Advertisement

Theoretical and Applied Genetics

, Volume 132, Issue 8, pp 2325–2351 | Cite as

Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium)

  • Steve LarsonEmail author
  • Lee DeHaan
  • Jesse Poland
  • Xiaofei Zhang
  • Kevin Dorn
  • Traci Kantarski
  • James Anderson
  • Jeremy Schmutz
  • Jane Grimwood
  • Jerry Jenkins
  • Shengqiang Shu
  • Jared Crain
  • Matthew Robbins
  • Kevin Jensen
Original Article

Abstract

Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.

Notes

Acknowledgements

This research was supported by the Malone Family Land Preservation Foundation. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. KD is supported by USDA-NIFA Post-doctoral Fellowships Grant No. 2017-67012-26129/Project Accession No. 1011622 “Exploring the Genomic Landscape of Perenniality within the Triticeae.” The authors wish to thank Martin Mascher and LiangLiang Gao for advice and contributions to the continuing development of the Thinopyrum intermedium genome assembly.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

122_2019_3357_MOESM1_ESM.xlsx (81 kb)
Supplementary material 1 (XLSX 81 kb)
122_2019_3357_MOESM2_ESM.xlsx (32 kb)
Supplementary material 2 (XLSX 31 kb)

References

  1. Abbo S, Pinhasi van-Oss R, Gopher A, Saranga Y, Ofner I, Peleg Z (2014) Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes. Trends Plant Sci 19:351–360.  https://doi.org/10.1016/j.tplants.2013.12.002 Google Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410.  https://doi.org/10.1016/S0022-2836(05)80360-2 Google Scholar
  3. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402.  https://doi.org/10.1093/nar/25.17.3389 Google Scholar
  4. Armstead IP, Turner LB, Marshall AH, Humphreys MO, King IP, Thorogood D (2008) Identifying genetic components controlling fertility in the outcrossing grass species perennial ryegrass (Lolium perenne) by quantitative trait loci analysis and comparative genetics. New Phytol 178:559–571.  https://doi.org/10.1111/j.1469-8137.2008.02413.x Google Scholar
  5. Ashikari M et al (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745.  https://doi.org/10.1126/science.1113373 Google Scholar
  6. Balanzà V, Roig-Villanova I, Di Marzo M, Masiero S, Colombo L (2016) Seed abscission and fruit dehiscence required for seed dispersal rely on similar genetic networks. Development 143:3372–3381.  https://doi.org/10.1242/dev.135202 Google Scholar
  7. Bell LW, Harrison MT, Kirkegaard JA (2015) Dual-purpose cropping: capitalising on potential grain crop grazing to enhance mixed-farming profitability. Crop Pasture Sci 66:i–iv.  https://doi.org/10.1071/CPv66n4_FO Google Scholar
  8. Berdahl JD, Frank AB (1998) Seed maturity in four cool-season forage grasses. Agron J 90:483–488Google Scholar
  9. Cattani DJ (2017) Selection of a perennial grain for seed productivity across years: intermediate wheatgrass as a test species. Can J Plant Sci 97:516–524.  https://doi.org/10.1139/cjps-2016-0280 Google Scholar
  10. Cattani DJ, Asselin SR (2017) Extending the growing season: forage seed production and perennial grains. Can J Plant Sci 98:235–246.  https://doi.org/10.1139/cjps-2017-0212 Google Scholar
  11. Cattani D, Asselin S (2018) Has selection for grain yield altered intermediate wheatgrass? Sustainability 10:688Google Scholar
  12. Ceoloni C, Kuzmanovic L, Forte P, Virili ME, Bitti A (2015) Wheat-perennial Triticeae introgressions: major achievements and prospects. In: Alien introgression in wheat: cytogenetics, molecular biology, and genomics, pp 273–313.  https://doi.org/10.1007/978-3-319-23494-6-11
  13. Chen G, Li H, Wei Y, Zheng Y-L, Zhou M, Liu C (2016) Pleiotropic effects of the semi-dwarfing gene uzu in barley. Euphytica 209:749–755.  https://doi.org/10.1007/s10681-016-1668-4 Google Scholar
  14. Chono M et al (2003) A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinosteroid receptor. Plant Physiol 133:1209–1219.  https://doi.org/10.1104/pp.103.026195 Google Scholar
  15. Clauß K et al (2011) Overexpression of sinapine esterase BnSCE3 in oilseed rape seeds triggers global changes in seed metabolism. Plant Physiol 155:1127–1145.  https://doi.org/10.1104/pp.110.169821 Google Scholar
  16. Cockram J, Jones H, Leigh FJ, O’Sullivan D, Powell W, Laurie DA, Greenland AJ (2007) Control of flowering time in temperate cereals: genes, domestication, and sustainable productivity. J Exp Bot 58:1231–1244Google Scholar
  17. Cox TS, Glover JD, van Tassel DL, Cox CM, DeHaan LR (2006) Prospects for developing perennial grain crops. Bioscience 56:649–659Google Scholar
  18. Cox TS, Van Tassel DL, Cox C, DeHaan L (2010) Progress in breeding perennial grains. Crop Pasture Sci 61:513–521.  https://doi.org/10.1071/CP09201 Google Scholar
  19. Culman SW, Snapp SS, Ollenburger M, Basso B, DeHaan LR (2013) Soil and water quality rapidly responds to the perennial grain Kernza wheatgrass. Agron J 105:735–744.  https://doi.org/10.2134/agronj2012.0273 Google Scholar
  20. Curwen-McAdams C, Jones SS (2017) Breeding perennial grain crops based on wheat. Crop Sci 57:1172–1188.  https://doi.org/10.2135/cropsci2016.10.0869 Google Scholar
  21. DeHaan LR, Ismail BP (2017) Perennial cereals provide ecosystem benefits. Cereal Foods World 62:278–281.  https://doi.org/10.1094/CFW-62-6-0278 Google Scholar
  22. DeHaan LR et al (2016) A pipeline strategy for grain crop domestication. Crop Sci 56:917–930.  https://doi.org/10.2135/cropsci2015.06.0356 Google Scholar
  23. DeHaan L, Christians M, Crain J, Poland J (2018) Development and evolution of an intermediate wheatgrass domestication program. Sustainability 10:1499Google Scholar
  24. Devos KM, Dubcovsky J, Dvorak J, Chinoy CN, Gale MD (1995) Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination. Theor Appl Genet 91:282–288.  https://doi.org/10.1007/BF00220890 Google Scholar
  25. Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321.  https://doi.org/10.1016/j.cell.2006.12.006 Google Scholar
  26. Doust AN, Mauro-Herrera M, Francis AD, Shand LC (2014) Morphological diversity and genetic regulation of inflorescence abscission zones in grasses. Am J Bot 101:1759–1769Google Scholar
  27. Dubcovsky J, Lijavetzky D, Appendino L, Tranquilli G (1998) Comparative RFLP mapping of Triticum monococcum genes controlling vernalization requirement. Theor Appl Genet 97:968–975.  https://doi.org/10.1007/s001220050978 Google Scholar
  28. Dubcovsky J, Chen CL, Yan LL (2005) Molecular characterization of the allelic variation at the VRN-H2 vernalization locus in barley. Mol Breed 15:395–407.  https://doi.org/10.1007/s11032-005-0084-6 Google Scholar
  29. Faris JD, Gill BS (2002) Genomic targeting and high-resolution mapping of the domestication gene Q in wheat. Genome 45:706–718Google Scholar
  30. Faris JD, Fellers JP, Brooks SA, Gill BS (2003) A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene. Genetics 164:311–321Google Scholar
  31. Fuller DQ (2007) Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the old world. Ann Bot 100:903–924.  https://doi.org/10.1093/aob/mcm048 Google Scholar
  32. Gallavotti A et al (2004) The role of barren stalk1 in the architecture of maize. Nature 432:630.  https://doi.org/10.1038/nature03148 Google Scholar
  33. Galli M et al (2015) Auxin signaling modules regulate maize inflorescence architecture. Proc Natl Acad Sci USA 112:13372–13377.  https://doi.org/10.1073/pnas.1516473112 Google Scholar
  34. Gegas VC et al (2010) A genetic framework for grain size and shape variation in wheat. Plant Cell 22:1046–1056.  https://doi.org/10.1105/tpc.110.074153 Google Scholar
  35. Griffiths S, Dunford RP, Coupland G, Laurie DA (2003) The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol 131:1855–1867.  https://doi.org/10.1104/pp.102.016188 Google Scholar
  36. Hackauf B, Wehling P (2005) Approaching the self-incompatibility locus Z in rye (Secale cereale L.) via comparative genetics. Theor Appl Genet 110:832–845.  https://doi.org/10.1007/s00122-004-1869-4 Google Scholar
  37. Harmoney KR (2015) Cool-season grass biomass in the southern mixed-grass prairie region of the USA. Bioenergy Res 8:203–210.  https://doi.org/10.1007/s12155-014-9514-9 Google Scholar
  38. Hayes R et al (2018) The performance of early-generation perennial winter cereals at 21 sites across four continents. Sustainability 10:1124Google Scholar
  39. Holland JB, Nyquist WE, Cervantes-Martínez CT (2010) Estimating and interpreting heritability for plant breeding: an update. In: Plant breeding reviews.  https://doi.org/10.1002/9780470650202.ch2
  40. Hou J, Jiang Q, Hao C, Wang Y, Zhang H, Zhang X (2014) Global selection on sucrose synthase haplotypes during a century of wheat breeding. Plant Physiol 164:1918–1929.  https://doi.org/10.1104/pp.113.232454 Google Scholar
  41. Houston K et al (2013) Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence. Proc Natl Acad Sci USA 110:16675–16680.  https://doi.org/10.1073/pnas.1311681110 Google Scholar
  42. Hu M-J et al (2016) Cloning and characterization of TaTGW-7A gene associated with grain weight in wheat via SLAF-seq-BSA. Front Plant Sci 7:1902.  https://doi.org/10.3389/fpls.2016.01902 Google Scholar
  43. Huang X et al (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494–497.  https://doi.org/10.1038/ng.352 Google Scholar
  44. Huang L-M, Lai C-P, Chen L-FO, Chan M-T, Shaw J-F (2015) Arabidopsis SFAR4 is a novel GDSL-type esterase involved in fatty acid degradation and glucose tolerance. Bot Stud 56:33.  https://doi.org/10.1186/s40529-015-0114-6 Google Scholar
  45. Ishimaru K et al (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet 45:707.  https://doi.org/10.1038/ng.2612 Google Scholar
  46. Jensen KB, Zhang YF, Dewey DR (1990) Mode of pollination of perennial species of the triticeae in relation to genomically defined genera. Can J Plant Sci 70:215–225Google Scholar
  47. Jensen JK et al (2008) Identification of a Xylogalacturonan Xylosyltransferase involved in pectin biosynthesis in Arabidopsis. Plant Cell 20:1289–1302.  https://doi.org/10.1105/tpc.107.050906 Google Scholar
  48. Jensen KB, Yan X, Larson SR, Wang RRC, Robins JG, McIntosch RA (2016) Agronomic and genetic diversity in intermediate wheatgrass (Thinopyrum intermedium). Plant Breeding 135:751–758.  https://doi.org/10.1111/pbr.12420 Google Scholar
  49. Jia QJ, Zhang JJ, Westcott S, Zhang XQ, Bellgard M, Lance R, Li CD (2009) GA-20 oxidase as a candidate for the semidwarf gene sdw1/denso in barley. Funct Integr Genomics 9:255–262Google Scholar
  50. Jiang Q, Hou J, Hao C, Wang L, Ge H, Dong Y, Zhang X (2011) The wheat (T. aestivum) sucrose synthase 2 gene (TaSus2) active in endosperm development is associated with yield traits. Funct Integr Genomics 11:49–61.  https://doi.org/10.1007/s10142-010-0188-x Google Scholar
  51. Jiang Y, Chen R, Dong J, Xu Z, Gao X (2012) Analysis of GDSL lipase (GLIP) family genes in rice (Oryza sativa). Plant OMICS 5:351–358Google Scholar
  52. Jungers JM, DeHaan LR, Betts KJ, Sheaffer CC, Wyse DL (2017) Intermediate wheatgrass grain and forage yield responses to nitrogen fertilization. Agron J 109:462–472.  https://doi.org/10.2134/agronj2016.07.0438 Google Scholar
  53. Kantarski T, Larson S, Zhang X, DeHaan L, Borevitz J, Anderson J, Poland J (2017) Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing. Theor Appl Genet 130:137–150.  https://doi.org/10.1007/s00122-016-2799-7 Google Scholar
  54. Kapazoglou A et al (2010) Epigenetic chromatin modifiers in barley: IV. The study of barley Polycomb group (PcG) genes during seed development and in response to external ABA. BMC Plant Biol 10:73.  https://doi.org/10.1186/1471-2229-10-73 Google Scholar
  55. Karsai I et al (2005) The Vrn-H2 locus is a major determinant of flowering time in a facultative x winter growth habit barley (Hordeum vulgare L.) mapping population. Theor Appl Genet 110:1458–1466.  https://doi.org/10.1007/s00122-005-1979-7 Google Scholar
  56. Kenneth PV, Kevin JJ (2001) Adaptation of perennial Triticeae to the eastern Central Great Plains. J Range Manag 54:674–679.  https://doi.org/10.2307/4003670 Google Scholar
  57. Klaas M et al (2011) Progress towards elucidating the mechanisms of self-incompatibility in the grasses: further insights from studies in Lolium. Ann Bot 108:677–685.  https://doi.org/10.1093/aob/mcr186 Google Scholar
  58. Knowles RP (1977) Recurrent mass selection for improved seed yields in intermediate wheatgrass. Crop Sci 17:51–54.  https://doi.org/10.2135/cropsci1977.0011183X001700010015x Google Scholar
  59. Komatsuda T et al (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104:1424–1429Google Scholar
  60. Koppolu R et al (2013) Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. Proc Natl Acad Sci USA 110:13198–13203.  https://doi.org/10.1073/pnas.1221950110 Google Scholar
  61. Kovach MJ, Sweeney MT, McCouch SR (2007) New insights into the history of rice domestication. Trends Genet 23:578–587.  https://doi.org/10.1016/j.tig.2007.08.012 Google Scholar
  62. Krupinsky JM, Berdahl JD (2000) Selecting resistance to Bipolaris sorokiniana and Fusarium graminearum in intermediate wheatgrass. Plant Dis 84:1299–1302.  https://doi.org/10.1094/PDIS.2000.84.12.1299 Google Scholar
  63. Kuczyńska A, Mikołajczak K, Ćwiek H (2014) Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination. Electron J Biotechnol 17:217–223.  https://doi.org/10.1016/j.ejbt.2014.07.005 Google Scholar
  64. La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4:34–46.  https://doi.org/10.1007/s10142-003-0098-2 Google Scholar
  65. Lai Y et al (2017) Association mapping of grain weight, length and width in barley (Hordeum vulgare) breeding germplasm. Int J Agric Biol 19:1175–1186.  https://doi.org/10.17957/IJAB/15.0406 Google Scholar
  66. Lang T et al (2018) Precise identification of wheat—Thinopyrum intermedium translocation chromosomes carrying resistance to wheat stripe rust in line Z4 and its derived progenies. Genome 61:177–185.  https://doi.org/10.1139/gen-2017-0229 Google Scholar
  67. Larson SR, Kellogg EA (2009) Genetic dissection of seed production traits and identification of a major-effect seed retention QTL in hybrid Leymus (Triticeae) wildryes. Crop Sci 49:29–40.  https://doi.org/10.2135/cropsci2008.05.0277 Google Scholar
  68. Larson SR et al (2012) Leymus EST linkage maps identify 4NsL-5NsL reciprocal translocation, wheat-Leymus chromosome introgressions, and functionally important gene loci. Theor Appl Genet 124:189–206.  https://doi.org/10.1007/s00122-011-1698-1 Google Scholar
  69. Larson S et al (2017) Development and testing of cool-season grass species, varieties and hybrids for biomass feedstock production in western North America. Agronomy 7:3Google Scholar
  70. Laurie DA, Pratchett N, Snape JW, Bezant JH (1995) RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter x spring barley (Hordeum vulgare L.) cross. Genome 38:575–585Google Scholar
  71. Lee D, Owens VN, Boe A, Koo BC (2009) Biomass and seed yields of big bluestem, switchgrass, and intermediate wheatgrass in response to manure and harvest timing at two topographic positions. Glob Change Biol Bioenergy 1:171–179.  https://doi.org/10.1111/j.1757-1707.2009.01008.x Google Scholar
  72. Lenser T, Theißen G (2013) Molecular mechanisms involved in convergent crop domestication. Trends Plant Sci 18:704–714.  https://doi.org/10.1016/j.tplants.2013.08.007 Google Scholar
  73. Li W, Gill BS (2006) Multiple genetic pathways for seed shattering in the grasses. Funct Integr Genomics 6:300–309.  https://doi.org/10.1007/s10142-005-0015-y Google Scholar
  74. Li Y et al (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266.  https://doi.org/10.1038/ng.977 Google Scholar
  75. Li B et al (2013) Constitutive expression of cell wall invertase genes increases grain yield and starch content in maize. Plant Biotechnol J 11:1080–1091.  https://doi.org/10.1111/pbi.12102 Google Scholar
  76. Li J et al (2017) Introduction of Thinopyrum intermedium ssp. trichophorum chromosomes to wheat by trigeneric hybridization involving Triticum, Secale and Thinopyrum genera. Planta 245:1121–1135.  https://doi.org/10.1007/s00425-017-2669-9 Google Scholar
  77. Liu Z, Garcia A, McMullen MD, Flint-Garcia SA (2016) Genetic analysis of kernel traits in maize-teosinte introgression populations. G3 Genes Genomes Genetics 6:2523–2530.  https://doi.org/10.1534/g3.116.030155 Google Scholar
  78. Liu H et al (2017) Production and molecular cytogenetic characterization of a durum wheat-Thinopyrum elongatum 7E disomic addition line with resistance to Fusarium head blight. Cytogenet Genome Res 153:165–173Google Scholar
  79. Ma L, Li T, Hao C, Wang Y, Chen X, Zhang X (2016) TaGS5-3A, a grain size gene selected during wheat improvement for larger kernel and yield. Plant Biotechnol J 14:1269–1280.  https://doi.org/10.1111/pbi.12492 Google Scholar
  80. Ma R, Yuan H, An J, Hao X, Li H (2018) A Gossypium hirsutum GDSL lipase/hydrolase gene (GhGLIP) appears to be involved in promoting seed growth in Arabidopsis. PLoS ONE.  https://doi.org/10.1371/journal.pone.0195556 Google Scholar
  81. Manzanares C et al (2016) A gene encoding a DUF247 domain protein cosegregates with the S self-incompatibility locus in perennial ryegrass. Mol Biol Evol 33:870–884.  https://doi.org/10.1093/molbev/msv335 Google Scholar
  82. Marti A, Bock JE, Pagani MA, Ismail B, Seetharaman K (2016) Structural characterization of proteins in wheat flour doughs enriched with intermediate wheatgrass (Thinopyrum intermedium) flour. Food Chem 194:994–1002.  https://doi.org/10.1016/j.foodchem.2015.08.082 Google Scholar
  83. Mathews S, Sharrock RA (1996) The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms. Mol Biol Evol 13:1141–1150.  https://doi.org/10.1093/oxfordjournals.molbev.a025677 Google Scholar
  84. McSteen P, Malcomber S, Skirpan A, Lunde C, Wu X, Kellogg E, Hake S (2007) barren inflorescence2 Encodes a co-ortholog of the PINOID serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize. Plant Physiol 144:1000–1011.  https://doi.org/10.1104/pp.107.098558 Google Scholar
  85. Meyer RS, Purugganan MD (2013) Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 14:840.  https://doi.org/10.1038/nrg3605 Google Scholar
  86. Monono EM, Nyren PE, Berti MT, Pryor SW (2013) Variability in biomass yield, chemical composition, and ethanol potential of individual and mixed herbaceous biomass species grown in North Dakota. Ind Crops Prod 41:331–339.  https://doi.org/10.1016/j.indcrop.2012.04.051 Google Scholar
  87. Nadolska-Orczyk A, Rajchel IK, Orczyk W, Gasparis S (2017) Major genes determining yield-related traits in wheat and barley. Theor Appl Genet 130:1081–1098.  https://doi.org/10.1007/s00122-017-2880-x Google Scholar
  88. Nallamilli BRR, Zhang J, Mujahid H, Malone BM, Bridges SM, Peng Z (2013) Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PLoS Genet 9:e1003322.  https://doi.org/10.1371/journal.pgen.1003322 Google Scholar
  89. Namikawa S, Kawakami Z (1934) On the occurrence of the haploid, triploid, and tetraploid plants in twin seedlings of common wheat. Proc Imp Acad Jap 10:668–671Google Scholar
  90. Ouellette LA, Reid RW, Blanchard SG, Brouwer CR (2018) LinkageMapView—rendering high-resolution linkage and QTL maps. Bioinformatics 34:306–307.  https://doi.org/10.1093/bioinformatics/btx576 Google Scholar
  91. Pearson CH, Larson SR, Keske CMH, Jensen KB (2015) Native grasss for biomass production at high elevations. In: Cruz VMV, Dierig DA (eds) Handbook of plant breeding, vol 9. Springer, New York, pp 101–132Google Scholar
  92. Peng JR et al (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–261Google Scholar
  93. Pourkheirandish M et al (2015) Evolution of the grain dispersal system in barley. Cell 162:527–539.  https://doi.org/10.1016/j.cell.2015.07.002 Google Scholar
  94. R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. https://www.R-project.org/
  95. Ral JP et al (2012) Down-regulation of Glucan, Water-Dikinase activity in wheat endosperm increases vegetative biomass and yield. Plant Biotechnol J 10:871–882.  https://doi.org/10.1111/j.1467-7652.2012.00711.x Google Scholar
  96. Revelle W (2018) psych: procedures for psychological, psychometric, and personality research. Northwestern University. Evanston, Illinois, USA. https://CRAN.R-project.org/package=psych
  97. Robins JG (2010) Cool-season grasses produce more total biomass across the growing season than do warm-season grasses when managed with an applied irrigation gradient. Biomass Bioenergy 34:500–505.  https://doi.org/10.1016/j.biombioe.2009.12.015 Google Scholar
  98. Ross JG (1963) Registration of Oahe Intermediate Wheatgrass (Reg. No. 5). Crop Sci 3:373–373.  https://doi.org/10.2135/cropsci1963.0011183X000300040046x Google Scholar
  99. Ryan MR, Crews TE, Culman SW, DeHaan LR, Hayes RC, Jungers JM, Bakker MG (2018) Managing for multifunctionality in perennial grain crops. Bioscience 68:294–304.  https://doi.org/10.1093/biosci/biy014 Google Scholar
  100. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675Google Scholar
  101. Schulz-Schaeffer J, Haller SE (1987) Registration of Montana-2 perennial × Agrotriticum intermediodurum Khizhnyak. Crop Sci 27:822–823.  https://doi.org/10.2135/cropsci1987.0011183X002700040058x Google Scholar
  102. Shinozuka H, Cogan NO, Smith KF, Spangenberg GC, Forster JW (2010) Fine-scale comparative genetic and physical mapping supports map-based cloning strategies for the self-incompatibility loci of perennial ryegrass (Lolium perenne L.). Plant Mol Biol 72:343–355.  https://doi.org/10.1007/s11103-009-9574-y Google Scholar
  103. Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028.  https://doi.org/10.1038/ng.169 Google Scholar
  104. Shu X, Rasmussen S (2014) Quantification of amylose, amylopectin, and β-glucan in search for genes controlling the three major quality traits in barley by genome-wide association studies. Front Plant Sci 5:197.  https://doi.org/10.3389/fpls.2014.00197 Google Scholar
  105. Simons KJ, Fellers JP, Trick HN, Zhang ZC, Tai YS, Gill BS, Faris JD (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555.  https://doi.org/10.1534/genetics.105.044727 Google Scholar
  106. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630.  https://doi.org/10.1038/ng2014 Google Scholar
  107. Studer B, Jensen LB, Hentrup S, Brazauskas G, Kölliker R, Lübberstedt T (2008) Genetic characterisation of seed yield and fertility traits in perennial ryegrass (Lolium perenne L.). Theor Appl Genet 117:781–791.  https://doi.org/10.1007/s00122-008-0819-y Google Scholar
  108. Su Z, Hao C, Wang L, Dong Y, Zhang X (2011) Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 122:211–223.  https://doi.org/10.1007/s00122-010-1437-z Google Scholar
  109. Sun PY et al (2016) OsGRF4 controls grain shape, panicle length and seed shattering in rice. J Integr Plant Biol 58:836–847.  https://doi.org/10.1111/jipb.12473 Google Scholar
  110. Taketa S et al (2008) Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Proc Natl Acad Sci USA 105:4062–4067.  https://doi.org/10.1073/pnas.0711034105 Google Scholar
  111. Tanabata T, Shibaya T, Hori K, Ebana K, Yano M (2012) SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis. Plant Physiol 160:1871–1880.  https://doi.org/10.1104/pp.112.205120 Google Scholar
  112. Tang H, Sezen U, Paterson AH (2010) Domestication and plant genomes. Curr Opin Plant Biol 13:160–166.  https://doi.org/10.1016/j.pbi.2009.10.008 Google Scholar
  113. Thorogood D et al (2017) A novel multivariate approach to phenotyping and association mapping of multi-locus gametophytic self-incompatibility reveals S, Z, and other loci in a perennial ryegrass (Poaceae) population. Front Plant Sci.  https://doi.org/10.3389/fpls.2017.01331 Google Scholar
  114. Tiwari GJ, Chiang MY, De Silva JR, Song BK, Lau YL, Rahman S (2016) Lipase genes expressed in rice bran: LOC_Os11g43510 encodes a novel rice lipase. J Cereal Sci 71:43–52.  https://doi.org/10.1016/j.jcs.2016.07.008 Google Scholar
  115. Tulpan D, Leger S (2017) The plant orthology browser: an orthology and gene-order visualizer for plant comparative genomics. Plant Genome.  https://doi.org/10.3835/plantgenome2016.08.0078 Google Scholar
  116. Uzma, Kubra G, Gul A, Mujeeb-Kazi A (2015) Use of alien diversity to combat some major biotic stresses in Triticum aestivum L. In: Hakeem KR (ed) Crop production and global environmental issues, pp 319–347.  https://doi.org/10.1007/978-3-319-23162-4_14
  117. Van Ooijen JW (2006) JoinMap 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
  118. Van Ooijen JW (2009) MapQTL 6, Software for the mapping of quantitative trait loci in experimental populations of diploid species. Wageningen, Kyazma B.V.Google Scholar
  119. Vogel KP, Tober D, Reece PE, Baltsensperger DD, Schuman G, Nicholson RA (2005) Registration of ‘Haymaker’ Intermediate Wheatgrass Registration by CSSA. Crop Sci 45:415–416.  https://doi.org/10.2135/cropsci2005.0415 Google Scholar
  120. Vu GT, Wicker T, Buchmann JP, Chandler PM, Matsumoto T, Graner A, Stein N (2010) Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley. Funct Integr Genomics 10:509–521.  https://doi.org/10.1007/s10142-010-0173-4 Google Scholar
  121. Wagoner P (1990) Perennial grain new use for intermediate wheatgrass. J Soil Water Conserv 45:81–82Google Scholar
  122. Wang H et al (2005) The origin of the naked grains of maize. Nature 436:714–719.  https://doi.org/10.1038/nature03863 Google Scholar
  123. Wang E et al (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374.  https://doi.org/10.1038/ng.220 Google Scholar
  124. Wang J, Liao X, Li Y, Zhou R, Yang X, Gao L, Jia J (2010) Fine mapping a domestication-related QTL for spike-related traits in a synthetic wheat. Genome 53:798–804.  https://doi.org/10.1139/g10-066 Google Scholar
  125. Wang S et al (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954.  https://doi.org/10.1038/ng.2327 Google Scholar
  126. Wang GJ et al (2014) Establishment and yield of perennial grass monocultures and binary mixtures for bioenergy in North Dakota. Agron J 106:1605–1613.  https://doi.org/10.2134/agronj14.0068 Google Scholar
  127. Wang Y et al (2015) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47:944–948.  https://doi.org/10.1038/ng.3346 Google Scholar
  128. Wendt T et al (2016) HvDep1 is a positive regulator of culm elongation and grain size in barley and impacts yield in an environment-dependent manner. PLoS One.  https://doi.org/10.1371/journal.pone.0168924 Google Scholar
  129. Weng J et al (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209.  https://doi.org/10.1038/cr.2008.307 Google Scholar
  130. Wu YZ, Fu YC, Zhao SS, Gu P, Zhu ZF, Sun CQ, Tan LB (2016) CLUSTERED PRIMARY BRANCH 1, a new allele of DWARF11, controls panicle architecture and seed size in rice. Plant Biotechnol J 14:377–386.  https://doi.org/10.1111/pbi.12391 Google Scholar
  131. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268.  https://doi.org/10.1073/pnas.0937399100 Google Scholar
  132. Yan LL et al (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644.  https://doi.org/10.1126/science.1094305 Google Scholar
  133. Yan S et al (2011) Seed size is determined by the combinations of the genes controlling different seed characteristics in rice. Theor Appl Genet 123:1173–1181.  https://doi.org/10.1007/s00122-011-1657-x Google Scholar
  134. Yang W-Y, Lu B-R, Hu X-R, Yu Y, Zhang Y (2005) Inheritance of the triple-spikelet character in a Tibetan landrace of common wheat. Genet Resour Crop Evol 52:847–851.  https://doi.org/10.1007/s10722-003-6089-2 Google Scholar
  135. Zadoks JC, Chang TT, Konzak CF (1974) A decimal code for the growth stages of cereals. Weed Res 14:415–421Google Scholar
  136. Zair W, Maxted N, Amri A (2018) Setting conservation priorities for crop wild relatives in the Fertile Crescent. Genet Resour Crop Evol 65:855–863.  https://doi.org/10.1007/s10722-017-0576-3 Google Scholar
  137. Zhang L, Zhao YL, Gao LF, Zhao GY, Zhou RH, Zhang BS, Jia JZ (2012a) TaCKX6-D1, the ortholog of rice OsCKX2, is associated with grain weight in hexaploid wheat. New Phytol 195:574–584.  https://doi.org/10.1111/j.1469-8137.2012.04194.x Google Scholar
  138. Zhang X et al (2012b) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci USA 109:21534–21539.  https://doi.org/10.1073/pnas.1219776110 Google Scholar
  139. Zhang Y et al (2015) Establishment of a 100-seed weight quantitative trait locus–allele matrix of the germplasm population for optimal recombination design in soybean breeding programmes. J Exp Bot 66:6311–6325.  https://doi.org/10.1093/jxb/erv342 Google Scholar
  140. Zhang XF et al (2016) Establishment and optimization of genomic selection to accelerate the domestication and improvement of intermediate wheatgrass. Plant Genome.  https://doi.org/10.3835/plantgenome2015.07.0059 Google Scholar
  141. Zhang X et al (2017) Uncovering the genetic architecture of seed weight and size in intermediate wheatgrass through linkage and association mapping. Plant Genome 10:10.  https://doi.org/10.3835/plantgenome2017.03.0022 Google Scholar

Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2019

Authors and Affiliations

  1. 1.United States Department of Agriculture, Agriculture Research Service, Forage and Range ResearchUtah State UniversityLoganUSA
  2. 2.The Land InstituteSalinaUSA
  3. 3.Department of Plant PathologyKansas State UniversityManhattanUSA
  4. 4.Department of Horticultural ScienceNorth Carolina State UniversityRaleighUSA
  5. 5.American Association for the Advancement of Science, Science and Technology Policy Fellow at the United States Department of AgricultureAnimal and Plant Health Inspection ServiceRiverdaleUSA
  6. 6.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA
  7. 7.Department of EnergyJoint Genome InstituteWalnut CreekUSA
  8. 8.Hudson Alpha Institute for BiotechnologyHuntsvilleUSA

Personalised recommendations