Genome-wide investigation of SnRK2 gene family in two jute species: \u3ci\u3eCorchorus olitorius\u3c/i\u3e and \u3ci\u3eCorchorus capsularis\u3c/i\u3e

Background Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specifc serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family. Result We identifed seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene family showed an evolutionarily distinct trend. Highly variable C-terminal and conserved N-terminal regions were observed. Co- and CcSnRK2.3, Co- and CcSnRk2.5, Co- and CcSnRk2.7, and Co- and CcSnRK2.8 were upregulated in response to drought and salinity stresses. In waterlogging conditions, Co- and CcSnRk2.6 and Co- and CcSnRK2.8 showed higher activity when exposed to hypoxic conditions. Expression analysis in diferent plant parts showed that SnRK2.5 in both Corchorus species is highly expressed in fber cells providing evidence of the role of fber formation. Conclusion This is the frst comprehensive study of SnRK2 genes in both Corchorus species. All seven genes identifed in this study showed an almost similar pattern of gene structures and molecular properties. Gene expression patterns of these genes varied depending on the plant parts and in response to abiotic stresses

Genome-Wide Association Study for Abscission Failure of Fruit Pericarps (Stick-Tights) in Wild Macadamia Germplasm

Macadamia pericarps that fail to abscise (‘stick-tights’) are an important trait to select against in breeding as they can harbour pests and diseases. Traditional macadamia breeding cycles are lengthy and expensive due to long juvenilities and large tree sizes. Thus, genome-wide association studies (GWAS) are an important investigative tool to identify candidate trait-linked markers to enable potential reductions in evaluation and selection cycles via marker-assisted selection (MAS) in young seedlings. This study assessed 199 wild macadamia germplasm accessions for stick-tight prevalence across two years. As the number of stick-tights per tree is limited by the number of nuts per tree, we conducted association analyses to identify SNPs linked with the number of stick-tights per tree, and examined whether such SNPs were also associated with, and thus confounded with, the number of nuts per tree. We also assessed associations with the proportion of stick-tights per total number of nuts. Thirty-two SNPs were associated with at least one of the stick-tight traits in one year (p < 0.001). Of all such SNPs, only one was associated with the number of nuts per tree (p < 0.001), indicating that most associations were not confounded with yield

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8 years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8 years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations

A physiological framework to explain genetic and environmental regulation of tillering in sorghum

Tillering determines the plant size of sorghum (Sorghum bicolor) and an understanding of its regulation is important to match genotypes to prevalent growing conditions in target production environments. The aim of this study was to determine the physiological and environmental regulation of variability in tillering among sorghum genotypes, and to develop a framework for this regulation. * Diverse sorghum genotypes were grown in three experiments with contrasting temperature, radiation and plant density to create variation in tillering. Data on phenology, tillering, and leaf and plant size were collected. A carbohydrate supply/demand (S/D) index that incorporated environmental and genotypic parameters was developed to represent the effects of assimilate availability on tillering. Genotypic differences in tillering not explained by this index were defined as propensity to tiller (PTT) and probably represented hormonal effects. * Genotypic variation in tillering was associated with differences in leaf width, stem diameter and PTT. The S/D index captured most of the environmental effects on tillering and PTT most of the genotypic effects. * A framework that captures genetic and environmental regulation of tillering through assimilate availability and PTT was developed, and provides a basis for the development of a model that connects genetic control of tillering to its phenotypic consequences

DArTseq based silicoDArT and SNP data

Molecular dat

Estimating genetic parameters of architectural and reproductive traits in young macadamia cultivars

Macadamia in the orchard environment is relatively unaltered from its natural form, and there is considerable scope to alter vegetative and reproductive architecture with the aim of improving yield efficiency through breeding. An understanding of the genetic and environmental control of architecture and the dynamics between vegetative and reproductive characteristics are fundamental to identifying traits for yield improvement. This experiment calculated the broad-sense heritability (H) of architectural traits and genetic correlations between vegetative and reproductive traits over 2 years. Cutting-grown clones (n = 3) of 15 macadamia genotypes were subsampled from a randomised high-density plot planted in 2011 in South East Queensland, Australia, and observed for two seasons between 2015 and 2017. Clonal values from independent linear mixed models for multiple traits were combined in principal component analysis (PCA) to provide an insight to potential genetic relationships between traits, and genetic correlations were calculated from multivariate linear mixed model analysis. At the tree scale, canopy volume and yield had low H (0.07 and 0.14, respectively), implying a strong environmental influence on these complex traits. Architectural components of canopy volume and yield were considered at multiple scales, for which H ranged from 0.06 to 0.68, suggesting architectural traits at lower scales may be manipulated by breeding. Specific traits displayed strong genetic relationships with yield and canopy volume, suggesting that indirect selection for yield efficiency may be possible via selection for architectural and floral traits, to improve future macadamia cultivars

DArTseq markers of wild macadamia species

Molecular marker data of wild macadamia specie