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

BMC Genomics

Jeffrey D Ehlers¹  Steve Wanamaker³  Stefano Lonardi²  Timothy J Close³  Philip A Roberts⁴  Marti Pottorff³ 

[1] Bill & Melinda Gates Foundation, Seattle, Washington, USA;Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA;Department of Botany & Plant Sciences, University of California Riverside, Riverside, CA, USA;Department of Nematology, University of California Riverside, Riverside, CA, USA

关键词: Ethylene;    Candidate genes;    Seed coat discoloration;    Heat-stress;    Marker-assisted selection;    Genomics;    Legumes;    Synteny;    Cowpea;   

Others  :  1217331
DOI  :  10.1186/1471-2164-15-328

 received in 2014-01-27, accepted in 2014-04-24,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Pottorff et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Wang D, Ram MS, Dowell FE: Classification of damaged soybean seeds using near-infrared spectroscopy. Trans Am Soc Agric Eng 2002, 45(6):1943-1950.
• [2]Park D, Maga JA: Dry bean (Phaseolus vulgaris): color stability as influenced by time and moisture content. J Food Process Preservation 1999, 23(6):515-522.
• [3]Junk DC: Seedcoat darkening in pinto bean (Phaseolus vulgaris L.). Saskatoon: University of Saskatchewan; 2005.
• [4]Elsadr HT, Wright LC, Pauls KP, Bett KE: Characterization of seed coat post harvest darkening in common bean (Phaseolus vulgaris L.). Theor Appl Genet 2011, 123(8):1467-1472.
• [5]Hall A, Patel P: Inheritance of heat-induced brown discoloration in seed coats of cowpea. Crop Sci 1988, 28(6):929-932.
• [6]Nasar-Abbas S, Siddique K, Plummer J, White P, Harris D, Dods K, D’Antuono M: 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 2009, 42(10):1703-1711.
• [7]Matus A, Slinkard A, Vandenberg A: The Potential of Zero Tannin Lentil. In New Crops. Edited by Janick J, Simon JE. New York: Wiley; 1993:279-282.
• [8]Nielsen CL, Hall AE: 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 1985, 10:167-179.
• [9]Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD: A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci U S A 2009, 106(43):18159-18164.
• [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 Enhancing Cowpea Value Chains Through Research Advances. Edited by Boukar O, Coulibaly O, Fatokun C, Lopez K, Tamò M. Ibadan, Nigeria: International Institute of Tropical Agriculture (IITA); 2012. In press
• [11]Lucas MR, Diop NN, Wanamaker S, Ehlers JD, Roberts PA, Close TJ: Cowpea–soybean synteny clarified through an improved genetic map. Plant Genome J 2011, 4(3):218-225.
• [12]HarvEST: EST databases http://harvest.ucr.edu/ webcite
• [13]Physical Map of cowpea http://phymap.ucdavis.edu/cowpea/ webcite
• [14]HarvEST BLAST search http://harvest-blast.org/ webcite
• [15]Lucas MR, Ehlers JD, Huynh B-L, Diop N-N, Roberts PA, Close TJ: Markers for breeding heat-tolerant cowpea. Mol Breed 2013, 31(3):529-536.
• [16]Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar Daniel S: Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 2012, 40(D1):D1178-D1186.
• [17]Kende H: Ethylene biosynthesis. Annu Rev Plant Physiol Plant Mol Biol 1993, 44(1):283-307.
• [18]Yang SF, Hoffman NE: Ethylene biosynthesis and its regulation in higher plants. Annu Rev Plant Physiol 1984, 35(1):155-189.
• [19]Kende H: Enzymes of ethylene biosynthesis. Plant Physiol 1989, 91(1):1-4.
• [20]Larkindale J, Knight MR: Protection against heat stress-induced oxidative damage in Arabidopsis involves calcium, abscisic acid, ethylene, and salicylic acid. Plant Physiol 2002, 128(2):682-695.
• [21]Larkindale J, Huang B: Effects of abscisic acid, salicylic acid, ethylene and hydrogen peroxide in thermotolerance and recovery for creeping bentgrass. Plant Growth Regul 2005, 47(1):17-28.
• [22]Munné-Bosch S, Peñuelas J, Asensio D, Llusià J: Airborne ethylene may alter antioxidant protection and reduce tolerance of holm oak to heat and drought stress. Plant Physiol 2004, 136(2):2937-2947.
• [23]Hays DB, Do JH, Mason RE, Morgan G, Finlayson SA: Heat stress induced ethylene production in developing wheat grains induces kernel abortion and increased maturation in a susceptible cultivar. Plant Sci 2007, 172(6):1113-1123.
• [24]Muchero W, Ehlers JD, Close TJ, Roberts PA: Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.]. Theor Appl Genet 2009, 118(5):849-863.
• [25]Pottorff M, Wanamaker S, Ma YQ, Ehlers JD, Roberts PA, Close TJ: 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 2012, 7(7):e41600.
• [26]Pottorff M, Li G, Ehlers JD, Close TJ, Roberts PA: 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 2014, 33(4):779-791.
• [27]Muchero W, Ehlers JD, Close TJ, Roberts PA: 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 2011, 12:8. BioMed Central Full Text
• [28]Davis RM, Frate CA: UC IPM Pest Management Guidelines: Dry Beans Fusarium Wilt (Blackeyes/Cowpeas). Oakland, CA: UC ANR Publication; 2007:3446.
• [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 Challenges and Opportunities for Enhancing Sustainable Cowpea Production. Edited by Fatokun C, Tarawali S, Singh B, Kormawa P. M T. Ibadan, Nigeria: International Institute of Tropical Agriculture (IITA); 2002:433.
• [30]Singh B, Mohan Raj D, Dashiell K, Jackai L: Recent Advances in Cowpea Breeding. In Advances in Cowpea Research. Edited by IITA, Singh B, Mohan Raj D, Dashiell K, Jackai L. Ibadan, Nigeria: Copublished by International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki; 1997:375.
• [31]Timko M, Gowda B, Ouedraogo J, Ousmane B, Ejeta G, Gressel J: Molecular Markers for Analysis of Resistance to Striga Gesnerioides in Cowpea. In Integrating new Technologies for Striga Control: Towards Ending the Witch-Hunt. Singapore: World Scientific Publishing Co Pte Ltd; 2007:115-128.
• [32]Matkin OA, Chandler PA: The UC type soil mixes. The UC System for producing healthy container grown plants. University of California Extension Service; 68-85.
• [33]Van Ooijen JW: MapQTL® 5, Software for the Mapping of Quantitative Trait Loci in Experimental Populations. Wageningen, Netherlands: Kyazma BV; 2004.
• [34]Voorrips RE: MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 2002, 93(1):77-78.
• [35]Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WTB, Flavell AJ, Marshall D: Flapjack—graphical genotype visualization. Bioinformatics 2010, 26(24):3133-3134.
• [36]Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J: High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 2003, 82(3):378-389.
• [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: Combinatorial pooling enables selective sequencing of the barley gene space. PLoS Comput Biol 2013, 9(4):e1003010.
• [38]Zerbino DR: Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics 2010, Chapter 11:Unit 11.15.
• [39]Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829.