Biology subjects

Cruickshank, A.

Publications and source records attributed to Cruickshank, A..

4 recordsLinked to original sources

bioRxiv2025

Scaling up orphan crop research: A global genetic perspective of cowpea (Vigna unguiculata) diversity from 10,617 accessions

Cowpea (Vigna unguiculata L. Walp) is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia, and Latin America. However, as a typical "orphan crop", cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10,617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterized the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

plant biology↗

bioRxiv2025

Sialylated CD43 is a glyco-immune checkpoint for macrophage phagocytosis

Macrophages in the tumor microenvironment exert potent anti-tumorigenic activity through phagocytosis. Yet therapeutics that enhance macrophage phagocytosis have not improved outcomes in clinical trials for patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). To systematically identify regulators of phagocytosis, we performed genome-scale CRISPR knockout screens in human leukemia cells co-cultured with human monocyte-derived macrophages. Surprisingly, we found that whereas the classic "dont eat me" signal CD47 inhibited mouse macrophages, it did not inhibit phagocytosis by human macrophages. In contrast, the O-linked glycosylation and sialylation pathways were strong negative regulators of phagocytosis. In AML, the cell surface O-linked glycoprotein CD43 was the major effector of the O-linked glycosylation and sialylation pathways. Genetic deletion or antibody blockade of CD43 enhanced macrophage phagocytosis. This work highlights the importance of using human platforms to identify immune checkpoints, and nominates CD43 as a glyco-immune regulator of human macrophage phagocytosis.

cancer biology↗

bioRxiv2019

Large scale genome-wide association study reveals that drought induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

Sorghum is generally grown in water limited conditions and often lodges under post-anthesis drought, which reduces yield and quality. Due to its complexity, our understanding on the genetic control of lodging is very limited. We dissected the genetic architecture of lodging in grain sorghum through genome-wide association study (GWAS) on 2308 unique hybrids grown in 17 Australian sorghum trials over 3 years. The GWAS detected 213 QTL, the majority of which showed a significant association with leaf senescence and plant height (72% and 71% respectively). Only 16 lodging QTL were not associated with either leaf senescence or plant height. The high incidence of multi-trait association for the lodging QTL indicates that lodging in grain sorghum is mainly associated with plant height and traits linked to carbohydrate remobilisation. This result supported the selection for stay-green (delayed leaf senescence) to reduce lodging susceptibility, rather than selection for short stature and lodging resistance per se, which likely reduces yield. Additionally, our data suggested a protective effect of stay-green on weakening the association between lodging susceptibility and plant height. Our study also showed that lodging resistance might be improved by selection for stem composition but was unlikely to be improved by selection for classical resistance to stalk rots. Key messageWe detected 213 lodging QTL and demonstrated that drought induced stem lodging in grain sorghum is substantially associated with stay-green and plant height, suggesting a critical role of carbon remobilisation.

genetics↗

bioRxiv2019

Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals

O_LIGrain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotypes genetic potential and its capacity to fill the grains.\nC_LIO_LIThis study aims to dissect the genetic architecture of grain size in sorghum via an integrated genome wide association study (GWAS) using a diversity panel of 837 individuals and a BC-NAM population of 1,421 individuals.\nC_LIO_LIIn order to isolate genetic effects associated with grain size, rather than the genotypes capacity to fill grain, a field treatment of removing half of the panicle during flowering was imposed. Extensive variation in grain size with high heritability was observed in both populations across 5 field trials. Subsequent GWAS analyses uncovered 92 grain size QTL, which were significantly enriched for orthologues of known grain size genes in rice and maize. Significant overlap between the 92 QTL and grain size QTL in rice and maize was also found, supporting common genetic control of this trait among cereals. Further analysis found grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size rather than the capacity to fill the grain.\nC_LIO_LIThese results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms in cereal crops and manipulation of this trait in breeding practices.\nC_LI

genetics↗