Molecular breeding tools for improving morphological traits and biotic and abiotic stress responses in perennial ryegrass
Creators: name: Vines, Phillip Lavelle
Publisher: name: No Publisher Supplied
Year: 2019

description: Perennial ryegrass (Lolium perenne L.) is a widely used cool-season turfgrass species. The primary breeding objectives for turf-type perennial ryegrass include improving tolerance to abiotic and biotic factors such as salinity stress and dollar spot disease, which is caused by Clarireedia jacksonii C. Salgado, L.A. Beirn, B.B. Clarke, and J.A. Crouch. These types of traits are often quantitatively inherited and present difficulties for the phenotypic selection breeding technique. Quantitative trait locus (QTL) mapping has been implemented in modern plant breeding programs as a basis for marker-assisted selection for complex, quantitatively inherited traits. The preliminary components for QTL mapping include developing an appropriate mapping population and constructing a genetic linkage map that is densely populated with markers. After these prerequisite tasks have been completed, and phenotypic data for the traits of interest have been collected, QTL analyses may be conducted. The purpose of this dissertation was to exploit the QTL mapping technique for developing molecular breeding tools to help improve these complex traits in perennial ryegrass. The specific research objectives of this work were (i) to develop a diverse perennial ryegrass mapping population that would accommodate QTL mapping studies for salinity tolerance and dollar spot resistance in perennial ryegrass, (ii) to construct a high-density, single nucleotide polymorphism (SNP)-based genetic linkage map for perennial ryegrass, (iii) to conduct QTL analyses for salinity tolerance, dollar spot resistance, and growth habit morphology traits in perennial ryegrass. For the first objective, candidate parental genotypes were selected from a large population of perennial ryegrass clones in the Rutgers turfgrass breeding program. These genotypes were studied for response to salinity stress and dollar spot disease. Additionally, phenotypic variation in growth habit and leaf color was also observed among the candidate parental genotypes. Although these two traits were not of primary interest in developing the mapping population, they were also considered when pairing parents for cross-fertilization events. Nine biparental crosses were made in the summer of 2016. The selected population consisted of 118 pseudo-F2 progeny derived from a cross between 15-8325 (maternal parent, referenced as I06) and 15-8343 (paternal parent, referenced as A89). Thus, the population is commonly referenced as the I06 × A89 perennial ryegrass mapping population and is comprised of the 2 parent genotypes and 118 progeny genotypes. For the second objective, greater than 1.8 Gb of raw sequencing reads were generated for the 2 parent genotypes and the 118 progeny genotypes from the I06 × A89 population. In addition to the SNP markers that were generated in this study, a set of framework simple sequence repeat (SSR) markers from previous studies were also used for linkage map construction. Two linkage maps, one for each parent, were developed. After screening markers for polymorphisms, segregation distortion, redundancy, and insufficient grouping support, 848 SNP markers and 52 SSR markers were included in the marker dataset for parent I06 while 769 SNP markers and 35 SSR markers were included in the marker dataset for parent A89. The 900 markers included in the I06 dataset mapped to a total distance of 677.5 cM with an average marker density of 0.75 cM. The 804 markers included in the A89 dataset mapped to a total distance of 687.9 cM with an average marker density of 0.86 cM. For the third objective, the I06 × A89 population was evaluated for the traits of salinity tolerance, dollar spot resistance, and growth habit morphology using multiple field trials during 2017 and 2018 at the Rutgers Plant Science Research and Extension Farm in Adelphia, NJ. Subsequently, QTL analyses were conducted with the individual I06 and A89 parent maps and phenotypic data for the traits of interest.The QTL analyses for salinity tolerance resulted in the identification of fifteen major-effect QTL and forty-three minor-effect QTL. Eleven salinity tolerance QTL were identified using two distinct assessment methods for salinity tolerance, seven salinity tolerance QTL were identified at multiple environmental locations, and one salinity tolerance QTL was identified on both parent maps. The QTL analyses for dollar spot resistance resulted in the identification of twelve major-effect QTL and nine minor-effect QTL. Coincident dollar spot resistance QTL were mapped to four distinct genomic regions and were consistently identified using multiple evaluation methods for dollar spot severity and/or multiple environments. The growth habit morphology QTL analyses resulted in the identification of twenty-one major effect QTL and seven minor-effect QTL. Four growth habit morphology QTL were identified across multiple environments, and two growth habit morphology QTL were significantly associated with multiple morphological traits. These are the first reported efforts for QTL mapping of salinity tolerance and dollar spot resistance in perennial ryegrass. Further, this is the first report of QTL mapping for growth habit traits in turf-type perennial ryegrass. These findings will be useful for future studies involving development of marker-assisted selection techniques for breeding applications, gene and mechanism discovery, and comparative genomics investigations using closely related plant species. These efforts will be used to develop improved perennial ryegrass cultivars, which will ultimately contribute to the sustainability of the turfgrass industry. Moreover, the I06 × A89 perennial ryegrass population will be useful to further study these and additional traits in perennial ryegrass, and the high-density genetic linkage map constructed herein will be a valuable resource for future QTL studies in turf-type perennial ryegrass breeding.