Genomes published for major agricultural weeds

Date:
August 27, 2020
Source:
University of Illinois College of Agricultural, Consumer and
Environmental Sciences
Summary:
Representing some of the most troublesome agricultural weeds,
waterhemp, smooth pigweed, and Palmer amaranth impact crop
production systems across the US and elsewhere with ripple effects
felt by economies worldwide. In a landmark study, scientists have
published the most comprehensive genome information to date for
all three species, marking a new era of scientific discovery toward
potential solutions.



FULL STORY ========================================================================== Representing some of the most troublesome agricultural weeds, waterhemp,
smooth pigweed, and Palmer amaranth impact crop production systems
across the U.S. and elsewhere with ripple effects felt by economies
worldwide. In a landmark study, scientists have published the most comprehensive genome information to date for all three species, marking
a new era of scientific discovery toward potential solutions.


========================================================================== "These genome assemblies will greatly foster further research on these difficult weed species, including better understanding the ways in
which they evade damage from herbicides," says Pat Tranel, professor and associate head of the Department of Crop Sciences at the University of
Illinois and co-author on the Genome Biology and Evolution study.

Draft genomes had already been published for waterhemp and Palmer
amaranth, but techniques used in the Genome Biology and Evolution study
provide a much clearer and richer picture of the species' gene sequences,
a requisite for many genomic studies.

All three genomes were assembled using advanced long-read sequencing,
which maintains the integrity and continuity of the genome similar to
the way large puzzle pieces provide a clearer picture of the whole than
small pieces. In Palmer amaranth, an additional sequencing technology (chromatin conformation capture sequencing) was used to further order
pieces of the genome that were assembled using the long-read information.

"The goal of any genome assembly is to reveal the complete
arrangement of genes in the genome, broken into chromosome-sized
fragments. Unfortunately, until recently, quality genome assemblies have
been very labor intensive and expensive. The previously published draft
genomes for these species reported the genome broken into thousands of
pieces, while the assemblies we report are down to hundreds. The vast
majority of the sequence is now assembled into very large fragments,"
says Jacob Montgomery, a graduate student working with Tranel and first
author on the study.

To further improve the assembly of the genomes for waterhemp and smooth pigweed, the team used an innovative approach known as trio binning,
developed in cattle. Not only had this technique never before been
fully utilized in plants, it had also not been used with parents from
different species.



==========================================================================
In normal reproduction, male and female parents each contribute one copy
of every gene to their offspring. In this case, offspring are diploid,
meaning they have two copies of every gene. In the study, the team
created hybrid offspring from two separate species: waterhemp and smooth pigweed. These offspring are still diploid, but the trio binning technique allowed the researchers to pull apart and isolate the two copies from
each parent species, resulting in haploid (single copy) genomes for each.

"This approach resolved a problem in the previous waterhemp genome
assembly.

When parent alleles (copies of each gene) 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," Tranel
says. "With only one allele from each species, we were able to obtain a
much cleaner assembly of their gene sequences." Detlef Weigel, director
of the Max Planck Institute for Developmental Biology and co-author on the study, adds, "I am a big fan of the new advanced sequencing techniques,
but even though they should theoretically be sufficient to sort out the arrangement of genes, in practice they are not. This is where genetics
can help out, using information on whether genes were inherited from
mom or dad. This allowed us to assign each gene to either a maternal
or paternal chromosome." The researchers specifically chose waterhemp
as the male parent in the smooth pigweed x 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 my group to make rapid progress on identifying the potential
genes that could be responsible for the determination of sex (male or
female) in both species," Tranel says.

Importantly, the genomes for all three species could start to chip away
at the problem of herbicide resistance in these weeds. More and more, scientists are uncovering evidence of non-target-site or metabolic
resistance in waterhemp and Palmer amaranth, allowing the weeds to
detoxify herbicides before they can cause damage. Unfortunately, it is
usually very difficult to determine which specific enzyme, among hundreds,
is responsible for detoxifying the herbicide.

Now, researchers will essentially be able to sort through a list to find
the culprit with the hope of either knocking out the enzyme responsible
or modifying the herbicide molecule to evade detoxification.

"Innovation is essential for the future of agriculture. We at BASF are
working continuously on improving our products and services including sustainable solutions for the management of herbicide-resistant weeds. We
want to better understand the amaranth biochemical resistance mechanisms
in order to offer farmers new products and solutions for optimal control
of key weeds," says Jens Lerchl, head of early biology research on
herbicides at BASF and study co- author. Lerchl coordinated the Palmer
amaranth genome work with KeyGene/ Wageningen -The Netherlands.

"The area of genome sequencing is highly dynamic. That is why BASF
chose KeyGene as the partner for both latest sequencing technology and bioinformatics. Together with the expertise of the University of Illinois
and Max Planck Society, we were able to compare genomes and address
specific biological topics," Lerchl says. In addition to collaborating
on this research, BASF is also a founding member of the International
Weed Genomics Consortium, led by Colorado State University aiming at
the sequencing and analysis of ten high priority key weeds.


========================================================================== Story Source: Materials provided by University_of_Illinois_College_of_Agricultural,_Consumer and_Environmental_Sciences. Original written by Lauren Quinn. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Jacob S Montgomery, Darci Giacomini, Bridgit Waithaka, Christa Lanz,
Brent P Murphy, Ruth Campe, Jens Lerchl, Andreas Landes, Fanny
Gatzmann, Antoine Janssen, Rudie Antonise, Eric Patterson, Detlef
Weigel, Patrick J Tranel. Draft genomes of Amaranthus tuberculatus,
Amaranthus hybridus and Amaranthus palmeri. Genome Biology and
Evolution, 2020; DOI: 10.1093/gbe/ evaa177 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200827105926.htm

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