Abstract Detail

Phylogenomics

Dzurlic, Jasmina [1], Eaton, Deren [2], Cohen, Rachel [3].

The phylogenetic distribution of sex-determining genomic regions in Amaranthus identified from a new reference-free GWAS approach.

Genome-wide association studies (GWAS) are used to identify candidate loci to connect genotype to phenotype. Sex-determining loci are highly conserved and often the first genes to be mapped when constructing linkage maps of species. Here I identify the genetic basis of multiple evolutionary origins of dioecy in Amaranthus by performing a gwas with K-merkit, a novel program that detects genetic variants using a k-mer based method. Traditional GWAS rely on microarrays and reference genomes that limit the scope of association studies and preclude mapping beyond the reference. K-merkit is an alignment-free method for association studies of categorical phenotypes based on counting k-mers, testing for associations between k-mers and phenotype, and local assembly of the statistically significant k-mers. Kmerkit contains six modules: Kcount, Kfilter, Kextract, Kassemble, and Kgwas. Each module can be used independently or consecutively in a pipeline to perform a reference-free GWAS. To investigate the phylogenetic evolution of dioecy in Amaranthus, Kmerkit was used to perform a GWAS of monoecious and dioecious species. We performed whole-genome sequencing at 20 X coverage using KAPA Hyper Prep and Illumina 2x150 sequencing for 62 million reads per sample for A. cruentus, A. cannabinus, A. retroflexus, A. tricolor, A. caduatus, A. dubious, A. fimbriatus, A. spinosus and A. tuberculatus. The genome of A. hypondriacus obtained from NCBI and two pooled samples from two populations of A. palmeri from Neves et al. 2020 were included in the analysis. Using Kmer-kit, k-mers were compared between and within monoecious and dioecious species. Male and female k-mers were compared across species. Results from associations provide insight into the genetic architecture of sex determination regions in Amaranthus and the phylogenomic evolution of dioecy in the genus.

1 - Columbia University, Ecology, Evolution, and Environmental Biology, 1200 Amsterdam Avenue, Schermerhorm Ext. , New York, NY, 10027, United States
2 - Columbia University, Ecology, Evolution, And Environmental Biology, 1200 Amsterdam Ave. , Schermerhorn Ext. Office 1007, New York, NY, 10027, United States
3 - Columbia University, 1190 Amsterdam Ave, New York, NY, 10027, United States

Keywords:
Dioecy
GWAS
k-mers
evolution of sex
Amaranthus.

Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL022
Abstract ID:818
Candidate for Awards:Phytochemical Best Poster Award