The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop

Muhammad Munir Iqbal; Mark Huynh; Joshua A Udall; Andrzej Kilian; Kedar N Adhikari; Jens D Berger; William Erskine; Matthew N Nelson

doi:10.1186/s12863-019-0767-3

The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop

BMC Genet. 2019 Aug 14;20(1):68. doi: 10.1186/s12863-019-0767-3.

Authors

Muhammad Munir Iqbal^{1

2}, Mark Huynh³, Joshua A Udall⁴, Andrzej Kilian⁵, Kedar N Adhikari⁶, Jens D Berger⁷, William Erskine^{8

9}, Matthew N Nelson^{7

10}

Affiliations

¹ School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia. munirqbl@gmail.com.
² Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia. munirqbl@gmail.com.
³ The College of Life Sciences, Brigham Young University, Provo, UT, USA.
⁴ USDA-ARS Southern Plains Agricultural Research Center, 2881 F&B Rd., College Station, TX, 77845, USA.
⁵ Diversity Arrays Technology, University of Canberra, Canberra, Australia.
⁶ School of Life and Environmental Sciences, I A Watson Grains Research Centre, The University of Sydney, Narrabri, NSW, Australia.
⁷ Agriculture and Food, CSIRO, Floreat, WA, Australia.
⁸ School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.
⁹ Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
¹⁰ The UWA Institute of Agriculture, Perth, WA, Australia.

Abstract

Background: Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits.

Results: We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation.

Conclusion: These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin.

Keywords: Adaptation traits; Linkage map; Phenology; QTL analysis; Yellow lupin.

Publication types

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

MeSH terms

Analysis of Variance
Chromosome Mapping*
Crops, Agricultural / genetics*
Edible Grain / genetics*
Genetic Linkage
Genetic Markers
Genotype
Inbreeding
Lupinus / genetics*
Phenotype
Plant Breeding
Quantitative Trait Loci*
Quantitative Trait, Heritable*

Substances

Genetic Markers