Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin

Theoretical and Applied Genetics

Volumn 131, Issue 4, 2018, Pages 887-901

  Mousavi Derazmahalleh, Mahsa ^a   Bayer, Philipp E ^a   Nevado, Bruno ^b   Hurgobin, Bhavna ^c   Filatov, Dmitry ^b   Kilian, Andrzej ^d   Kamphuis, Lars G ^a,e   Singh, Karam B ^a,e   Berger, Jens D ^a,e   Hane, James K ^f   Edwards, David ^a   Erskine, William ^a   Nelson, Matthew N ^a,g  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d DArT P/L   (Australia)

^e CSIRO   (Australia)

^f CURTIN UNIVERSITY   (Australia)

^g ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CLIMATE MODELS; CROPS; PLANTS (BOTANY);

CLIMATIC ADAPTATION; EASTERN MEDITERRANEAN; GENETIC DIFFERENTIATION; GENOME-WIDE ASSOCIATION STUDIES; LINKAGE DISEQUILIBRIUM; LUPINUS ANGUSTIFOLIUS; MEDITERRANEAN REGION; SINGLE-NUCLEOTIDE POLYMORPHISM MARKERS;

CLIMATE CHANGE;

ADAPTATION; FLOWER; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION STUDY; GENETIC MARKER; GENETIC VARIATION; GENETICS; GENOTYPE; LUPIN; PHYLOGENY; PHYSIOLOGY; PLANT GENOME; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTHERN EUROPE;

ADAPTATION, BIOLOGICAL; FLOWERS; GENETIC ASSOCIATION STUDIES; GENETIC MARKERS; GENETIC VARIATION; GENETICS, POPULATION; GENOME, PLANT; GENOTYPE; LINKAGE DISEQUILIBRIUM; LUPINUS; MEDITERRANEAN REGION; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 85040663358     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-017-3045-7     Document Type: Article

References (60)

1. Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Tuberosa R, Valliyodan B, Varshney RK, Yano M (2015) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnol J 14:1095–1098
2. Awika J (2011) Major cereal grains production and use around the world. In: Advances in cereal science: implications to food processing and health promotion. ACS symposium series. American Chemical Society, Washington DC, pp 1–13
3. Barbero M, Loisel R, Quézel P (1992) Biogeography, ecology and history of Mediterranean Quercus ilex ecosystems. In: Romane F, Terradas J (eds) Quercus ilex L. ecosystems: function, dynamics and management. Springer Netherlands, Dordrecht, pp 19–34
4. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263–265
5. Berger J, Ludwig C (2014) Contrasting adaptive strategies to terminal drought-stress gradients in Mediterranean legumes: phenology, productivity, and water relations in wild and domesticated Lupinus luteus L. J Exp Bot 65(21):6219–6229
6. Berger J, Buirchell B, Luckett D, Nelson M (2012a) Domestication bottlenecks limit genetic diversity and constrain adaptation in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 124(4):637–652
7. Berger J, Buirchell B, Luckett D, Palta J, Ludwig C, Liu DL (2012b) How has narrow-leafed lupin changed in its 1st 40 years as an industrial, broad-acre crop? AG × E-based characterization of yield-related traits in Australian cultivars. Field Crops Res 126:152–164
8. Berger JD, Clements JC, Nelson MN, Kamphuis LG, Singh KB, Buirchell B (2013) The essential role of genetic resources in narrow-leafed lupin improvement. Crop Pasture Sci 64(4):361–373
9. Berger JD, Shrestha D, Ludwig C (2017) Reproductive strategies in Mediterranean legumes: trade- offs between phenology, seed Size and vigor within and between wild and domesticated Lupinus species collected along aridity gradients. Front Plant Sci 8:548
10. Caballero B, Finglas P, Toldrá F (2015) Encyclopedia of food and health, 1st edn. Academic Press, Oxford, UK
11. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6(2):80–92
12. Clements J, Cowling W (1994) Patterns of morphological diversity in relation to geographical origins of wild Lupinus angustifolius from the Aegean region. Genet Resour Crop Evol 41(2):109–122
13. Dai F, Nevo E, Wu D, Comadran J, Zhou M, Qiu L, Chen Z, Beiles A, Chen G, Zhang G (2012) Tibet is one of the centers of domestication of cultivated barley. Proc Natl Acad Sci 109(42):16969–16973
14. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL (1999) Alignment of whole genomes. Nucleic Acids Res 27(11):2369–2376
15. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12(1):13–15
16. 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
17. FAO (2014) FAOSTAT database collections. Food and agriculture organization of the United Nations. http://faostat.fao.org. Accessed 03 Nov 2016
18. Felsenstein J (1989) PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164–166
19. Foyer CH, Lam H-M, Nguyen HT, Siddique KH, Varshney RK, Colmer TD, Cowling W, Bramley H, Mori TA, Hodgson JM, Cooper JW, Miller AJ, Kunert K, Vorster J, Cullis C, Ozga JA, Wahlqvist ML, Liang Y, Shou H, Shi K, Yu J, Fodor N, Kaiser BN, Wong F-L, Valliyodan B, Considine MJ (2016) Neglecting legumes has compromised human health and sustainable food production. Nat Plants 2:16112
20. Franks SJ, Sim S, Weis AE (2007) Rapid evolution of flowering time by an annual plant in response to a climate fluctuation. Proc Natl Acad Sci 104(4):1278–1282
21. Friesen ML, Cordeiro MA, Penmetsa RV, Badri M, Huguet T, Aouani ME, Cook DR, Nuzhdin SV (2010) Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation. Plant J 63(4):623–635
22. Gepts P (2010) Crop domestication as a long-term selection experiment. Plant Breed Rev 24(Part 2):1–44
23. Gladstones J (1970) Lupins as crop plants. Field Crop Abstr 23(2):123–148
24. Gladstones J (1998) Distribution, origin, taxonomy, history and importance. In: Gladstones JS, Atkins C, Hamblin J (eds) Lupins as crop plants: biology, production and utilization. Cambridge University Press, Cambridge, UK, pp 1–40
25. Gladstones JS, Crosbie G (1979) Lupin wild types introduced into Western Australia to 1973. Collection site data, preliminary ratings of field characteristics and disease reactions, and measurements of seed protein and oil contents. Technical Bulletin-Western Australian Department of Agriculture (Australia)
26. Gómez A, Lunt DH (2007) Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. In: Weiss S, Ferrand N (eds) Phylogeography of southern european refugia: evolutionary perspectives on the origins and conservation of European biodiversity. Springer Netherlands, Dordrecht, pp 155–188
27. Gomiero T (2016) Soil degradation, land scarcity and food security: reviewing a complex challenge. Sustainability 8(3):281
28. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5(10):e1000695
29. Hane JK, Ming Y, Kamphuis LG, Nelson MN, Garg G, Atkins CA, Bayer PE, Bravo A, Bringans S, Cannon S (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
30. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25(15):1965–1978
31. Hoffmann AA, Sgro CM (2011) Climate change and evolutionary adaptation. Nature 470(7335):479–485
32. Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 888:67–89
33. 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
34. Kurlovich BS, Heinanen J (2002) Biological features. In: Kurlovich BS (ed) Lupins (geography, classification, genetic resources and breeding). OY International North Express, St. Petersburg, p 468
35. 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
36. Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE (2015) Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv 1(6):e1400218
37. Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28(18):2397–2399
38. Maxted N, Kell S, Ford-Lloyd B, Dulloo E, Toledo Á (2012) Toward the systematic conservation of global crop wild relative diversity. Crop Sci 52(2):774–785
39. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303
40. Nelson MN, Książkiewicz M, Rychel S, Besharat N, Taylor CM, Wyrwa K, Jost R, Erskine W, Cowling WA, Berger JD, Berger J, Batley J, Weller J, Naganowska B, Wolko B (2017) The loss of vernalization requirement in narrow-leafed lupin is associated with a deletion in the promoter and de-repressed expression of a Flowering Locus T (FT) homologue. New Phytol 213(1):220–232
41. Nevado B, Atchison GW, Hughes CE, Filatov DA (2016) Widespread adaptive evolution during repeated evolutionary radiations in New World lupins. Nat Commun. https://doi.org/10.1038/ncomms12384
42. Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MG, Beiko RG (2013) GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One 8(7):e69885
43. Parmesan C, Yohe G (2003) A globally coherent fingerprint of climate change impacts across natural systems. Nature 421(6918):37–42
44. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904–909
45. Pulido F, Berthold P (2010) Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population. Proc Natl Acad Sci 107(16):7341–7346
46. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575
47. R Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
48. Raj A, Stephens M, Pritchard JK (2014) fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197(2):573–589
49. Roberts N, Moreno A, Valero-Garcés BL, Corella JP, Jones M, Allcock S, Woodbridge J, Morellón M, Luterbacher J, Xoplaki E (2012) Palaeolimnological evidence for an east–west climate see-saw in the Mediterranean since AD 900. Glob Planet Change 84:23–34
50. Sansaloni C, Petroli C, Jaccoud D, Carling J, Detering F, Grattapaglia D, Kilian A (2011) Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. In: BMC proceedings, 2011, vol 5, Supplementary 7. BioMed Central, p P54
51. Seymour M, Kirkegaard JA, Peoples MB, White PF, French RJ (2012) Break-crop benefits to wheat in Western Australia—insights from over three decades of research. Crop Pasture Sci 63(1):1–16
52. Stapley J, Reger J, Feulner PG, Smadja C, Galindo J, Ekblom R, Bennison C, Ball AD, Beckerman AP, Slate J (2010) Adaptation genomics: the next generation. Trends Ecol Evol 25(12):705–712
53. Thompson JD (2005) Plant evolution in the Mediterranean, 1st edn. Oxford University Press, Oxford, UK
54. Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV (2010) Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet 42(3):260–263
55. Vincent H, Wiersema J, Kell S, Fielder H, Dobbie S, Castañeda-Álvarez NP, Guarino L, Eastwood R, Leόn B, Maxted N (2013) A prioritized crop wild relative inventory to help underpin global food security. Biol Conserv 167:265–275
56. VSN International (2011) GenStat for windows 14th edition. http://GenStat.co.uk. Accessed 1 Dec 2016
57. Weigel D, Nordborg M (2015) Population genomics for understanding adaptation in wild plant species. Annu Rev Genet 49:315–338
58. Wolko B, Clements JC, Naganowska B, Nelson MN, Yang H (2011) Lupinus. In: Kole C (ed) Wild crop relatives: genomic and breeding resources: legume crops and forages. Springer, Berlin, Heidelberg, pp 153–206
59. WorldClim (2006) WorldClim—global climate data. http://www.worldclim.org/. Accessed 1 Dec 2016
60. Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND, Tiffin P (2014) Genomic signature of adaptation to climate in Medicago truncatula. Genetics 196(4):1263–1275