Repository logo

Browsing by Author "Morris, Geoffrey, advisor"

Now showing 1 - 4 of 4
  • Thumbnail Image
    ItemOpen Access
    An NLR gene likely underlying RMES1 provides global sorghum resistance bolstered by RMES2
    (Colorado State University. Libraries, 2023) VanGessel, Carl, author; Morris, Geoffrey, advisor; Nalam, Vamsi, committee member; Roberts, Robyn, committee member; Mason, Esten, committee member
    Breeding for aphid host plant resistance in sorghum has been an area of interest since the emergence of Melanaphis sorghi in North America a decade ago. In order to develop durable sorghum aphid resistance, breeders must be equipped with tools (trait package) and knowledge (molecular mechanisms) of host plant resistance. In this dissertation, I characterize the current state of sorghum aphid breeding and propose a genotype to phenotype map for the major source of global resistance, Resistance to Melanaphis sorghi 1. Relying on near-isogenic lines, I demonstrate that RMES1 is applying selection pressure to sorghum aphid through reduction in fecundity that discriminates among aphid species. In global sorghum lines, RMES1 is rare whereas a second resistance source, RMES2, is common and present in historic breeding germplasm. I mapped RMES2 in Haitian breeding populations where it contributes fitness increases while lacking antagonistic pleiotropy and is selected for alongside RMES1. These results suggest breeding programs may unknowingly be deploying both sources of resistance which in combination are reducing the likelihood of M. sorghi biotype shifts to overcome RMES1. As aphid resistance may rely on phytochemical and/or induction with extended phenotypes regarding aphid populations, I used pan-genomic, transcriptomic, and metabolomic resources to describe the molecular mechanism of RMES1. Structural variation at the Chr06 locus underlies presence/absence variation of several nucleotide-binding leucine-rich repeat receptor (NLR) genes. Two of these candidate genes, SbPI276837.06G016400 and SbPI276837.06G016600, are representatives of two orthologous NLR groups which have genomic and transcriptomic evidence of underlying RMES1 resistance. The PAL branch of the salicylic acid pathway is the primary phytohormone pathway responsible for RMES1-induced resistance. Finally, metabolome reorganization mirroring transcriptome changes suggest RMES1 is inducing multiple downstream mechanisms responsible for reducing aphid fecundity. While the causal gene underlying RMES1 remains to be cloned and the eliciting aphid factor is unknown, this research suggests that gene-for-gene dynamics could lead to resistance-breaking biotype shifts and combining RMES1 with additional resistance genes e.g. RMES2, will help achieve durability.
  • Thumbnail Image
    ItemOpen Access
    Phenotyping tools and genetic knowledge to facilitate breeding of dhurrin content and cyanogenic potential in sorghum
    (Colorado State University. Libraries, 2023) Johnson, Kristen, author; Morris, Geoffrey, advisor; Mason, Esten, committee member; Prenni, Jessica, committee member
    Cyanogenic glucosides are important secondary compounds found in plants serving roles such as plant defense, pollinator attraction, nitrogen (N) sources, and drought tolerance. Sorghum (S. bicolor [L.] Moench), an important grain crop predominantly grown in drought-prone environments, contains a cyanogenic glucoside known as dhurrin where it functions as a source of hydrogen cyanide (HCN) after the leaf tissue is disrupted. Dhurrin has been hypothesized to serve as an osmoprotectant, N turnover source, and sorghum aphid resistance mechanism. In addition, dhurrin concentrations can vary due to growth stage, environment, and genotype, and this variability can cause limitations for effective dhurrin phenotyping. To facilitate the breeding of dhurrin and HCNp, we developed a semi-quantitative phenotyping method to detect HCNp and investigated the genetics of dhurrin and HCN variation in global sorghum germplasm. In the first study, we developed a simple, semi-quantitative, high-throughput phenotyping method to detect HCNp in sorghum leaf tissue. Biochemical methods have been used to determine dhurrin content quantitatively, however these methods are laborious and costly. As a result, we developed a semi-quantitative phenotypic assay using commercial test strip paper to measure HCNp utilizing a F13 Stg Recombinant Inbred Line (RIL) population with previously reported dhurrin concentrations. We found that later sampling time improved the detection of HCNp variation with broad-sense heritability (H2) values highest at flowering. In addition, we found that other covariates such as leaf number may play a role in effective phenotyping. Altogether this assay can be used to screen a sorghum breeding population in both a greenhouse and field setting for smallholder breeding programs looking to advance their breeding generations more efficiently. In the second study we sought to understand the genetics underlying HCN and dhurrin variability, as well as investigate the relationship between drought and dhurrin using diverse sorghum landraces. We found no direct correlation between dhurrin and drought, but the slight positive correlation could suggest other environmental factors, such as pest pressures, are driving HCN and dhurrin variation. To further understand the biological relationship between dhurrin and HCN, we conducted a genome-wide association study (GWAS) for HCNp and dhurrin. We identified several significant associations between HCNp and known dhurrin biosynthetic and catabolic genetic markers, but major biosynthesis loci were not all significantly associated with HCNp. In addition, we performed a GWAS on dhurrin and found peaks associated with the dhurrin biosynthetic gene cluster, as well as other unknown loci that could contribute to dhurrin variation. This suggests that genetic variation for genes in the dhurrin biosynthesis, catabolism, and recycling pathway contributes to HCNp variability, and they are not direct proxies for each other. As a result, breeders should de-couple phenotyping methods for dhurrin and HCNp depending on the trait of interest.
  • Thumbnail Image
    ItemOpen Access
    Unlocking sorghum adaptive potential through investigations into pleiotropic control of chilling tolerance by Tannin1
    (Colorado State University. Libraries, 2023) Schuh, Anthony, author; Morris, Geoffrey, advisor; Argueso, Cristiana, committee member; Wrighton, Kelly, committee member
    Chilling tolerant crops can positively impact agricultural sustainability through lengthened growing seasons and improved water and nitrogen use efficiency. In sorghum (Sorghum bicolor [L.] Moench), the fourth most grown grain, coinheritance of qSbCT04.62, the largest effect chilling tolerance locus, with Tannin1, the major gene underlying undesirable grain proanthocyanidins, has stymied breeding for chilling tolerance. To investigate the genetic basis of qSbCT04.62, including its coinheritance with Tan1, we developed near isogenic lines (NILs) with chilling tolerant haplotypes around qCT04.62. In the first study we genotype the NILs and investigate the introgressions physiological control over the cold stress response. Genome sequencing revealed that the CT04.62+ NILs introgressions on chr04 include Tannin1, a homolog of Arabidopsis cold regulator CBF, peak SNPs for qCT04.62 from multi-family NAM, and 61.2-62 Mb of HKZ ✕ BTx623 NAM family qCT04.62 confidence interval. Grain tannins were correlated with Tan1 genotype, revealing heterogeneity in one NIL at Tannin1. Controlled environment chilling assays found no genotype by environment interaction on growth by chilling per se in parents or NILs. Cold germination was reduced at 15°C and superior at 20 and 25°C in the chilling tolerant parent compared to chilling sensitive, but unchanged between NILs. The introgression also did not regulate a chilling induced increase in non-photochemical quenching. In the second study we investigated Tan1 function with a transcriptome analysis of the NIL's response to chilling stress. Tannin1 was widely expressed in sorghum tissues but did not promote a transcriptional response in chilling tolerance related molecular pathways including lipid remodeling, phytohormone signaling, CBF upregulation, photoprotection, and ROS mitigation. GO analysis also found no significant term enrichments at the p < 0.1 threshold. Only 17 genes had expression patterns regulated by polymorphisms in the introgressions, seven cis, and ten trans, with little evidence of co-regulation. Further, Tannin1 was functionally divergent from its Arabidopsis ortholog TTG1 and other WD40 orthologs in regulating leaf anthocyanin biosynthesis. Overall, these findings suggest that linkage, not pleiotropy, underpins the coinheritance of Tan1 and CT04.62+, unlocking the use of CT04.62+ for sorghum improvement. Further, these results imply a lack of deleterious fitness effects of tan1 alleles in commercial grain sorghum varieties and suggest the possibility of an unknown cold tolerance regulator which, if identified, could have implications for crop improvement of chilling tolerance outside sorghum.
  • Thumbnail Image
    ItemOpen Access
    Utilizing plant genetic resources for pre-breeding of water-efficient sorghum: genetics of the limited transpiration trait
    (Colorado State University. Libraries, 2022) Cerimele, Gina, author; Morris, Geoffrey, advisor; Cotrufo, Francesca, committee member; McKay, John, committee member
    Shifting precipitation patterns driven by the changing climate threaten productivity of dryland agricultural systems. Increasing the efficiency of water use by crops grown in dryland regions, such as sorghum (Sorghum bicolor), is a target for plant breeding to address this issue. c variants conferring efficient water use in sorghum may be found within collections of plant genetic resources (PGR). However, tropical sorghum PGR require adaptation to the target temperate environment to begin the pre-breeding trait discovery process. The landmark Sorghum Conversion Program unlocked diverse sorghum genetics for temperate breeding by adapting tropical African lines to temperate height and maturity standards. In the U.S. Sorghum Belt, spanning South Dakota to central Texas, the limited transpiration (LT) trait could provide growers a 5% yield increase in water-limited conditions with high vapor pressure deficit (VPD) according to crop modeling. To transfer the LT trait into commercial breeding programs, an elite donor line must be developed. Characterizing the genetic architecture of LT informs markers and breeding strategy for development of an elite donor. To characterize the genetic architecture of LT, two biparental recombinant inbred line (RIL) mapping families were developed from crossing putative LT parents SC979 and BTx2752 by putative non-LT parent RTx430. For this study, the families were grown together as a mapping population in three locations (continental-humid eastern Kansas, semi-arid western Kansas, and semi-arid Colorado) in one year. The families were phenotyped for the LT trait using UAS- collected thermal imaging and canopy temperature as a proxy. The families were initially designed with the goal of controlling phenotypic covariates of canopy temperature associated with height and flowering time, like neighbor-shading and artifactual temperature inflation related to panicle imaging. To test whether the family design controlled for height and flowering time covariates, the populations were phenotyped for both traits. High broad-sense heritability (H2) > 0.86 for all traits and families across locations indicates that the traits are not fixed. However, phenotypic distributions reveal that most lines are within an agronomically-relevant range that limits confounding covariates. Using DArTseq-LD genotyping data, GWAS analyses of height and flowering time reveal putatively significant marker-trait associations (MTA) with known loci underlying height and maturity in sorghum. These results collectively indicate that, while genetic variation for height and flowering exist in the LT mapping families, the resulting phenotypes are homogeneous enough to be suitable for LT genetic mapping. To test hypotheses on the monogenic, oligogenic, or polygenic architecture of the LT trait, canopy temperature data collected by the UAS-thermal imaging missions was used. Non-zero H2 of canopy temperature in most location-timepoints indicates genetic variation is present for LT in the population. Continuous phenotypic distributions imply a quantitative architecture. GWAS analyses revealed moderate marker-trait association peaks visible within timepoints and across locations, indicating oligogenic architecture of LT. Some of those peaks also colocalize with sorghum homologs of aquaporin genes in Arabidopsis thaliana, suggesting that aquaporin variation could be a molecular basis underlying the trait. These results provide a basis for marker-assisted selection in developing an LT donor line.