Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia

Abstract

Flowering time (i.e., heading date in crops) is an important ecological trait that determines growing seasons and regional adaptability of plants to specific natural environments. Rice (Oryza sativa L.) is a short-day plant that originated in the tropics. Increasing evidence suggests that the northward expansion of cultivated rice was accompanied by human selection of the heading date under noninductive long-day (LD) conditions. We report here the molecular cloning and characterization of DTH2 (for Days to heading on chromosome 2), a minor-effect quantitative trait locus that promotes heading under LD conditions. We show that DTH2 encodes a CONSTANS-like protein that promotes heading by inducing the florigen genes Heading date 3a and RICE FLOWERING LOCUS T 1, and it acts independently of the known floral integrators Heading date 1 and Early heading date 1. Moreover, association analysis and transgenic experiments identified two functional nucleotide polymorphisms in DTH2 that correlated with early heading and increased reproductive fitness under natural LD conditions in northern Asia. Our combined population genetics and network analyses suggest that DTH2 likely represents a target of human selection for adaptation to LD conditions during rice domestication and/or improvement, demonstrating an important role of minor-effect quantitative trait loci in crop adaptation and breeding.

Days to heading 7 , a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice

“…Generally its flowering is delayed when days are long and nights are short but accelerated when days are getting shorter. Cultivars with reduced PS response are characterized with early flowering and were developed to suit for growing at higher latitudes in the temperate zone (the northern limit is ∼53°N) or for two (even three) successive rounds of planting in the long growing season areas (e.g., some provinces in South China) (3,4). By contrast, cultivars with enhanced PS (late flowering) have been developed for increased grain yield in most rice planting regions (5,6).…”

“…Recently it was found that RICE FLOWERING LOCUS T 1 (RFT1), the closest paralog of Hd3a, also functions as a mobile flowering signal that works mainly under long day conditions (LDs) (11,12). Both of the "florigen" genes are regulated by Hd1, Early heading date 1 (Ehd1), and Days to heading 2 (DTH2) (4,7,13). Heading date 1 (Hd1) (counterpart of Arabidopsis CON-STANS, CO) (14) promotes Hd3a expression under SDs but suppresses it under LDs (7, 10, 11), whereas DTH2, another COlike protein, induces flowering by promoting the expression of Hd3a and RFT1 under LDs (4).…”

“…Molecular genetic studies in the past few decades have uncovered a number of flowering-time loci (3)(4)(5)(6)(7)(8)(9). Among them, a major quantitative trait locus (QTL), Heading date 3a (Hd3a), which encodes a rice ortholog of the Arabidopsis Flowering locus T (FT), promotes floral transition under short day conditions (SDs) (9).…”

Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana

“…At difference from most plant QTL identified so far, which are due to single functional polymorphisms 31 , natural variation at AtARQ1 involves several structural nucleotide polymorphisms that act in a non-additive manner on As(V) reductase function. Recent studies showed the first large effect natural alleles from plants due to multiple additive functional polymorphisms 32,33 . Our results provide evidence of the higher complexity that can underlie natural alleles and the combinatorial impact of multiple intraallelic mutations with little or no additive effect, in the generation of large effect alleles that contribute to quantitative variation and evolution in plants 34 .…”

Storytelling and story testing in domestication

“…Furthermore, because the number of genes that can be under selection simultaneously is constrained (80), it is necessary to consider gene interactions in models of adaptation (75,81). A case in point is the adaptation of crops to higher latitudes as they were moved out of their location(s) of origin (82)(83)(84). A reduction in crop adaptability may have led to population collapse in mid-Holocene Europe (85), resulting into regional agricultural abandonment (86).…”