Skip to main content
Log in

Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages

Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

This is the first report on association analysis of salt tolerance and identification of SNP markers associated with salt tolerance in cowpea.

Abstract

Cowpea (Vigna unguiculata (L.) Walp) is one of the most important cultivated legumes in Africa. The worldwide annual production in cowpea dry seed is 5.4 million metric tons. However, cowpea is unfavorably affected by salinity stress at germination and seedling stages, which is exacerbated by the effects of climate change. The lack of knowledge on the genetic underlying salt tolerance in cowpea limits the establishment of a breeding strategy for developing salt-tolerant cowpea cultivars. The objectives of this study were to conduct association mapping for salt tolerance at germination and seedling stages and to identify SNP markers associated with salt tolerance in cowpea. We analyzed the salt tolerance index of 116 and 155 cowpea accessions at germination and seedling stages, respectively. A total of 1049 SNPs postulated from genotyping-by-sequencing were used for association analysis. Population structure was inferred using Structure 2.3.4; K optimal was determined using Structure Harvester. TASSEL 5, GAPIT, and FarmCPU involving three models such as single marker regression, general linear model, and mixed linear model were used for the association study. Substantial variation in salt tolerance index for germination rate, plant height reduction, fresh and dry shoot biomass reduction, foliar leaf injury, and inhibition of the first trifoliate leaf was observed. The cowpea accessions were structured into two subpopulations. Three SNPs, Scaffold87490_622, Scaffold87490_630, and C35017374_128 were highly associated with salt tolerance at germination stage. Seven SNPs, Scaffold93827_270, Scaffold68489_600, Scaffold87490_633, Scaffold87490_640, Scaffold82042_3387, C35069468_1916, and Scaffold93942_1089 were found to be associated with salt tolerance at seedling stage. The SNP markers were consistent across the three models and could be used as a tool to select salt-tolerant lines for breeding improved cowpea tolerance to salinity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Abeer H, Abd_Allah EF, Alqarawi AA, Egamberdieva D (2015) Induction of salt stress tolerance in cowpea [Vigna unguiculata (L.) Walp.] by arbuscular mycorrhizal fungi. Legume Res 38(5):579–588

    Google Scholar 

  • Agbicodo EM, Fatokun CA, Bandyopadhyay R, Wydra K, Diop NN, Muchero 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(2):215–226

    Article  CAS  Google Scholar 

  • Ashebir G, Mebeasilassie A, Manikanidan M (2013) The response of some cowpea (Vigna unguiculata (L.) Walp.) genotypes for salt stress during germination and seedling stage. J Stress Physiol Biochem 9:73–84

    Google Scholar 

  • Bastien M, Sonah H, Belzile F (2014) Genome wide association mapping of resistance in soybean with a genotyping-by-sequencing approach. Plant Genome 7(1):1–13

    Article  Google Scholar 

  • Ben-Hayyim G, Moore GA (2007) Recent advances in breeding citrus for drought and saline stress tolerance. Springer Netherlands, Dordrecht, pp 627–642

    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(19):2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Biol Sci 363(1491):557–572

    Article  CAS  Google Scholar 

  • Earl DA, VonHoldt BM (2011) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res 4(2):359–361

    Article  Google Scholar 

  • Egbadzor KF, Yeboah M, Danquah EY, Ofori K, Offei SK (2013) Identification of SNP markers associated with seed size in cowpea [Vigna unguiculata (L) Walp]. Int J Plant Breed Genet 7(2):115–123

    Article  CAS  Google Scholar 

  • Egbadzor KF, Ofori K, Yeboah M, Aboagye LM, Opoku-Agyeman MO, Danquah EY, Offei SK (2014) Diversity in 113 Cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers. SpringerPlus 3(1):541

    Article  PubMed  PubMed Central  Google Scholar 

  • Elakhdar A, EL-Sattar MA, Amer K, Rady A (2016) Population structure and marker–trait association of salt tolerance in barley (Hordeum vulgare L.). C R Biol 339(11):454–461

    Article  PubMed  Google Scholar 

  • 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(5):e19379

    Article  CAS  PubMed  PubMed Central  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(8):2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Fehr WR, Caviness CE, Burmood DT, Pennington JS (1971) Stage of development descriptions for soybeans, Glycine max (L.) Merrill. Crop Sci 11(6):929–931

    Article  Google Scholar 

  • Fernandez GCJ (1992) Effective selection criteria for assessing plant stress tolerance. In: Proceedings of the international symposium on adaptation of vegetables and other food crops in temperature and water stress, pp 257–270

  • Foolad MR (1999) Comparison of salt tolerance during seed germination and vegetative growth in tomato by QTL mapping. Genome 42(4):727–734

    Article  CAS  Google Scholar 

  • Foolad MR (2007) Current status of breeding tomoatoes for salt and drought tolerance. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant crops, chap 27. Springer, Netherlands, pp 261–283

    Google Scholar 

  • Foolad MR, Jones RA (1993) Mapping salt-tolerance genes in tomato (Lycopersicon esculentum) using trait-based marker analysis. Theor Appl Genet 87(1–2):184–192

    CAS  PubMed  Google Scholar 

  • Foolad MR, Stoltz T, Dervinis C, Rodriguez RL, Jones RA (1997) Mapping QTLs conferring salt tolerance during germination in tomato by selective genotyping. Mol Breed 3(4):269–277

    Article  CAS  Google Scholar 

  • Foolad MR, Chen FQ, Lin GY (1998) RFLP Mapping of QTLs conferring cold tolerance during seed germination in an interspecific cross of tomato. Mol Breed 4(6):519–529

    Article  CAS  Google Scholar 

  • Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12(2):211–217

    Article  CAS  PubMed  Google Scholar 

  • Kan G, Zhang W, Yang W, Ma D, Zhang D, Hao D, Hu Z, Yu D (2015) Association mapping of soybean seed germination under salt stress. Mol Gen Genomics 290(6):2147–2162

    Article  CAS  Google Scholar 

  • Kan G, Ning L, Li Y, Hu Z, Zhang W, He X, Yu D (2016) Identification of novel loci for salt stress at the seed germination stage in soybean. Breed Sci 66(4):530

    Article  PubMed  PubMed Central  Google Scholar 

  • Kisha TJ, Sneller CH, Diers BW (1997) Relationship between genetic distance among parents and genetic variance in populations of soybean. Crop Sci 37(4):1317–1325

    Article  Google Scholar 

  • Kordrostami M, Rabiei B, Kumleh HH (2016) Association analysis, genetic diversity and haplotyping of rice plants under salt stress using SSR markers linked to salTol and morpho-physiological characteristics. Plant Syst Evol 302(7):871–890

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  PubMed  Google Scholar 

  • Lander ES, Botsteins’b D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121(1):185–199

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li ZK, Xu JL (2007) Breeding for drought and salt tolerant rice (Oryza sativa L.): progress and perspectives. In: Advances in molecular breeding toward drought and salt tolerant crops. Springer Netherlands, pp 531–564

  • Li C, Zhang G, Lance R (2007) Recent advances in breeding barley for drought and saline stress tolerance. Adv Mol Breed Toward Drought Salt Toler Crops. Springer, Netherlands, pp 603–626

    Chapter  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Liu X, Huang M, Fan B, Buckler ES, Zhang Z, Bradbury PJ (2016) Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genet 12(2):e1005767

    Article  PubMed  PubMed Central  Google Scholar 

  • Lobato AKS, Filho BGS, Costa RCL, Gonçalves-Vidigal MC, Moraes EC, Oliveira Neto CF, Rodrigues VLF, Cruz FJR, Ferreira AS, Pita JD, Barreto AGT (2009) Morphological, physiological and biochemical responses during germination of the cowpea (Vigna unguiculata Cv. Pitiuba) seeds under salt stress. World J Agric Sci 5(5):590–596

    CAS  Google Scholar 

  • Long NV, Dolstra O, Malosetti M, Kilian B, Graner A, Visser RGF, Van der Linden CG (2013) Association mapping of salt tolerance in barley (Hordeum vulgare L.). Theor Appl Genet 126(9):2335–2351

    Article  CAS  PubMed  Google Scholar 

  • Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147(3):969–977

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA (2009) A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci 106(43):18159–18164

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Munns R, Schachtman DP, Condon AG, Munns R, Schachtman DP, Condon AG (1995) The significance of a two-phase growth response to salinity in wheat and barley. Funct Plant Biol 22(4):561–569

    CAS  Google Scholar 

  • Neumann P (1997) Salinity resistance and plant growth revisited. Plant Cell Env 20(9):1193–1198

    Article  CAS  Google Scholar 

  • Olufajo OO (2012) Agronomic Performance of improved cowpea varieties under natural infestation with Alectra vogelii (Benth.) in the northern Guinea savannah of Nigeria. Agric Tropic Subtropic 45(2):66–71

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Qin J, Shi A, Xiong H, Mou B, Motes DR, Lu W, Miller JJ, Scheuring DC, Nzaramba MN, Weng Y, Yang W (2016) Population structure analysis and association mapping of seed antioxidant content in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs. Can J Plant Sci 96(6):1026–1036

    CAS  Google Scholar 

  • Ramasamy RK, Ramasamy S, Bindroo BB, Naik VG (2014) STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. SpringerPlus 3(1):431

    Article  PubMed  PubMed Central  Google Scholar 

  • Saad FF, El-Mohsen AAA, Abd MA, Al-Soudan IH (2014) Effective selection criteria for evaluating some barley crosses for water stress tolerance. Adv Agric Biol 1(3):112–123

    Article  Google Scholar 

  • Shannon MC (1997) Adaptation of plants to salinity. Adv Agron 60:75–120

    Article  Google Scholar 

  • Shi A, Buckley B, Mou B, Motes D, Morris JB, Ma J, Xiong H, Qin J, Yang W, Chitwood J, Weng Y (2016) Association analysis of cowpea bacterial blight resistance in USDA cowpea germplasm. Euphytica 208(1):143–155

    Article  CAS  Google Scholar 

  • Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M, Belzile F (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 8(1):e54603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Souza RP, Machado EC, Silva JAB, Lagôa AMMA, Silveira JAG (2004) Photosynthetic gas exchange, chlorophyll fluorescence and some associated metabolic changes in cowpea (Vigna unguiculata) during water stress and recovery. Environ Exp Bot 51(1):45–56

    Article  CAS  Google Scholar 

  • Stratonovitch P, Semenov MA (2015) Heat tolerance around flowering in wheat identified as a key trait for increased yield potential in Europe under climate change. J Exp Bot 66(12):3599–3609

    Article  CAS  PubMed  PubMed Central  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(9):522–530

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Chen G, Zhang H, Liu B, Yang Y, Qin L, Chen E, Guan Y (2014) Identification of QTLs for salt tolerance at germination and seedling stage of Sorghum bicolor L. Moench. Euphytica 196(1):117–127

    Article  CAS  Google Scholar 

  • Win KT, Oo AZ (2015) Genotypic difference in salinity tolerance during early vegetative growth of cowpea (Vigna unguiculata L. Walp.) from Myanmar. Biocatal Agric Biotechnol 4:449–455

    Google Scholar 

  • Xiong H, Shi A, Mou B, Qin J, Motes D, Lu W, Ma J (2016) Genetic diversity and population structure of cowpea (Vigna unguiculata L. Walp). PLoS One 11(8):e0160941

    Article  PubMed  PubMed Central  Google Scholar 

  • Xu Y (2010) Molecular plant breeding. CABI, pp 752

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48(2):391–407

    Article  Google Scholar 

  • Xu Y, Li S, Li L, Zhang X, Xu H, An D (2013) Mapping QTLs for salt tolerance with additive, epistatic and QTL × treatment interaction effects at seedling stage in wheat. Plant Breed 132(3):276–283

    Article  CAS  Google Scholar 

  • Yeo AR, Flowers TJ (1983) Varietal differences in the toxicity of sodium ions in rice leaves. Physiol Planta 59(2):189–195

    Article  CAS  Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38(2):203

    Article  CAS  PubMed  Google Scholar 

  • Zhang HJ, Dong HZ, Li WJ, Zhang DM (2012) Effects of soil salinity and plant density on yield and leaf senescence of field-grown cotton. J Agron Crop Sci 198(1):27–37

    Article  CAS  Google Scholar 

  • Zhang WJ, Niu BuSH, Li M, Feng JY, Zhang J, Yang SX, Odinga MM, Wei SP, Liu XF, Zhang YM (2014) Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage. PLoS One 9(1):e84750

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ainong Shi.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Communicated by Peter Langridge.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 75 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ravelombola, W., Shi, A., Weng, Y. et al. Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages. Theor Appl Genet 131, 79–91 (2018). https://doi.org/10.1007/s00122-017-2987-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-017-2987-0

Navigation