A genome wide association study to dissect the genetic architecture of agronomic traits in Andean lupin (Lupinus mutabilis)

Abstract

Establishing Lupinus mutabilis as a protein and oil crop requires improved varieties adapted to EU climates. The genetic regulation of strategic breeding traits, including plant architecture, growing cycle length and yield, is unknown. This study aimed to identify associations between 16 669 single nucleotide polymorphisms (SNPs) and 9 agronomic traits on a panel of 223 L. mutabilis accessions, grown in four environments, by applying a genome wide association study (GWAS). Seven environment-specific QTLs linked to vegetative yield, plant height, pods number and flowering time, were identified as major effect QTLs, being able to capture 6 to 20% of the phenotypic variation observed in these traits. Furthermore, two QTLs across environments were identified for flowering time on chromosome 8. The genes FAF, GAMYB and LNK, regulating major pathways involved in flowering and growth habit, as well as GA30X1, BIM1, Dr1, HDA15, HAT3, interacting with these pathways in response to hormonal and environmental cues, were prosed as candidate genes. These results are pivotal to accelerate the development of L. mutabilis varieties adapted to European cropping conditions by using marker-assisted selection (MAS), as well as to provide a framework for further functional studies on plant development and phenology in this species.

<em>Lupinus mutabilis</em> Breeding in the Andes of Ecuador, Peru, and Bolivia: A Review

“…Two recent studies evaluated accessions from the Ecuadorian germplasm bank on four environments (Portugal, Ecuador and two locations in The Netherlands), and high phenotypic variability has been reported for some characteristics such as flowering time, plant height, number of branch orders, vegetative yield, pods and seeds on the central axis, total number of pods and seeds per plant and seed weight. High heritability values were reported for flowering (0.88), plant height (0.82) and production of pods and seeds on the main stem (0.6), as well as strong correlation between plant height, flowering time and seed yield was reported [36,37]. In addition, using GWAS (genome wide association study) 10 Markers linked to flowering time, plant height, vegetative yield, and number of pods and seeds on the main stem were identified (Table 3).…”

“…The most of the SNPs reported were identified as single location markers. The reference genome used in this study was L angistifolius [37]. L. mutabilis shows a wide diversity in plant architecture, plant height, grain and flower color [13,34]; likewise, it varies in crop cycle, protein, oil and alkaloid content, yield, and tolerance to insect pests and diseases [1].…”

Lupinus mutabilis Breeding in the Andes of Ecuador, Peru, and Bolivia: A Review

“…Two recent studies evaluated accessions from the Ecuadorian germplasm bank on four environments (Portugal, Ecuador, and two locations in The Netherlands), and high phenotypic variability has been reported for some characteristics, such as the flowering time, plant height, number of branch orders, vegetative yield, pods and seeds on the central axis, total number of pods and seeds per plant, and seed weight. High heritability values were reported for flowering (0.88), plant height (0.82), and production of pods and seeds on the main stem (0.6), as well as a strong correlation between plant height, flowering time, and seed yield [34,35]. In addition, using a genome wide association study (GWAS), 10 markers linked to flowering time, plant height, vegetative yield, and number of pods and seeds on the main stem were identified (Table 3).…”

“…Most of the reported SNPs were identified as single location markers. The reference genome used in this study was L. angistifolius [35].…”