922
Views
0
CrossRef citations to date
0
Altmetric
Articles

Analysis of the genetic diversity of grain legume germplasm resources in China and the development of universal SSR primers

, , , , , , , , , , , , , & show all
Pages 1706-1721 | Received 16 Jul 2021, Accepted 11 Nov 2021, Published online: 13 Jan 2022

References

  • Smýkal P, J CC, J AM, et al. Legume crops phylogeny and genetic diversity for science and breeding. Crit Rev Plant Sci. 2015;34(1–3):43–104.
  • Nacira M, Ailin I, Leo K, et al. Potential uses of wild germplasms of grain legumes for crop improvement. IJMS. 2017;18(2):328.
  • Foyer CH, Lam HM, Nguyen HT, et al. Neglecting legumes has compromised human health and sustainable food production. Nat Plants. 2016; 2:16112.
  • Rong L, Chen HF, Yang ZL, et al. Research status of soybean symbiosis nitrogen fixation. Oil Crop Science. 2020; 5:6–10.
  • Wang LX, Wang J, Cheng XZ. Adzuki bean (vigna angularis (willd.) ohwi & ohashi) breeding. In: Advances in plant breeding strategies: Legumes: Volume 7. Springer International Publishing: Cham, 2019. pp. 1–23.
  • Xu XZ, Akito K, Norihiko T, et al. The genetic diversity of the Vigna angularis complex in Asia. Genome. 2003; 46:647–658.
  • Jin WL, Wen ZX, Pu SJ, et al. Genetic diversity of adzuki bean germplasm resources based on RAPD markers. Zuo Wu Xue Bao. 2004; 30:686–691.
  • Noble TJ, Tao YF, Mace ES, et al. Characterization of linkage disequilibrium and population structure in a mungbean diversity panel. Front Plant Sci. 2017; 8:2102.
  • Bangar P, Chaudhury A, Umdale S, et al. Detection and characterization of polymorphic simple sequence repeats markers for the analysis of genetic diversity in indian mungbean [vigna radiata (L.) wilczek]. Ind J Gen Plnt Bree. 2017;78(1):111–117.
  • Kaur G, Joshi A, Jain D. SSR-marker assisted evaluation of genetic diversity in mung bean (Vigna radiata) genotypes. Braz Arch Biol Technol. 2018;61(0):e180613.
  • Gepts P. A Middle american and an andean common bean gene Pool. Springer Netherlands. 1988. 375–390.
  • Gepts P, Debouck DG. Origin, domestication, and evolution of the common bean (Phaseolus vulgaris L.). In: van Schoonhoven A, Voysest O., editors. Common beans: research for crop improvement. Commonwealth Agricultural Bureaux International, Wallingford, United Kingdom; 1991. p. 7–53.
  • Schmutz J, McClean PE, Mamidi S, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 2014; 46(7):707–713.
  • Gepts P, Osborn TC, Rashka K, et al. Phaseolin-protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris): evidence for multiple centers of domestication. Econ Bot. 1986;40(4):451–468.
  • Chen ML, Wu J, Wang LF, et al. Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation. Mol Breeding. 2014; 33(2):489–496.
  • Decroocq V, Favé MG, Hagen L, et al. Development and transferability of apricot and grape Est microsatellite markers across taxa. Theor Appl Genet. 2003; 106(5):912–922.
  • Varshney RK, Sigmund R, Börner A, et al. Interspecific transferability and comparative mapping of barley Est-SSR markers in wheat, rye and rice. Plant Sci. 2005; 168(1):195–202.
  • Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079.
  • Zhao D, Cheng XZ, Wang LX, et al. Construction of mungbean genetic linkage map. Acta Agron Sin. 2010; 36(6):932–939.
  • Xu RQ, Tomooka N, Vaughan DA, et al. The vigna angularis complex: Genetic variation and relationships revealed by RAPD analysis, and their implications for in situ conservation and domestication. Genet Resour Crop Evol. 2000;47(2):123–134.
  • Chen HL, Liu LP, Wang LX, et al. Development of SSR markers and assessment of genetic diversity of adzuki bean in the chinese germplasm collection. Mol Breeding. 2015;35(10):191.
  • Chen HL, Wang LX, Wang SL, et al. Transcriptome sequencing of mung bean (Vigna radiate L.) genes and the identification of Est-SSR markers. Plos One. 2015; 10(4):e0120273.
  • Gill-Langarica HR, Muruaga-Martínez JS, Vargas-Vázquez MLP, et al. Genetic diversity analysis of common beans based on molecular markers. Genet Mol Biol. 2011; 34(4):595–605.
  • Kang YJ, Satyawan D, Shim S, et al. Draft genome sequence of adzuki bean, Vigna angularis. Sci Rep. 2015; 5:8069.
  • Kang YJ, Kim SK, Kim MY, et al. Genome sequence of mungbean and insights into evolution within vigna species. Nat Commun. 2014; 5:5443.
  • Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, et al. Genome and transcriptome analysis of the mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol. 2016; 17(1):32.
  • Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25(16):2078–2079.
  • Untergasser A, Cutcutache I, Koressaar T, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.
  • Koressaar T, Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007; 23(10):1289–1291.
  • Page M, MacLean D, Schudoma C. Blastjs: a BLAST + wrapper for node.js. BMC Res Notes. 2016; 9(1):1–4.
  • Yeh FC, Yang RC, Boyle T. POPGENE, version 1.32. microsoft window-based Freeware for population genetic analysis. University of Alberta. Edmonton; 1999.
  • Raza A, Mehmood SS, Ashraf F, et al. Genetic diversity analysis of brassica species using PCR-based SSR markers. Gesunde Pflanzen. 2019; 71(1):1–7.
  • Zhang J, Waryani B, Zhou QH. Isolation and characterization of microsatellite loci from an ice fish, neosalanx tangkahkeii (osmeriformes, salangidae). PJZ. 2019; 51(5):1853.
  • Oduoye OT, Oluwasanya OA, Arikawe OO, et al. Genetic variation via SSR polymorphic information content and ecological distribution of nigerian sesame. African J Biotechnol. 2020; 19(4):165–170.
  • Yang W, Dan Y, Xin ZL. Genetic diversity of toona ciliata populations based on SSR markers. J Resour Ecol. 2020; 11(5):466–474.
  • Daghighi S, Alizadeh Z, Habibi H. Determination of chromosome number and genetic diversity using SSR and RAPD markers in ziziphus jujuba mill. Iran J Sci Technol Trans Sci. 2021;45(1):77–89.
  • Gu XZ, Cao YC, Zhang ZH, et al. Genetic diversity and population structure analysis of capsicum germplasm accessions. J Integr Agricult. 2019; 18(6):1312–1320.
  • Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2):945–959.
  • Gopalan P, Hao W, Blei DM, et al. Scaling probabilistic models of genetic variation to millions of humans. Nat Genet. 2016;48(12):1587–1590.
  • Dennis JRDR, Nico K, Tom VDS, et al. Dispersal limitation of the mangrove avicennia marina at its South african range limit in strong contrast to connectivity in its core east african region. Mar Ecol Prog Ser. 2016; 545:123–134.
  • Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005; 14(8):2611–2620.
  • Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007; 23(14):1801–1806.
  • Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–W259.
  • Scaramozzino N, Crance J, Jouan A, et al. Comparison of flavivirus universal primer pairs and development of a rapid, highly sensitive heminested reverse transcription-PCR assay for detection of flaviviruses targeted to a conserved region of the NS5 gene sequences. J Clin Microbiol. 2001; 39(5):1922–1927.
  • Elbrecht V, Leese F. Validation and development of COI metabarcoding primers for freshwater macroinvertebrate bioassessment. Front Environ Sci. 2017; 5:11.
  • Hu H, Jung K, Wang QH, et al. Development of a one-step RT-PCR assay for detection of pancoronaviruses (α-, β-, γ-, and δ-coronaviruses) using newly designed degenerate primers for porcine and avian ‘fecal samples. J Virol Methods. 2018; 256:116–122.
  • Ivanova NV, Zemlak TS, Hanner RH, et al. Universal primer cocktails for fish DNA barcoding. Food Chem. 2007; 7(4):544–548.
  • Meiyu F, Huosheng C, Cuihua C, et al. Detection of flaviviruses by reverse transcriptase-polymerase chain reaction with the universal primer set. Microbiol Immunol. 1997; 41(3):209–213.
  • Yang J, Vázquez L, Chen XD, et al. Development of chloroplast and nuclear DNA markers for chinese oaks (quercus subgenus quercus) and assessment of their utility as DNA barcodes. Front Plant Sci. 2017; 8:816.
  • Xue CB, Wang PY, Zhao J, et al. Development and validation of a universal primer pair for the simultaneous detection of eight animal species. Food Chem. 2017; 221:790–796.