First Records on Genetic Diversity and Population Structure of Algerian Peanut (Arachis hypogaea) Using Microsatellite Markers
Tóm tắt
Peanut (Arachis hypogaea L) is one of the wide cultivated plants with a narrow genetic base, hence the interest in prospecting, rescuing, and characterizing germplasm of this species is continuously carried out. In this work, eleven microsatellite markers were used to assess the genetic diversity and population structure of 68 Algerian peanut accessions originated from four geographic regions in the north and south of Algeria. A total of 83 alleles were amplified with a mean number of 7.545 alleles per locus and polymorphic information content (PIC) ranged from 0.625 to 0.874. The observed and expected heterozygosity varied from 0.31 to 1.00 and from 0.61 to 0.84 with a mean of 0.704 and 0.732, respectively. Genetic structure analysis showed a strong population at K = 2, separating accessions according to their subspecies affiliation (hypogeae ssp. and fastigiata ssp.). It was also able to quantify the genetic correlations between genotypes using principal component analysis (PCA) and the method of groups of unweighted pairings with arithmetic means (UPGMA). Analysis of molecular variance (AMOVA) revealed high genetic variation within individuals (90.7%) and low genetic differentiation between subspecies (10.3%) and among populations (8.9%) from different geographical origin. Genetic diversity analysis in this study provides useful information for the exploration and utilization of these peanut cultivars.
Tài liệu tham khảo
Barkley NA, Dean RE, Pittman RN, Wang ML, Holbrook CC, Pederson GA (2007) Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing. Genet Res 89:93–106. https://doi.org/10.1017/S0016672307008695
Benbouza H, Jacquemin JM, Baudoin JP, Mergeai G (2006) Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol Agron Soc Environ 10:77–81
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkagemap in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Boudchicha RH, Hormaza JI, Benbouza H (2018) Diversity analysis and genetic relationships among local Algerian fig cultivars (Ficus carica l.) using SSR markers. S Afr J Bot 116:207–215. https://doi.org/10.1016/j.sajb.2018.03.015
Clark LV, Schreier AD (2017) Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables. Mol Ecol Resour 17:1090–1103. https://doi.org/10.1111/1755-0998.12639
Clark LV, Jasieniuk M (2011) POLYSAT : an R package for polyploid microsatellite analysis. Mol Ecol Resour 11:562–566. https://doi.org/10.1111/j.1755-0998.2011.02985.x
Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15
Da E, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
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. https://doi.org/10.1111/j.1365-294X.2005.02553.x
FAO (2018) Food and Agricultural Organization of the United Nations. FAO Statistical database. http://faostat.fao.org. Accessed 29 June 2020
Ferguson ME, Burow M, Schulze SR, Bramel P, Paterson AH, Kresovich S, and Mitchell S (2005) Sequence-tagged Microsatellites reveal Polymorphism in Peanut (A. hypogaea L.): Microsatellite identification and characterization. Unpublished. Database. https://www.ncbi.nlm.nih.gov/nuccore/BZ999636
Gimenes MA, Hoshino AA, Barbosa AV, Palmieri DA, Lopes CR (2007) Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea). BMC Plant Biol 7(1): 1–13.https://doi.org/10.1186/1471-2229-7-9
Guo HY, Wang ZL, Huang Z, Chen Z, Yang HB, Kang XY (2019) Genetic diversity and population structure of alnuscremastogyne as revealed by microsatellite markers. Forests 10:278. https://doi.org/10.3390/f10030278
He G, Meng R, Newman M, Gao G, Pittman RN, Prakash CS (2003) Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol 3(1): 1–6. https://doi.org/10.1186/1471-2229-3-3
Henderson ST, Petes TD (1992) Instability of simple sequence DNA in Saccharomyces cerevisiae. Mol Cell Biol 12:2749–2757. https://doi.org/10.1128/MCB.12.6.2749
Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD, Kresovich S (1999) Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Sci 39(4):1243–1247. https://doi.org/10.2135/cropsci1999.0011183X003900040047x
Hong Y, Chen X, Liang X, Liu H, Zhou G, Li S, Wen S, Holbrook CC, Guo, B (2010) A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. BMC Plant Biol 10:17. https://doi.org/10.1186/1471-2229-10-17
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. https://doi.org/10.1093/bioinformatics/btm233
Krapovickas A, Gregory WC (1994) TAXONOMIA DEL GENERO ARACHIS (LEGUMINOSAE). Bonplandia, pp 1–186
Krapovickas A, Gregory WC, Williams DE, Simpson CE (2007) Taxonomy of the genus Arachis (Leguminosae). Bonplandia 16:7–205
Li Y, Chen CY, Knapp SJ, Culbreath AK, Holbrook CC, Guo B (2011) Characterization of simple sequence repeat (SSR) markers and genetic relationships within cultivated peanut (Arachis hypogaea L.). Peanut Sci 38(1): 1–10. https://doi.org/10.3146/PS10-10.1
Mace ES, Yuejin W, Boshou L, Upadhyaya HD, Chandra S, Crouch JH (2007) Simple sequence repeat (SSR)-based diversity analysis of groundnut (Arachis hypogaea L.) germplasm resistant to bacterial wilt. Plant Genet Resour: Characterization and Utilization 5:27–36. https://doi.org/10.1017/S1479262107390916
Meirmans PG (2020) genodive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids. Mol Ecol Resour 20:1126–1131. https://doi.org/10.1111/1755-0998.13145
Moretzsohn MC, Leoi L, Proite K, Guimaraes PM, Leal-Bertioli SCM, Gimenes MA et al (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111(6): 1060–1071. https://doi.org/10.1007/2Fs00122-005-0028-x
Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182. https://doi.org/10.1046/j.1365-313X.1993.t01-9-00999.x
Nei M (1987) Molecular evolutionary genetics. Annu Rev Genet 30:371–403. https://doi.org/10.1146/annurev.genet.30.1.371
Pandey MK, Gautami B, Jayakumar T, Sriswathi M, Upadhyaya HD, Chennabyregowda MV, Radhakrishnan T, Bertioli DJ, Knapp SJ, Cook DR, Varshney RK (2012) Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea). Plant Breed 131:139–147. https://doi.org/10.1111/j.1439-0523.2011.01911.x
Pasupuleti J, Nigam SN (2013) Phenotyping for groundnut (Arachis hypogaea L.) improvement. In: PasupuletiJand Nigam SN (ed) Phenotyping for Plant Breeding. Springer, New York, pp 129–167. https://doi.org/10.1007/978-1-4614-8320-5_5
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959. https://doi.org/10.1093/genetics/155.2.945
Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV (1996) Generating and using DNA markers in plants. In: Birren B, Lai E (ed) Nonmammalian genomic analysis. Academic Press, pp 75–134
Ramasamy RK, Ramasamy S, Bindroo BB, Naik VG (2014) STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. Springer plus 3:431. https://doi.org/10.1186/2193-1801-3-431
Ren X, Jiang H, Yan Z, Chen Y, Zhou X, Huang L, Lei Y, Huang J, Yan L, Qi Y, Wei W, Liao B (2014) Genetic diversity and population structure of the major peanut (Arachis hypogaea L.) cultivars grown in China by SSR markers. PLoS One 9: e88091.https://doi.org/10.1371/journal.pone.0088091
Rohlf FJ (1997) NTSYS-pc. Numerical taxonomy and multivariance analysis system version 2.02 e. Exeter Software. New York. USA
Schlötterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20:211–215. https://doi.org/10.1093/nar/20.2.211
Seijo G, Lavia GI, Fernández A, Krapovickas A, Ducasse DA, Bertioli DJ, Moscone EA (2007) Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH. Am J Bot 94:1963–1971. https://doi.org/10.3732/ajb.94.12.1963
Seijo JG, Lavia GI, Fernández A, Krapovickas A, Ducasse D, Moscone EA (2004) Physical mapping of the 5S and 18S–25S rRNA genes by FISH as evidence that Arachis duranensis and A. ipaensis are the wild diploid progenitors of A. hypogaea (Leguminosae). Am J Bot 91:1294–1303. https://doi.org/10.3732/ajb.91.9.1294
Tang Wang C, Dao Yang X, Xu Chen D, Lin YuS, Zhen Liu G, Yi Tang Y, Zhi XuJ (2007) Isolation of simple sequence repeats from groundnut. Electron J Biotechnol 10(3):473–480. https://doi.org/10.2225/vol10-issue3-fulltext-10
Valls JF, Simpson CE (2005) New species of Arachis (leguminosae) from Brazil, Paraguay, and Bolivia. Bonplandia 14:35–63
Van De Peer Y, De Wachter R (1994) Treecon for windows: a software package for the construction and drawing of evolutionary trees for the microsoft windows environment. Bioinformatics 10:569–570. https://doi.org/10.1093/bioinformatics/10.5.569
Varshney RK, Mahendar T, Aruna R, Nigam SN, Neelima K, Vadez V, Hoisington DA (2009) High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers. Plant Breeding 128:486–494. https://doi.org/10.1111/j.1439-0523.2009.01638.x
Wang H, Khera P, Huang B, Yuan M, Katam R, Zhuang W, Harris-Shultz K, M. Moore K, K. Culbreath A, Zhang X, K. Varshney R, Xie L, Guo B (2016) Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers. J Integr Plant Biol 58:452–465. https://doi.org/10.1111/jipb.12380
Wang ML, Sukumaran S, Barkley NA, Chen Z, Chen CY, Guo B, Pittman RN, Stalker HT, Holbrook CC, Pederson GA, Yu J (2011) Population structure and marker-trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection. Theor Appl Genet 123:1307–1317. https://doi.org/10.1007/2Fs00122-011-1668-7