Abstract
Pigeon pea Cajanus cajan (L.) Millsp. and cowpea Vigna unguiculata (L.) Walp. are two of the important seed legumes of Africa and are relatively more drought-tolerant than many other legumes. Nigeria is the largest producer of cowpea in Africa, while pigeon pea is yet to be commercially cultivated in Nigeria. The genomic information on cowpea is known but not for pigeon pea, and this has hindered the development of superior varieties. Most importantly, although various genetic markers have been used in both legumes to elucidate their genetic diversity, simple sequence repeats and single nucleotide polymorphism markers are preferred for genetic and plant breeding applications. We investigated the genetic diversity in the two legumes and traced the evolutionary relationship of the large subunit of the ribulose-bisphosphate carboxylase/oxygenase (RuBisCo) (rbcl) gene in selected organisms using cowpea and pigeon pea rbcl gene sequences as queries. The genetic diversity study analysed 25 pigeon pea and 22 cowpea accessions using rbcl gene region primers. A total of 432 polymorphic sites were detected from the obtained legume DNA sequences. The phylogeny of the two legumes was a location/origin of adoption to the germplasm. Analysis of molecular variance of the rbcl gene showed that among-population variance was 0% and within-population variance was 100%, suggesting a wide genetic diversity among pigeon pea and cowpea populations. This study provided a basis for the understanding of the evolutionary relatedness and the genetic diversity of cowpea and pigeon pea accessions. To substantiate the diversity of these legumes, wider regional sampling of seeds in Nigeria should be implemented.
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References
Abbo S, Berger J, Turner NC (2003) Viewpoint: evolution of cultivated chickpea: four bottlenecks limit diversity andconstrain adaptation. Funct Plant Biol 30(10):1081. https://doi.org/10.1071/FP03084
Aryamanesh N, Nelson MN, Yan G, Clarke HJ, Siddique KHM (2010) Mapping a major gene for growth habit and QTLs for ascochyta blight resistance and flowering time in a population between chickpea and Cicer reticulatum. Euphytica 173(3):307–319. https://doi.org/10.1007/s10681-009-0086-2
Bohra A, Jha R, Pandey G, Patil PG, Saxena RK, Singh IPSD et al (2017) New hypervariable SSR markers for diversity analysis, hybrid purity testing and trait mapping in pigeonpea [Cajanus Cajan (L.) Millspaugh]. Front Res Found 8:377. https://doi.org/10.3389/fpls.2017.00377
Chetia P, Phukan BC, Tamang D (2016) RbcL gene based molecular phylogenetic studies of certain pteridophytes of Assam. Res Rev J Bioinform 3(1):18–21
Close TJ, Bhat PR, Lonardi S, Yonghui W, Rostoks N, Ramsay L, Druka A et al (2009) Development and implementation of high-throughput SNP genotyping in Barley. BMC Genom 10(1):582. https://doi.org/10.1186/1471-2164-10-582
Cooper DH, Spillane C, Hodgkin T (2001) Broadening the genetic base of crop production. In: Broadening the genetic base of crop production. CABI Pub. in association with Food and Agriculture Organization of the United Nations and International Plant Genetic Resources Institute, New York. https://doi.org/10.1079/9780851994116.0000
Daniell H, Lin CS, Ming Y, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17(1):1–29. https://doi.org/10.1186/s13059-016-1004-2
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1(4):19–21
Deokar A, Sagi M, Taran B (2019) Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer Arietinum L.). Theor Appl Genet 132(6):1861–1872. https://doi.org/10.1007/s00122-019-03322-3
Dong W, Liu J, Jing Y, Wang L, Zhou S (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7:4. https://doi.org/10.1371/journal.pone.0035071
Duczek LJ, Sutherland KA, Reed SL, Bailey KL, Lafond GP (1999) Survival of leaf spot pathogens on crop residues of wheat and barley in Saskatchewan. Can J Plant Pathol 21:165–173. https://doi.org/10.1080/07060669909501208
Duminil J, Pemonge M-H, Petit RJ (2002) A set of 35 consensus primer pairs amplifying genes and introns of plant mitochondrial DNA. Mol Ecol Notes 2(4):428–430. https://doi.org/10.1046/j.1471-8286.2002.00263.x
Ghalmi N, Marie AE, Ae M, Jean-Marie Jacquemin AE, Sidi MO, Leila AE et al (2010) Morphological and molecular diversity within Algerian Cowpea (Vigna unguiculata (L.) Walp.) landraces. Genet Resour Crop Evol 57:371–386. https://doi.org/10.1007/s10722-009-9476-5
Hall BG (2013) Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol 30(5):1229–1235. https://doi.org/10.1093/molbev/mst012
Jha AB, Gali KK, Banniza S, Warkentin TD (2019) “Validation of SNP markers associated with ascochyta blight resistance in pea” Edited by Christian Willenborg. Can J Plant Sci 99(2):243–249. https://doi.org/10.1139/cjps-2018-0211
Kassa MT, You FM, Hiebert CW, Pozniak CJ, Fobert PR, Sharpe AG, Menzies JG et al (2017) Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16. BMC Plant Biol 17(1):45. https://doi.org/10.1186/s12870-017-0993-7
Kenicer G (2005) Legumes of the world. In: Lewis G, Schrire B, MacKinder B, Lock M (eds) Edinburgh journal of botany, vol 62. Cambridge University Press, Cambridge
Knauth LP, Kennedy MJ (2009) The late precambrian greening of the earth. Nature 460(7256):728–732. https://doi.org/10.1038/nature08213
Li J, Xiao J, Grandillo S, Jiang L, Wan Y, Deng Q, Yuan L, McCouch SR (2004) QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated asian (O. Sativa L.) and African (O. Glaberrima S.) rice. Genome 47(4):697–704. https://doi.org/10.1139/G04-029
Ludke WH, Schuster I, Silva FLD, Montecelli TDN, de Almeida B, Soares AB, Oliveira De, Volpato L (2019) SNP markers associated with soybean partial resistance to phytophthora sojae. Crop Breed Appl Biotechnol 19(1):31–39. https://doi.org/10.1590/1984-70332019v19n1a05
Mikolajczyk K, Dabert M, Karlowski WM, Spasibionek S, Nowakowska J, Cegielska-Taras T, Bartkowiak-Broda I (2010) Allele-specific SNP markers for the new low linolenic mutant genotype of winter oilseed rape. Plant Breed 129(5):502–507. https://doi.org/10.1111/j.1439-0523.2009.01730.x
Mondal K, Sunil SS, Kundu S (2013) A comparative computational study of the ‘rbcL’ gene in plants and in the three prokaryotic families-Archaea, cyanobacteria and proteobacteria. Indian J Biotechnol 12:58–66
Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S et al (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(43):18159–18164. https://doi.org/10.1073/pnas.0905886106
Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, Jüngling R et al (2010) Integration of novel SSR and gene-based SNP Marker Loci in the Chickpea genetic map and establishment of new anchor points with medicago truncatula genome. Theor Appl Genet 120(7):1415–1441. https://doi.org/10.1007/s00122-010-1265-1
Nei M, Kumar S (2002) Molecular evolution and phylogenetics-Masatoshi Nei, Sudhir Kumar. Oxford University Press, New York
Njung’e V, Deshpande S, Siambi M, Jones R, Silim S, De Villiers S (2016) SSR genetic diversity assessment of popular pigeonpea varieties in malawi reveals unique fingerprints. Electron J Biotechnol 21:65–71. https://doi.org/10.1016/j.ejbt.2016.02.004
Pasquet RS (2000) Allozyme diversity of cultivated cowpea (Vigna unguiculata (L.) Walp). Theor Appl Genet 101(1–2):211–219. https://doi.org/10.1007/s001220051471
Peakall R, Smouse PE (2012) GenALEx 6.5: genetic analysis in excel. population genetic software for teaching and research-an update. Bioinformatics 28(19):2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Penny D, Felsenstein J (2004) Inferring phylogenies. System Biol 53(4):669–670. https://doi.org/10.1080/10635150490468530
Prasanthi L, Geetha B, Ramya Jyothi BN, Raja Reddy K (2012) Evaluation of genetic diversity in cowpea, (Vigna unguiculata (L.) Walp) gentotypes using random amplified polymorphic DNA (RAPD). Curr Biotica 6(1):22–31
Raju NL, Gnanesh BN, Lekha P, Jayashree B, Pande S, Hiremath PJ, Byregowda M, Singh NK, Varshney RK (2010) The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus Cajan L.). BMC Plant Biol. https://doi.org/10.1186/1471-2229-10-45
Rashid J, Tamanna FM, Hossain MAR, Samsul Alam Md (2012) Genetic variation in endangered butter catfish, Ompok Bimaculatus (Bloch) populations revealed by random amplified polymorphic DNA (RAPD) fingerprinting. Int J Biosci 2(9):85–93
Rauf S, Shahzad M, Naveed A, Munir H (2010) Response of wheat species to the contrasting saline regimes. Pak J Bot 42(5):3039–3045
Sarhan S, Hamed F, Al-Youssef W (2016) The RbcL gene sequence variations among and within prunus species. J Agric Sci Technol 18:1105–1115
Sattin SR, Cleveland CC, Hood E, Reed SC, King AJ, Schmidt SK, Robeson MS, Ascarrunz N, Nemergut DR (2010) Functional shifts in unvegetated, perhumid, recently deglaciated soils do not correlate with shifts in soil bacterial community composition. J Microbiol 47:673–681
Singh S, Singh KN, Kant R, Mehfooz S, Dutta S (2008) Assessment of genetic diversity among pigeonpea genotypes using SSR markers. Indian J Genet 68(3):255–260
Singh A, Negi G, Mohanty A (2016) In silico analysis of sequence variation in rbcl gene to assess phylogenetic relations in setaria species. J Exp Bot 16–18
Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR (2017) Interspecific plastome recombination reflects ancient reticulate evolution in picea (Pinaceae). Mol Biol Evol 34(7):1689–1701. https://doi.org/10.1093/molbev/msx111
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729. https://doi.org/10.1093/molbev/mst197
Teyioué BJB, Souleymane O, Tignegre JB, Huynh BL, Kusi F, Leandre PS, Timothy JC et al (2018) Single nucleotide polymorphism (SNP)-based genetic diversity in a set of Burkina Faso Cowpea germplasm. Afr J Agric Res 13(19):978–987. https://doi.org/10.5897/ajar2018.13121
Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Varma Penmetsa R, Thirunavukkarasu N et al (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1291 marker loci for chickpea (Cicer arietinum L.). PLoS ONE 6:11. https://doi.org/10.1371/journal.pone.0027275
Tomkowiak A, Bocianowski J, Wolko Ł, Adamczyk J, Mikołajczyk S, Kowalczewski PŁ (2019) Identification of markers associated with yield traits and morphological features in maize (Zea mays L.). Plants 8:9. https://doi.org/10.3390/plants8090330
Udensi OU, Okon EA, Ikpeme EV, Onung OO, Ogban FU (2016) Assessing the genetic diversity in cowpea (Vigna unguiculata (L.) Walp) accessions obtained from IITA, Nigeria using random amplified polymorphic DNA (RAPD). Int J Plant Breed Genet 10(1):12–22. https://doi.org/10.3923/ijpbg.2016.12.22
Udensi OU, Edu N, Ikpeme E, Onung O, Emeagi L, Nwanze B, Ejiyere E (2017) Genotyping of pigeon pea [Cajanus Cajan (L.) Millsp.] accessions obtained from international institute of tropical agriculture (IITA) germplasm using random amplified polymorphic DNA. J Exp Agric Int 17(3):1–12. https://doi.org/10.9734/jeai/2017/26971
Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR (2009) Orphan legume crops enter the genomics era! Curr Opin Plant Biol. https://doi.org/10.1016/j.pbi.2008.12.004
Varshney RK, Thundi M, May GD, Jackson SA (2010) Legume genomics and breeding. Plant Breed Rev 33:257–304. https://doi.org/10.1002/9780470535486.ch6
Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA et al (2012) Draft genome sequence of pigeonpea (Cajanus Cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30(1):83–89. https://doi.org/10.1038/nbt.2022
Voss I, Sunil B, Scheibe R, Raghavendra AS (2013) Emerging concept for the role of photorespiration as an important part of abiotic stress response. Plant Biol. https://doi.org/10.1111/j.1438-8677.2012.00710.x
Xiong H, Shi A, Mou B, Qin J, Motes D, Weiguo L, Ma J, Weng Y, Yang W, Dianxing W (2016) “Genetic diversity and population structure of Cowpea (Vigna unguiculata (L.) Walp.)” Edited by Swarup Kumar Parida. PLoS ONE 11(8):e0160941. https://doi.org/10.1371/journal.pone.0160941
Yahara T, Javadi F, Onoda Y, Paganucci L, de Queiroz DP, Faith DE, Prado MA et al (2013) Global legume diversity assessment: concepts, key indicators, and strategies. Taxon 62(2):249–266. https://doi.org/10.12705/622.12
Yu QB, Jiang Y, Chong K, Yang ZN (2009) AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accd rna editing and early chloroplast biogenesis in Arabidopsis Thaliana. Plant J 59(6):1011–1023. https://doi.org/10.1111/j.1365-313X.2009.03930.x
Zavinon F, Adoukonou-Sagbadja H, Keilwagen J, Lehnert H, Ordon F, Perovic D (2020) Genetic diversity and population structure in beninese pigeon pea [Cajanus Cajan (L.) Millsp.] landraces collection revealed by SSR and genome wide SNP markers. Genet Resour Crop Evol 67(1):191–208. https://doi.org/10.1007/s10722-019-00864-9
Zhou T, Wang J, Jia Y, Li W, Fusheng X, Wang X (2018) Comparative chloroplast genome analyses of species in gentiana section cruciata (Gentianaceae) and the development of authentication markers. Int J Mol Sci 19:7. https://doi.org/10.3390/ijms19071962
Acknowledgements
The authors thank the Department of Genetics and Biotechnology, Plant Genetics and Genomics Unit, University of Calabar, Nigeria for financial assistance. We acknowledge the Genetic Resource Unit (GRU) of International Institute Tropical Agriculture (IITA), Ibadan, Nigeria and International Crops Research Institute for the Semi-Arid Tropical (ICRISAT) Niger, for providing the pigeon pea and cowpea accessions used in this research.
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Udensi, U.O., Emeagi, I.L., Daniel, V.E. et al. Insight to the genetic diversity of pigeon pea Cajanus cajan (L.) Millsp. and cowpea Vigna unguiculata (L.) Walp. germplasm cultivated in Nigeria based on rbcl gene region. Genet Resour Crop Evol 69, 2231–2248 (2022). https://doi.org/10.1007/s10722-022-01373-y
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DOI: https://doi.org/10.1007/s10722-022-01373-y