Comprehensive genome information for three of the most troublesome weed species recently was published.
Waterhemp, smooth pigweed and Palmer amaranth adversely affect crop production across the United States and elsewhere.
“The genome assemblies will foster further research on difficult weed species, including better understanding of the ways in which they evade control by herbicides,” Pat Tranel, a professor and associate head of the crop-sciences department at the University of Illinois, said in a news release. Tranel also is co-author of the study.
The three genomes were assembled using advanced long-read sequencing, which maintains the integrity and continuity of the genome. It’s similar to the way large puzzle pieces provide a clearer picture of the whole than small pieces.
“The goal of any genome assembly is to reveal the complete arrangement of genes in the genome, broken into chromosome-sized fragments,” said Jacob Montgomery, a graduate student working with Tranel and first author on the study.
“Until recently, quality genome assemblies have been labor intensive and expensive. The previously published draft genomes for these species reported the genome broken into thousands of pieces. The assemblies we report are down to hundreds. The majority of the sequence is now assembled into very large fragments.”
To further improve the assembly of the genomes for waterhemp and smooth pigweed, the researchers used an approach known as trio binning, which was developed in cattle. The technique hadn’t been fully utilized in plants before.
The researchers created hybrid offspring from two separate species — waterhemp and smooth pigweed.
“This approach resolved a problem in the previous waterhemp genome assembly,” Tranel said. “When parent alleles are very different from each other, as is often the case in outcrossing species such as waterhemp, the genome-assembly program interprets them to be different genes. With only one allele from each species we were able to obtain a cleaner assembly of their gene sequences.”
The researchers chose waterhemp as the male parent in the smooth pigweed-waterhemp cross because the previously published waterhemp genome was from a female plant. Tranel is pursuing research to understand the genetic basis for maleness and femaleness in waterhemp and Palmer amaranth, with potential applications toward introducing female sterility as a future control method.
“The genomes of the male waterhemp and Palmer amaranth already have enabled us to make rapid progress on identifying potential genes that could be responsible for the determination of sex in both species,” Tranel said.
The genomes for all three species could help address the problem of herbicide resistance. Scientists are uncovering evidence of non-target site or metabolic resistance in waterhemp and Palmer amaranth. That would enable weeds to detoxify herbicides before they cause damage. But it’s usually difficult to determine which specific enzyme, among hundreds, is responsible for detoxifying the herbicide, according to the researchers.
The researchers will now be able to sort through a list to find the culprit in hopes of either knocking out the enzyme responsible or modifying the herbicide molecule to evade detoxification.
The study recently was published in “Genome Biology and Evolution.”