Projects | Lucas K. Bobadilla

Gender determination mechanism in dioecious Amaranthus species

Wed, 31 Aug 2022 17:32:05 -0500

Contemporary agriculture must evolve to meet the challenges of achieving high yields in a sustainable fashion to feed a growing population. Among these challenges, weed management continues to be of high priority due to the constant evolution and adaptation of weeds to chemical management practices (Perotti et al. 2020, Renton et al. 2014). Collectively, waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are considered driver weed species throughout much of the US. In fact, recent surveys by the Weed Science Society of America (WSSA) classified these two weeds as the most troublesome in corn, and two of the three most troublesome in soybean.

The two species are herbaceous, annual plants native to the American Midwest and Southwest (Sauer 1955), with many attributes contributing to weediness, including high photosynthetic rates, rapid growth rates, and germination periods that extend throughout much of the growing season (Costea et al. 2005, Ward et al. 2013). However, the main attribute that makes these weeds so troublesome is their ability to rapidly and repeatedly evolve resistance to herbicides (Steckel 2007): to date, waterhemp and Palmer amaranth have evolved resistance to herbicides spanning seven and eight modes of action, respectively.

The weediness characteristics of waterhemp and Palmer amaranth are shared—at least to some extent—by many of the other Amaranthus weeds [e.g., redroot pigweed (A. retroflexus)]. Setting waterhemp and Palmer amaranth apart, however, is their dioecy characteristic. Whereas most other Amaranthus species are monoecious and predominantly self-pollinated, separate female and male plants of the dioecious species ensures outcrossing. This high rate of outcrossing promotes genetic diversity, rapid adaptation, and efficient “stacking” of multiple herbicide-resistance traits, leaving producers with few effective herbicide choices.

Dioecy can be defined as the presence of male and female individuals within a plant species. Dioecy is not common, present in about 6% of angiosperms. Despite its infrequency, however, dioecy has evolved independently in several lineages and is found in many important species [e.g., spinach (Spinacia oleracea), asparagus (Asparagus spp.), hops (Humulus spp.), cannabis (Cannabis spp.), kiwifruit (Actinidia spp.), papaya (Carica papaya), fig (Ficus carica), persimmon (Diospyros kaki), grape (Vitis vinifera), strawberry (Fragaria spp.) and willow (Salix spp.)

Dioecy provides several advantages and potential disadvantages to the success of a species. Separate sexes enforce outcrossing, favor high heterozygosity and associated heterosis, and can lead to plants being more efficient in their reproductive role. For example, female plants could invest more energy into seed production, providing more resources to their progeny.

Recent advances were made to identify male-specific Y (MSY) regions within A. tuberculatus and A. palmeri utilizing male-specific markers with the genome sequence and the identification of the MSY region in each species. The MSY regions in A. palmeri and A. tuberculatus span about 1.3 Mbp and 4.6 Mbp, respectively. Consistent with the hypothesis that dioecy evolved separately in the two species, synteny was not detected between the two species’ MSY regions. Even though the MSY identification led to a considerable advance in the diecious mechanism elucidation, no precise candidate gene was identified. This gap can be filled by the transcriptomics comparisons across genders to narrow down further putative candidates for sex-determination in dioecious weedy Amaranthus species.

The focus of my studies is to fill this gap via RNA-seq and comparative genomics analyses to narrow down de list of putative candidates for sex-determination in Amaranthus species.

Currently, the manuscript for it was submitted and it is under review.

Dicamba resistance evolution in Amaranthus tuberculatus

Sun, 24 Apr 2022 17:32:05 -0500

Waterhemp [Amaranthus tuberculatus (Moq.) Sauer] is one of the most troublesome weed species in the midwestern United States. Amaranthus tuberculatus has prolific seed production and can drastically reduce soybean and corn yields by 40% to 70%, respectively. The rapid evolution and selection of herbicide-resistance traits in A. tuberculatus represent a major challenge in managing this species. Amaranthus tuberculatus resistant to acetolactate synthase (ALS) and photosystem II (PSII) inhibitors was first identified in the 1990s; currently, resistance to herbicides from seven SOA groups (Groups 2, 4, 5, 9, 14, 15, 27) has been documented.

Dicamba is a synthetic auxin herbicide that has been commercially available since the late 1960s to control a wide range of broadleaf weeds. Dicamba is an important herbicide in corn production and also in soybean following the release of dicamba-resistant soybean cultivars.

This project has the focus the characterization of first documented dicamba resistance case in Amaranthus tuberculatus. The project was divided into two steps:

Step 1: Quantification of the resistance level and understanding of the inheritance patterns

This step was recently published on Weed Science and details can be found in the peer reviewed manuscript. In fact, the paper was featured in the cover of the journal edition and was featured in multiple News outlet.

Step 2: Transcriptome and expression variation in Dicamba resistance waterhemp

This second step consists of an RNA-seq study to identify the putative candidate genes involved with dicamba resistance. Currently, I already identified key genes that could play a role in dicamba resistance and a manuscript is on the writing process.

Herbicide resistance genetics and evolution in Lolium spp.

Sun, 24 Apr 2022 17:32:05 -0500

The Lolium genus contains many species of economic importance. L. perenne L. ssp. perenne (L. perenne), L. perenne L. spp. multiflorum (L. multiflorum), and L. rigidum are of particular relevance due to their widespread presence globally. These three species (hereinafter referred collectively to as Lolium spp.) are diploid (2n = 2x = 14), obligate outcrossing, and interfertile grass species that are widely planted for cover crop, turf, and pasture. These species are also considered weeds of agricultural and non-agricultural areas, and exhibit a distinctive ability to rapidly adapt to different environments.

Weed control is one of the most important components of cropping systems that results in significant yield and financial loss to growers if not properly performed. This scenario is exacerbated by the evolution of herbicide resistant weed populations, with 514 unique cases reported globally. Herbicide resistance in Lolium spp. populations has been widely documented. There are at least 125 reports of herbicide resistance in this genus to date, where multiple- and cross-resistance represent approximately 40% of the reports. In some regions of the world where environmental conditions for Lolium spp. development are ideal and there is an overreliance on herbicides as the main weed management tool, proportion of populations with multiple- and cross-resistance may be as high as 61%.

Herbicide resistance in Lolium spp. has been reported to 14 mechanisms of action, with an example of one population of L. rigidum from Australia with evolved resistance to seven mechanisms of action (HRAC/WSSA numbers 1, 2, 3, 8, 15, 13, and 23)

My studies during my MS at Oregon State University focused on the modelling and understanding of the geographical distribution of herbicide resistant populations across the Willamette Valley region. A secondary study was conducted to identify alternative control methods via seed sterilization using synthetic auxins. Both studies were published at Weed Science and Weed technology.

Recently I was also part of a incredible group that wrote a review article about non-target site resistance in Lolium species published at Frontiers plant science.

Currently, I am working with transcriptomics data from multiple populations of Lolium from Europe. This project as being divided into two manuscripts (Currently under review for publication):

Characterization of non-target site resistance in populations of Lolium from Western Europe with focus in the characterization of CYP81A.
Identification of local adaptation patterns in weedy lolium across Western Europe