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Genome wide association study to map genetic loci underlying important agronomic traits of wild emmer wheat (Triticum dicoccoides)

Rahman, Shanjida (2022) Genome wide association study to map genetic loci underlying important agronomic traits of wild emmer wheat (Triticum dicoccoides). PhD thesis, Murdoch University.

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Wild emmer (Triticum dicoccoides) is a progenitor of modern wheat that played the central role in wheat evolution. During the long process of evolution, rapid alteration and sporadic genomic changes occurred in wheat which resulted in gene modifications and some genes were lost in modern wheats. Thus, wild emmer contains a high number of novel genes which are absent in durum or bread wheat. Despite of huge diversity on morphological, grain quality and stress related traits, very few genes have been explored from wild emmer in the past. Particularly, only few shoots morphological trait related alleles have been well characterised. Likewise, root traits of wild emmer are almost unexplored. In this study, diversity of important shoot and root morphological traits across 263 wild emmer accessions were investigated and their genetics was studied. Accessions were collected from different parts of Israel, Turkey, Lebanon, and Syria. Shoot phenotyping was carried out on 19 traits by conducting three individual experiments, including two glasshouse experiments in 2019 and 2020 and one field trial in 2020. Root phenotyping was conducted on 10 traits in two independent glasshouse experiments in 2020 and 2021. All traits showed a wide range of variations, indicating a huge phenotypic diversity in wild emmer germplasm. The key traits identified with breeding potential include flowering time, tiller number, spike length, leaf area, shoot biomass, lateral root count, primary root count, and root biomass. Based on collection region, the germplasm was grouped into eight populations which demonstrated considerable variations for a few traits such as plant height, spike length and flag leaf area, but not for any root trait. Clustering based on shoot and root traits formed two broad groups where the Turkish germplasm grouped with that of Israeli, while the Lebanese and Syrian germplasm formed a separate group. Genotyping of the 263 wild emmer accessions was carried out using 90K SNP (Single Nucleotide Polymorphism) array. After quality checking, a total of 11,393 SNPs were selected for downstream analysis. A high level of diversity was observed, with an overall genetic diversity value of 0.4294 and a polymorphism information content (PIC) value of 0.3808. Structure analysis and phylogenetic analysis based on SNP markers divided the wild emmer germplasm into two sub-populations. GWAS (Genome Wide Association Study) was conducted using TASSEL (Trait Analysis by Association, Evolution and Linkage) software with the Mixed Linear Model (MLM). A total of 857 significant MTAs (Marker Trait Associations) were identified for shoot traits, among which 81 were highly significant. For root traits, 255 significant MTAs were identified, among which 31 were highly significant. Putative candidate genes and annotations were identified for all highly significant MTAs using specialized bioinformatics platform for wild emmer called ‘GrainGene’. The selected MTAs on phenotypes showed significant allelic effects among alternative alleles in most cases. However, the most promising MTAs belong to growth stage related traits, tiller number, shoot biomass, yield related traits, lateral and primary root count, and root biomass. Some of the novel alleles identified in the study include IWB19587 on 2A, IWB5392 on 4A, IWB58299 and IWB9063 on 7A for growth stage related traits; IWB3715 on 1B, IWA24354 and IWA4622 on 5B, IWB4154 on 7B for total tiller number; IWB64507 and IWB73323 on 4A for effective tiller number; IWB57171 on 7A for shoot biomass; IWB41324 and IWB57707 on 5A for yield; IWB44730 on 1B, IWB24094 and IWA1214 on 5A, IWA4622 on 5B, IWB67213 on 6B for lateral root count; IWB69753 and IWB32014 on 6B, IWB3235 on 7B for primary root count; and IWB70454 on 6A, IWA4249 on 7B for root biomass. The new alleles identified from this study have the potential to be incorporated into bread and durum wheat as wild emmer is easily crossable with both, which will ultimately accelerate wheat improvement.

Item Type: Thesis (PhD)
Murdoch Affiliation(s): College of Science, Health, Engineering and Education
Supervisor(s): Ma, Wujun, Islam, Shahidul, Sharma, Darshan and She, Maoyun
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