Association mapping of agronomic and quality traits in USDA pea single-plant collection

Molecular Breeding

Volumn 35, Issue 2, 2015, Pages

  Cheng, Peng ^a   Holdsworth, William ^b   Ma, Yu ^a   Coyne, Clarice J ^d   Mazourek, Michael ^b   Grusak, Michael A ^c   Fuchs, Sam ^d   McGee, Rebecca J ^d  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b Cornell University ^*  (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Association mapping; Marker assisted selection; Pea single plant collection; Pisum sativum; Single nucleotide polymorphism

Indexed keywords

AGRONOMY; CROPS; CULTIVATION; DESORPTION; MAPPING; SEED; VALUE ENGINEERING;

AGRONOMIC TRAITS; ASSOCIATION MAPPING; CROP PLANTS; LANDRACES; MARKER-ASSISTED SELECTION; MOLECULAR BASIS; PEA SINGLE-PLANT COLLECTION; PISUM SATIVUM; SINGLE NUCLEOTIDE POLYMORPHISMS; SINGLE PLANTS;

MASS SPECTROMETRY;

PISUM SATIVUM; PISUM SATIVUM SUBSP. SATIVUM;

EID: 84923238769     PISSN: 13803743     EISSN: 15729788     Source Type: Journal    
DOI: 10.1007/s11032-015-0277-6     Document Type: Article

References (72)

1. Bastianelli D, Grosjean F, Peyronnet C, Duparque M, Regnier JM (1998) Feeding value of pea (Pisum sativum L.) 1. Chemical composition of different categories of pea. Anim Sci 67:609–619
2. Benhamou N, Grenier J, Chrispeels MJ (1991) Accumulation of β-fructosidase in the cell walls of tomato roots following infection by a fungal wilt pathogen. Plant Physiol 97:739–750
3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B Met 57:289–300
4. Blair MW, Astudillo C, Grusak MA, Graham R, Beebe SE (2009) Inheritance of seed iron and zinc concentrations in common bean (Phaseolus vulgaris L.). Mol Breed 23:197–207
5. Bordat A, Savois V, Nicolas M, Salse J, Chauveau A, Bourgeois M, Potier J, Houtin H, Rond C, Murat F, Marget P, Aubert G, Burstin J (2011) Translational genomics in legumes allowed placing in silico 5460 unigenes on the pea functional map and identified candidate genes in Pisum sativum L. G3 1:93–103
6. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
7. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177
8. Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo ZW, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Liu H, Liu H, Liu H, Stein N, Schulte D, Steuernagel B, Marshall DF, Thomas WTB, Ramsay L, Mackay I, Balding DJ, Waugh R, O’Sullivan DM, Consortium A (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Acad Sci USA 107:21611–21616
9. Coyne CJ, Brown AF, Timmerman-Vaughan GM, McPhee K, Grusak MA (2005a) USDA-ARS refined pea core collection for 26 qualitative traits. Pisum Genetics 37:3–6
10. Coyne CJ, Grusak MA, Razai L, Baik BK (2005b) Variation for pea seed protein concentration in the USDA Pisum core collection. Pisum Genetics 37:5–9
11. Dabney A, Storey JD (2004) Q-value estimation for false discovery rate control. Medicine 344:539–548
12. Deulvot C, Charrel H, Marty A, Jacquin F, Donnadieu C, Lejeune-Henaut I, Burstin J, Aubert G (2010) Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea. BMC Genom 11:468
13. Dolezel J, Greilhuber J (2010) Nuclear genome size: are we getting closer? Cytom Part A 77A:635–642
14. Duarte J, Rivière N, Baranger A, Aubert G, Burstin J, Cornet L, Lavaud C, Lejeune-Hénaut I, Martinant JP, Pichon JP, Pilet-Nayel ML, Boutet G (2014) Transcriptome sequencing for high throughput SNP development and genetic mapping in pea. BMC Genom 15:126
15. Earl DA, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361
16. Ekvall J, Stegmark R, Nyman M (2006) Content of low molecular weight carbohydrates in vining peas (Pisum sativum) related to harvest time, size and brine grade. Food Chem 94:513–519
17. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379
18. Esquinas-Alcazar J (2005) Protecting crop genetic diversity for food security: political, ethical and technical challenges. Nat Rev Genet 6:946–953
19. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
20. Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallel SNP genotyping. Cold Spring Harb Sym 68:69–78
21. FAOSTAT (2012) http://faostat.fao.org
22. Flint-Garcia SA, Thornsberry JM, Buckler EST (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374
23. Gabriel S, Ziaugra L, Tabbaa D (2009) SNP genotyping using the Sequenom MassARRAY iPLEX platform. Curr Protoc Hum Genet 60:2.12.1–2.12.16
24. Greene C (2008) A history of food. 2d edition. Libr J 133:96
25. Grusak MA, Burgett CL, Knewtson SJ, Lopez-Millan A, Ellis DR, Li C, Musetti VM, Blair MW (2004) Novel approaches to improve legume seed mineral nutrition. Proceedings of the 5th AEP-2nd ICLGG conference, pp 37–38
26. Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12
27. Herbers K, Meuwly P, Frommer WB, Metraux JP, Sonnewald U (1996) Systemic acquired resistance mediated by the ectopic expression of invertase: possible hexose sensing in the secretory pathway. Plant Cell 8:793–803
28. Jia L, Yan W, Zhu C, Agrama HA, Jackson A, Yeater K, Li X, Huang B, Hu B, McClung A, Wu D (2012) Allelic analysis of sheath blight resistance with association mapping in rice. PLoS One 7:e32703
29. Jing RC, Johnson R, Seres A, Kiss G, Ambrose MJ, Knox MR, Ellis THN, Flavell AJ (2007) Gene-based sequence diversity analysis of field pea (Pisum). Genetics 177:2263–2275
30. Jing RC, Vershinin A, Grzebyta J, Shaw P, Smýkal P, Marshall D, Ambrose MJ, Ellis THN, Flavell AJ (2010) The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol 10:44
31. Jones DA, DuPont MS, Ambrose MJ, Frias J, Hedley CL (1999) The discovery of compositional variation for the raffinose family of oligosaccharides in pea seeds. Seed Sci Res 9:305–310
32. Kang YJ, Kim KH, Shim S, Yoon MY, Sun S, Kim MY, Van K, Lee SH (2012) Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean. BMC Plant Biol 12:139
33. Knudsen KEB, Li BW (1991) Determination of oligosaccharides in protein-rich feedstuffs by gas-liquid chromatography and high-performance liquid chromatography. J Agric Food Chem 39:689–694
34. Kwon SJ, Brown AF, Hu J, McGee R, Watt C, Kisha T, Timmerman-Vaughan G, Grusak M, McPhee KE, Coyne CJ (2012) Genetic diversity, population structure and genome-wide marker-trait association analysis emphasizing seed nutrients of the USDA pea (Pisum sativum L.) core collection. Genes Genom 34:305–320
35. Kwon SJ, Smýkal P, Hu J, McGee RJ, McPhee KE, Coyne CJ (2013) User-friendly markers linked to Fusarium wilt race 1 resistance gene in pea for marker-assisted selection. Plant Breed 132:642–648
36. Leonforte A, Sudheesh S, Cogan NOI, Salisbury PA, Nicolas ME, Materne M, Forster JW, Kaur S (2013) SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.). BMC Plant Biol 13:161
37. Loridon K, McPhee KE, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne CJ, Lejeune-Hénault I, Burstin J (2005) Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). Theor Appl Genet 111:1022–1031
38. Malvick DK, Percich JA (1999) Identification of Pisum sativum germ plasm with resistance to root rot caused by multiple strains of Aphanomyces euteiches. Plant Dis 83:51–54
39. Martínez-Villaluenga C, Frias J, Vidal-Valverde C (2008) Alpha-galactosides: antinutritional factors or functional ingredients? Crit Rev Food Sci Nutr 48:301–316
40. McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D (2013) Agriculture: feeding the future. Nature 499:23–24
41. McPhee K (2005) Variation for seedling root architecture in the core collection of pea germplasm. Crop Sci 45:1758–1763
42. McPhee KE, Muehlbauer FJ (1999) Stem strength in the core collection of Pisum germplasm. Pisum Genet 31:21–23
43. McPhee KE, Tullu A, Kraft JM, Muehlbauer FJ (1999) Resistance to Fusarium wilt race 2 in the Pisum core collection. J Am Soc Hortic Sci 124:28–31
44. Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 102:2442–2447
45. Nallu S, Silverstein KA, Zhou P, Young ND, VandenBosch KA (2014) Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions of Medicago truncatula. Plant J 78:697–705
46. Nikolopoulou D, Grigorakis K, Stasini M, Alexis MN, Iliadis K (2007) Differences in chemical composition of field pea (Pisum sativum) cultivars: effects of cultivation area and year. Food Chem 103:847–852
47. Pasam RK, Sharma R, Malosetti M, van Eeuwijk FA, Haseneyer G, Kilian B, Graner A (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biol 12:16
48. Peterbauer T, Richter A (2001) Biochemistry and physiology of raffinose family oligosaccharides and galactosyl cyclitols in seeds. Seed Sci Res 11:185–198
49. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
50. Proels RK, Hückelhoven R (2014) Cell-wall invertases, key enzymes in the modulation of plant metabolism during defence responses. Mol Plant Pathol 15:858–864
51. R Core Team (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. www.R-project.org
52. Ramamurthy RK, Jedlicka J, Graef GL, Waters BM (2014) Identification of new QTLs for seed mineral, cysteine, and methionine concentrations in soybean [Glycine max (L.) Merr.]. Mol Breed 34:431–445
53. Ray H, Bett K, Tar’an B, Vandenberg A, Thavarajah D, Warkentin T (2014) Mineral micronutrient content of cultivars of field pea, chickpea, common bean, and lentil grown in Saskatchewan, Canada. Crop Sci 54(4):1698–1708
54. Riedelsheimer C, Lisec J, Czedik-Eysenberg A, Sulpice R, Flis A, Grieder C, Altmann T, Stitt M, Willmitzer L, Melchinger AE (2012) Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize. Proc Natl Acad Sci 109:8872–8877
55. Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G, Papa R (2009) Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2:504–522
56. Saha GC, Vandemark GJ (2012) Evaluation of expression stability of candidate references genes among green and yellow pea cultivars (Pisum sativum L.) subjected to abiotic and biotic stress. Am J Plant Sci 3:235–242
57. Sankaran RP, Huguet T, Grusak MA (2009) Identification of QTL affecting seed mineral concentrations and content in the model legume Medicago truncatula. Theor Appl Genet 119:241–253
58. Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14
59. Sindhu A, Ramsay L, Sanderson LA, Stonehouse R, Li R, Condie J, Shunmugam ASK, Liu Y, Jha AB, Diapari M, Burstin J, Aubert G, Tar’an B, Bett KE, Warkentin TD, Sharpe AG (2014) Gene-based SNP discovery and genetic mapping in pea. Theor Appl Genet 127:2225–2241
60. Smýkal P, Aubert G, Burstin J, Coyne CJ, Ellis NTH, Flavell AJ, Ford R, Hýbl M, Macas J, Neumann P, McPhee KE, Redden RJ, Rubiales D, Weller JL, Warkentin TD (2012) Pea (Pisum sativum L.) in the genomic era. Agronomy 2:74–115
61. Storey JD, Tibshirani R (2003) Statistical significance for genome-wide studies. Proc Natl Acad Sci USA 100:9440–9445
62. Tedford EC, Inglis DA (1999) Evaluation of legumes common to the Pacific northwest as hosts for the pea cyst nematode, Heterodera goettingiana. J Nematol 31:155–163
63. Upadhyaya HD, Wang YH, Sharma S, Singh S (2012) Association mapping of height and maturity across five environments using the sorghum mini core collection. Genome 55:471–479
64. Van Inghelandt D, Melchinger AE, Martinant JP, Stich B (2012) Genome-wide association mapping of flowering time and northern corn leaf blight (Setosphaeria turcica) resistance in a vast commercial maize germplasm set. BMC Plant Biol 12:56
65. Vidal-Valverde C, Frias J, Hernandez A, Martín-Alvarez PJ, Sierra I, Rodríguez C, Blazquez I, Vicente G (2003) Assessment of nutritional compounds and antinutritional factors in pea (Pisum sativum) seeds. J Sci Food Agri 83:298–306
66. Wang TL, Domoney C, Hedley CL, Casey R, Grusak MA (2003) Can we improve the nutritional quality of legume seeds? Plant Physiol 131:886–891
67. Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler EST (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733
68. Xu J, Ranc N, Munos S, Rolland S, Bouchet JP, Desplat N, Le Paslier MC, Liang Y, Brunel D, Causse M (2013) Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet 126:567–581
69. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
70. Zhang L, Cohn NS, Mitchell JP (1996) Induction of a pea cell-wall invertase gene by wounding and its localized expression in phloem. Plant Physiol 112:1111–1117
71. Zhao H, Nettleton D, Soller M, Dekkers JCM (2005) Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL. Genet Res 86:77–87
72. Zhu CS, Gore M, Buckler ES, Yu JM (2008) Status and prospects of association mapping in plants. Plant Genet 1:5–20