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Items: 1 to 50 of 128

1.

Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp).

Lo S, Muñoz-Amatriaín M, Boukar O, Herniter I, Cisse N, Guo YN, Roberts PA, Xu S, Fatokun C, Close TJ.

Sci Rep. 2018 Apr 19;8(1):6261. doi: 10.1038/s41598-018-24349-4.

2.

A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.).

Huynh BL, Ehlers JD, Huang BE, Muñoz-Amatriaín M, Lonardi S, Santos JRP, Ndeve A, Batieno BJ, Boukar O, Cisse N, Drabo I, Fatokun C, Kusi F, Agyare RY, Guo YN, Herniter I, Lo S, Wanamaker SI, Xu S, Close TJ, Roberts PA.

Plant J. 2018 Mar;93(6):1129-1142. doi: 10.1111/tpj.13827. Epub 2018 Feb 24.

PMID:
29356213
3.

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M.

Sci Data. 2017 Apr 27;4:170044. doi: 10.1038/sdata.2017.44.

4.

A chromosome conformation capture ordered sequence of the barley genome.

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N.

Nature. 2017 Apr 26;544(7651):427-433. doi: 10.1038/nature22043.

PMID:
28447635
5.

Genome resources for climate-resilient cowpea, an essential crop for food security.

Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, Fatokun C, Gu YQ, Guo YN, Huynh BL, Jackson SA, Kusi F, Lawley CT, Lucas MR, Ma Y, Timko MP, Wu J, You F, Barkley NA, Roberts PA, Lonardi S, Close TJ.

Plant J. 2017 Mar;89(5):1042-1054. doi: 10.1111/tpj.13404. Epub 2017 Feb 3.

6.

Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp).

Xu P, Wu X, Muñoz-Amatriaín M, Wang B, Wu X, Hu Y, Huynh BL, Close TJ, Roberts PA, Zhou W, Lu Z, Li G.

Plant Biotechnol J. 2017 May;15(5):547-557. doi: 10.1111/pbi.12639. Epub 2016 Oct 17.

7.

Genomic Tools in Cowpea Breeding Programs: Status and Perspectives.

Boukar O, Fatokun CA, Huynh BL, Roberts PA, Close TJ.

Front Plant Sci. 2016 Jun 3;7:757. doi: 10.3389/fpls.2016.00757. eCollection 2016. Review.

8.

A major QTL corresponding to the Rk locus for resistance to root-knot nematodes in cowpea (Vigna unguiculata L. Walp.).

Huynh BL, Matthews WC, Ehlers JD, Lucas MR, Santos JR, Ndeve A, Close TJ, Roberts PA.

Theor Appl Genet. 2016 Jan;129(1):87-95. doi: 10.1007/s00122-015-2611-0. Epub 2015 Oct 8.

9.

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.

Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ.

Plant J. 2015 Oct;84(1):216-27. doi: 10.1111/tpj.12959. Epub 2015 Sep 21.

10.

De novo meta-assembly of ultra-deep sequencing data.

Mirebrahim H, Close TJ, Lonardi S.

Bioinformatics. 2015 Jun 15;31(12):i9-16. doi: 10.1093/bioinformatics/btv226.

11.

When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality.

Lonardi S, Mirebrahim H, Wanamaker S, Alpert M, Ciardo G, Duma D, Close TJ.

Bioinformatics. 2015 Sep 15;31(18):2972-80. doi: 10.1093/bioinformatics/btv311. Epub 2015 May 20.

PMID:
25995232
12.

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.

Ounit R, Wanamaker S, Close TJ, Lonardi S.

BMC Genomics. 2015 Mar 25;16:236. doi: 10.1186/s12864-015-1419-2.

13.

Introgression of a rare haplotype from Southeastern Africa to breed California blackeyes with larger seeds.

Lucas MR, Huynh BL, Roberts PA, Close TJ.

Front Plant Sci. 2015 Mar 9;6:126. doi: 10.3389/fpls.2015.00126. eCollection 2015.

14.

The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning.

Tavakol E, Okagaki R, Verderio G, Shariati J V, Hussien A, Bilgic H, Scanlon MJ, Todt NR, Close TJ, Druka A, Waugh R, Steuernagel B, Ariyadasa R, Himmelbach A, Stein N, Muehlbauer GJ, Rossini L.

Plant Physiol. 2015 May;168(1):164-74. doi: 10.1104/pp.114.252882. Epub 2015 Mar 27.

15.

Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California.

Huynh BL, Ehlers JD, Ndeve A, Wanamaker S, Lucas MR, Close TJ, Roberts PA.

Mol Breed. 2015;35:36. Epub 2015 Jan 21.

16.

Identification of candidate genes and molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp].

Pottorff M, Roberts PA, Close TJ, Lonardi S, Wanamaker S, Ehlers JD.

BMC Genomics. 2014 May 1;15:328. doi: 10.1186/1471-2164-15-328.

17.
18.

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).

Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KF, Scholz U, Poland JA, Stein N, Waugh R.

Plant J. 2013 Nov;76(4):718-27. doi: 10.1111/tpj.12319. Epub 2013 Oct 10.

19.

Genetic architecture of delayed senescence, biomass, and grain yield under drought stress in cowpea.

Muchero W, Roberts PA, Diop NN, Drabo I, Cisse N, Close TJ, Muranaka S, Boukar O, Ehlers JD.

PLoS One. 2013 Jul 30;8(7):e70041. doi: 10.1371/journal.pone.0070041. Print 2013.

20.

A graph-theoretical approach to the selection of the minimum tiling path from a physical map.

Bozdag S, Close TJ, Lonardi S.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):352-60. doi: 10.1109/TCBB.2013.26.

PMID:
23929859
21.

Association Studies and Legume Synteny Reveal Haplotypes Determining Seed Size in Vigna unguiculata.

Lucas MR, Huynh BL, da Silva Vinholes P, Cisse N, Drabo I, Ehlers JD, Roberts PA, Close TJ.

Front Plant Sci. 2013 Apr 15;4:95. doi: 10.3389/fpls.2013.00095. eCollection 2013.

22.

Combinatorial pooling enables selective sequencing of the barley gene space.

Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Bhat PR, Wu Y, Ciardo G, Alsaihati B, Ma Y, Wanamaker S, Resnik J, Bozdag S, Luo MC, Close TJ.

PLoS Comput Biol. 2013 Apr;9(4):e1003010. doi: 10.1371/journal.pcbi.1003010. Epub 2013 Apr 4.

23.

Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus huanglongbing disease.

Zhao H, Sun R, Albrecht U, Padmanabhan C, Wang A, Coffey MD, Girke T, Wang Z, Close TJ, Roose M, Yokomi RK, Folimonova S, Vidalakis G, Rouse R, Bowman KD, Jin H.

Mol Plant. 2013 Mar;6(2):301-10. doi: 10.1093/mp/sst002. Epub 2013 Jan 5.

24.

A physical, genetic and functional sequence assembly of the barley genome.

International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N.

Nature. 2012 Nov 29;491(7426):711-6. doi: 10.1038/nature11543. Epub 2012 Oct 17.

25.

Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum race 3 in cowpea [Vigna unguiculata (L.) Walp].

Pottorff M, Wanamaker S, Ma YQ, Ehlers JD, Roberts PA, Close TJ.

PLoS One. 2012;7(7):e41600. doi: 10.1371/journal.pone.0041600. Epub 2012 Jul 31.

26.

Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species.

Pottorff M, Ehlers JD, Fatokun C, Roberts PA, Close TJ.

BMC Genomics. 2012 Jun 12;13:234. doi: 10.1186/1471-2164-13-234.

27.

Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies.

Xu P, Wu X, Wang B, Luo J, Liu Y, Ehlers JD, Close TJ, Roberts PA, Lu Z, Wang S, Li G.

Heredity (Edinb). 2012 Jul;109(1):34-40. doi: 10.1038/hdy.2012.8. Epub 2012 Feb 29.

28.

ParentChecker: a computer program for automated inference of missing parental genotype calls and linkage phase correction.

Hu Z, Ehlers JD, Roberts PA, Close TJ, Lucas MR, Wanamaker S, Xu S.

BMC Genet. 2012 Feb 23;13:9. doi: 10.1186/1471-2156-13-9.

29.

Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava.

Ferguson ME, Hearne SJ, Close TJ, Wanamaker S, Moskal WA, Town CD, de Young J, Marri PR, Rabbi IY, de Villiers EP.

Theor Appl Genet. 2012 Mar;124(4):685-95. doi: 10.1007/s00122-011-1739-9. Epub 2011 Nov 9.

PMID:
22069119
30.

Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes.

Barrera-Figueroa BE, Gao L, Diop NN, Wu Z, Ehlers JD, Roberts PA, Close TJ, Zhu JK, Liu R.

BMC Plant Biol. 2011 Sep 17;11:127. doi: 10.1186/1471-2229-11-127.

31.

Expression of the H+-ATPase AHA10 proton pump is associated with citric acid accumulation in lemon juice sac cells.

Aprile A, Federici C, Close TJ, De Bellis L, Cattivelli L, Roose ML.

Funct Integr Genomics. 2011 Dec;11(4):551-63. doi: 10.1007/s10142-011-0226-3. Epub 2011 May 10.

PMID:
21556928
32.

Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.).

Saxena RK, Cui X, Thakur V, Walter B, Close TJ, Varshney RK.

Funct Integr Genomics. 2011 Dec;11(4):651-7. doi: 10.1007/s10142-011-0227-2. Epub 2011 May 6.

33.

Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley.

Sato K, Close TJ, Bhat P, Muñoz-Amatriaín M, Muehlbauer GJ.

Plant Cell Physiol. 2011 May;52(5):728-37. doi: 10.1093/pcp/pcr024. Epub 2011 Mar 21.

PMID:
21427110
34.

A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. sesquipedialis) and comparison with the broader species.

Xu P, Wu X, Wang B, Liu Y, Ehlers JD, Close TJ, Roberts PA, Diop NN, Qin D, Hu T, Lu Z, Li G.

PLoS One. 2011 Jan 6;6(1):e15952. doi: 10.1371/journal.pone.0015952.

35.

INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1.

Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WT, Macaulay M, MacKenzie K, Simpson C, Fuller J, Bonar N, Hayes PM, Lundqvist U, Franckowiak JD, Close TJ, Muehlbauer GJ, Waugh R.

Nat Genet. 2011 Feb;43(2):169-72. doi: 10.1038/ng.745. Epub 2011 Jan 9.

PMID:
21217754
36.
37.

Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure.

Cuesta-Marcos A, Szucs P, Close TJ, Filichkin T, Muehlbauer GJ, Smith KP, Hayes PM.

BMC Genomics. 2010 Dec 15;11:707. doi: 10.1186/1471-2164-11-707.

38.

Dissection of QTL effects for root traits using a chromosome arm-specific mapping population in bread wheat.

Sharma S, Xu S, Ehdaie B, Hoops A, Close TJ, Lukaszewski AJ, Waines JG.

Theor Appl Genet. 2011 Mar;122(4):759-69. doi: 10.1007/s00122-010-1484-5. Epub 2010 Dec 11.

39.

Patterns of polymorphism and linkage disequilibrium in cultivated barley.

Comadran J, Ramsay L, MacKenzie K, Hayes P, Close TJ, Muehlbauer G, Stein N, Waugh R.

Theor Appl Genet. 2011 Feb;122(3):523-31. doi: 10.1007/s00122-010-1466-7. Epub 2010 Nov 13.

40.

Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress.

Cotsaftis O, Plett D, Johnson AA, Walia H, Wilson C, Ismail AM, Close TJ, Tester M, Baumann U.

Mol Plant. 2011 Jan;4(1):25-41. doi: 10.1093/mp/ssq056. Epub 2010 Oct 5.

41.

Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array.

Das S, Ehlers JD, Close TJ, Roberts PA.

BMC Genomics. 2010 Aug 19;11:480. doi: 10.1186/1471-2164-11-480.

42.

Association mapping of spot blotch resistance in wild barley.

Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ.

Mol Breed. 2010 Aug;26(2):243-256. Epub 2010 Mar 10.

43.

Accurate construction of consensus genetic maps via integer linear programming.

Wu Y, Close TJ, Lonardi S.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):381-94. doi: 10.1109/TCBB.2010.35.

PMID:
20479505
44.

Response to zinc deficiency of two rice lines with contrasting tolerance is determined by root growth maintenance and organic acid exudation rates, and not by zinc-transporter activity.

Widodo B, Broadley MR, Rose T, Frei M, Pariasca-Tanaka J, Yoshihashi T, Thomson M, Hammond JP, Aprile A, Close TJ, Ismail AM, Wissuwa M.

New Phytol. 2010 Apr;186(2):400-14. doi: 10.1111/j.1469-8137.2009.03177.x. Epub 2010 Jan 22.

45.

Development and implementation of high-throughput SNP genotyping in barley.

Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R.

BMC Genomics. 2009 Dec 4;10:582. doi: 10.1186/1471-2164-10-582.

46.

A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs.

Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ.

Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18159-64. doi: 10.1073/pnas.0905886106. Epub 2009 Oct 13.

47.

Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals.

Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C.

Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14908-13. doi: 10.1073/pnas.0902350106. Epub 2009 Aug 13.

48.

Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress.

Walia H, Wilson C, Ismail AM, Close TJ, Cui X.

BMC Genomics. 2009 Aug 25;10:398. doi: 10.1186/1471-2164-10-398.

49.

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice.

Thiel T, Graner A, Waugh R, Grosse I, Close TJ, Stein N.

BMC Evol Biol. 2009 Aug 22;9:209. doi: 10.1186/1471-2148-9-209.

50.

A compartmentalized approach to the assembly of physical maps.

Bozdag S, Close TJ, Lonardi S.

BMC Bioinformatics. 2009 Jul 15;10:217. doi: 10.1186/1471-2105-10-217.

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