Haplotype variations of major flowering time genes in quinoa unveil their role in the adaptation to different environmental conditions

Abstract

Response to photoperiod is of major importance in crop production. It defines the adaptation of plants to local environments. Quinoa is a short-day plant which had been domesticated in the Andeans regions. We wanted to understand the adaptation to long-day conditions by studying orthologues of two major flowering time regulators of Arabidopsis, FLOWERING LOCUS T (FT) and CONSTANS (CO) in quinoa accessions with contrasting photoperiod response. By searching the quinoa reference genome sequence, we identified 24 FT and six CO homologs. CqFT genes displayed remarkably different expression patterns between long-and short-day conditions, whereas the influence of the photoperiod on CqCOL expressions was moderate. Cultivation of 276 quinoa accessions under short-and long-day conditions revealed great differences in photoperiod sensitivity. After sequencing their genomes, we identified large sequence variations in 12 flowering time genes. We found nonrandom distribution of haplotypes across accessions from different geographical origins, highlighting the role of CqFT and CqCOL genes in the adaptation to different day-length conditions. We identified five haplotypes causing early flowering under long days. This study provides assets for quinoa breeding because superior haplotypes can be assembled in a predictive breeding approach to produce well-adapted early flowering lines under long-day photoperiods.

High-density mapping of QTL controlling agronomically important traits in quinoa (Chenopodium quinoaWilld.)

“…Besides, we identified FLOWERING LOCUS T (CqFT2A) within pleio7.1, a QTL found in the F 2 population, exclusively. Although FT genes are described in studies related to flowering time regulation in quinoa and in C. rubrum, no flowering-time function has been specified particularly for the CqFT2A paralog (Patiranage et al 2021;Štorchová 2020). To continue towards identification of candidate genes, we mainly focused on the two pleiotropic QTL detected in F 2 and F 3 populations and identified putative candidate genes based on their known functions in flowering time and yield regulation in other species.…”

Yield and Nutritional Characterization of Thirteen Quinoa (Chenopodium quinoa Willd.) Varieties Grown in North-West Europe—Part I

“…The newest varieties show early maturity and are almost completely day-length neutral [3,9]. Moreover, Patiranage et al [10] recently identified haplotypes that induce photoperiod insensitivity associated with early flowering under long day lengths. A haplotype-based breeding strategy of pyramiding favorable alleles is suggested by the authors to breed quinoa varieties that are early maturing under long day lengths and are, thus, suitable for cultivation in northern latitudes [10].…”

High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (Chenopodium quinoa Willd.)

“…This is correlated with the additive effects calculated for the markers with the highest LOD score within each QTL ( Table 4 ). The observed contrasting effects of PI-614889 alleles at pleio4.1 and pleio14.1 would probably complicate breeding processes, whose aim is to reduce days to flowering and plant height and increase TKW, simultaneously ( Murphy et al, 2018 ; Patiranage et al, 2021 ). In a broader sense, our results from the genome-wide epistasis analysis revealed the complexity of the regulation of days to flowering, plant height, and TKW in quinoa, which was expected given the intricated processes, such as DNA methylation, histone modification, and non-coding RNA-associated gene silencing, which underlie these traits ( Pandey et al, 2021 ).…”

“…Besides, we identified FLOWERING LOCUS T ( CqFT2A ) within pleio7.1 , a QTL found in the F 2 population, exclusively. Although FT genes are described in studies related to flowering time regulation in quinoa and C. rubrum , no flowering-time function has been specified particularly for the CqFT2A paralog ( Štorchová, 2020 ; Patiranage et al, 2021 ). To continue toward the identification of candidate genes, we mainly focused on the two pleiotropic QTL detected in F 2 and F 3 populations and identified putative candidate genes based on their known functions in flowering time and yield regulation in other species.…”

“…Quinoa breeding aims for short, non-branching plants with a compact panicle, as well as increased tolerance to abiotic and biotic stresses. Nevertheless, the main breeding objective in quinoa remains to be the development of high-yielding varieties and, in temperate regions and high latitudes of Europe, North America, and China, the adaptation to long-day conditions ( Murphy et al, 2018 ; Patiranage et al, 2021 ). Thus, for breeding quinoa, a better understanding of the molecular regulation of flowering time and day-length responsiveness is essential since yield potential and local adaptation are largely determined by these processes.…”