Strawberry Breeding & Research

University of California, Davis

Knapp Publications

  1. Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P (2017) Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. GigaScience
  2. Slabaugh MB, Cooper LD, Kishore VK, Knapp SJ Kling JG. (2015) Genes affecting novel seed constituents in Limnanthes alba Benth: transcriptome analysis of developing embryos and a new genetic map of meadowfoam. PeerJ 3: e915.
  3. Barb J, Bowers JE, Renaut S, Rey JI, Knapp SJ, Rieseberg LH, Burke JM (2014) Chromosomal evolution and patterns of introgression in Helianthus. Genetics 197: 969-979
  4. Bertioli DJ, Ozias-Akins P, Chu Y, Dantas KM, Santos SP, Gouvea E, Guimarães PM, Leal-Bertioli SC, Knapp SJ, Moretzsohn MC (2014) The use of SNP markers for linkage mapping in diploid and tetraploid peanuts. G3: Genes, Genomes, Genetics 4(1):89-96
  5. Ziebell AL, Barb JG, Sandhu S, Moyers B, Sykes RW, Doeppke C, Gracom KL, Carlile M, Marek LF, Davis MF, Knapp SJ, Burke JM (2013) Sunflower as a biofuels crop:  an analysis of lignocellulosic chemical properties. Biomass Bioenergy 59: 208-217
  6. Maren L, Yu W, Wieckhorst S, Haseneyer G, Seidel M, Hahn V, Knapp SJ, Taudien S, Schön C.C., Bauer E (2013) WBSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower.  BMC Genomics 14: 628
  7. Khera P, Upadhyaya HD, Pandey MK, Roorkiwal M, Sriswathi M, Janila P, Guo Y, McKain MR, Nagy ED, Knapp SJ, Leebens-Mack J, Conner JA, Ozias-Akins P, Varshney RK (2013) Single nucleotide polymorphism-based genetic diversity in the reference set of peanut (Arachis spp.) by developing and applying cost-effective kompetitive allele specific polymerase chain reaction genotyping assays.  The Plant Genome 6: 1-11
  8. Mandel JR, Milton EF, Donovan LA, Knapp SJ, Burke JM (2013) Genetic diversity and population structure in the rare Algodones sunflower (Helianthus niveus ssp. tephrodes) and comparison to related sunflowers.  Conserv Genet 14: 31-40
  9. Mandel JR, Nambeesan S, Bowers JE, Marek LF, Ebert D, Rieseberg LH, Knapp SJ, Burke JM (2013) Association mapping and the genomic consequences of selection in sunflower. PLoS Genet 9: e1003378
  10. Bowers JE, Nambeesan S, Corbi J, Barker MS, Rieseberg LH, Knapp SJ, Burke JM (2012) Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms.  PLoS One 7: e51360
  11. Sujay V, Gowda MV, Pandey MK, Bhat RS, Khedikar YP, Nadaf HL, Gautami B, Sarvamangala C, Lingaraju S, Radhakrishan T, Knapp SJ, Varshney RK (2012) Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Mol Breed 30: 773-788
  12. Sandlin K, Prothro J, Heesacker A, Khalilian N, Okashah R, Xiang W, Bachlava E, Caldwell DG, Taylor CA, Seymour DK, White V, Chan E, Tolla G, White C, Safran D, Graham E, Knapp S, McGregor C (2012) Comparative mapping in watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai]. Theor Appl Genet 125: 1603-18
  13. Bowers JE, Bachlava E, Brunick RL, Rieseberg LH, Knapp SJ, Burke JM (2012) Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3 (Bethesda) 2: 721-9
  14. Staton SE, Bakken BH, Blackman BK, Chapman MA, Kane NC, Tang S, Ungerer MC, Knapp SJ, Rieseberg LH, Burke JM (2012) The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant J 72: 142-53
  15. Ballerini ES, Brothers AN, Tang S, Knapp SJ, Bouck A, Taylor SJ, Arnold ML, Martin NH (2012) QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris. BMC Plant Biol 12:91
  16. Gautami B, Pandey MK, Vadez V, Nigam SN, Ratnakumar P, Krishnamurthy L, Radhakrishnan T, Gowda MV, Narasu ML, Hoisington DA, Knapp SJ, Varshney RK (2012) Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Mol Breed. 30:757-772
  17. Chen X, Zhu W, Azam S, Li H, Zhu F, Li H, Hong Y, Liu H, Zhang E, Wu H, Yu S, Zhou G, Li S, Zhong N, Wen S, Li X, Knapp SJ, Ozias-Akins P, Varshney RK, Liang X (2013) Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotechnol J 11:115-27
  18. Kane NC, Burke JM, Marek L, Seiler G, Vear F, Baute G, Knapp SJ, Vincourt P, Rieseberg LH (2013) Sunflower genetic, genomic, and ecological resources. Mol Ecol Resour 13:10-20.
  19. Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.  BMC Genomics 13:3
  20. Portis E, Scaglione D, Acquadro, Mauromicale G, Mauro R, Knapp SJ, Lanteri S (2012) Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex. BMC Res Notes 5: 252
  21. Scaglione D, Lanteri S, Acquadro A, Lai Z, Knapp SJ, Rieseberg LH, Portis E (2012) Large-scale transcriptome characterization and mass discovery of SNPs in globe artichoke and its related taxa. Plant Biotech J 10: 956-69
  22. Nagy ED, Guo Y, Tang S, Bowers JE, Okashah RA, Taylor CA, Zhang D, Khanal S, Heesacker AF, Khalilian N, Farmer AD, Carrasquilla-Garcia N, Penmetsa RV, Cook D, Stalker HT, Nielsen N, Ozias-Akins P, Knapp SJ (2012) A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genomics 13:469
  23. Guo Y, Khanal S, Tang S, Bowers JE, Heesacker AF, Khalilian N, Nagy ED, Zhang D, Taylor CA, Stalker HT, Ozias-Akins P, Knapp SJ (2011) Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A and B genome diploid species of peanut. BMC Genomics 13:608
  24. Mandel JR, Milton EF, Donovan LA, Knapp SJ, Burke JM (2011) Genetic diversity and population structure in the rare Algodones sunflower (Helianthus niveus ssp. tephrodes) and comparison to related sunflowers. Conserv Genet 14: 31-40
  25. Kane NC, Burke JM, Knapp SJ, Seiler G, Marek L, Vincourt P, Rieseberg LH (2011) Sunflower genetic, genomic, and ecological resources. Mol Ecol Resources 13:10-20
  26. Chapman MC, Tang S, Draeger D, Nambeesan S, Shaffer H, Barb JG, Knapp SJ, Burke JM (2011) Genetic analysis of floral symmetry in Van Gogh’s sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae. PLoS Genet 8:e1002628
  27. Bachlava E, Taylor CA, Tang S, Bower JE, Mandel JR, Burke JM, Knapp SJ (2011) SNP discovery and development of a high-density genotyping array for sunflower. PLoS One 7: e298
  28. Gautami B, Pandey MK, Vadez V, Nigam SN, Ratnakumar P, Krishnamurthy L, Radhakrishnan T, Gowda MVC, Narasu ML, Hoisington DA, Knapp SJ, Varshney RK (2011) Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Mol Breed 30:757-772
  29. Sujay V, Gowda MVC, Pandey MK, Bhat RS, Khedikar YP, Nadaf, Gautami B, Sarvamangala C, Lingaraju S, Radkakrishan T, Knapp SJ, Varshney RK (2011) Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.). Mol Breed 30:773-788
  30. Pandey MSK, Gautami B, Jayakumar T, Sriswathi M, Upadhyaya HD, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Cook DR, Varshney RK (2011) Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea).  Plant Breeding 131:139–147
  31. Qin H, Feng S, Chen C, Guo Y, Knapp SJ, Culbreath A, He G, Wang ML, Zhang X, Holbrook CC, Osias-Akins P (2011) An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations. Theor Appl Genet 124: 653-64
  32. Kane NC, Gill N, K, King MG, Bowers JE, Berges H, Gouzy J, Bachlava E, Langlade Z, Lai Z, Stewart M, Burke JM, Vincourt P, Knapp SJ, Rieseberg LH (2011) Progress towards a reference genome for sunflower. Botany 89: 429–437
  33. Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Varshney RK (2011) Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theor Appl Genet 122: 1119-1132
  34. Bachlava E, Radwan OE, Abratti G, Tang S, Gao W, Heesacker AF, Bazzalo ME, Zambelli A, Leon AJ, Knapp SJ (2011) Downy mildew (Pl8 and Pl14) and rust (RAdv) resistance genes reside in close proximity to tandemly duplicated clusters of non-TIR-like NBS-LRR-encoding genes on sunflower chromosomes 1 and 13. Theor Appl Genet 122: 1211-1221
  35. Blackman BK, Rasmussen DA, Strasburg JL, Raduski AR, Burke JM, Knapp SJ, Michaels SD, Rieseberg LH (2010) Contributions of flowering time genes to sunflower domestication and improvement.  Genetics 187: 271-287
  36. Wieckhorst S, Bachlava E, Dussle CM, Tang S, Gao W, Knapp SJ, Schoen CC, Hahn V, Bauer E (2010) Fine mapping of the sunflower resistance locus PlARG introduced from the wild species Helianthus argophyllus. Theor Appl Genet 121: 1633-1644
  37. Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L, Aruna R, Nigam SN, Moss BJ, Seetha K, Ravi K, He G, Knapp SJ, Hoisington DA (2009) The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor Appl Genet 118: 729-739
  38. Arnold ML, Tang S, Knapp SJ, Martin NH (2010) Asymmetric introgressive hybridization among Louisiana Iris species. Genes 1: 9-22
  39. Wills DM, Abdel-Haleem H, Knapp SJ, Burke JM (2010) Genetic architecture of novel traits in the Hopi sunflower.  J Hered 101: 727-736
  40. Tang S, Okashah RA, Knapp SJ, Arnold ML, Martin NH (2010) Transmission ratio distortion results in asymmetric introgression in Louisiana Iris.  BMC Plant Biology 10: 48
  41. Dechaine JM, Burger JC, Chapman MA, Seiler GJ, Brunick R, Knapp SJ, Burke JM (2009) Fitness effects and genetic architecture of plant-herbivore interactions in sunflower crop-wild hybrids. New Phytol 184: 741-743
  42. Nagy ED, Chu Y, Guo Y, Khanal S, Tang S, Li Y, Dong WB, Timper P, Taylor C, Ozias-Akins P, Holbrook CC, Beilinson V, Nielsen NC, Stalker HT, Knapp SJ (2009) Recombination is suppressed in an alien introgression on chromosome 5A of peanut harboring Rma, a dominant root-knot nematode resistance gene.  Mol Breeding 26: 357-370
  43. Scaglione, D, A Acquadro, E Portis, S. Lanteri, C Taylor, SJ Knapp (2009) Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database.  BMC Genomics 10: 454
  44. Bachlava E, Draeger D, Tang S, Knapp SJ (2009) Pleiotropy of the branching locus (B) masks linked and unlinked quantitative trait loci affecting seed traits in sunflower.  Theor Appl Genet 120: 829-842
  45. Heesacker AF, Brunick RL, Bachlava E, Burke JM, Rieseberg LH, Knapp SJ (2009) Karyotypic evolution of the common and silverleaf sunflower genomes.  The Plant Genome 2: 233-246
  46. Chapman, M, Hvala J, Stever J, Matvienko M, Kozik A, Michelmore RW, Tang S, Knapp SJ, Burke JM (2009) Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.).  Theor Appl Genet 120: 85-91
  47. Tang S, Okashah RA, Cordonnier-Pratt MM, Pratt LH, Virgil Ed Johnson VE, Taylor CA, Arnold ML, Knapp SJ (2009) EST and EST-SSR marker resources for Iris.  BMC Plant Biology 9: 72
  48. Gandhi SD, Kishore VK, Crane JM, Slabaugh MB, and Knapp SJ (2009) Selection for low erucic acid and genetic mapping of loci affecting the accumulation of very long-chain fatty acids in meadowfoam seed storage lipids.  Genome 52: 547-556
  49. Kane NC, Barker MS, Whitlock MC, Raduski A, Karenberg S, Knapp SJ, Rieseberg LH (2009) Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species.  Evolution 63: 2061-2075
  50. McHale LK, Truco MJ, Kozik A, Wroblewski T, Ochoa OE, Lahre KA, Knapp SJ, Michelmore RW (2009) The genomic architecture of disease resistance in lettuce. Theor Appl Genet 118: 565-580
  51. Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH (2008) Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol 25: 2445-2455
  52. Chapman MA, Pashley CH, Wenzler J, Hvala J, Tang S, Knapp SJ, Burke JM (2008) A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus).  Plant Cell 20: 2931-2945
  53. Heesacker, A, Kishore VK, Gao W, Tang S, Kolkman J, Gingle A, Matvienko M, Kozik A, Michelmore RW, Lai Z, Rieseberg LH, Knapp SJ (2008) SSRs mined from the sunflower EST database:  abundance, polymorphisms, and cross-taxa utility.  Theor Appl Genet 117: 1021-9
  54. Yue B, Radi SA, Vick BA, Cai X, Tang S, Knapp SJ, Gulya TJ, Miller JF, Hu J (2008) Identifying quantitative trait loci for resistance to Sclerotinia head rot in two USDA sunflower germplasms.  Phytopathology 98: 926-931
  55. Radwan O, Gandhi S, Heesacker A, Whitaker B, Taylor C, Plozik A, Kesseli R, Kozik A, Michelmore RM, Knapp SJ (2008) Genetic diversity and genomic distribution of homologs encoding NBS-LRR disease resistance proteins in sunflower.  Mol Genetics Genomics 280: 111-125
  56. Xu X, Martin B, Jonathan P. Comstock JP, Vision TJ, Tauer CG, Baige Zhao B, Pausch RC, Knapp SJ (2008) Fine mapping a QTL for carbon isotope composition in tomato. Theor Appl Genet 117: 221-233
  57. Kolkman JM, Berry ST, Leon AJ, Slabaugh MB, Tang S, Gao W, Shintani DK, Burke JM, Knapp SJ (2007) Single nucleotide polymorphisms and linkage disequilibrium in sunflower. Genetics 177: 457-68.
  58. Hajduch M, Casteel JE, Tang S, Hearne LB, Knapp S, Thelen JJ (2007) Proteomic analysis of near-isogenic sunflower varieties differing in seed oil traits. J Proteome Res 6: 3232-41.
  59. Church SA, Livingstone K, Lai Z, Kozik A, Knapp SJ, Michelmore RW, Rieseberg LH (2007) Using variable rate models to identify genes under selection in sequence pairs:  their validity and limitations for EST sequences.  J. Mol. Evol. 64: 171-80.
  60. Bushman BS, Scholte AA, Cornish K, Scott DJ, Brichta JL, Vederas JC, Ochoa O, Michelmore RW, Shintani DK, Knapp SJ (2006) Identification and comparison of natural rubber from two Lactuca species.  Phytochemistry 67: 2590-6.
  61. Filichkin S, Slabaugh MB, Knapp SJ (2006) Thioesterases isolated from Cuphea calophylla, a high laurate species, have broad substrate specificities and complement an Arabidopsis fatb mutant. Eur J Lipid Sci Tech 108: 979-990
  62. Timms, L., R. Jimenez, M. Chase, L. McHale, D. Lavelle, A. Kozik, Z. Lai, R.W. Michelmore, S.J. Knapp, A. Heesacker, L. Rieseberg, R. Kesseli (2006) Analyses of synteny between Arabidopsis thaliana and species in the Compositae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics 173: 2227-35.
  63. Schuppert, G.F., Tang, S., Slabaugh, M.B., and Knapp, S.J. (2006) The sunflower high-oleic mutant Ol carries variable tandem repeats of FAD2-1, a seed-specific oleoyl-phosphatidyl choline desaturase. Mol. Breeding 17: 241-256.
  64. Tang, S., Hass, C., and Knapp, S.J. (2006) Ty3/gypsy-like retrotransposon knockout of a 2-methyl-6-phytyl-1,4-benzoquinone methyltransferase is non-lethal, uncovers a cryptic paralogous mutation, and produces novel tocopherol (vitamin E) profiles in sunflower. Theor Appl Genet 113: 767-82
  65. Tang, S., A. Leon, W. C. Bridges, and S.J. Knapp (2006) Quantitative trait loci for genetically correlated seed traits are tightly linked to branching and pericarp pigment loci in sunflower. Crop Sci. 46: 721-734.
  66. Hass, C., Tang, S., Leonard, S., Miller, J.F., Traber, M., and Knapp, S.J. (2006) Three non-allelic epistatically interacting methyltransferase mutations produce novel tocopherol (vitamin E) profiles in sunflower. Theor Appl Genet 113: 783-99
  67. Filichkin S, Slabaugh MB, Knapp SJ (2006) Thioesterases isolated from Cuphea calophylla, a high laurate species, have broad substrate specificities and complement an Arabidopsis fatb mutant. Eur J Lipid Sci Tech 108: 979–990
  68. Bushman BS, Scholte AA, Cornish K, Scott DJ, Brichta JL, Vederas JC, Ochoa O, Michelmore RW, Shintani DK, Knapp SJ (2006) Identification and comparison of natural rubber from two Lactuca species. Phytochemistry 67:  2590–2596
  69. Timms L, Jimenez, R, Chase M, McHale L, Lavelle D, Kosik A, Lai Z, Michelmore RW, Knapp S, Heesacker A, Rieseberg L, Kesseli R (2006) Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics173: 2227-2235
  70. Schuppert GF, Tang S, Slabaugh MB, Knapp SJ (2006) The sunflower high-oleic mutant Ol carries variable tandem repeats of FAD2-1, a seed-specific oleoyl-phosphatidyl choline desaturase. Mol. Breeding 17: 241-256.
  71. Lai Z, Livingstone K, Zou Y, Church SA, Knapp SJ, Andrews J, Rieseberg LH (2005) Identification and mapping of SNPs from ESTs in sunflower. Theor. Appl. Genet. 111: 1532-44.
  72. Burke JH, Knapp SJ, Rieseberg LH (2005) Genetic consequences of selection during the evolution of cultivated sunflower. Genetics 171: 1933-40.
  73. Lai Z, Nakazato T, Salmaso M, Burke JM, Tang S, Knapp SJ, Rieseberg LH (2005) Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species. Genetics 171: 291-303.
  74. Argyris J, Truco MJ, Ochoa O, Knapp SJ, Still DW, Lenssen G, Schut J, Michelmore RW, Bradford KJ (2005) Quantitative trait loci associated with seed and seedling traits in Lactuca. Theor. Appl. Genet. 111: 1365-76.
  75. Pérez-Vich B, Berry ST, Velasco L, Fernandez-Martinez JM, Gandhi S, Freeman C, Heesacker A, Knapp SJ, Leon AJ (2005) Genetic mapping of nuclear male-sterility genes in sunflower. Crop Sci. 45: 1851-1857.
  76. Knapp SJ, Brunick R, Crane JM (2005) Registration of Ross meadowfoam. Crop Sci. 45: 407.
  77. Micic Z, Hahn V, Bauer E, Schoen CC, Knapp SJ, Tangm S, Melchinger AE (2005) Identification and validation of QTL for Sclerotinia midstalk rot resistance in sunflower by selective genotyping. Theor Appl Genet 111: 233-42
  78. Bushman BS, Phillips B,Isbell T, Ou B, Crane JM, Knapp SJ (2004) Chemical composition of caneberry (Rubus spp.) seeds and oils and their antioxidant potential. J. Agric. Food Chem. 52: 7982-7.
  79. Gandhi S, Heesacker AF, Freeman CA, Argyris J, Bradford K, Knapp SJ (2004) The self-incompatibility locus (S) and quantitative trait loci for self-pollination and seed dormancy in sunflower. Theor Appl Genet 111: 619-29
  80. Micic Z, Hahn V, Bauer E, Schoen CC, Knapp SJ, Tang S, Melchinger AE (2004) QTL mapping of Sclerotinia midstalk rot resistance in sunflower. Theor. Appl. Genet. 109: 1474-84.
  81. Dussel CM, Hahn V, Knapp SJ, Bauer E (2004) PlArg from Helianthus argophyllus is unlinked to other known downy mildew resistance genes in sunflower. Theor. Appl. Genet. 109: 1083-1086.
  82. Pérez-Vich B, Knapp SJ, Leon AJ, Fernandez-Martinez JM, Berry ST (2004) Mapping minor QTL for increased stearic acid content in sunflower seed oil. Mol. Breeding 13: 313-322.
  83. Kolkman JM, Slabaugh MB, Bruniard JM, Berry ST, Bushman SB, Abratti G, Zambelli A, Miller JF, Leon A, Knapp SJ (2004) Acetohydroxyacid synthase mutations conferring resistance to imidazolinone or sulfonylurea herbicides in wild sunflower biotypes. Theor. Appl. Genet. 109:1147-1159.
  84. Burke JM, Lai Z, Salmaso M, Nakazato T, Tang S, Heesacker A, Knapp SJ, Rieseberg LH (2004) Comparative mapping and rapid karyotypic evolution in Helianthus. Genetics 167:449-457
  85. Kishore VK, Velasco P, Shintani DK, Rowe J, Rosato C, Adair N, Slabaugh MB, Knapp SJ (2004) Conserved simple sequence repeats in the Limnanthaceae (Brassicales).  Theor. Appl. Genet. 108: 450-457.
  86. Pérez-Vich B, Akhtouch B, Knapp SJ, Leon AJ, Velasco L, Fernández-Martínez JM, Berry ST 2004) Quantitative trait loci for broomrape (Orobanche cumana Wallr.) resistance in sunflower. Theor. Appl. Genet. 109:92-102.
  87. Tang S, Kishore VK, Knapp SJ (2003) PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower. Theor Appl Genet 107: 6-19.
  88. Slabaugh MG, Yu JK, Tang S, Heesacker A, Hu X, Lu G, F. Han, Bidney D, Knapp SJ (2003) Haplotyping and mapping a large cluster of resistance gene candidates in sunflower using multilocus intron fragment length polymorphisms. Plant Biotech J. 1: 167-185.
  89. Tang S, Heesacker A, Kishore VK, Fernandez A, Sadik ES, Cole G, Knapp SJ (2003) Genetic mapping of the Or5 gene for resistance to Orobanche race E in sunflower. Crop Sci. 43: 1021-1028.
  90. Tang S, Knapp SJ (2003) Microsatellites uncover extraordinary molecular genetic diversity in Native American land races and wild populations of cultivated sunflower. Theor Appl Genet 106: 990-1003.
  91. Kozik A, Michelmore RW, Knapp SJ, Matvienko MS, Rieseberg L, Lin H, van Damme M, Lavelle D, Chevalier P, Ziegle J, Ellison P, Kolkman J, Slaubaugh MS, Livingston K, Zhou LZ, Church S, Edberg S, Jackson L, Bradford K (2002) Lettuce and sunflower expressed sequences tags (ESTs). http://compgenomics.ucdavis.edu/.
  92. Yu JK, Tang S, Slabaugh MB, Heesacker A, Cole G, Herring M, J. Soper J, Han F, Chu WC, Webb DM, Thompson L, Edwards KJ, Berry S, Leon A, Olungu C, Maes N, Knapp SJ (2002) Towards a saturated molecular genetic linkage map for cultivated sunflower. Crop Sci 43: 367-387
  93. Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161: 1257-1267.
  94. Tang S, Yu JK, Slabaugh MB, Shintani DK, Knapp SJ (2002) Simple sequence repeat map of the sunflower genome. Theor Appl Genet 105: 1124-1136
  95. Pérez-Vich B, Fernández-Martínez JM, Grondona M, Knapp SJ, Berry ST (2002) Stearoyl-ACP and oleoyl-PC desaturase genes cosegregate with quantitative trait loci underlying high stearic and high oleic acid mutant phenotypes in sunflower.  Theor. Appl. Genet. 104: 338-349.
  96. Knapp SJ, Crane JM (2002) Registration of Wheeler meadowfoam.  Crop Sci. 42: 2208-2209.
  97. Burke JM, Tang S, Knapp SJ, Rieseberg LH (2002) Genetic analysis of sunflower domestication. Genetics 161: 1257-1267.
  98. Tang S, Yu JK, Slabaugh MB, Shintani DK, Knapp SJ (2002) Simple sequence repeat map of the sunflower genome. Theor Appl Genet 105:1124-1136
  99. Pérez-Vich B, Fernández-Martínez JM, Grondona M, Knapp SJ, Berry ST (2002) Stearoyl-ACP and oleoyl-PC desaturase genes cosegregate with quantitative trait loci underlying high stearic and high oleic acid mutant phenotypes in sunflower.  Theor. Appl. Genet. 104:338-349.
  100. Castro AJ, Chen X, Hayes PM, Knapp SJ, Line R, Toojinda T, Vivar H (2002) Coincident QTL which determine seedling and adult plant resistance to stripe rust in barley.  Crop Sci 42: 1701-1708
  101. Yu JK, Mangor J, Thompson L, Edwards KJ, Slabaugh MB, Knapp SJ (2002) Allelic diversity of simple sequence repeat markers among elite inbred lines in cultivated sunflower. Genome 45: 652-660
  102. Katengam S, Crane JM, Knapp SJ (2001) The development of a genetic map for meadowfoam comprised of amplified fragment length polymorphisms.  Theor. Appl. Genet. 104: 92-96.
  103. Katengam S, Crane JM, Knapp SJ (2001) Genetic mapping of a macromutation and quantitative trait loci underlying fatty acid composition differences in meadowfoam oil.  Crop Sci. 41: 1927-1930.
  104. Gelid MA, Berry SK, Jones R, Leon A, Wye C, Peleman J, Knapp SJ (2001) An integrated RFLP-AFLP linkage map for cultivated sunflower.  Genome 44: 213-221.
  105. Gelid MA, Slabaugh MB, Berry SK, Jones R, Michelmore R, Miller JF, Gulya T, Knapp SJ (2001) Candidate disease resistance genes in sunflower cloned using conserved nucleotide binding site motifs:  genetic mapping and linkage to the downy mildew resistance gene Pl1.  Genome 44: 205-212.
  106. Knapp SJ, Berry S, Rieseberg LH (2001) Genetic mapping in sunflowers.  pp. 379-403.  In R.L. Phillips and I.K. Vasil (ed.).  DNA markers in plants.  Kluwer, Dordrecht, the Netherlands.
  107. Crane JM, Knapp SJ (2000) Registration of Knowles meadowfoam. Crop Sci. 40: 291-292.
  108. Crane JM, Knapp SJ (2000) Registration of the self-pollinated meadowfoam germplasm line OMF64. Crop Sci. 40: 1511-1512.
  109. Knapp SJ, Crane JM (2000) Registration of self-pollinated fully non-dormant Cuphea germplasm VL160.  Crop Sci. 40: 300-301.
  110. Knapp SJ, Crane JM (2000) Registration of high oil Cuphea germplasm VL186.  Crop Sci. 40: 301.
  111. Knapp SJ, Crane JM(2000) Registration of reduced seed-shattering Cuphea germplasm PSR23.  Crop Sci. 40: 299-300.
  112. Cheers MT, Crane JM, Miller JF, Knapp SJ (2000) Genetic distance as a predictor of heterosis and hybrid performance in sunflower.  Theor. Appl. Genet. 100: 889-894.
  113. Cheers MT, Miller JF, Knapp SJ (1999) Donor inbred lines for enhancing the performance of elite single-cross hybrids in sunflower.  Crop Sci. 39: 1325-1331.
  114. Knapp SJ, Crane JM(1999) The development of meadowfoam as an industrial oilseed:  breeding challenges and germplasm resources.  In J. Janick (ed.).  pp. 225-233.  Proceedings of the Fourth National Symposium on New Crops.  Wiley, New York.
  115. Keller DP, Goodrum JW, Knapp SJ (1999) Fuel properties of oil from a genetically altered Cuphea viscosissima.  Indus. Crop Prod. 9: 85-91.
  116. Knapp SJ, Crane JM (1998) A dominant mutation affecting the erucic and dienoic acid contents of meadowfoam subspecies.  Crop Sci. 38: 1541-1544.
  117. Cheres M, Knapp SJ (1998) Ancestral origins and genetic diversity of cultivated sunflower:  coancestry analysis of public germplasm sources.  Crop Sci. 38: 1476-1482.
  118. Knapp SJ (1998) Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes.  Crop Sci. 38: 1164-1174.
  119. Hongtrakul V, Slabaugh MB, Knapp SJ (1998) A seed specific delta-12 oleate desaturase is duplicated, rearranged, and weakly expressed in high oleic sunflower lines.  Crop Sci. 38: 1245-1249.
  120. Slabaugh MB, Leonard JM, Knapp SJ (1998) Condensing enzymes from Cuphea wrightii associated with medium-chain fatty acid biosynthesis.  Plant J. 13: 611-620.
  121. Leonard JM, Knapp SJ, Slabaugh MB (1998) Cuphea beta-ketoacyl-ACP synthase shifts the synthesis of fatty acids towards shorter chains in Arabidopsis seeds expressing Cuphea FatB thioesterases.  Plant J. 13: 621-628.
  122. Hongtrakul V, Slabaugh MB, Knapp SJ (1998) DFLP, SSCP, and SSR markers for delta-9-stearoyl-acyl carrier protein desaturases strongly expressed in developing seeds of sunflower:  intron lengths are hypervariable among elite inbred lines.  Mol. Breeding 4: 195-203.
  123. Krutovskii KV, Vollmer SS, Sorensen FC, Adams WT, Knapp SJ, Strauss SH (1998) RAPD genome maps of douglas-fir.  J. Heredity 89: 197-205.
  124. Knapp, S.J. and J.M. Crane (1997) The development of self-pollinated inbred lines of meadowfoam by direct selection in open-pollinated populations.  Crop Sci. 37: 1770-1775.
  125. Leonard JM, Slabaugh MB, Knapp SJ (1997) Cuphea wrightii thioesterases have unexpected broad specificities on saturated fatty acids.  Plant Mol. Biol. 34: 669-679.
  126. Hongtrakul V, Huestis G, Knapp SJ (1997) Amplified fragment length polymorphisms as a tool for DNA fingerprinting sunflower germplasm:  genetic diversity among oilseed inbred lines.  Theor. Appl. Genet. 95: 400-407.
  127. Knapp SJ, Crane JM, Tagliani LA, Slabaugh MB (1997) Cuphea viscosissima mutants with decreased capric acid.  Crop Sci. 37: 352-357.
  128. Liu B-H, Knapp SJ, Birkes D (1997) Sampling distributions, biases, variances, and confidence intervals for genetic correlations.  Theor. Appl. Genet. 36: 8-20.
  129. Slabaugh MB, Huestis GM, Leonard J, Holloway JL, Rosato C, Hongtrakul V, Martini N, Toepfer R, Voetz M, Schell J, Knapp SJ (1997) Sequence-based genetic markers for genes and gene families:  single-strand conformational polymorphisms for the fatty acid synthesis genes of Cuphea.  Theor. Appl. Genet. 94: 400-408.
  130. Ali MS, Knapp SJ (1996) Heterosis of Cuphea lanceolata single-cross hybrids.  Crop Sci. 36: 278-284.
  131. Ali MS, Knapp SJ (1996) Cytogenetics of Cuphea lanceolata interpopulation hybrids.  Genome 38: 1148-1152.
  132. Knapp SJ, Bridges WC, Holloway J, Liu B-H (1995) Mapping dominant markers using F2 matings.  Theor. Appl. Genet. 91: 74-81.
  133. Knapp SJ, Crane JM (1995) Fatty acid diversity of Section Inflexae Limnanthes.  Industrial Crops Products 4: 219-227.
  134. Crane JM, Tagliani LA, Knapp SJ (1995) Registration of self-fertile non-dormant Cuphea viscosissima x lanceolata germplasm.  Crop Sci. 35: 1516-1517.
  135. Crane JM, Tagliani LA, Knapp SJ (1995) Registration of four fatty acid mutant lines (VS-6-CPR-1, VS-6-CPR-4, VS-6-CPY-1, and VS-6-MYR-1) of Cuphea viscosissima Jacq.  Crop Sci. 35: 1517.
  136. Slabaugh MB, Tai H, Jaworski J, Knapp SJ (1995) Two cDNAs encoding beta-ketoacyl-ACP synthase III from C. wrightii.  Plant Physiol. 108: 443-444.
  137. Deavy ME, Fiddler TA, Liu B-H, Knapp SJ, Neale D (1995) An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree.  Theor. Appl. Genet. 88: 273-278.
  138. Knapp SJ (1994) Selection using molecular marker indexes.  In Proc. Second Plant Breeding Symposium of the Crop Sci. Soc. Amer. and Amer. Soc. Hort. Sci., Corvallis, Oregon., pp. 1-11.  Amer. Soc. Hort. Sci., Alexandria, Virginia.
  139. Crane JM, Webb DM, Tagliani LA, Knapp SJ (1994) Registration of a non-dormant population (LN-183) of Cuphea lanceolata Ait.  Crop Sci. 34: 1423.
  140. Knapp SJ (1994) Mapping quantitative trait loci.  In R.L. Phillips and I.K. Vasil (ed.), pp. 58-96.  DNA markers in plants.  Kluwer, Dordrecht, the Netherlands.
  141. Echt CS, Tidwell KK, Knapp SJ, Osborn TS, McCoy T (1994) Linkage mapping in diploid alfalfa.  Genome 37: 61-71.
  142. Slabaugh MB, Leanord JM, Huestis GM, Crane JM, Knapp SJ (1994) Genetic and biochemical studies of medium-chain fatty acid synthesis.  In Proc. Eleventh Intl. Symp. Plant Lipids, Paris, France, pp. 1-4.  Kluwer, Dordrecht, the Netherlands.
  143. Leonards-Schippers C, Gieffers W, Schaefer-Pregl R, Ritter E, Knapp SJ, Salamini F, Gebhardt C (1994) Quantitative resistance to Phytophora infestans in potato:  a case study for QTL mapping in an allogamous plant species.  Genetics 137: 67-77.
  144. Hayes PM, Liu B-H, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmussen D, Sorrels M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm.  Theor. Appl. Genet. 87: 392-401.
  145. Knapp SJ,Bridges WC, Liu B-H (1993) Mapping quantitative trait loci using nonsimultaneous and simultaneous estimators and hypothesis tests.  In Beckmann, J.S. and T.S. Osborn (ed.), pp. 209-237.  Plant genomes:  Methods for genetic and physical mapping.  Kluwer, Dordrecht, the Netherlands.
  146. Kleinhofs A, Kilian A, Saghai Maroof MA, Biyashev RM, Hayes PM, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahlien L, Kudrna D, Bollinger J, Knapp SJ, Liu B-H, Sorrells M, Heun M, Fanckowiak JD, Hoffman D, Skadsen R, Steffens BJ (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome.  Theor. Appl. Genet. 86: 705-712.
  147. Brandt T, Knapp SJ (1993) Gametic selection at fatty acid synthesis and allozyme marker loci and meiosis of Cuphea lanceolata x Cuphea viscosissima populations.  Crop Sci. 33: 1138-1143.
  148. Knapp SJ (1993) Modifying the seed oils of Cuphea–a new commercial source of caprylic, capric, lauric, and myristic acid.  In S. MacKenzie and D. Taylor (ed.), pp. 142-154.  Seed oils for the future.  Amer. Oil Chem. Soc., Champaign, Illinois.
  149. Holloway JL, Knapp SJ (1993) G-MENDEL 3.0:  Software for the analysis of genetic markers and maps.  pp. 1-130.  Oregon State University, Corvallis.
  150. Knapp, SJ (1992) Mapping quantitative trait loci using lines tested across environments.  Proc. Intl. Biometric Congress, Hamilton, New Zealand.
  151. Knapp SJ (1992) Breakthroughs towards the domestication of Cuphea.  In Janick, J. and J.E. Simon (eds.), pp. 372-379.  New crops.  Wiley and Sons, New York.
  152. Galbraith DW, Harkins KR, Knapp SJ (1992) Systematic endopolyploidy in Arabidopsis thaliana.  Plant Physiol. 96: 985-989.
  153. Schoen CC, Hayes PM, Blake TK, Knapp SJ (1992) Gametophytic selection in a winter x spring barley cross.  Genome 34: 918-922.
  154. Webb DM, Knapp SJ, Tagliani LA(1992) An RFLP and allozyme linkage map of Cuphea lanceolata.  Theor. Appl. Genet. 83: 528-532.
  155. Knapp SJ, Tagliani LA (1991) Two medium-chain fatty acid mutants of C. viscosissima.  Plant Breeding 106: 338-341.
  156. Knapp SJ, Tagliani LA, Roath WR (1991) Fatty acid and oil diversity of Cuphea viscosissima:  A source of medium-chain fatty acids.  J. Am. Oil Chem. Soc. 68: 515-517.
  157. Bridges WC, Knapp SJ, Cornelius PJ (1991) Standard errors and confidence interval estimators for expected selection response.  Crop Sci. 31: 253-255.
  158. Knapp SJ (1991) Mapping quantitative trait loci using molecular markers: multilocus estimators of backcross, recombinant inbred, and doubled haploid parameters.  Theor. Appl. Genet. 81: 333-338.
  159. Krueger SK, Knapp SJ (1991) Mating systems of Cuphea laminuligera and Cuphea lutea.  Theor. Appl. Genet. 82: 221-226.
  160. Webb DM, Knapp SJ (1991) Estimates of genetic parameters for oil yield of a Cuphea lanceolata population.  Crop Sci. 31: 621-624.
  161. Thompson AE, Dierig D, Knapp SJ, Kleiman R (1991) Variation in seed oil and fatty acid content within and among lauric-acid rich Cuphea species.  J. Am. Oil Chem. Soc. 67: 611-617.
  162. Knapp SJ, Tagliani LA, Liu BH (1991) Outcrossing rates of experimental populations of Cuphea lanceolata.  Plant Breeding 106: 334-337.
  163. Knapp SJ, Bridges WC, Birkes D (1990) Mapping quantitative trait loci using molecular marker linkage maps.  Theor. Appl. Genet. 79: 583-592.
  164. Krueger S, Knapp SJ (1990) Genetics of allozyme variation in Cuphea laminuligera and Cuphea lutea.  J. Hered. 81: 351-358.
  165. Knapp SJ(1990) Recurrent mass selection for reduced seed dormancy in Cuphea laminuligera and Cuphea lanceolata.  Plant Breeding 104: 46-52.
  166. Knapp, SJ (1990) New temperate industrial oilseed crops.  In Janick, J. and J.E. Simon (eds.), pp. 203-210.  Advances in New Crops.  Timber Press, Portland, Oregon.
  167. Knapp SJ, Bridges WC (1990) Programs for mapping quantitative trait loci using flanking molecular markers.  J. Hered. 81: 234-235.
  168. Webb DM, Knapp SJ (1990) DNA extraction from a previously recalcitrant plant genus. Pl. Mol. Biol. Rept. 8: 180-185.
  169. Knapp SJ, Bridges WC (1990) Using molecular markers to estimate quantitative trait locus parameters:  Power and genetic variances for unreplicated and replicated progeny.  Genetics 126: 769-777.
  170. Liu BH, Knapp SJ (1990) GMENDEL:  A program for Mendelian segregation and linkage analysis of individual or multiple progeny populations using log-likelihood ratios.  J. Hered. 81: 407.
  171. Knapp SJ, Bridges WC, Yang MH (1989) Nonparametric confidence interval estimators for heritability and expected selection response. Genetics 121: 891-898.
  172. Knapp SJ, Tagliani LA (1989) Genetics of allozyme variation in Cuphea lanceolata Ait. Genome 32: 57-63.
  173. Knapp SJ, Tagliani LA (1989) Genetic variation for seed dormancy in Cuphea laminuligera and Cuphea lanceolata.  Euphytica 47: 65-70.
  174. Knapp SJ (1989) Quasi-Mendelian genetic analysis of quantitative trait loci using molecular marker linkage maps.  In Roebbelen, G. (ed.),  Proc. XIIth Eucarpia Congress (European Plant Breeding Congress), Goettingen, Germany.
  175. Knapp SJ, Bridges WC (1988) Parametric and jackknife confidence interval estimators for two-factor mating design genetic variance ratios.  Theor. Appl. Genet. 76: 385-392.
  176. Yang MH, Knapp SJ (1988) FORTRAN programs for calculating percentage points from F- and t-distributions.  J. Hered. 79: 122.
  177. Knapp SJ, Cox TS (1988) S1 family recurrent selection in autogamous crops based on dominant genetic male-sterility.  Crop Sci. 28: 227-231.
  178. Knapp SJ, Ross WM, Stroup WW (1987) Precision of genetic variance and heritability estimates from sorghum populations.  Crop Sci. 27: 265-268.
  179. Knapp SJ, Bridges WC (1987) Confidence interval estimators for heritability for several mating and experiment designs.  Theor. Appl. Genet. 73: 759-763.
  180. Bridges WC, Knapp SJ (1987) Probabilities of negative estimates of genetic variances.  Theor. Appl. Genet. 74: 269-274.
  181. Knapp, SJ (1986) Confidence intervals for heritability for two-factor mating design single environment linear models.  Theor. Appl. Genet. 72: 587-591.
  182. Knapp SJ, Stroup WW, Ross WM (1985) Exact confidence intervals for heritability on a progeny mean basis.  Crop Sci. 25: 192-194.