4.3 Article

Natural variation and improved genome annotation of the emerging biofuel crop field pennycress (Thlaspi arvense)

期刊

G3-GENES GENOMES GENETICS
卷 12, 期 6, 页码 -

出版社

OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkac084

关键词

Thlaspi arvense (pennycress); genome annotation; accessions; RNA-seq; SNPs

资金

  1. DOE Office of Science, Office of Biological and Environmental Research (BER) [DE-SC0019233]
  2. U.S. Department of Energy (DOE) [DE-SC0019233] Funding Source: U.S. Department of Energy (DOE)

向作者/读者索取更多资源

Pennycress, a plant with suitable seed oil composition for biodiesel and aviation fuel production, requires domestication of its wild traits for cultivation. This study improved the genome annotation of pennycress and identified protein-coding genes and biallelic SNPs. Several candidate genes under likely recent positive selection were also discovered, which could be potential targets for crop improvement efforts in pennycress.
The Brassicaceae family comprises more than 3,700 species with a diversity of phenotypic characteristics, including seed oil content and composition. Recently, the global interest in Thlaspi arvense L. (pennycress) has grown as the seed oil composition makes it a suitable source for biodiesel and aviation fuel production. However, many wild traits of this species need to be domesticated to make pennycress ideal for cultivation. Molecular breeding and engineering efforts require the availability of an accurate genome sequence of the species. Here, we describe pennycress genome annotation improvements, using a combination of long- and short-read transcriptome data obtained from RNA derived from embryos of 22 accessions, in addition to public genome and gene expression information. Our analysis identified 27,213 protein-coding genes, as well as on average 6,188 biallelic SNPs. In addition, we used the identified SNPs to evaluate the population structure of our accessions. The data from this analysis support that the accession Ames 32872, originally from Armenia, is highly divergent from the other accessions, while the accessions originating from Canada and the United States cluster together. When we evaluated the likely signatures of natural selection from alternative SNPs, we found 7 candidate genes under likely recent positive selection. These genes are enriched with functions related to amino acid metabolism and lipid biosynthesis and highlight possible future targets for crop improvement efforts in pennycress.

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