A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

Nat Genet. 2021 Apr;53(4):574-584. doi: 10.1038/s41588-021-00808-z. Epub 2021 Mar 18.

Abstract

Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Contig Mapping / methods*
  • Crops, Agricultural / genetics*
  • Gene Duplication
  • Gene Expression Regulation, Plant
  • Genetic Loci
  • Genome Size
  • Genome, Plant*
  • High-Throughput Nucleotide Sequencing
  • Plant Breeding
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Quantitative Trait, Heritable*
  • Retroelements
  • Secale / genetics*
  • Starch / biosynthesis
  • Triticum / genetics

Substances

  • Plant Proteins
  • Retroelements
  • Starch