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

详细信息    查看全文

• 作者：Marti Pottorff (11)
  Philip A Roberts (12)
  Timothy J Close (11)
  Stefano Lonardi (13)
  Steve Wanamaker (11)
  Jeffrey D Ehlers (11) (14)
  
  11. Department of Botany & Plant Sciences ; University of California Riverside ; Riverside ; CA ; USA
  12. Department of Nematology ; University of California Riverside ; Riverside ; CA ; USA
  13. Department of Computer Science and Engineering ; University of California Riverside ; Riverside ; CA ; USA
  14. Bill & Melinda Gates Foundation ; Seattle ; Washington ; USA
  
• 关键词：Cowpea ; Synteny ; Legumes ; Genomics ; Marker ; assisted selection ; Heat ; stress ; Seed coat discoloration ; Candidate genes ; Ethylene
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：907 KB
• 参考文献：1. Wang, D, Ram, MS, Dowell, FE (2002) Classification of damaged soybean seeds using near-infrared spectroscopy. Trans Am Soc Agric Eng 45: pp. 1943-1950 11410" target="_blank" title="It opens in new window">CrossRef
  2. Park, D, Maga, JA (1999) Dry bean (Phaseolus vulgaris): color stability as influenced by time and moisture content. J Food Process Preservation 23: pp. 515-522 1111/j.1745-4549.1999.tb00401.x" target="_blank" title="It opens in new window">CrossRef
  3. Junk, DC (2005) Seedcoat darkening in pinto bean (Phaseolus vulgaris L.). University of Saskatchewan, Saskatoon
  4. Elsadr, HT, Wright, LC, Pauls, KP, Bett, KE (2011) Characterization of seed coat post harvest darkening in common bean (Phaseolus vulgaris L.). Theor Appl Genet 123: pp. 1467-1472 11-1683-8" target="_blank" title="It opens in new window">CrossRef
  5. Hall, A, Patel, P (1988) Inheritance of heat-induced brown discoloration in seed coats of cowpea. Crop Sci 28: pp. 929-932 11183X002800060020x" target="_blank" title="It opens in new window">CrossRef
  6. Nasar-Abbas, S, Siddique, K, Plummer, J, White, P, Harris, D, Dods, K, D鈥橝ntuono, M (2009) Faba bean (vicia faba L.) seeds darken rapidly and Phenolic content falls when stored at higher temperature, moisture and light intensity. LWT-Food Sci Technol 42: pp. 1703-1711 CrossRef
  7. Matus, A, Slinkard, A, Vandenberg, A The Potential of Zero Tannin Lentil. In: Janick, J, Simon, JE eds. (1993) New Crops. Wiley, New York, pp. 279-282
  8. Nielsen, CL, Hall, AE (1985) Responses of cowpea (Vigna unguiculata (L.) walp.) in the field to high night air temperature during flowering. I. Thermal regimes of production regions and field experimental system. Field Crop Res 10: pp. 167-179 CrossRef
  9. Muchero, W, Diop, NN, Bhat, PR, Fenton, RD, Wanamaker, S, Pottorff, M, Hearne, S, Cisse, N, Fatokun, C, Ehlers, JD (2009) A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci U S A 106: pp. 18159-18164 CrossRef
  10. Diop, N, Ehlers, J, Wanamaker, S, Muchero, W, Fatokun, C, Guojing, L, Roberts, P, Close, T An Improved Consensus Genetic Linkage map of Cowpea [Vigna Unguiculata (L) Walp.]. In: Boukar, O, Coulibaly, O, Fatokun, C, Lopez, K, Tam貌, M eds. (2012) Enhancing Cowpea Value Chains Through Research Advances. International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
  11. Lucas, MR, Diop, NN, Wanamaker, S, Ehlers, JD, Roberts, PA, Close, TJ (2011) Cowpea鈥搒oybean synteny clarified through an improved genetic map. Plant Genome J 4: pp. 218-225 11.06.0019" target="_blank" title="It opens in new window">CrossRef
  12. HarvEST: EST databases. http://harvest.ucr.edu/
  13. Physical Map of cowpea. http://phymap.ucdavis.edu/cowpea/
  14. HarvEST BLAST search. http://harvest-blast.org/
  15. Lucas, MR, Ehlers, JD, Huynh, B-L, Diop, N-N, Roberts, PA, Close, TJ (2013) Markers for breeding heat-tolerant cowpea. Mol Breed 31: pp. 529-536 11032-012-9810-z" target="_blank" title="It opens in new window">CrossRef
  16. Goodstein, DM, Shu, S, Howson, R, Neupane, R, Hayes, RD, Fazo, J, Mitros, T, Dirks, W, Hellsten, U, Putnam, N, Rokhsar Daniel, S (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40: pp. D1178-D1186 CrossRef
  17. Kende, H (1993) Ethylene biosynthesis. Annu Rev Plant Physiol Plant Mol Biol 44: pp. 283-307 1146/annurev.pp.44.060193.001435" target="_blank" title="It opens in new window">CrossRef
  18. Yang, SF, Hoffman, NE (1984) Ethylene biosynthesis and its regulation in higher plants. Annu Rev Plant Physiol 35: pp. 155-189 1146/annurev.pp.35.060184.001103" target="_blank" title="It opens in new window">CrossRef
  19. Kende, H (1989) Enzymes of ethylene biosynthesis. Plant Physiol 91: pp. 1-4 1104/pp.91.1.1" target="_blank" title="It opens in new window">CrossRef
  20. Larkindale, J, Knight, MR (2002) Protection against heat stress-induced oxidative damage in Arabidopsis involves calcium, abscisic acid, ethylene, and salicylic acid. Plant Physiol 128: pp. 682-695 1104/pp.010320" target="_blank" title="It opens in new window">CrossRef
  21. Larkindale, J, Huang, B (2005) Effects of abscisic acid, salicylic acid, ethylene and hydrogen peroxide in thermotolerance and recovery for creeping bentgrass. Plant Growth Regul 47: pp. 17-28 CrossRef
  22. Munn茅-Bosch, S, Pe帽uelas, J, Asensio, D, Llusi脿, J (2004) Airborne ethylene may alter antioxidant protection and reduce tolerance of holm oak to heat and drought stress. Plant Physiol 136: pp. 2937-2947 1104/pp.104.050005" target="_blank" title="It opens in new window">CrossRef
  23. Hays, DB, Do, JH, Mason, RE, Morgan, G, Finlayson, SA (2007) Heat stress induced ethylene production in developing wheat grains induces kernel abortion and increased maturation in a susceptible cultivar. Plant Sci 172: pp. 1113-1123 CrossRef
  24. Muchero, W, Ehlers, JD, Close, TJ, Roberts, PA (2009) Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.]. Theor Appl Genet 118: pp. 849-863 CrossRef
  25. Pottorff, M, Wanamaker, S, Ma, YQ, Ehlers, JD, Roberts, PA, Close, TJ (2012) Genetic and physical mapping of candidate genes for resistance to Fusarium oxysporum f.sp. tracheiphilum race 3 in cowpea [Vigna unguiculata (L.) Walp]. PLoS One 7: pp. e41600 CrossRef
  26. Pottorff, M, Li, G, Ehlers, JD, Close, TJ, Roberts, PA (2014) Genetic mapping, synteny, and physical location of two loci for Fusarium oxysporum f. sp. tracheiphilum race 4 resistance in cowpea [Vigna unguiculata (L.) Walp]. Mol Breed 33: pp. 779-791 11032-013-9991-0" target="_blank" title="It opens in new window">CrossRef
  27. Muchero, W, Ehlers, JD, Close, TJ, Roberts, PA (2011) Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.]. BMC Genomics 12: pp. 8 1186/1471-2164-12-8" target="_blank" title="It opens in new window">CrossRef
  28. Davis, RM, Frate, CA (2007) UC IPM Pest Management Guidelines: Dry Beans Fusarium Wilt (Blackeyes/Cowpeas). UC ANR Publication, Oakland, CA
  29. Ehlers, JD, Matthews, WC, Hall, AE, Roberts, PA Breeding and Evaluation of Cowpeas With High Levels of Broad-Based Resistance to Root-Knot Nematodes. In: Fatokun, C, Tarawali, S, Singh, B, Kormawa, P eds. (2002) Challenges and Opportunities for Enhancing Sustainable Cowpea Production. International Institute of Tropical Agriculture (IITA), M T. Ibadan, Nigeriapp. 433
  30. Singh, B, Mohan Raj, D, Dashiell, K, Jackai, L Recent Advances in Cowpea Breeding. In: Singh, B, Mohan Raj, D, Dashiell, K, Jackai, L eds. (1997) Advances in Cowpea Research. Copublished by International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Ibadan, Nigeriapp. 375
  31. Timko, M, Gowda, B, Ouedraogo, J, Ousmane, B, Ejeta, G, Gressel, J (2007) Molecular Markers for Analysis of Resistance to Striga Gesnerioides in Cowpea. Integrating new Technologies for Striga Control: Towards Ending the Witch-Hunt. World Scientific Publishing Co Pte Ltd, Singapore, pp. 115-128 1142/9789812771506_0009" target="_blank" title="It opens in new window">CrossRef
  32. Matkin OA, Chandler PA: / The UC type soil mixes. The UC System for producing healthy container grown plants. University of California Extension Service; 68鈥?5.
  33. Van Ooijen, JW (2004) MapQTL庐 5, Software for the Mapping of Quantitative Trait Loci in Experimental Populations. Kyazma BV, Wageningen, Netherlands
  34. Voorrips, RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: pp. 77-78 CrossRef
  35. Milne, I, Shaw, P, Stephen, G, Bayer, M, Cardle, L, Thomas, WTB, Flavell, AJ, Marshall, D (2010) Flapjack鈥攇raphical genotype visualization. Bioinformatics 26: pp. 3133-3134 CrossRef
  36. Luo, MC, Thomas, C, You, FM, Hsiao, J, Ouyang, S, Buell, CR, Malandro, M, McGuire, PE, Anderson, OD, Dvorak, J (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: pp. 378-389 CrossRef
  37. 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, M-C, Close Timothy, J (2013) Combinatorial pooling enables selective sequencing of the barley gene space. PLoS Comput Biol 9: pp. e1003010 CrossRef
  38. Zerbino, DR (2010) Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics Chapter 11: pp. Unit 11.15
  39. Zerbino, DR, Birney, E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: pp. 821-829 1101/gr.074492.107" target="_blank" title="It opens in new window">CrossRef
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Heat-induced browning (Hbs) of seed coats is caused by high temperatures which discolors the seed coats of many legumes, affecting the visual appearance and quality of seeds. The genetic determinants underlying Hbs in cowpea are unknown. Results We identified three QTL associated with the heat-induced browning of seed coats trait, Hbs-1, Hbs-2 and Hbs-3, using cowpea RIL populations IT93K-503-1 (Hbs positive) x CB46 (hbs negative) and IT84S-2246 (Hbs positive) x TVu14676 (hbs negative). Hbs-1 was identified in both populations, accounting for 28.3% -77.3% of the phenotypic variation. SNP markers 1_0032 and 1_1128 co-segregated with the trait. Within the syntenic regions of Hbs-1 in soybean, Medicago and common bean, several ethylene forming enzymes, ethylene responsive element binding factors and an ACC oxidase 2 were observed. Hbs-1 was identified in a BAC clone in contig 217 of the cowpea physical map, where ethylene forming enzymes were present. Hbs-2 was identified in the IT93K-503-1 x CB46 population and accounted for of 9.5 to 12.3% of the phenotypic variance. Hbs-3 was identified in the IT84S-2246 x TVu14676 population and accounted for 6.2 to 6.8% of the phenotypic variance. SNP marker 1_0640 co-segregated with the heat-induced browning phenotype. Hbs-3 was positioned on BAC clones in contig512 of the cowpea physical map, where several ACC synthase 1 genes were present. Conclusion The identification of loci determining heat-induced browning of seed coats and co-segregating molecular markers will enable transfer of hbs alleles into cowpea varieties, contributing to higher quality seeds.