Genomic and transcriptomic insight into the evolution and breeding of turfgrass species, Poa annua and Bouteloua dactyloides
Open Access
- Author:
- Benson, Christopher
- Graduate Program:
- Plant Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- July 14, 2023
- Committee Members:
- Sally Mackenzie, Major Field Member
David Huff, Chair & Dissertation Advisor
Claude Depamphilis, Outside Field Member
Gary Felton, Outside Unit Member
Teh-Hui Kao, Program Head/Chair - Keywords:
- Poa annua
turfgrass
genetics
genomics
polyploidy
sequencing
breeding
annual bluegrass
annual meadowgrass
pistil smut
Bouteloua dactyloides
Buffalograss
Salmacisia buchloëana
the genome balance hypothesis
dioecy
tilletia
golf
putting green
homoeolog
polyploid plasticity hypothesis
chromosome modification
chromosome restructuring
fractionation
retrotransposon
synteny
RNA-seq
comparative genomics
pan-genome
transposable element
host manipulation
amphihapoid
haploid plants
allotetraploid
DNA methylation
Poa infirma
Poa supina - Abstract:
- Turfgrasses, in their broadest definition, are plants that form a roughly continuous ground cover that persists with regular mowing and foot traffic. Over the past 100 years, the turfgrass industry has blossomed from its infancy into a $60 billion industry with an estimated 60 million acres of land covered in turf in the US. As a result of its recent onset, much of the genetic advancement in turf has been attained using conventional breeding methods and recurrent selection. In the coming decades, turfgrass breeders, like food crop breeders, will benefit extensively from integrating modern tools in multi-omic surveys on diversity, high-throughput phenotyping, and large-scale measures of plant performance. In this work, I use multi-omic sequencing, global measures of DNA methylation, and whole-plant phenotyping to investigate the agronomic components of two widely used turfgrass species, Poa annua and Bouteloua dactyloides. Poa annua (2n=4x=28) is a cool-season (C3) grass. It is an allotetraploid resulting from an interspecific cross between diploid species, Poa infirma (2n=2x=14) and Poa supina (2n=2x=14). Poa annua is highly morphologically variable and spans the continuum from annual to perennial biotypes with seeding populations on all seven continents. As a result of its wide phenotypic plasticity and range of morphologies, it occupies the juxtaposing cultural niches of being both a pervasive weed and a highly valued turfgrass species. In chapter two, I use methyl-sensitive molecular markers and 5-mC-targeted ELISAs to compare global DNA methylation status in clonal populations of abiotically stressed P. annua. I find that golf course-style mowing stress increases global DNA methylation and that methylation status in the offspring of mowed plants remains elevated when compared to their unmowed clone. The observed partial heritability of the DNA methylation landscape is correlated with phenotypic differences, where the progeny of mowed clones are more dwarf. I conclude that DNA methylation may play a role in epigenetically priming P. annua seedlings to its local environment. In chapter 3, I sequence, assemble, and annotate the chromosome-level genomes of Poa annua’s diploid progenitors, Poa infirma and Poa supina. I find that P. infirma and P. supina diverged from their common ancestor 5.5 - 6.3 Mya and hybridized to form P. annua ≤ 50,000 years ago. Poa annua’s allotetraploid subgenomes remain remarkably intact with ~1,300 small (averaging 15 kb in length) homoeologous exchanges (HEs) evenly split between subgenomes. Although HEs do not have a subgenome bias in terms of number and length, there does appear to be a bias in gene density within HEs, such that 68% of genes within HEs move from the A (infirma) subgenome to the B (supina) subgenome. Poa annua’s subgenomes appear to be heavily structured by disparate bursts of long terminal repeats (LTR) activity that pre-date hybridization but continue into present day. In addition, I show that active LTRs preferentially land in the B subgenome regardless of their subgenome origin. On the basis of biased LTR movement and biased reshuffling of genes, I conclude that both retrotransposons and host genes are preferentially drawn to B subgenome homoeologs. To better understand subgenome dominance and to test subgenome expression bias under environmental stress, I conducted a subgenome-specific RNA-seq experiment on abiotically stressed P. annua. I observe a small but statistically significant gene expression bias favoring B homoeologs and find that P. annua appears to have partitioned its primary metabolic processes irrespective of the environmental condition used here. Whole-genome resequencing of 15 additional P. annua genotypes revealed large-scale chromosomal variation in the species with some genotypes shedding as much as 224 Mb of repetitive sequence from the largest and most TE-dense chromosome. This result supports the Genome Balance hypothesis, which predicts that subgenomes with vastly different amounts of paracentric heterochromatin will segregate unequally during meiosis and that the centromeric and pericentromeric sequence of one of the homoeologs will be retained to solve those segregational issues. In chapter 4, I used whole-genome and RNA sequencing to explore the biotrophic relationship between fungal pathogen, Salmacisia buchloëana, and its sole host, Bouteloua dactyloides (buffalograss). Buffalograss is dioecious with variable ploidy and high genetic heterogeneity. It is a valued turfgrass species for its heat and drought tolerance and low maintenance requirement. Infection with S. buchloëana results in increased reproductive allocation and higher seed yield potential in buffalograss. I show that S. buchloëana is a closely related to the genus Tilletia and identify a novel chromosome arm that contains no syntenic relationship to related Tilletia fungi. I find that genes on the novel chromosome arm are preferentially upregulated during infection and contain an enrichment of tandemly duplicated serine-type peptidases. In addition, I show that buffalograss upregulates serine-type peptidase inhibitors when infected with S. buchloëana. This work establishes a framework for the genetic underpinnings of biotically-induced seed yield potential in buffalograss. In this dissertation, I explore the genetic and genomic components contributing to stress tolerance, phenotypic plasticity, plant performance, and seed yield potential in two agronomically significant turfgrass species. The resources generated as a result of this work (available at www.ncbi.nlm.nih.gov/sra/?term=Christopher%20Benson) will be a valuable tool for turfgrass breeders and help to fast-track genome-guided breeding decisions and enable precise genome editing to accelerate turfgrass cultivar development and facilitate technological advancement in the grass seed industry and in other polyploid crops.