Adapting legume crops to climate change using genomic approaches.

Mahsa Mousavi-Derazmahalleh, Philipp E Bayer, James K Hane, Babu Valliyodan, Henry T Nguyen, Matthew N Nelson, William Erskine, Rajeev K Varshney, Roberto Papa, David Edwards
Author Information
  1. Mahsa Mousavi-Derazmahalleh: UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia. ORCID
  2. Philipp E Bayer: School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia. ORCID
  3. James K Hane: CCDM Bioinformatics, Centre for Crop Disease Management, Curtin University, Bentley, Western Australia, 6102, Australia. ORCID
  4. Babu Valliyodan: Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. ORCID
  5. Henry T Nguyen: Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA. ORCID
  6. Matthew N Nelson: UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia. ORCID
  7. William Erskine: UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia. ORCID
  8. Rajeev K Varshney: UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia. ORCID
  9. Roberto Papa: Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131, Ancona, Italy. ORCID
  10. David Edwards: School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia. ORCID

Abstract

Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.

Keywords

References

  1. Nat Genet. 2017 Jul;49(7):1082-1088 [PMID: 28530677]
  2. Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16666-71 [PMID: 17068128]
  3. Hortic Res. 2015 May 13;2:15019 [PMID: 26504570]
  4. Sci Rep. 2017 May 15;7(1):1911 [PMID: 28507291]
  5. BMC Genomics. 2014 May 01;15:328 [PMID: 24885083]
  6. Plant Cell Environ. 2019 Jan;42(1):6-19 [PMID: 29603775]
  7. J Biosci. 2014 Jun;39(3):513-7 [PMID: 24845514]
  8. Front Plant Sci. 2017 Sep 05;8:1463 [PMID: 28928752]
  9. BMC Plant Biol. 2010 Jan 27;10:17 [PMID: 20105299]
  10. Front Plant Sci. 2017 Mar 17;8:359 [PMID: 28367154]
  11. Genome. 2002 Feb;45(1):175-88 [PMID: 11908660]
  12. J Hered. 2010 Mar-Apr;101(2):251-6 [PMID: 19959597]
  13. Trends Ecol Evol. 2007 Aug;22(8):432-9 [PMID: 17573151]
  14. Front Plant Sci. 2017 Jan 06;7:2005 [PMID: 28111584]
  15. Nature. 2011 Nov 16;480(7378):520-4 [PMID: 22089132]
  16. Plant Physiol. 2003 Mar;131(3):872-7 [PMID: 12644639]
  17. Plant Physiol. 2005 Apr;137(4):1189-96 [PMID: 15824281]
  18. New Phytol. 2016 Mar;209(4):1781-94 [PMID: 26526745]
  19. Plant Genome. 2017 Mar;10(1): [PMID: 28464065]
  20. Genetics. 2014 Apr;196(4):1263-75 [PMID: 24443444]
  21. Nat Rev Genet. 2017 Sep;18(9):563-575 [PMID: 28669983]
  22. BMC Genomics. 2011 Jan 05;12:8 [PMID: 21208448]
  23. Theor Appl Genet. 2005 Feb;110(4):669-77 [PMID: 15650814]
  24. Funct Plant Biol. 2016 Feb;44(1):76-93 [PMID: 32480548]
  25. Sci Rep. 2016 Mar 31;6:23598 [PMID: 27029319]
  26. Nature. 2010 Jan 14;463(7278):178-83 [PMID: 20075913]
  27. J Exp Bot. 2017 Apr 1;68(8):2055-2063 [PMID: 27927999]
  28. New Phytol. 2013 Jan;197(1):300-313 [PMID: 23126683]
  29. BMC Plant Biol. 2011 Mar 29;11:56 [PMID: 21447154]
  30. Sci Rep. 2017 Feb 21;7:42839 [PMID: 28220807]
  31. Theor Appl Genet. 2018 Apr;131(4):887-901 [PMID: 29353413]
  32. Microbiol Mol Biol Rev. 1999 Dec;63(4):968-89, table of contents [PMID: 10585971]
  33. Plant Cell. 2014 May 21;26(5):1901-1912 [PMID: 24850850]
  34. Biology (Basel). 2017 Mar 11;6(1): [PMID: 28287462]
  35. Am J Bot. 2015 Sep;102(9):1401-2 [PMID: 26391705]
  36. Plant J. 2013 Apr;74(1):174-83 [PMID: 23289725]
  37. Science. 2011 Oct 7;334(6052):83-6 [PMID: 21980108]
  38. Sci Rep. 2017 Nov 10;7(1):15335 [PMID: 29127429]
  39. Curr Opin Plant Biol. 2015 Apr;24:93-9 [PMID: 25733069]
  40. PLoS One. 2014 Aug 20;9(8):e105228 [PMID: 25140620]
  41. Genome Biol. 2017 May 31;18(1):99 [PMID: 28558752]
  42. Plant Physiol. 2005 Apr;137(4):1228-35 [PMID: 15824285]
  43. Nat Biotechnol. 2015 Apr;33(4):408-14 [PMID: 25643055]
  44. Plant J. 2010 Aug;63(4):623-35 [PMID: 20545888]
  45. BMC Genomics. 2014 Dec 22;15:1160 [PMID: 25534372]
  46. Nat Biotechnol. 2014 Oct;32(10):1045-52 [PMID: 25218520]
  47. Trends Plant Sci. 2007 Oct;12(10):433-6 [PMID: 17719833]
  48. Sci Rep. 2017 Jun 12;7(1):3231 [PMID: 28607439]
  49. Nature. 2002 Aug 8;418(6898):700-7 [PMID: 12167878]
  50. Mol Genet Genomics. 2015 Apr;290(2):559-71 [PMID: 25344290]
  51. BMC Genet. 2012 Oct 08;13:84 [PMID: 23043321]
  52. Nucleic Acids Res. 2016 Jan 4;44(D1):D1181-8 [PMID: 26546515]
  53. PLoS One. 2017 Feb 2;12(2):e0171105 [PMID: 28152092]
  54. Sci Adv. 2015 Jul 03;1(6):e1400218 [PMID: 26601206]
  55. Plant Physiol. 2003 Mar;131(3):900-10 [PMID: 12644643]
  56. Nat Biotechnol. 2013 Mar;31(3):240-6 [PMID: 23354103]
  57. Science. 2017 Mar 17;355(6330):1122-1123 [PMID: 28302807]
  58. Plant Biotechnol J. 2017 Mar;15(3):318-330 [PMID: 27557478]
  59. Nat Biotechnol. 2011 Nov 06;30(1):83-9 [PMID: 22057054]
  60. Sci Rep. 2016 Aug 22;6:30358 [PMID: 27545089]
  61. BMC Genomics. 2013 Aug 28;14:579 [PMID: 23984715]
  62. Nat Genet. 2010 Dec;42(12):1053-9 [PMID: 21076406]
  63. Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8641-8 [PMID: 17494757]
  64. Nat Genet. 2016 Apr;48(4):438-46 [PMID: 26901068]
  65. Theor Appl Genet. 2006 Apr;112(6):1149-63 [PMID: 16432734]
  66. Proc Biol Sci. 2005 Dec 22;272(1581):2561-9 [PMID: 16321776]
  67. New Phytol. 2009;183(2):273-290 [PMID: 19515223]
  68. Sci Rep. 2017 May 12;7(1):1813 [PMID: 28500330]
  69. PLoS One. 2013 May 31;8(5):e65688 [PMID: 23741505]
  70. Mol Biol Evol. 2016 Jul;33(7):1740-53 [PMID: 27189559]
  71. BMC Genomics. 2007 Nov 21;8:427 [PMID: 18031571]
  72. Theor Appl Genet. 2014 Feb;127(2):445-62 [PMID: 24326458]
  73. DNA Res. 2001 Apr 27;8(2):61-72 [PMID: 11347903]
  74. Genome Biol. 2016 Feb 25;17:32 [PMID: 26911872]
  75. Theor Appl Genet. 2004 Nov;109(8):1610-9 [PMID: 15365627]
  76. Genetics. 1990 Nov;126(3):735-42 [PMID: 1979039]
  77. Theor Appl Genet. 2012 Mar;124(4):637-52 [PMID: 22069118]
  78. Plant Cell Rep. 2017 Feb;36(2):371-374 [PMID: 27834007]
  79. Annu Rev Genet. 2005;39:197-218 [PMID: 16285858]
  80. Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22032-7 [PMID: 21131573]
  81. Br J Nutr. 2011 Oct;106(7):1045-51 [PMID: 21736844]
  82. New Phytol. 2014 Mar;201(4):1328-1342 [PMID: 24283472]
  83. New Phytol. 2017 Nov;216(3):682-698 [PMID: 28762506]
  84. Funct Plant Biol. 2014 Oct;41(11):1178-1190 [PMID: 32481067]
  85. BMC Genomics. 2017 Mar 27;18(1):261 [PMID: 28347275]
  86. Sci Rep. 2015 Oct 19;5:15296 [PMID: 26478518]
  87. Genetics. 2003 Dec;165(4):2259-68 [PMID: 14704201]
  88. Mol Biol Evol. 2005 Mar;22(3):506-19 [PMID: 15525701]
  89. Front Plant Sci. 2017 May 08;8:722 [PMID: 28533789]
  90. Int J Plant Genomics. 2011;2011:314829 [PMID: 22315587]
  91. New Phytol. 2013 Jan;197(1):314-322 [PMID: 23121242]
  92. Plant Biotechnol J. 2016 May;14(5):1183-94 [PMID: 26397045]
  93. Plant Biotechnol J. 2017 Aug;15(8):1034-1046 [PMID: 28111887]
  94. PLoS One. 2013 Aug 21;8(8):e72590 [PMID: 23991125]
  95. Nat Genet. 2014 Jul;46(7):707-13 [PMID: 24908249]
  96. Science. 2012 Aug 17;337(6096):816-21 [PMID: 22745249]
  97. Plant Biotechnol J. 2015 Jan;13(1):14-25 [PMID: 25060816]
  98. Nat Genet. 2010 Mar;42(3):260-3 [PMID: 20101244]
  99. Front Plant Sci. 2015 Apr 09;6:207 [PMID: 25914700]
  100. Plant Methods. 2013 Jul 22;9:29 [PMID: 23876160]
  101. PLoS One. 2012;7(8):e41304 [PMID: 22876284]
  102. Theor Appl Genet. 2018 Mar;131(3):513-524 [PMID: 29151146]
  103. GM Crops Food. 2015;6(4):243-52 [PMID: 26479970]
  104. Theor Appl Genet. 2010 May;120(7):1415-41 [PMID: 20098978]
  105. Plant Biotechnol J. 2016 Apr;14(4):1095-8 [PMID: 26360509]
  106. DNA Res. 2008 Aug;15(4):227-39 [PMID: 18511435]
  107. Curr Opin Plant Biol. 2003 Apr;6(2):199-204 [PMID: 12667879]
  108. Theor Appl Genet. 2018 Jan;131(1):79-91 [PMID: 28948303]
  109. Plant Genome. 2015 Jul;8(2):eplantgenome2014.09.0059 [PMID: 33228312]
  110. PLoS One. 2014 May 06;9(5):e96758 [PMID: 24801366]
  111. BMC Genomics. 2010 Aug 11;11:469 [PMID: 20701770]
  112. Plant Biotechnol J. 2016 Nov;14(11):2110-2119 [PMID: 27107184]
  113. Plant Genome. 2016 Nov;9(3): [PMID: 27902795]
  114. Front Plant Sci. 2017 Sep 26;8:1611 [PMID: 29018458]
  115. Theor Appl Genet. 2009 Feb;118(4):729-39 [PMID: 19048225]
  116. Saudi J Biol Sci. 2015 Mar;22(2):123-31 [PMID: 25737642]
  117. Trends Plant Sci. 2005 Dec;10(12):621-30 [PMID: 16290213]
  118. Front Plant Sci. 2016 Dec 26;7:1940 [PMID: 28082996]
  119. Theor Appl Genet. 2006 Jul;113(2):225-38 [PMID: 16791689]
  120. Cell. 2006 Dec 29;127(7):1309-21 [PMID: 17190597]

Grants

  1. /Bill & Melinda Gates Foundation

MeSH Term

Climate Change
Crops, Agricultural
Fabaceae
Genes, Plant
Genomics
Plant Breeding

Word Cloud

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