Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum

High-throughput genomic and phenomic data have enhanced the ability to detect genotype-to-phenotype associations that can resolve broad pleiotropic effects of mutations on plant phenotypes. As the scale of genotyping and phenotyping has advanced, rigorous methodologies have been developed to accommodate larger datasets and maintain statistical precision. However, determining the functional effects of associated genes/loci is expensive and limited due to the complexity associated with cloning and subsequent characterization. Here, we utilized phenomic imputation of a multi-year, multi-environment dataset using PHENIX which imputes missing data using kinship and correlated traits, and we screened insertions and deletions (InDels) from the recently whole-genome sequenced Sorghum Association Panel for putative loss-of-function effects. Candidate loci from genome-wide association results were screened for potential loss of function using a Bayesian Genome-Phenome Wide Association Study (BGPWAS) model across both functionally characterized and uncharacterized loci. Our approach is designed to facilitate in silico validation of associations beyond traditional candidate gene and literature-search approaches and to facilitate the identification of putative variants for functional analysis and reduce the incidence of false-positive candidates in current functional validation methods. Using this Bayesian GPWAS model, we identified associations for previously characterized genes with known loss-of-function alleles, specific genes falling within known quantitative trait loci, and genes without any previous genome-wide associations while additionally detecting putative pleiotropic effects. In particular, we were able to identify the major tannin haplotypes at the Tan1 locus and effects of InDels on the protein folding. Depending on the haplotype present, heterodimer formation with Tan2 was significantly affected. We also identified major effect InDels in Dw2 and Ma1, where proteins were truncated due to frameshift mutations that resulted in early stop codons. These truncated proteins also lost most of their functional domains, suggesting that these indels likely result in loss of function. Here, we show that the Bayesian GPWAS model is able to identify loss-of-function alleles that can have significant effects upon protein structure and folding as well as multimer formation. Our approach to characterize loss-of-function mutations and their functional repercussions will facilitate precision genomics and breeding by identifying key targets for gene editing and trait integration

A rare new species of the genus Wiborgiella (Crotalarieae, Fabaceae)

The new species Wiborgiella argentea is described. It is closely similar to Wiborgiella leipoldtiana and W. fasciculata but differs in its single-stemmed habit, densely sericeous leaves, wing petals that are longer than the keel and de- tails of the fruit. It is known from the Robertson area where it occurs in Robertson Karoo, on rocky, south facing shale slopes. The genus Wiborgiella Boatwr. & B.-E.van Wyk comprises nine species of legumes endemic to the Greater Cape Floristic Region of South Africa (Boatwright et al., 2010). It was described to accommo- date several anomalous species of the genus Lebeckia Thunb. s.l. as well as one species of Wiborgia Thunb

A rare new species of the genus Wiborgiella (Crotalarieae, Fabaceae)

The new species Wiborgiella argentea is described. It is closely similar to Wiborgiella leipoldtiana and W. fasciculata but differs in its single-stemmed habit, densely sericeous leaves, wing petals that are longer than the keel and de- tails of the fruit. It is known from the Robertson area where it occurs in Robertson Karoo, on rocky, south facing shale slopes. The genus Wiborgiella Boatwr. & B.-E.van Wyk comprises nine species of legumes endemic to the Greater Cape Floristic Region of South Africa (Boatwright et al., 2010). It was described to accommo- date several anomalous species of the genus Lebeckia Thunb. s.l. as well as one species of Wiborgia Thunb

Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole-genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high-density genomic marker set of 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5-kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources

Discovering useful genetic variation in the seed parent gene pool for sorghum improvement

Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding

Exchange Bias in Fe@Cr Core–Shell Nanoparticles

We have used X-ray magnetic circular dichroism and magnetometry to study isolated Fe@Cr core−shell nanoparticles with an Fe core diameter of 2.7 nm (850 atoms) and a Cr shell thickness varying between 1 and 2 monolayers. The addition of Cr shells significantly reduces the spin moment but does not change the orbital moment. At least two Cr atomic layers are required to stabilize a ferromagnetic/antiferromagnetic interface and generate the associated exchange bias and increase in coercivity

A phylogenetic study of the tribe Podalyrieae (Fabaceae)

M.Sc.The tribe Podalyrieae is a group of Papilionoid legumes that are largely endemic to the Cape Floristic Region of southern Africa. A phylogenetic study of the tribe was undertaken using gene sequences obtained from the internal transcribed spacer (ITS) as well as the plastid gene rbcL. Although the resolution was poor in the resulting trees, several groupings were noted within the tribe. The subtribe Xiphothecinae remains relatively unchanged and consists of the genera Amphithalea and Xiphotheca. The subtribe Podalyriinae was found to be paraphyletic. A close relationship was observed between the genera Liparia and Podalyria with Stirtonanthus as sister. Additional chloroplast genes (trnL-F and trnS-trnG) were sequenced to obtain better resolution within this group. While Podalyria and Stirtonanthus are monophyletic, the monophyly of Liparia is still uncertain. Virgilia and Calpurnia are closely related and Cyclopia retains its isolated, monophyletic position sister to the tribe. The species of Cadia included in the phylogenetic analysis formed a sister grouping to the tribe Podalyrieae and the inclusion of this genus in Podalyrieae is discussed. A date for the root node of the tribe was estimated at 28.55 MYA, using non-parametric rate smoothing (NPRS), indicating a major radiation to have taken place during the Pliocene. By means of independent contrasts it was determined that the rate of molecular evolution is higher in reseeders than resprouters, perhaps due to more reproductive cycles in these individuals, that would in turn affect the rate of DNA substitution

Systematic studies of the genus Lebeckia and related genera of the tribe Crotalarieae (Fabaceae)

Ph.D.Relationships within the Crotalarieae are explored using DNA sequences (ITS and rbcL) and morphological data and the monophyly of the various genera is assessed. A literature review of chemical characters (mainly alkaloids) was needed in order to evaluate the congruence between molecular, morphological and chemical data and how these patterns should be interpreted within the context of new generic and suprageneric concepts. The DNA study was also aimed at confirming the suspected polyphyly of Lebeckia and Lotononis (as currently circumscribed) and at improving generic circumscriptions. The aim was to propose and formalize new generic concepts for Lebeckia s.l. and Lotononis s.l. in order to ensure that all of the resultant genera are monophyletic

Mapping mental spaces : how we organize perceptual and cognitive information

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 1997.Vita.Includes bibliographical references.by Stephen A.B. Gilbert.Ph.D

A taxonomic revision of the Argyrolobium robustum and A. transvaalense groups (Fabaceae) in southern Africa

Previous studies on the genus Argyrolobium (Genisteae, Fabaceae) in southern Africa recognized a group of species defined by a suffrutescent habit, monomorphic flowers and leaves, and the plants not turning black when dried as 'section A. transvaalense'. A formal rank was never published for this group. Here a taxonomic study of this group is conducted, including comprehensive descriptions of and a key to the species, nomenclature, typifications, diagnostic characters, and geographical distribution. Based on an assessment of morphological characters, two groups can be recognised; 1) the A. robustum group that comprises four species with a herbaceous habit with up to 55-flowered inflorescences, flowers drying black or turning black when damaged, keel petals lacking pockets, and staminal sheaths fully open above, and 2) the A. transvaalense group comprising five species with a suffruticose habit with up to 24-flowered inflorescences, flowers becoming discoloured (darker coloured or brown) when dried, keel petals with pockets except in A. megarhizum, and staminal sheaths variously fused into a closed tube.Funding provided by: Botanical Education Trust*Crossref Funder Registry ID: Award Number: Funding provided by: National Research FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001321Award Number: FBIP210331591471Literature and herbarium material (including types) from JSTOR Global Plants (2022), AMD, B, BM, BOL, E, G, HBG, J, JE, K, L, M, MEL, MO, NBG (including SAM), NH, NU, PRE, REG, S, TCD, TUB, and UPS (herbarium acronyms according to Thiers 2023) were studied and used to delimit species following standard alpha-taxonomic methods. Specimens were arranged into morpho types based on overall morphological similarities and distributions. For each morpho type, three measurements of each vegetative and some reproductive (inflorescences, bracts, bracteoles, fruits and seeds) characters were taken from a minimum of five specimens, and where available, representative of the full range of variation. From these, one flower (where available) per specimen was rehydrated, dissected, and flower parts measured. Larger plant parts were measured with a ruler while micromorphological characters were photographed and measured using an Olympus DSX110 digital microscope with Olympus DSX software v. 3.1.9 (Olympus Corporation 2011-2019). Diagnostic characters were identified and used to describe taxa. In addition, fieldwork was conducted in the Limpopo, Mpumalanga, and KwaZulu-Natal Provinces (South Africa) to observe plants in their natural habitat. Photos were taken using a Canon EOS 450D with a 100 mm Canon macro lens (Canon Inc.). Specimens with sufficient locality information were georeferenced following the Natural Science Collections Facility protocol (Englebrecht 2021) and distribution maps generated with QGIS v. 3.22.7-Bialozieza software (© 1989, 1991 Free Software Foundation, Inc.)