The galling insect, Leptocybe invasa, causes significant losses in plantations of various Eucalyptus species and hybrids, threatening its economic viability. We applied a Genome-Wide Association Study (GWAS) to identify single nucleotide polymorphism (SNP) markers associated with resistance to L. invasa. A total of 563 insect-challenged Eucalyptus grandis trees, from 61 half-sib families, were genotyped using the EUChip60K SNP chip and we identified 15,445 informative SNP markers in the test population. Multi-Locus Mixed Model (MLMM) analysis identified 35 SNP markers putatively associated with resistance to L. invasa based on four discreet classes of insect damage scores: (0)- not infested, (1)- infested showing evidence of oviposition but no gall development, (2)- infested with galls on leaves, mid-ribs or petioles and (3)- stunting and lethal gall formation. MLMM analysis identified three associated genomic regions on chromosomes 3, 7 and 8 jointly explaining 17.6% of the total phenotypic variation. SNP analysis of a validation population of 494 E. grandis trees confirmed seven SNP markers that were also detected in the initial association analysis. Based on transcriptome profiles of resistant and susceptible genotypes from an independent experiment we identified several putative candidate genes in associated genomic loci including NB-ARC and TIR-NBS-LRR genes. Our results suggest that Leptocybe resistance in E. grandis may be influenced by a few large-effect loci in combination with minor effect loci segregating in our test and validation populations.

Detailed knowledge on genetic diversity among germplasm is important for hybrid maize (Zea mays L.) breeding. The objective of the study was to determine genetic diversity in widely grown hybrids in Southern Africa, and compare effectiveness of phenotypic analysis models for determining genetic distances between hybrids. Fifty hybrids were evaluated at one site with two replicates. The experiment was a randomized complete block design. Phenotypic and genotypic data were analyzed using SAS and Power Marker respectively. There was significant (p < 0.01) variation and diversity among hybrid brands but small within brand clusters. Polymorphic Information Content (PIC) ranged from 0.07 to 0.38 with an average of 0.34 and genetic distance ranged from 0.08 to 0.50 with an average of 0.43. SAH23 and SAH21 (0.48) and SAH33 and SAH3 (0.47) were the most distantly related hybrids. Both single nucleotide polymorphism (SNP) markers and phenotypic data models were effective for discriminating genotypes according to genetic distance. SNP markers revealed nine clusters of hybrids. The 12-trait phenotypic analysis model, revealed eight clusters at 85%, while the five-trait model revealed six clusters. Path analysis revealed significant direct and indirect effects of secondary traits on yield. Plant height and ear height were negatively correlated with grain yield meaning shorter hybrids gave high yield. Ear weight, days to anthesis, and number of ears had highest positive direct effects on yield. These traits can provide good selection index for high yielding maize hybrids. Results confirmed that diversity of hybrids is small within brands and also confirm that phenotypic trait models are effective for discriminating hybrids.

Terpenes are an important group of plant specialized metabolites (PSM) influencing, amongst other functions, defence mechanisms against pests. We used a Genome-Wide Association Study (GWAS) to identify single nucleotide polymorphism (SNP) markers and putative candidate genes for terpene traits. We tested 15,387 informative SNP markers derived from genotyping 416 Eucalyptus grandis individuals for association with three terpene traits, 1,8-cineole, γ-terpinene and p-cymene. A Multi-Locus Mixed Model (MLMM) analysis identified 21 SNP markers for 1,8-cineole on chromosomes 2, 4, 6, 7, 8, 9, 10 and 11, that individually explained 3.0% to 8.4% and jointly 42.7% of the phenotypic variation. Association analysis of γ-terpinene found 32 significant SNP markers on chromosomes 1, 2, 4, 5, 6, 9 and 11, explaining 3.4 to 15.5% and jointly 54.5% of phenotypic variation. For p-cymene 28 significant SNP markers were identified on chromosomes 1, 2, 3, 5, 6, 7, 10 and 11, explaining 3.4% to 16.1% of the phenotypic variation and jointly 46.9%. Our results show that variation underlying the three terpene traits is influenced by a few minor loci in combination with a few major effect loci, suggesting an oligogenic nature of the traits.