ABSTRACT The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory

sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (_Oryza sativa_). We inferred fitCons

scores (_ρ_) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA

methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference

elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs. Access through

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OTHERS EPIALLELIC VARIATION OF NON-CODING RNA GENES AND THEIR PHENOTYPIC CONSEQUENCES Article Open access 14 February 2024 A SUPER PAN-GENOMIC LANDSCAPE OF RICE Article Open access 12 July

2022 SEQUENCE-BASED ANALYSIS OF THE RICE CAMTA FAMILY: HAPLOTYPE AND NETWORK ANALYSES Article Open access 05 October 2024 DATA AVAILABILITY The read data used to generate the ChromHMM model

and genomic classes have been deposited at the NCBI SRA (https://www.ncbi.nlm.nih.gov/sra) and can be accessed through BioProject ID PRJNA586887. Genome assemblies of _O. officinalis_ and

_O. australiensis_ are available from the CoGe CyVerse website (https://genomevolution.org/coge/) with genome IDs id56031 and id56030, respectively. Access to genomic class annotation and

INSIGHT scoring of the rice genome is available via a genome browser linked from the project’s website (http://purugganan-genomebrowser.bio.nyu.edu/insightJuly2018/greenInsight.html). All

epigenomic data tracks, genome annotations, multiple alignments, conservation scores, fitCons scores and site classes are available for visualization and download on a local installation on

the USCSC Genome Browser at http://purugganan-genomebrowser.bio.nyu.edu/cgi-bin/hgTracks?db=Osaj&position=Osaj.1%3A166356–178595, and are also available for download from the NCBI SRA

(PRJNA586887). The greenINSIGHT-specific data used to generate the greenINSIGHT online tool are available in the “Additional information, scripts & data” section at

http://purugganan-genomebrowser.bio.nyu.edu/insightJuly2018/greenInsight.html. The greenINSIGHT-specific code used to generate the greenINSIGHT online tool, as well as the code described in

the Methods, are available in the “Additional information, scripts & data” section at http://purugganan-genomebrowser.bio.nyu.edu/insightJuly2018/greenInsight.html. CODE AVAILABILITY The

greenINSIGHT-specific data used to generate the greenINSIGHT online tool are available in the “Additional information, scripts & data” section at

http://purugganan-genomebrowser.bio.nyu.edu/insightJuly2018/greenInsight.html. The greenINSIGHT-specific code used to generate the greenINSIGHT online tool, as well as the code described in

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ACKNOWLEDGEMENTS We thank the New York University Center for Genomics and Systems Biology GenCore Facility and the Next Generation Sequencing core at Cold Spring Harbor Laboratory for

sequencing support. We thank O. Wilkins and C. Danko for valuable suggestions relating to the ATAC and PRO-Seq protocols, respectively. This work was supported primarily by a grant from the

Zegar Family Foundation (no. A16-0051-004), as well as some support from the National Science Foundation Plant Genome Research Program (no. IOS-1546218) and NYU Abu Dhabi Research Institute

to M.D.P., the National Science Foundation CAREER award (no. MCB-1552455), the US National Institutes of Health (no. R35GM124806) and US Department of Agriculture Hatch Program (no. 1012915)

to X.Z., the US National Institutes of Health (no. R35GM127070) to A.S., and fellowships from the Gordon and Betty Moore Foundation and Life Sciences Research Foundation (no. GBMF2550.06)

to S.C.G. and from the Natural Sciences and Engineering Research Council of Canada (no. PDF-502464-2017) to Z.J.-L. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Center for Genomics and

Systems Biology, Department of Biology, New York University, New York, NY, USA Zoé Joly-Lopez, Adrian E. Platts, Jae Young Choi, Simon C. Groen & Michael D. Purugganan * Simons Center

for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA Adrian E. Platts, Brad Gulko & Adam Siepel * Laboratory of Genetics and Wisconsin Institute for

Discovery, University of Wisconsin-Madison, Madison, WI, USA Xuehua Zhong * Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, NYU Abu Dhabi, Abu Dhabi, United Arab

Emirates Michael D. Purugganan Authors * Zoé Joly-Lopez View author publications You can also search for this author inPubMed Google Scholar * Adrian E. Platts View author publications You

can also search for this author inPubMed Google Scholar * Brad Gulko View author publications You can also search for this author inPubMed Google Scholar * Jae Young Choi View author

publications You can also search for this author inPubMed Google Scholar * Simon C. Groen View author publications You can also search for this author inPubMed Google Scholar * Xuehua Zhong

View author publications You can also search for this author inPubMed Google Scholar * Adam Siepel View author publications You can also search for this author inPubMed Google Scholar *

Michael D. Purugganan View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS M.D.P. conceived of the study idea. M.D.P., Z.J.-L., A.E.P. and A.S.

designed the study. M.D.P. directed the study. Z.J.-L. and X.Z. collected the data, A.E.P., Z.J.-L., J.Y.C., B.G., S.C.G. and M.D.P. analysed the data. Z.J.-L., A.E.P., A.S. and M.D.P. wrote

the paper. CORRESPONDING AUTHOR Correspondence to Michael D. Purugganan. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PEER

REVIEW INFORMATION _Nature Plants_ thanks Robin Allaby, Peter Civan and Peter Morrell for their contribution to the peer review of this work. PUBLISHER’S NOTE Springer Nature remains neutral

with regard to jurisdictional claims in published maps and institutional affiliations. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Figs. 1–12. REPORTING SUMMARY

SUPPLEMENTARY TABLES Supplementary Tables 1–11. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Joly-Lopez, Z., Platts, A.E., Gulko, B. _et al._ An

inferred fitness consequence map of the rice genome. _Nat. Plants_ 6, 119–130 (2020). https://doi.org/10.1038/s41477-019-0589-3 Download citation * Received: 18 July 2019 * Accepted: 20

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