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ARS Home » Pacific West Area » Logan, Utah » Forage and Range Research » Research » Publications at this Location » Publication #359425
Title: Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass

Author
item HUANG, LINKAI - Sichuan Agricultural University
item FENG, GUANGYAN - Sichuan Agricultural University
item YAN, HAIDONG - Sichuan Agricultural University
item ZHANG, ZHONGREN - Novogene Bioinformatics Institue
item Bushman, Shaun
item WANG, JIANPING - University Of Florida
item BOMBARELY, AURELIANO - Virginia Tech
item YANG, ZONGFU - Sichuan Agricultural University
item NIE, GANG - Sichuan Agricultural University
item XIE, WENGANG - Sichuan Agricultural University
item XU, LEI - Sichuan Agricultural University
item CHEN, PEILIN - Sichuan Agricultural University

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2019
Publication Date: 7/30/2019
Citation: Huang, L., Feng, G., Yan, H., Zhang, Z., Bushman, B.S., Wang, J., Bombarely, A., Yang, Z., Nie, G., Xie, W., Xu, L., Chen, P. 2019. Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. Plant Biotechnology Journal. 18(2):373-388. https://doi.org/10.1111/pbi.13205.
DOI: https://doi.org/10.1111/pbi.13205

Interpretive Summary: This study reports an assembly of the first chromosome-scale reference genome of a diploid orchardgrass via PacBio and Hi-C techniques. The reference genome of 1.78 Gb was assembled with contig N50 of 1.05 Mb and scaffold N50 of 3.41 Mb, accouting for 91.75% of the estimated genome size. Our results suggested that TE/LTRs in orchardgrass were likely activated during Pleistocene epoch betwen 0.1 million years ago responsive to extreme environmental conditions. Seventy-six orchardgrass accessions displayed low intension of domestication. The materials from Northern Europe and East Asia were clustered together, potentially resulting from diffusion along the silk road. Four candidate genes controlling orchardgrass flowering time were identified via transcriptome, quantitative genetic, and bulk segregant analysis. This paper presents a genome assembly model and comparative genetic resources for other forage grasses.

Technical Abstract: This study reports an assembly of the first chromosome-scale reference genome of a diploid orchardgrass via PacBio and Hi-C techniques. The reference genome of 1.78 Gb was assembled with contig N50 of 1.05 Mb and scaffold N50 of 3.41 Mb, accounting for 91.75% of the estimated genome size. Our results suggested that TE/LTRs in orchardgrass were likely activated during Pleistocene epoch between 0-1 million years ago responsive to extreme environmental conditions. Seventy-six orchardgrass accessions displayed low intension of domestication. The materials from Northern Europe and East Asia were clustered together, potentially resulting from diffusion along the silk road. Four candidate genes controlling orchardgrass flowering time were identified via transcriptome, quantitative genetic, and bulk segregant analysis. This paper presents a genome assembly model and comparative genetic resources for other forage grasses.