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Association analysis of cowpea bacterial blight resistance in USDA cowpea germplasm

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Abstract

Cowpea bacterial blight (CoBB, Xanthomonas axonopodis pv. vignicola, Xav) is the most important bacterial disease of cowpea (Vigna unguiculata) because it prevalent in all major cowpea growing areas worldwide, and the use of host resistance is the primary method to control this disease. Genetic diversity and association analysis were conducted for CoBB resistance in 249 USDA germplasm accessions, originally collected from 42 countries. Genotyping by sequencing (GBS) was used for single nucleotide polymorphism (SNP) discovery. A total of 1031 SNPs were used for genetic diversity and association analysis in this study. Three well-differentiated genetic populations and admixtures were postulated in the cowpea panel by STRUCTURE 2.3.4 and MEGA 6. Association analysis for CoBB resistance was done using single marker regression, general linear mode, and mixed linear mode using Tassel 5, GAPIT and QGene 4. Four SNP markers (C35046071_1260, C35084634_455, scaffold96328_3387, and scaffold96765_4430) were identified to be strongly associated with CoBB resistance with >70 % selection accuracy. These markers can be utilized in cowpea breeding for CoBB resistance through marker-assisted selection.

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References

  • Agbicodo EM, Fatokun CA, Bandyopadhyay R, Wydra K, Diop NN, Mucher W, Ehlers JD, Roberts PA, Close TJ, Visser RGF, van der Linden CG (2010) Identification of markers associated with bacterial blight resistance loci in cowpea [Vigna unguiculata (L.) Walp.]. Euphytica 175:215–226

    Article  CAS  Google Scholar 

  • Ajeigbe HA, Singh BB, Emechebe AM (2008) Field evaluation of improved cowpea lines for resistance to bacterial blight, virus and striga under natural infestation in the West African Savannas. Afr J Biotechnol 7:3563–3568

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Bua B, Adipala E, Opio F (1998) Screening cowpea germplasm for resistance to bacterial blight in Uganda. Int J Pest Manag 44:185–189

    Article  Google Scholar 

  • Buckley B, Clark CA (1997) Reaction of cowpea cultivars, breeding lines, and PIs to bacterial blight. HortScience 32:606

    Google Scholar 

  • Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 12(363):557–572

    Article  Google Scholar 

  • Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196

    Article  CAS  Google Scholar 

  • Davis DW, Oelke EA, Oplinger ES, Doll JD, Hanson CV, Putnam DH (1991) Cowpea alternative field crops manual (http://www.hort.purdue.edu/newcrop/afcm/cowpea.html)

  • Duke JA (1981) Handbook of legumes of world economic importance. Plenum Press, New York 345p

    Book  Google Scholar 

  • Ehlers JD, Hall AE (1997) Cowpea (Vigna unguiculata L Walp). Field Crops Res 53:187–204

    Article  Google Scholar 

  • Ehlers JD, Fery RL, Hall AE (2007) Cowpea breeding in the USA: new varieties and improved germplasm. In: IITA Conference Proceedings

  • Elshire RJ, Glaubitz JC, Sun Q (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6(5):e19379

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Fery RL (1990) The Cowpea: production, utilization, and research in the United States. Hortic Rev 12:197–222

    Google Scholar 

  • Fery RL (2002) New opportunities in Vigna. In: Janick J, Whipkey A (eds) Trends in new crops and new uses. ASHS Press, Alexandria, pp 424–428

    Google Scholar 

  • Fery RL, Singh BB (1997) Cowpea genetics: a review of the recent literature In: Singh BB, Dr Mohan Raj, Dashiell KE, Jackai LEN (eds) Advances in cowpea research. International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS) IITA, Ibadan, Nigeria pp 13–30

  • Gitaitis RD (1983) Two resistant responses in cowpea induced by different strains of Xanthomonas campestris pv vignicola. Plant Dis 67:1025–1028

    Article  Google Scholar 

  • Hayatu M, Kutama AS, Aisha WA, Nura S (2013) Screening of some genotypes of cowpea (Vigna unguiculata L (Walp) against bacterial blight caused by Xanthomonas compestris Pv Translucens. Glob Adv Res J Agric Sci 2(10):276–282

    Google Scholar 

  • He J, Zhao X, Laroche A, Lu Z-X, Liu H, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:484

    Article  PubMed Central  PubMed  Google Scholar 

  • Iquira E, Humira S, Francois B (2015) Association mapping of QTLs for Sclerotinia stem rot resistance in a collection of soybean plant introductions using a genotyping by sequencing (GBS) approach. BMC Plant Biol 15:5. doi:10.1186/s12870-014-0408-y

    Article  PubMed Central  PubMed  Google Scholar 

  • Joehanes R, Nelson JC (2008) QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics 24:2788–2789

    Article  CAS  PubMed  Google Scholar 

  • Kisha T, Sneller CH, Diers BW (1997) Relationship between genetic distance among parents and genetic variance in populations of soybean. Crop Sci 37:1317–1325

    Article  Google Scholar 

  • Langyintuo AS, Lowenberg-DeBoer J, Faye M, Lambert D, Ibro G, Moussa B, Kergna A, Kushwaha S, Musa S, Ntoukam G (2003) Cowpea supply and demand in west and central Africa. Field Crops Res 82:215–231

    Article  Google Scholar 

  • Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K, Wnag J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967

    Article  CAS  PubMed  Google Scholar 

  • Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbur PJ, Gore MA, Buckler ES, Zhang Z (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28:2397–2399

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Bayer M, Druka A, Russell JR, Hackett CA, Poland J, Ramsay L, Hedley PE, Waugh R (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genom 15:104

    Article  Google Scholar 

  • Lucas MR, Diop NN, Wanamaker S, Ehlers JD, Roberts PA, Close TJ (2011) Cowpea–soybean synteny clarified through an improved genetic map. Plant Genome 4:218–225

    Article  CAS  Google Scholar 

  • Lv J, Qi J, Shi Q, Shen D, Zhang S, Zhang A, Shao G, Li H, Sun Z, Weng Y, Shang Y, Gu X, Li X, Zhu X, Zhang J, van Treuren R, van Dooijeweert W, Zhang Z, Huang S (2012) Genetic diversity and population STRUCTURE of cucumber (Cucumis sativus L). PLoS One 7(10):e46919

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M (2009) A consensus genetic map of cowpea [Vigna unguiculata (L) Walp] and synteny based on EST-derived SNPs. PNAS 106(43):18159–18164

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nimmakayala P, Levi A, Abburi L, Abburi VL, Tomason YR, Saminathan T, Vajja VG, Malkaram S, Reddy R, Wehner TC, Mitchell SE, Reddy UK (2014) Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genom 15:767. doi:10.1186/1471-2164-15-767

    Article  Google Scholar 

  • Okechukwu RU, Ekpo EJA (2004) Sources of resistance to cowpea bacterial blight disease in Nigeria. J Phytopathol 152:345–351

    Article  Google Scholar 

  • Poland JA, Brown PJ, Sorrells ME, Jannik JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7(2):e32253. doi:10.1371/journalpone0032253

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed Central  CAS  PubMed  Google Scholar 

  • Sim SC (2015) Tutorial of the STRUCTURE software. http://pbgworks.org/sites/pbgworks.org/files/Tutorial%20of%20STRUCTURE%20software.pdf. Accessed 1 Aug 2015)

  • Singh BB (2007) Recent progress in cowpea genetics and breeding. In: Chadha ML (ed) Proceedings of 1st international conference on indigenous vegetables and legumes pp 69–75

  • Singh BB, Mohan-Raj DR, Dashiell DR, Jackai LEN (1997) Advances in cowpea research. International Institute of Tropical Agriculture, Ibadan

    Google Scholar 

  • Singh BB, Ehlers JD, Sharma B, Freire-Filho FR (2002) Recent progress in cowpea breeding: challenges and opportunities for enhancing sustainable cowpea production. International Institute of Tropical Agriculture, Ibadan, pp 22–40

    Google Scholar 

  • Singh BB, Ajeigbe HA, Tarawali SA, Fernandez-Rivera S, Abubakar M (2003) Improving the production and utilization of cowpea as food and fodder. Field Crops Res 84(1–2):169–177

    Article  Google Scholar 

  • Sonah H, Bastien M, Iquira E, Tardivel A, Legare G (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 8(1):e54603

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sonah H, O’Donoughue L, Cober E, Rajcan I, Belzile F (2015) Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean. Plant Biotechnol J 13(2):211–221

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Ailipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tan H, Tie M, Luo Q, Zhu Y, Lai J, Li H (2012) A review of molecular makers applied in cowpea (Vigna unguiculata L Walp) breeding. J Life Sci 6:1190–1199

    Google Scholar 

  • Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530

    Article  CAS  PubMed  Google Scholar 

  • Verdier V, Assigbetse K, Khatri-Chhetri G, Wydra K, Rudolph K, Geiger J (1998) Molecular characterization of the incitant of cowpea bacterial blight and pustule, Xanthomonas campestris pv vignicola. Eur J Plant Pathol 104:595–602

    Article  CAS  Google Scholar 

  • Wydra K, Singh BB (1998) Breeding for resistance to multiple strains of cowpea bacterial blight. IITA Annual Report, Project 11, pp 25–27

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407

    Article  Google Scholar 

  • Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355–360

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by USDA-ARS GRIN GERMPLASM EVALUATION PROPOSAL for National Plant Germplasm System (NPGS) by Crop Germplasm Committee (CGC) with Project Number: 6046-21000-011-15. Cowpea germplasm accessions were provide by USDA-ARS at GRIFFIN, GA Station. The cowpea_Genome_0.03.fa (6750 scaffolds or contigs) (http://harvest-blast.org/) was kindly provided by Dr. Timothy J. Close at University of California Riverside, CA, USA.

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Authors and Affiliations

  1. Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA

    Ainong Shi, Jianbing Ma, Haizheng Xiong, Jun Qin, Wei Yang, Jessica Chitwood, Yuejin Weng & Weiguo Lu

  2. LSU AgCenter, Red River Research Station, 262 Research Station Drive, Bossier City, LA, 71112, USA

    Blair Buckley

  3. Crop Improvement and Protection Research Unit, USDA-ARS, Salinas, CA, 93905, USA

    Beiquan Mou

  4. Vegetable Research Center, University of Arkansas, Alma, AR, 72921, USA

    Dennis Motes

  5. Plant Genetic Resources Conservation Unit, USDA, 1109 Experiment St., Griffin, GA, 30223, USA

    J. Bradley Morris

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  1. Ainong Shi
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  2. Blair Buckley
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Correspondence to Ainong Shi, Blair Buckley or Beiquan Mou.

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Shi, A., Buckley, B., Mou, B. et al. Association analysis of cowpea bacterial blight resistance in USDA cowpea germplasm. Euphytica 208, 143–155 (2016). https://doi.org/10.1007/s10681-015-1610-1

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