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Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes

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Abstract

Key message

Both SH and BHA weedy rice genotypes evolved independently and have distinct genomic composition. Different genetic mechanisms may be responsible for their competitiveness and adaptation to diverse environmental conditions.

Abstract

Two major types of weedy rice are recognized in the USA based on morphology: straw-hull (SH) and black-hull awned (BHA) weedy rice. We performed whole-genome resequencing of a SH weedy rice ‘PSRR-1’, a BHA weedy rice ‘BHA1115’, and a japonica cultivar ‘Cypress’ to delineate genome-wide differences and their relevance to genetics and evolution of weedy attributes. The high-quality reads were uniformly distributed with 82–88% genome coverage. The number of genotype-specific SNPs and InDels was highest in Cypress, followed by BHA1115 and PSRR-1. However, more genes were affected in BHA1115 compared with other two genotypes which is evident from the number of high-impact SNPs and InDels. Haplotype analysis of selected genes involved in domestication, adaptation, and agronomic performance not only differentiated SH from BHA weedy rice and supported evolution of weedy rice through de-domestication, but also validated the function of several genes such as qAn-1, qAn-2, Bh4, Rc, SD1, OsLG1, and OsC1. Several candidate genes were identified for previously reported seed dormancy and seed shattering QTLs. The SH and BHA weedy rice have distinct genomic composition, and the BHA weedy rice likely diverged earlier than SH weedy rice. The accumulation of plant development, reproduction, and defense-related genes in weedy rice possibly helped them to compete, survive, and spread under a wide range of environmental conditions by employing novel and diverse mechanisms. The genomic resources will be useful for both weed management and rice improvement by exploring the molecular basis of key agronomic, adaptive, and domestication attributes.

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All relevant data are provided as tables and figures with the paper and in the supplementary materials.

Abbreviations

SH:

Straw hulled

BHA:

Black-hulled awned

CPRS:

Cypress

QTL:

Quantitative trait locus

SNP:

Single-nucleotide polymorphism

InDel:

Insertions and deletions

RIL:

Recombinant inbred lines

CDS:

Coding sequences

UTR:

Untranslated regions

GO:

Gene ontology

NGS:

Next-generation sequencing

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Acknowledgements

This work is supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture (Grant No. 2006-35320-16555). This manuscript is approved for publication by the Director of Louisiana Agricultural Experiment Station, USA as Manuscript Number 2020-306-34605.

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Authors and Affiliations

  1. School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA

    Md. Shofiqul Islam, Sapphire Coronejo & Prasanta Kumar Subudhi

  2. Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

    Md. Shofiqul Islam

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  1. Md. Shofiqul Islam
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Contributions

PKS conceived and designed the experiment. MSI conducted the experiment and wrote the manuscript. MSI and SC analyzed data. PKS critically revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Prasanta Kumar Subudhi.

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Communicated by Takuji Sasaki.

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Islam, M.S., Coronejo, S. & Subudhi, P.K. Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes. Theor Appl Genet 133, 2461–2475 (2020). https://doi.org/10.1007/s00122-020-03611-2

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