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Items: 1 to 50 of 61

1.

African Orphan Crops Consortium (AOCC): status of developing genomic resources for African orphan crops.

Hendre PS, Muthemba S, Kariba R, Muchugi A, Fu Y, Chang Y, Song B, Liu H, Liu M, Liao X, Sahu SK, Wang S, Li L, Lu H, Peng S, Cheng S, Xu X, Yang H, Wang J, Liu X, Simons A, Shapiro HY, Mumm RH, Van Deynze A, Jamnadass R.

Planta. 2019 May 9. doi: 10.1007/s00425-019-03156-9. [Epub ahead of print] Review.

PMID:
31073657
2.

Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection.

Gonda I, Ashrafi H, Lyon DA, Strickler SR, Hulse-Kemp AM, Ma Q, Sun H, Stoffel K, Powell AF, Futrell S, Thannhauser TW, Fei Z, Van Deynze AE, Mueller LA, Giovannoni JJ, Foolad MR.

Plant Genome. 2019 Mar;12(1). doi: 10.3835/plantgenome2018.02.0010.

3.

Association between vitamin content, plant morphology and geographical origin in a worldwide collection of the orphan crop Gynandropsis gynandra (Cleomaceae).

Sogbohossou EOD, Kortekaas D, Achigan-Dako EG, Maundu P, Stoilova T, Van Deynze A, de Vos RCH, Schranz ME.

Planta. 2019 Mar 25. doi: 10.1007/s00425-019-03142-1. [Epub ahead of print]

PMID:
30911886
4.

The zinc-finger transcription factor CcLOL1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato.

Borovsky Y, Monsonego N, Mohan V, Shabtai S, Kamara I, Faigenboim A, Hill T, Chen S, Stoffel K, Van Deynze A, Paran I.

Plant J. 2019 Jul;99(1):41-55. doi: 10.1111/tpj.14305. Epub 2019 Apr 1.

PMID:
30828904
5.

The draft genomes of five agriculturally important African orphan crops.

Chang Y, Liu H, Liu M, Liao X, Sahu SK, Fu Y, Song B, Cheng S, Kariba R, Muthemba S, Hendre PS, Mayes S, Ho WK, Yssel AEJ, Kendabie P, Wang S, Li L, Muchugi A, Jamnadass R, Lu H, Peng S, Van Deynze A, Simons A, Yana-Shapiro H, Van de Peer Y, Xu X, Yang H, Wang J, Liu X.

Gigascience. 2019 Mar 1;8(3). pii: giy152. doi: 10.1093/gigascience/giy152.

6.

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota.

Van Deynze A, Zamora P, Delaux PM, Heitmann C, Jayaraman D, Rajasekar S, Graham D, Maeda J, Gibson D, Schwartz KD, Berry AM, Bhatnagar S, Jospin G, Darling A, Jeannotte R, Lopez J, Weimer BC, Eisen JA, Shapiro HY, Ané JM, Bennett AB.

PLoS Biol. 2018 Aug 7;16(8):e2006352. doi: 10.1371/journal.pbio.2006352. eCollection 2018 Aug.

7.

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace.

Li M, An H, Angelovici R, Bagaza C, Batushansky A, Clark L, Coneva V, Donoghue MJ, Edwards E, Fajardo D, Fang H, Frank MH, Gallaher T, Gebken S, Hill T, Jansky S, Kaur B, Klahs PC, Klein LL, Kuraparthy V, Londo J, Migicovsky Z, Miller A, Mohn R, Myles S, Otoni WC, Pires JC, Rieffer E, Schmerler S, Spriggs E, Topp CN, Van Deynze A, Zhang K, Zhu L, Zink BM, Chitwood DH.

Front Plant Sci. 2018 Apr 25;9:553. doi: 10.3389/fpls.2018.00553. eCollection 2018.

8.

Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae).

Spalink D, Stoffel K, Walden GK, Hulse-Kemp AM, Hill TA, Van Deynze A, Bohs L.

Mol Phylogenet Evol. 2018 Sep;126:293-302. doi: 10.1016/j.ympev.2018.04.030. Epub 2018 Apr 25.

PMID:
29702214
9.

Quantitative Trait Loci Controlling Fruit Size and Other Horticultural Traits in Bell Pepper (Capsicum annuum).

Chunthawodtiporn J, Hill T, Stoffel K, Van Deynze A.

Plant Genome. 2018 Mar;11(1). doi: 10.3835/plantgenome2016.12.0125.

10.

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

Hulse-Kemp AM, Maheshwari S, Stoffel K, Hill TA, Jaffe D, Williams SR, Weisenfeld N, Ramakrishnan S, Kumar V, Shah P, Schatz MC, Church DM, Van Deynze A.

Hortic Res. 2018 Jan 12;5:4. doi: 10.1038/s41438-017-0011-0. eCollection 2018.

11.

A roadmap for breeding orphan leafy vegetable species: a case study of Gynandropsis gynandra (Cleomaceae).

Sogbohossou EOD, Achigan-Dako EG, Maundu P, Solberg S, Deguenon EMS, Mumm RH, Hale I, Van Deynze A, Schranz ME.

Hortic Res. 2018 Jan 10;5:2. doi: 10.1038/s41438-017-0001-2. eCollection 2018.

12.

Regions Underlying Population Structure and the Genomics of Organ Size Determination in Capsicum annuum.

Hill TA, Chunthawodtiporn J, Ashrafi H, Stoffel K, Weir A, Van Deynze A.

Plant Genome. 2017 Nov;10(3). doi: 10.3835/plantgenome2017.03.0026.

13.

Disease Resistance to Multiple Fungal and Oomycete Pathogens Evaluated Using a Recombinant Inbred Line Population in Pepper.

Naegele RP, Granke LL, Fry J, Hill TA, Ashrafi H, Van Deynze A, Hausbeck MK.

Phytopathology. 2017 Dec;107(12):1522-1531. doi: 10.1094/PHYTO-02-17-0040-R. Epub 2017 Oct 2.

PMID:
28762287
14.

Early fruiting in Synsepalum dulcificum (Schumach. & Thonn.) Daniell juveniles induced by water and inorganic nutrient management.

Tchokponhoué DA, N'Danikou S, Hale I, Van Deynze A, Achigan-Dako EG.

F1000Res. 2017 Mar 30;6:399. doi: 10.12688/f1000research.11091.1. eCollection 2017.

15.

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.

Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM.

BMC Plant Biol. 2017 Feb 3;17(1):37. doi: 10.1186/s12870-017-0981-y.

16.

A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding.

Hulse-Kemp AM, Ashrafi H, Plieske J, Lemm J, Stoffel K, Hill T, Luerssen H, Pethiyagoda CL, Lawley CT, Ganal MW, Van Deynze A.

Hortic Res. 2016 Jul 27;3:16036. doi: 10.1038/hortres.2016.36. eCollection 2016.

17.

New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL.

Rinaldi R, Van Deynze A, Portis E, Rotino GL, Toppino L, Hill T, Ashrafi H, Barchi L, Lanteri S.

Front Plant Sci. 2016 Jul 18;7:1031. doi: 10.3389/fpls.2016.01031. eCollection 2016.

18.

Correction: DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.

Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA.

PLoS Genet. 2016 Jul 22;12(7):e1006206. doi: 10.1371/journal.pgen.1006206. eCollection 2016 Jul.

19.

Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing.

Ho WK, Muchugi A, Muthemba S, Kariba R, Mavenkeni BO, Hendre P, Song B, Van Deynze A, Massawe F, Mayes S.

Genome. 2016 Jun;59(6):427-31. doi: 10.1139/gen-2016-0029. Epub 2016 May 12.

PMID:
27244454
20.

DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.

Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA.

PLoS Genet. 2016 May 11;12(5):e1006012. doi: 10.1371/journal.pgen.1006012. eCollection 2016 May. Erratum in: PLoS Genet. 2016 Jul;12(7):e1006206.

21.

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.

Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, Bowman M, Iovene M, Sanseverino W, Cavagnaro P, Yildiz M, Macko-Podgórni A, Moranska E, Grzebelus E, Grzebelus D, Ashrafi H, Zheng Z, Cheng S, Spooner D, Van Deynze A, Simon P.

Nat Genet. 2016 Jun;48(6):657-66. doi: 10.1038/ng.3565. Epub 2016 May 9.

PMID:
27158781
22.

Ultra-High Density, Transcript-Based Genetic Maps of Pepper Define Recombination in the Genome and Synteny Among Related Species.

Hill T, Ashrafi H, Chin-Wo SR, Stoffel K, Truco MJ, Kozik A, Michelmore R, Van Deynze A.

G3 (Bethesda). 2015 Sep 8;5(11):2341-55. doi: 10.1534/g3.115.020040.

23.

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM.

G3 (Bethesda). 2015 Apr 22;5(6):1187-209. doi: 10.1534/g3.115.018416.

24.

BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping.

Hulse-Kemp AM, Ashrafi H, Stoffel K, Zheng X, Saski CA, Scheffler BE, Fang DD, Chen ZJ, Van Deynze A, Stelly DM.

G3 (Bethesda). 2015 Apr 9;5(6):1095-105. doi: 10.1534/g3.115.017749.

25.

Genetically engineered crops that fly under the US regulatory radar.

Camacho A, Van Deynze A, Chi-Ham C, Bennett AB.

Nat Biotechnol. 2014 Nov;32(11):1087-91. doi: 10.1038/nbt.3057. No abstract available.

26.

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts.

Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda AB, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM.

BMC Genomics. 2014 Oct 30;15:945. doi: 10.1186/1471-2164-15-945.

27.

CaGLK2 regulates natural variation of chlorophyll content and fruit color in pepper fruit.

Brand A, Borovsky Y, Hill T, Rahman KA, Bellalou A, Van Deynze A, Paran I.

Theor Appl Genet. 2014 Oct;127(10):2139-48. doi: 10.1007/s00122-014-2367-y. Epub 2014 Aug 6.

PMID:
25096887
28.

Selection and validation of reference genes for gene expression analysis in switchgrass (Panicum virgatum) using quantitative real-time RT-PCR.

Gimeno J, Eattock N, Van Deynze A, Blumwald E.

PLoS One. 2014 Mar 12;9(3):e91474. doi: 10.1371/journal.pone.0091474. eCollection 2014.

29.

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.

Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, Lee HY, Kim SY, Kim MS, Kang BC, Jo YD, Yang HB, Jeong HJ, Kang WH, Kwon JK, Shin C, Lim JY, Park JH, Huh JH, Kim JS, Kim BD, Cohen O, Paran I, Suh MC, Lee SB, Kim YK, Shin Y, Noh SJ, Park J, Seo YS, Kwon SY, Kim HA, Park JM, Kim HJ, Choi SB, Bosland PW, Reeves G, Jo SH, Lee BW, Cho HT, Choi HS, Lee MS, Yu Y, Do Choi Y, Park BS, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai HS, Ahn HK, Yeam I, Giovannoni JJ, Rose JK, Sørensen I, Lee SJ, Kim RW, Choi IY, Choi BS, Lim JS, Lee YH, Choi D.

Nat Genet. 2014 Mar;46(3):270-8. doi: 10.1038/ng.2877. Epub 2014 Jan 19.

PMID:
24441736
30.

QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population.

Naegele RP, Ashrafi H, Hill TA, Chin-Wo SR, Van Deynze AE, Hausbeck MK.

Phytopathology. 2014 May;104(5):479-83. doi: 10.1094/PHYTO-05-13-0143-R.

31.

Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

Page JT, Huynh MD, Liechty ZS, Grupp K, Stelly D, Hulse AM, Ashrafi H, Van Deynze A, Wendel JF, Udall JA.

G3 (Bethesda). 2013 Oct 3;3(10):1809-18. doi: 10.1534/g3.113.007229.

32.

Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae).

Iorizzo M, Senalik DA, Ellison SL, Grzebelus D, Cavagnaro PF, Allender C, Brunet J, Spooner DM, Van Deynze A, Simon PW.

Am J Bot. 2013 May;100(5):930-8. doi: 10.3732/ajb.1300055. Epub 2013 Apr 17.

33.

Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries.

Hirsch CN, Hirsch CD, Felcher K, Coombs J, Zarka D, Van Deynze A, De Jong W, Veilleux RE, Jansky S, Bethke P, Douches DS, Buell CR.

G3 (Bethesda). 2013 Jun 21;3(6):1003-13. doi: 10.1534/g3.113.005595.

34.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

Truco MJ, Ashrafi H, Kozik A, van Leeuwen H, Bowers J, Wo SR, Stoffel K, Xu H, Hill T, Van Deynze A, Michelmore RW.

G3 (Bethesda). 2013 Apr 9;3(4):617-631. doi: 10.1534/g3.112.004929.

35.

Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

Hill TA, Ashrafi H, Reyes-Chin-Wo S, Yao J, Stoffel K, Truco MJ, Kozik A, Michelmore RW, Van Deynze A.

PLoS One. 2013;8(2):e56200. doi: 10.1371/journal.pone.0056200. Epub 2013 Feb 8.

36.

Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population.

Yarnes SC, Ashrafi H, Reyes-Chin-Wo S, Hill TA, Stoffel KM, Van Deynze A.

Genome. 2013 Jan;56(1):61-74. doi: 10.1139/gen-2012-0083. Epub 2013 Jan 1.

PMID:
23379339
37.

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.

Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee TH, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z, Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR, Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, ur Rahman M, Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly DM, Triplett BA, Van Deynze A, Vaslin MF, Waghmare VN, Walford SA, Wright RJ, Zaki EA, Zhang T, Dennis ES, Mayer KF, Peterson DG, Rokhsar DS, Wang X, Schmutz J.

Nature. 2012 Dec 20;492(7429):423-7. doi: 10.1038/nature11798.

PMID:
23257886
38.

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.

Ashrafi H, Hill T, Stoffel K, Kozik A, Yao J, Chin-Wo SR, Van Deynze A.

BMC Genomics. 2012 Oct 30;13:571. doi: 10.1186/1471-2164-13-571.

39.

High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.

Sim SC, Van Deynze A, Stoffel K, Douches DS, Zarka D, Ganal MW, Chetelat RT, Hutton SF, Scott JW, Gardner RG, Panthee DR, Mutschler M, Myers JR, Francis DM.

PLoS One. 2012;7(9):e45520. doi: 10.1371/journal.pone.0045520. Epub 2012 Sep 20.

40.

Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.

Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM.

PLoS One. 2012;7(7):e40563. doi: 10.1371/journal.pone.0040563. Epub 2012 Jul 10.

41.

Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development.

Powell AL, Nguyen CV, Hill T, Cheng KL, Figueroa-Balderas R, Aktas H, Ashrafi H, Pons C, Fernández-Muñoz R, Vicente A, Lopez-Baltazar J, Barry CS, Liu Y, Chetelat R, Granell A, Van Deynze A, Giovannoni JJ, Bennett AB.

Science. 2012 Jun 29;336(6089):1711-5. doi: 10.1126/science.1222218.

42.

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).

Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S, Truco MJ, Michelmore RW, Van Deynze A.

BMC Genomics. 2012 May 14;13:185. doi: 10.1186/1471-2164-13-185.

43.

A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome.

Yu JZ, Kohel RJ, Fang DD, Cho J, Van Deynze A, Ulloa M, Hoffman SM, Pepper AE, Stelly DM, Jenkins JN, Saha S, Kumpatla SP, Shah MR, Hugie WV, Percy RG.

G3 (Bethesda). 2012 Jan;2(1):43-58. doi: 10.1534/g3.111.001552. Epub 2012 Jan 1.

44.

A method for distinctly marking honey bees, Apis mellifera, originating from multiple apiary locations.

Hagler J, Mueller S, Teuber LR, Van Deynze A, Martin J.

J Insect Sci. 2011;11:143. doi: 10.1673/031.011.14301.

45.

Foraging range of honey bees, Apis mellifera, in alfalfa seed production fields.

Hagler JR, Mueller S, Teuber LR, Machtley SA, Van Deynze A.

J Insect Sci. 2011;11:144. doi: 10.1673/031.011.14401.

46.

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.

Iorizzo M, Senalik DA, Grzebelus D, Bowman M, Cavagnaro PF, Matvienko M, Ashrafi H, Van Deynze A, Simon PW.

BMC Genomics. 2011 Aug 2;12:389. doi: 10.1186/1471-2164-12-389.

47.

Single nucleotide polymorphism discovery in elite North American potato germplasm.

Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR.

BMC Genomics. 2011 Jun 9;12:302. doi: 10.1186/1471-2164-12-302.

48.

Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato.

Robbins MD, Sim SC, Yang W, Van Deynze A, van der Knaap E, Joobeur T, Francis DM.

J Exp Bot. 2011 Mar;62(6):1831-45. doi: 10.1093/jxb/erq367. Epub 2010 Dec 30.

49.

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.).

Sim SC, Robbins MD, Van Deynze A, Michel AP, Francis DM.

Heredity (Edinb). 2011 Jun;106(6):927-35. doi: 10.1038/hdy.2010.139. Epub 2010 Nov 17.

50.

Enhanced cytokinin synthesis in tobacco plants expressing PSARK::IPT prevents the degradation of photosynthetic protein complexes during drought.

Rivero RM, Gimeno J, Van Deynze A, Walia H, Blumwald E.

Plant Cell Physiol. 2010 Nov;51(11):1929-41. doi: 10.1093/pcp/pcq143. Epub 2010 Sep 24.

PMID:
20871100

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