Characterisation of novel endogenous geminiviral elements in macadamia

Background The presence of geminivirus sequences in a preliminary analysis of sRNA sequences from the leaves of macadamia trees with abnormal vertical growth (AVG) syndrome was investigated. Results A locus of endogenous geminiviral elements (EGE) in the macadamia genome was analysed, and the sequences revealed a high level of deletions and/or partial integrations, thus rendering the EGE transcriptionally inactive. The replication defective EGE in the macadamia genome indicates its inability to be the source of new viral infections and thus cause AVG or any other disease in macadamia. The EGE sequences were detected in two edible Macadamia species that constitute commercial cultivars and the wild germplasm of edible and inedible species of Macadamia. This strongly suggests that the integration preceded speciation of the genus Macadamia. A draft genome of a locus of EGE in Macadamia was developed. The findings of this study provide evidence to suggest the endogenization of the geminiviral sequences in the macadamia genome and the ancestral relationship of EGE with Macadamia in the Proteaceae family. Random mutations accumulating in the EGE inform that the sequence is evolving. Conclusions The EGE in Macadamia is inactive and thus not a direct cause of any diseases or syndromes including AVG in macadamia. The insertion of the EGE in the macadamia genome preceded speciation of the genus Macadamia.

Resource evaluation and novel germplasm excavation of wild Chinese prickly ash in Qinling mountains

Wild Chinese prickly ash with elevated antioxidants is a valuable genetic resource for Zanthoxylum bungeanum Maxim improvement. There are rich wild germplasm resources in the Qinling Mountains. In a study with wild germplasm resources from different altitudes and six cultivated varieties, the phenolic and flavonoid compounds were analyzed by high performance liquid chromatography (HPLC). The chromatograms of them were basically the same, although their chemical composition content was greatly different. The thirty samples were divided into three categories through the hierarchical clustering analysis. And catechin, hyperoside and quercitrin were considered to be key compound for the quality evaluation, by contrast, the wild samples with an altitude of 2300±50 m (Ⅳ group) had the highest content of key compounds, and showed stronger antioxidant activity and antibacterial ability, indicating that these wild samples could be used as an excellent breeding resource. This is the first time to evaluate the quality of wild Chinese prickly ash in different altitude areas of Qinling Mountains. These excellent wild germplasm resources provided substantial potential accessions for use directly in Chinese prickly ash breeding programs.

Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

Evaluating Wild Germplasm Introgression into Autotetraploid Blueberry

Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii is a wild diploid blueberry species endemic to the southeastern United States that possesses highly desirable and economically important traits for blueberry breeding such as: short bloom to ripe period, adaptation to upland sandy soils, disease resistance, firmness, and pleasant flavor. To examine the potential of hybridization, we evaluated populations of interspecific hybrids across multiple stages of breeding (i.e., F1, F2, and backcrosses) in two crop seasons. We used our extensive pedigree data to generate breeding values for pre-breeding blueberry hybrid populations. Hybrid performance was evaluated considering fitness (i.e., plant vigor and plant height) in addition to evaluating six fruit-quality and marketable-related traits (i.e., size, firmness, acidity, soluble solids, weight, and yield). Overall, F2 and backcrosses rapidly achieved market thresholds, presenting values not significantly different from commercial blueberry germplasm. Our results confirmed the potential of exploiting the high genetic variability contained in V. elliottii for interspecific hybridization. Additionally, we developed germplasm resources that can be further evaluated and utilized in the breeding process, advancing selections for fruit quality and environmental adaptation.

Evaluating the Introgression of Wild Germplasm Into Autotetraploid Blueberry Breeding

Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii is a wild diploid blueberry species endemic to the southeastern United States that possesses highly desirable and economically important traits for blueberry breeding such as: short bloom to ripe period, adaptation to upland sandy soils, disease resistance, firmness, and pleasant flavor. To examine the potential of hybridization, we evaluated populations of interspecific hybrids across multiples stages of breeding (i.e., F1, F2, and backcrosses) in two crop seasons. We used our extensive pedigree data to generate breeding values for pre-breeding blueberry hybrid populations. Hybrid performance was evaluated considering fitness (i.e., plant vigor and plant height) in addition to evaluating six fruit-quality and marketable-related traits (i.e., size, firmness, acidity, soluble solids, weight, and yield). Overall, F2 and backcrosses rapidly achieved market thresholds, presenting values not significantly different from commercial blueberry germplasm. Our results confirmed the potential of exploiting the high genetic variability contained in V. elliotii for interspecific hybridization. Additionally, we developed germplasm resources that can be further evaluated and utilized in the breeding process, advancing selections for fruit quality and environmental adaptation.

The Embryo Characteristics and Genes Expression Analysis Involved in Apomixis of Wild Germplasm Materials of Kentucky Bluegrass in Gansu Province of China

Background: Apomixis is mainly used to maintain the heterosis, stability, and consistency of crops. Its main advantage is to reduce the costs of seed production and shorten the breeding process. In the field of hybrid breeding, apomixis has been referred to as the "asexual revolution" and has realized a new green revolution.Apomixis is mainly used to maintain the heterosis, stability, and consistency of crops. Its main advantage is to reduce the costs of seed production and shorten the breeding process. In the field of hybrid breeding, apomixis has been referred to as the "asexual revolution" and has realized a new green revolution. Kentucky bluegrass (Poa pratensis) is a natural apomictic species that mainly exhibits facultative apospory. Its main feature is that the somatic nucellar cells bypass meiosis and double fertilization to form unreduced embryos, and the development of the endosperm requires pseudogamy. Although apomixis is of great significance in breeding, the genetic control of apomixis remains unclear. Therefore, we report the results of a global gene expression analysis of wild germplasm materials of Kentucky bluegrass spikelets in Gansu province of China, exhibiting significant differences in apomictic rates to identify the genes, biological processes, and molecular functions related to apomixis.Result: At four reproductive periods, there were 5400 differentially expressed genes (DEGs) between the two genotypes, including 2476 downregulated and 2823 upregulated genes. Further analysis of the gene functions, pathways, expression patterns, networks, and transcription factors (TFs) showed that the occurrence of apomixis in Kentucky bluegrass was related to changes in the time- and space-related expression of genes associated with sexual reproduction, which led to disordered sexual reproduction and thus the production of offspring by apomixis. Conclusion: At the transcriptional level, the genesis and development of apomixis was regulated by TFs. It also involved the coexpression of many genes associated with disordered meiosis, hormone signal transduction, embryonic development, stress response pathways, and epigenetics. We also verified these 16 DEGs by real-time quantitative PCR. The expression results were basically consistent with the transcriptome expression profile, indicating that the transcriptome data were reliable. The results of this study may provide a theoretical basis for revealing the mechanism of occurrence and development of apomixis in Kentucky bluegrass.

Genetic diversity among wild and cultivated germplasm of the perennial pasture grass Phalaris aquatica, using DArTseq SNP marker analysis

Phalaris aquatica L. (phalaris) is a cool-season perennial grass originating from the Mediterranean Basin, north-west Africa and Middle Eastern regions that is used for livestock agriculture mainly in temperate areas with dry summers. It has been the subject of breeding programs in Australia, South America, New Zealand and the USA. Increased knowledge of relationships between wild and cultivated germplasm through use of molecular markers has the potential to facilitate future breeding gains. For this purpose, we conducted an analysis of P. aquatica by using 3905 polymorphic DArTseq SNP markers. Genetic diversity as measured by expected heterozygosity was similar for wild (HE = 0.14; n = 57) and cultivated (HE = 0.13; n = 37) accessions. Diversity in wild germplasm was generally continuous in nature, largely related to geographical location, with a division at the broadest scale into eastern and western clades, with more admixture in the western than the eastern clade. Structure analysis of wild germplasm indicated six subpopulations consistent with country of origin, with some admixture among subpopulations likely resulting from natural and human influences. There were nine subpopulations among wild and cultivated accessions combined. This population structure should be considered if genomic selection is applied in P. aquatica. Analysis of molecular variance indicated that 71% of the genetic variation occurred within subpopulations and 29% among subpopulations. Genetic distances were low among cultivated germplasm from most countries except the USA, which was more distinct. Evaluation of material from the US pool by breeding programs in other countries, and additional material from the less utilised eastern clade, may be worthwhile.