Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea reproductive phenology

Abstract

Water deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model and manipulate phenology. We define a new trait, drought effect on phenology (DEP = difference in flowering time between irrigated and rainfed crops), and use FST genome scanning to probe for genomic regions under selection for this trait. Owing to the negligible variation in daylength, variation in phenology with sowing date was attributed to temperature and water; hence, genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects. Thermal time to flowering was shortened with increasing water stress quantified with carbon isotope composition. Genomic regions on chromosomes 4, 5, 6, 7 and 8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2 and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1 and ERF1. Modelling showed DEP reduces the likelihood of drought and heat stress at the expense of cold stress. Accounting for DEP would improve genetic and phenotypic models of phenology.