Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius

Yinglong Chen; Fucheng Shan; Matthew N Nelson; Kadambot Hm Siddique; Zed Rengel

doi:10.1093/jxb/erw127

Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius

J Exp Bot. 2016 Jun;67(12):3683-97. doi: 10.1093/jxb/erw127. Epub 2016 Apr 5.

Authors

Yinglong Chen¹, Fucheng Shan², Matthew N Nelson³, Kadambot Hm Siddique⁴, Zed Rengel⁵

Affiliations

¹ School of Earth and Environment, The University of Western Australia, Perth, WA 6009, Australia The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia The State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi 712100, China yinglong.chen@uwa.edu.au.
² The Department of Agriculture and Food, Western Australia, Locked Bag 4, Bentley, WA 6983, Australia.
³ The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia School of Plant Biology, The University of Western Australia, Perth, WA 6009, Australia Current address: Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.
⁴ The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
⁵ School of Earth and Environment, The University of Western Australia, Perth, WA 6009, Australia The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.

Abstract

Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions.

Keywords: Diversity Arrays Technology (DArT); genetic diversity; molecular marker; narrow-leafed lupin; root trait; trait-marker association..

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genetic Markers*
Genetic Variation*
Lupinus / genetics*
Lupinus / growth & development*
Phenotype*
Plant Roots / genetics
Plant Roots / growth & development

Substances

Genetic Markers