Genetic and molecular analysis of epistatic interactions in flowering time pathways identified in a barley multi-parent advanced generation intercross (MAGIC) population
Final Report Abstract
The time of flowering is a key factor for global adaptability to diverse conditions and a critical agronomical factor for successful reproduction. The floral switch marked by the transition from vegetative to reproductive phase is regulated by a complex mechanism, based on responding to specific external environmental stimuli beside of endogenous signals. Present study aims to improve understanding of environment-dependent regulation of flowering time in and identify candidate gene(s) underlying novel barley flowering time pathway in two crops barley and wheat. This study used spring barley multi-parental advanced generation intercross (MAGIC) population which is constructed of an eight-way cross of barley landraces and one elite cultivar Barke. To investigate regulation of flowering time pathway of barley under field and semi-controlled conditions, a set of 534 spring barley MAGIC DH lines were used for analyzing of quantitative trait loci (QTLs), epistatic interactions, QTL × environment interactions and epistasis × environment interactions. A newlydetected QTL on chromosome H1 was investigated to identify the underlying candidate gene(s) by a targeted background effect elimination approach based on epistasis to compare flowering-timespecific-near-isogenic (comparable) pair of DH lines by microscopic phenotyping, RNAseq and RT- qPCR. Results revealed overall 18 QTLs and 2,420 epistatic interactions including a novel QTL harboring a flowering-delaying allele on chromosome 1H, engaged in epistatic and environment interactions, which we named “HvHeading”. Distinguishable epistatic interactions and environment interactions were detected in field and semi-controlled conditions suggesting the influence of temperature on regulators of flowering time pathway. To investigate the allele underlying HvHeading, microscopic phenotyping of comparable MAGIC DH lines and differential transcript expression analysis in main apical meristem identified up-regulation of Spt6 gene in delayed-flowering DH line. Precise epistasis mapping can help compose strategies to facilitate gene identification. This study gives new insights into environment-dependent regulation of flowering time in barley through a multidisciplinary approach which highlights importance of employing approaches that better explain complex traits in future research and breeding programs. Modern bread wheat has a huge genetic potential to adjust its heading date (HD) with favorable conditions that has remained largely unexplored so far. For this purpose, an association panel of cultivars adapted in Germany that was tested in multi-location field trials across Germany over three years. Spring temperature overdominates other factors in decreasing the days to heading whereas the higher amount of solar radiation is delaying it. Genome wide scan detected a so far unknown stable locus TaHd102 on chromosome 5A. Including non-adapted cultivars, the exotic allele TaHd044 on chromosome 3A could be identified. The later explains up to 33% of the genetic variance and accelerates HD by 5.6 days. The response to the competition of latitude dependent climatic variables detected fine tuning QTL responding to temperature and photoperiod in lower and higher latitudes, respectively. VRN-A2 showed potential epistatic interactions with 15 known operators of HD regulation. The epistatic power moved to QTL TaHd098, which interacts with the same regulatory elements as VRN-A2 when exotic cultivars were included in the analysis. By joining QTL mapping and RNA-seq, on orthologue of transcription factor ASYMMETRIC LEAVES 1 (AS1) could be identified in the late reproductive phase in leaf tissue and mapped in QTL TaHd102. Deletion of six nucleotides in the AS1 promoter could be identified in the binding site of the Suppressor of Constans Overexpression 1 (SOC1) gene. Both proteins AS1 and SOC1 are inducing HD in response to gibberellin (GA) biosynthesis. This later that is likely behind the HD variation in the adapted germplasm. Our results enrich the knowledge and understanding gained so far in flowering time pathway and inflorescence development in barley and wheat on genetic and molecular levels, and construct a solid basis that could be exploited for further researches studies and breeding programs.
Publications
- 2015. Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept. Molecular Breeding 35, 86
Sannemann W, Huang BE, Mathew B, Léon J
(See online at https://doi.org/10.1007/s11032-015-0284-7) - 2018. Detection of epistasis for flowering time using Bayesian multilocus estimation in a barley MAGIC population. Genetics 208: 525–536
Mathew B, Léon J, Sannemann W, Sillanpää MJ
(See online at https://doi.org/10.1534/genetics.117.300546) - Genetische und molekulare Analyse des Blühzeitpunktes in verschiedenen Weizen Populationen. Gemeinschaft zur Förderung von Pflanzeninnovation e. V.(GFPi) Tagung 23.05.2018 in Bonn/Klein-Altendorf Germany
Salma Benaouda, Jens Léon, Agim Ballvora
- (2020) Effect of epistasis and environment on flowering time in barley reveals a novel flowering-delaying QTL allele. Journal of Experimental Botany
Afsharyan N. P., Sannemann W., Léon J., Ballvora A.
(See online at https://doi.org/10.1093/jxb/erz477) - Genetic and molecular analysis of heading day trait in wheat under different climatic conditions. International Symposium of the Society for Plant Breeding, February 11-13, 2020 Tulln – Austria
Salma Benaouda, Said Dadshani, Jens Léon, Agim Ballvora
