Narrow-leafed lupin (Lupinus angustifolius L.) is used as grain legumes, fodder for livestock and green manure in the world and has a great potential to be developed as a new crop in China. In this study, we assessed the genetic diversity among a set of 109 newly introduced accessions of narrow-leafed lupin using 76 genomic SSR markers. Data analysis suggested that the average gene diversity index and average polymorphism information content (PIC) were 0.4758 and 0.4328, respectively. The mean allele number per loci (Na) was 6.3816. The population structure analysis identified two subgroups based on delta K (ΔK) values. This result is in accordance with that of a PCA. The AMOVA analysis showed that most of molecular variance were within population. These results will be useful to guide the genetic improvement of the narrow-leafed lupin crop in China.
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Yang H, Tao Y, Zheng Z, Zhang Q, Zhou G, Sweetingham MW, Howieson JG, Li C (2013) Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L. PLoS ONE 8(5):e64799
Kroc M, Koczyk G, Święcicki W, Kilian A, Nelson MN (2014) New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin). Theor Appl Genet 127(5):1237–1249
French RJ, Buirchell BJ (2005) Lupin: the largest grain legume crop in Western Australia, its adaptation and improvement through plant breeding. Aust J Agric Res 56(11):1169–1180
Hane JK, Ming Y, Kamphuis LG, Nelson MN, Garg G et al (2017) A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution. Plant Biotechnol J 15(3):318–330
Drummond CS, Eastwood RJ, Miotto ST, Hughes CE (2012) Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling. Syst Biol 61(3):443–460
Lee YP, Mori TA, Sipsas S, Barden A, Puddey IB et al (2006) Lupin-enriched bread increases satiety and reduces energy intake acutely. Am J Clin Nutr 84(5):975–980
Gladstones JS, Atkins CA, Hamblin J (1998) Lupins as crop plants. Field Crop Abstr 23:123–148
Lambers H, Clements JC, Nelson MN (2013) How a phosphorus-acquisition strategy based on carboxylate exudation powers the success and agronomic potential of lupines (Lupinus, Fabaceae). Am J Bot 100(2):263–288
Aïnouche A, Bayer RJ, Misset MT (2004) Molecular phylogeny, diversification and character evolution in Lupinus (Fabaceae) with special attention to Mediterranean and African lupines. Plant Syst Evol 246(3–4):211–222
Plitmann U (1981) Evolutionary history of the Old World Lupines. Taxon 30(2):430–437
Kłos P, Poreba E, Springer E, Lampart-Szczapa E, Goździcka Józefiak A (2010) Identification of a specific IgE-binding protein from narrow-leafed lupin (L. Angustifolius) seeds. J Food Sci 75(1):H39–H43
Berger JD, Buirchell BJ, Luckett DJ, Palta JA, Ludwig C et al (2012) How has narrow-leafed lupin changed in its 1st 40 years as an industrial, broad-acre crop? A G × E-based characterization of yield-related traits in Australian cultivars. Field Crops Res 126:152–164
Mousavi-Derazmahalleh M, Bayer PE, Nevado B, Hurgobin B, Filatov D, Kilian A, Kamphuis LG, Singh KB, Berger JD, Hane JK, Edwards D, Erskine W, Nelson MN (2018) Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin. Theor Appl Genet 131(4):887–901
Sońta M, Batorska M, Więcek J, Rekiel A (2020) Performance results and concentrations of biochemical indices and mineral elements in blood serum of fatteners fed diets containing mixtures of raw seeds of pea (Pisum sativum L.) or blue lupin (Lupinus angustifolius L.). Animals 10(5):858
Abraham EM, Ganopoulos I, Madesis P et al (2019) The use of lupin as a source of protein in animal feeding: genomic tools and breeding approaches. Int J Mol Sci 20(4):851
Ruiz-López MA, Barrientos-Ramírez L, García-López PM et al (2019) Nutritional and bioactive compounds in mexican lupin beans species: a mini-review. Nutrients 11(8):1785
Clements J, Galek R, Kozak B, Michalczyk DJ, Sawicka-Sienkiewicz E, Stawiński S, Zalewski D (2014) Diversity of selected Lupinus angustifolius L. genotypes at the phenotypic and DNA Level with respect to microscopic seed coat structure and thickness. PLoS ONE 9(8):e102874
Foley RC, Gao LL, Spriggs A, Soo LY, Goggin DE, Smith PM, Atkins CA, Singh KB (2011) Identification and characterisation of seed storage protein transcripts from Lupinus angustifolius. BMC Plant Biol 11:59
Berger JD, Buirchell BJ, Luckett DJ, Nelson MN (2012) Domestication bottlenecks limit genetic diversity and constrain adaptation in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 124(4):637–652
Chen Y, Shan F, Nelson MN, Siddique KH, Rengel Z (2016) Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius. J Exp Bot 67(12):3683–3697
Moore SS, Sargeant LL, King TJ, Mattick JS, Georges M, Hetzel DJ (1991) The conservation of dinucleotide microsatellites among mammalian genomes allows the use of heterologous PCR primer pairs in closely related species. Genomics 10(3):654–660
Zheng X, Cheng T, Yang L et al (2019) Genetic diversity and DNA fingerprints of three important aquatic vegetables by EST-SSR markers. Sci Rep 9(1):14074
Kumar M, Choi JY, Kumari N, Pareek A, Kim SR (2015) Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica. Front Plant Sci 6:688
Liu Q, Song Y, Liu L, Zhang M, Sun J, Zhang S, Wu J (2015) Genetic diversity and population structure of pear (Pyrus spp.) collections revealed by a set of core genome-wide SSR markers. Tree Genet Genom 11(6):128
Chen C, Xiao L, Li X, Du D (2018) Comparative mapping combined With map-based cloning of the Brassica juncea genome reveals a candidate gene for multilocular rapeseed. Front Plant Sci 9:1744
Fu XQ, Yang FX, Lu XK, Wang XG, Yang BX, Liu FJ, Liu Y, Peng J (2017) Molecular identification of variety purity in a cotton hybrid with unknown parentage using DNA-SSR markers. Genet Mol Res. https://doi.org/10.4238/gmr16039799
Kaldate R, Rana M, Sharma V, Hirakawa H, Kumar R et al (2017) Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis. Mol Breed 37(8):103
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: Version II. Plant Mol Biol Rep 1:19–21
Suzana M, Rahimah AR, Maizura I, Singh R (2015) A simple and rapid protocol for isolation of genomic DNA from oil palm leaf tissue. J Oil Palm Res 27(3):282–287
Yang H, Jian J, Li X, Renshaw D, Clements J, Sweetingham MW, Tan C, Li C (2015) Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius ). BMC Genom 16(1):660
Jarman SN (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics 20(10):1644–1645
Pauthenier C, Faulon JL (2014) PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling. Nucleic Acids Res 42(W1):W205–W209
da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FI, Costa de Oliveira A (2008) SSR locator: tool for simple sequence repeat discovery integrated with primer design and pcr simulation. Int J Plant Genom. https://doi.org/10.1155/2008/412696
Marjanović D, Bakal N, Kovacević L, Hodzić M, Haverić A, Haverić S, Ibrulj S, Durmić A (2006) Optimisation of forensic genetics procedures used in disputed paternity testing: adjustment of the PCR reaction volume. Bosn J Basic Med Sci 6(2):76–81
Wittig I, Schägger H (2005) Advantages and limitations of clear-native PAGE. Proteomics 5(17):4338–4346
Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129
Razavi FE, Zarban A, Hajipoor F, Naseri M (2017) The allele frequency of CYP2C9 and VKORC1 in the Southern Khorasan population. Res Pharm Sci 12(3):211–221
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
Niu S, Song Q, Koiwa H et al (2019) Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing. BMC Plant Biol 19(1):328
Gronau I, Moran S (2007) Optimal implementations of UPGMA and other common clustering algorithms. Inf Process Lett 104(6):205–210
Kumar S, Tamura K, Nei M (1994) MEGA: molecular evolutionary genetics analysis software for microcomputers. Comput Appl Biosci 10(2):189–191
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evolut 30(12):2725–2729
de Jager D, Swarts P, Harper C, Bloomer P (2017) Friends and family: a software program for identification of unrelated individuals from molecular marker data. Mol Ecol Resour 17(6):e225–e233
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
Nei M (1983) Genetic Polymorphism and the role of mutation in evolution. In: Nei M, Kohen RK (eds) Evolution of gene and proteins. Sinaver Associates, Sunderlans, pp 165–190
We acknowledge the financial support from National Infrastructure for Crop Germplasm Resources project from the Ministry of Science and Technology of China (NICGR2018), the international cooperation projects (2016-X16 and 2017YFE0105100), and also supported by Agricultural Science and Technology Innovation Program (ASTIP) in CAAS.
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Ji, Y., Liu, R., Hu, J. et al. Genetic diversity analysis for narrow-leafed lupin (Lupinus angustifolius L.) by SSR markers. Mol Biol Rep (2020). https://doi.org/10.1007/s11033-020-05596-z
- Simple sequence repeats
- Genetic relationships
- Molecular variance