Ancient relaxation of an obligate short-day requirement in common bean through loss of CONSTANS-like gene function

González, Ana M.; Schoor, Jacqueline K. Vander; Fang, Chao; Kong, Fanjiang; Wu, Jing; Weller, James L.; Santalla, Marta

doi:10.1016/j.cub.2021.01.075

Cited by 16 publications

(25 citation statements)

References 63 publications

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“…Well-documented examples are seen in the cereals, wheat and barley, where mutations in the Ppd and Vrn genes have adjusted photoperiod and vernalization sensitivity and have been linked to the expansion of these crops into northern Europe from south west Asia and Mediterranean regions ( Cockram et al , 2007 ). Similar adaptations are also seen during the evolution of legume crops, with a reduction in photoperiod sensitivity conferred by mutations in PRR3 , PHYA , E1 , and GI genes in soybean ( Glycine max ; Lin et al , 2021 ), PHYA3 and COL2 in common bean ( Phaseolus vulgaris ; Weller et al , 2019 ; Gonzalez et al , 2021 ), and ELF3 in pea ( Pisum sativum ), lentil ( Lens culinaris ), and chickpea ( Cicer arietinum ; Weller et al , 2012 ; Ridge et al , 2017 ), which have in each case contributed to expansion of their ecogeographical range.…”

Section: Introductionmentioning

confidence: 65%

The genetic architecture of flowering time changes in pea from wild to crop

Williams

Schoor

Butler

et al. 2022

Journal of Experimental Botany

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Change in phenology has been an important component in crop evolution, and selection for earlier flowering through a reduction in environmental sensitivity has helped broaden adaptation in many species. Natural variation for flowering in domesticated pea (Pisum sativum L.) has been noted and studied for decades, but there has been no clear account of change relative to its wild progenitor. Here we examined the genetic control of differences in flowering time between wild P. sativum ssp. humile and a typical late-flowering photoperiodic P. s. sativum accession in a recombinant inbred population under long and short photoperiods. Our results confirm the importance of the major photoperiod sensitivity locus Hr/PsELF3a and identify two other loci on chromosomes 1 (DTF1) and 3 (DTF3) that contribute to earlier flowering in the domesticated line under both photoperiods. The domesticated allele at a fourth locus on chromosome 6 (DTF6) delays flowering under long days only. Map positions, inheritance patterns, and expression analyses in near-isogenic comparisons imply that DTF1, DTF3 and DTF6 represent gain-of-function alleles of the florigen/antiflorigen genes FTa3, FTa1 and TFL1c/LF, respectively. This echoes similar variation in chickpea and lentil, and suggests a conserved route to reduced photoperiod sensitivity and early phenology in temperate pulses.

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Section: Introductionmentioning

confidence: 65%

The genetic architecture of flowering time changes in pea from wild to crop

Williams

Schoor

Butler

et al. 2022

Journal of Experimental Botany

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“…4a, d, Supplementary Figs. [22][23][24][25]. During domestication, these two alleles were retained and passed onto the landraces in this region (Fig.…”

Section: Discussionmentioning

confidence: 94%

“…Stepwise selection of different cis -regulatory variants in an FT homolog also occurred at different evolutionary times for local adaptation in maize 22 . A recent study also indicated that stepwise selection of a CONSTANS LIKE gene and a Phytochrome A gene facilitated the adaptation of common bean to high latitudes 23 . These findings suggest that the gradual selection of different genes or different alleles of one gene is a common strategy during crop evolution and adaptation.…”

Section: Discussionmentioning

confidence: 99%

Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

et al. 2021

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Soybean (Glycine max) serves as a major source of protein and edible oils worldwide. The genetic and genomic bases of the adaptation of soybean to tropical regions remain largely unclear. Here, we identify the novel locus Time of Flowering 16 (Tof16), which confers delay flowering and improve yield at low latitudes and determines that it harbors the soybean homolog of LATE ELONGATED HYPOCOTYL (LHY). Tof16 and the previously identified J locus genetically additively but independently control yield under short-day conditions. More than 80% accessions in low latitude harbor the mutations of tof16 and j, which suggests that loss of functions of Tof16 and J are the major genetic basis of soybean adaptation into tropics. We suggest that maturity and yield traits can be quantitatively improved by modulating the genetic complexity of various alleles of the LHY homologs, J and E1. Our findings uncover the adaptation trajectory of soybean from its temperate origin to the tropics.

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“…For example, Sh1 genes for seed shattering were under parallel selection during cereal crop domestication (Lin et al, 2012), and the major flowering time gene Hd1 experienced parallel selection during domestication in cereal crops (Liu et al, 2015). A parallel loss of photoperiod sensitivity occurred independently in two domesticated lineages through sequential loss of COL2 and PHYA3 function in common bean (Gonza ´lez et al, 2021). In addition, the domestication gene G orthologs controlling seed dormancy were selected in parallel in at least three crop species (soybean, rice, and tomato) from different families, likely representing the first domestication syndrome gene subject to parallel selection in independent crop families (Wang et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes

et al. 2022

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Photoperiod responsiveness is a key factor limiting the geographic distribution of cultivated soybean and its wild ancestor. In particular, the genetic basis of the adaptation in wild soybean remains poorly understood. In this study, by combining whole-genome resequencing and genome-wide association studies we identified a novel locus, Time of Flowering 5 (Tof5), which promotes flowering and enhances adaptation to high latitudes in both wild and cultivated soybean. By genomic, genetic and transgenic analyses we showed that Tof5 encodes a homolog of Arabidopsis thaliana FRUITFULL (FUL). Importantly, further analyses suggested that different alleles of Tof5 have undergone parallel selection. The Tof5 H1 allele was strongly selected by humans after the early domestication of cultivated soybean, while Tof5 H2 allele was naturally selected in wild soybean, and in each case facilitating adaptation to high latitudes. Moreover, we found that the key flowering repressor E1 suppresses the transcription of Tof5 by binding to its promoter. In turn, Tof5 physically associates with the promoters of two important FLOWERING LOCUS T (FT), FT2a and FT5a, to upregulate their transcription and promote flowering under long photoperiods. Collectively, our findings provide insights into how wild soybean adapted to high latitudes through natural selection and indicate that cultivated soybean underwent changes in the same gene but evolved a distinct allele that was artificially selected after domestication.

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Ancient relaxation of an obligate short-day requirement in common bean through loss of CONSTANS-like gene function

Cited by 16 publications

References 63 publications

The genetic architecture of flowering time changes in pea from wild to crop

The genetic architecture of flowering time changes in pea from wild to crop

Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes

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