Triticum aestivum L.).

He S, Zhao Y, Mette MF, Bothe R, Ebmeyer E, Sharbel TF, Reif JC, Jiang Y.

BMC Genomics. 2015 Mar 11;16:168. doi: 10.1186/s12864-015-1366-y.


First insights into the genotype-phenotype map of phenotypic stability in rye.

Wang Y, Mette MF, Miedaner T, Wilde P, Reif JC, Zhao Y.

J Exp Bot. 2015 Jun;66(11):3275-84. doi: 10.1093/jxb/erv145. Epub 2015 Apr 6.


Yield performance and stability of CMS-based triticale hybrids.

Mühleisen J, Piepho HP, Maurer HP, Reif JC.

Theor Appl Genet. 2015 Feb;128(2):291-301. doi: 10.1007/s00122-014-2429-1. Epub 2014 Dec 16.


Potential and limits to unravel the genetic architecture and predict the variation of Fusarium head blight resistance in European winter wheat (Triticum aestivum L.).

Jiang Y, Zhao Y, Rodemann B, Plieske J, Kollers S, Korzun V, Ebmeyer E, Argillier O, Hinze M, Ling J, Röder MS, Ganal MW, Mette MF, Reif JC.

Heredity (Edinb). 2015 Mar;114(3):318-26. doi: 10.1038/hdy.2014.104. Epub 2014 Nov 12.


Detecting SNPs underlying domestication-related traits in soybean.

Li YH, Reif JC, Jackson SA, Ma YS, Chang RZ, Qiu LJ.

BMC Plant Biol. 2014 Sep 26;14:251. doi: 10.1186/s12870-014-0251-1.

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