Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

Steed, Gareth; Ramirez, Dora Cano; Hannah, Matthew A.; Webb, Alex A. R.

doi:10.1126/science.abc9141

Cited by 95 publications

(92 citation statements)

References 77 publications

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“…Moreover, MQ had additional genes under positive selection in the photomorphogenesis, flowering and circadian pathway: LIGHT-DEPENDENT SHORT HYPOCOTYLS ( LSH ), ENHANCER OF AG-4 ( HUA2 ) and LHY . In addition to being under positive selection, LHY is also tandemly duplicated in Vmac (Figure 3B), suggesting it may play an important role in the domestication of cranberry consistent with the selection pressure on core circadian genes in other crops [39].…”

Section: Resultsmentioning

confidence: 88%

Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

Kawash

Colt

Hartwick

et al. 2021

Preprint

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Cranberry (Vaccinium macrocarpon) is a member of the Heath family (Ericaceae) and is a temperate low-growing woody perennial native to North America that is both economically important and has significant health benefits. While some native varieties are still grown today, breeding programs over the past 50 years have made significant contributions to improving disease resistance, fruit quality and yield. An initial genome sequence of an inbred line of the wild selection Ben Lear, which is parent to multiple breeding programs, provided insight into the gene repertoire as well as a platform for molecular breeding. Recent breeding efforts have focused on leveraging the circumboreal V. oxycoccos, which forms interspecific hybrids with V. macrocarpon, offering to bring in novel fruit chemistry and other desirable traits. Here we present an updated, chromosome-resolved V. macrocarpon reference genome, and compare it to a high-quality draft genome of V. oxycoccos. Leveraging the chromosome resolved cranberry reference genome, we confirmed that the Ericaceae has undergone two whole genome duplications that are shared with blueberry and rhododendron. Leveraging resequencing data for Ben Lear inbred lines, as well as several wild and elite selections, we identified common regions that are targets of improvement. These same syntenic regions in V. oxycoccos, were identified and represent environmental response and plant architecture genes. These data provide insight into early genomic selection in the domestication of a native North American berry crop.

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Section: Resultsmentioning

confidence: 88%

Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

Kawash

Colt

Hartwick

et al. 2021

Preprint

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“…For the purpose of exploring the relationship between CCA1-PRR9 and RVE4-PRR7 , a simplified model of their interactions was developed (Figure 1A) (Shalit-Kaneh et al, 2018); more detailed models can be found in recent reviews (McClung, 2021; Steed et al, 2021). In general, PRR7/9 are negatively and positively regulated by CCA1/LHY and RVE4/RVE8 respectively, while in turn PRR7/9 negatively regulate both.…”

Section: Resultsmentioning

confidence: 99%

“…The plant circadian clock ensures biological processes occur at the proper time-of-day (TOD) regardless of predictable as well as random environmental changes, which is why it has been a target for plant domestication (Bendix et al, 2015; Creux and Harmer, 2019; McClung, 2021; Steed et al, 2021). The molecular mechanisms of the plant circadian clock were initially worked out in the model plant Arabidopsis thaliana and now there is a growing body of work across an array of crop and ornamental plants (Sanchez and Kay, 2016; McClung, 2019).…”

Section: Introductionmentioning

confidence: 99%

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

Michael

2021

Preprint

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The circadian clock ensures that biological processes are phased to the correct time of day. In plants the circadian clock is conserved at both the level of transcriptional networks as well as core genes. In the model plant Arabidopsis thaliana, the core circadian singleMYB (sMYB) genes CCA1 and RVE4 are in genetic linkage with the PSEUDO-RESPONSE REGULATOR (PRR) genes PRR9 and PRR7 respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis it was possible to trace this genetic linkage back to the basal angiosperm Amborella and identify an additional evolutionarily conserved genetic linkage between PIF3 and PHYA. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7 and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of higher plant families representing distinct whole genome duplication and fractionation events. Soybean maintains all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae) such as maize where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The evolutionary conservation of the genetic linkage as well as its loss in the grasses provides new insight in the plant circadian clock, which has been a critical target of breeding and domestication.Summary SentenceThe genetic linkage of the core circadian clock components has evolutionary origins in bryophytes and sheds light on the current functioning and selection on the circadian clock in crops.

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“…The functions of the circadian clock system in crops are diverse and conservative, but the mechanism of the circadian clock components in regulating the growth and development of crops still needs further study. The general impact of the circadian clock system on crops suggests that, by modifying the circadian rhythm, designing the timing of transgene expression and applying agricultural treatments at the most effective time of the day, future food production may be improved ( Steed et al, 2021 ). Analyzing how the circadian clock system regulates the growth and development process of crops will hopefully illuminate the theoretical basis of chronobiology, provide high-quality genetic resources for crop molecular breeding, and increase crop yields ( Wei et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…However, in recent years, more and more reports suggested that Ppd-1 is a member of the circadian clock. Steed et al (2021) indicated that on the basis of its relationship to Arabidopsis , PRR37 is assumed to have potential roles in the oscillator. Cao et al (2021) described the PRRs, including the wheat Ppd-1 gene, as a major component of the circadian clock.…”

Section: Discussionmentioning

confidence: 99%

Functional Analysis of the “Green Revolution” Gene Photoperiod-1 and Its Selection Trends During Bread Wheat Breeding

Liu

et al. 2021

Front. Plant Sci.

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Flowering is central to the transformation of plants from vegetative growth to reproductive growth. The circadian clock system enables plants to sense the changes in the external environment and to modify the growth and development process at an appropriate time. Photoperiod-1 (Ppd-1), which is controlled by the output signal of the circadian clock, has played an important role in the wheat “Green Revolution.” In the current study, we systematically studied the relationship between Ppd-1 haplotypes and both wheat yield- and quality-related traits, using genome-wide association analysis and transgenic strategies, and found that highly appropriate haplotypes had been selected in the wheat breeding programs. Genome-wide association analysis showed that Ppd-1 is associated with significant differences in yield-related traits in wheat, including spike length (SL), heading date (HD), plant height (PH), and thousand-grain weight (TGW). Ppd-1-Hapl-A1 showed increased SL by 4.72–5.93%, whereas Ppd-1-Hapl-B1 and Ppd-1-Hapl-D1 displayed earlier HD by 0.58–0.75 and 1.24–2.93%, respectively, decreased PH by 5.64–13.08 and 13.62–27.30%, respectively, and increased TGW by 4.89–10.94 and 11.12–21.45%, respectively. Furthermore, the constitutive expression of the Ppd-D1 gene in rice significantly delayed heading date and resulted in reduced plant height, thousand-grain weight, grain width (GW), and total protein content. With reference to 40years of data from Chinese wheat breeding, it was found that the appropriate haplotypes Ppd-1-Hapl-A1, Ppd-1-Hapl-B1, and Ppd-1-Hapl-D1 had all been subjected to directional selection, and that their distribution frequencies had increased from 26.09, 60.00, and 52.00% in landraces to 42.55, 93.62, and 96.23% in wheat cultivars developed in the 2010s. A Ppd-B1 methylation molecular marker was also developed to assist molecular wheat breeding. This research is of significance for fully exploring the function of the Ppd-1 gene and its genetic resource diversity, to effectively use the most appropriate haplotypes and to improve crop yield and sustainability.

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Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

Cited by 95 publications

References 77 publications

Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

Functional Analysis of the “Green Revolution” Gene Photoperiod-1 and Its Selection Trends During Bread Wheat Breeding

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