Biology subjects

Morris, G. P.

Publications and source records attributed to Morris, G. P..

35 records · Page 2Linked to original sources

bioRxiv2023

Induced pluripotent stem cell derived pericytes respond to endogenous mediators of proliferation and contractility

BackgroundPericytes are multifunctional contractile cells that reside on capillaries. Pericytes are critical regulators of cerebral blood flow and blood-brain barrier function, and pericyte dysfunction may contribute to the pathophysiology of human neurological diseases including Alzheimers disease, multiple sclerosis, and stroke. Induced pluripotent stem cell (iPSC)-derived pericytes (iPericytes) are a promising tool for vascular research. However, it is unclear how iPericytes functionally compare to primary human brain vascular pericytes (HBVPs). We differentiated iPSCs into iPericytes of either the mesoderm or neural crest lineage using established protocols. We compared iPericyte and HBVP morphologies, quantified gene expression by qPCR and bulk RNA sequencing, and visualised pericyte protein markers by immunocytochemistry. To determine whether the gene expression of neural crest iPericytes, mesoderm iPericytes or HBVPs correlated with their functional characteristics in vitro, we quantified EdU incorporation following exposure to the key pericyte mitogen, platelet derived growth factor (PDGF)-BB and, contraction and relaxation in response to the vasoconstrictor endothelin-1 or vasodilator adenosine, respectively. iPericytes were morphologically similar to HBVPs and expressed canonical pericyte markers. However, iPericytes had 1864 differentially expressed genes compared to HBVPs, while there were 797 genes differentially expressed between neural crest and mesoderm iPericytes. Consistent with the ability of HBVPs to respond to PDGF-BB signalling, PDGF-BB enhanced and PDGF receptor-beta inhibitors impaired iPericyte proliferation. Administration of endothelin-1 led to iPericyte contraction and adenosine led to iPericyte relaxation, of a magnitude similar to the response evoked in HBVPs. We determined that neural crest iPericytes were less susceptible to PDGFR beta inhibition, but responded most robustly to vasoconstrictive meditators. iPericytes express pericyte-associated genes and proteins and, exhibit an appropriate physiological response upon exposure to a key endogenous mitogen or vasoactive mediators. Therefore, the generation of functional iPericytes would be suitable for use in future investigations exploring pericyte function or dysfunction in neurological diseases.

cell biology↗

bioRxiv2023

Crop modeling suggests limited transpiration would increase yield of sorghum across drought-prone regions of the United States

Breeding sorghum for drought adaptation is pivotal to secure crop production in drought-prone regions. Limited transpiration (LT) restricts water demand at high vapor pressure deficit, saving water for use in critical periods later in the growing season. Here we evaluated the hypothesis that LT would increase sorghum grain yield in the United States. We used a process-based crop model, APSIM, which simulates interactions of genotype, environment, and management (G x E x M). In this study, the G component includes the LT trait (GT) and maturity group (GM), the E component entails water deficit patterns, and the M component represents different planting dates. Simulations were conducted over 33 years (1986-2018) for representative locations across the US sorghum belt (Kansas, Texas, and Colorado) for three planting dates and maturity groups. The interaction of GT x E indicated a higher impact of LT sorghum on grain for LD, MD, and ED (8%), than on WW environments (4%). Thus significant impacts of LT can be achieved in western regions of the sorghum belt. Otherwise, the lack of interaction of GT x GM x M suggested that an LT sorghum would increase yield by around 8% across maturity groups and planting dates. Although the interaction GM x M revealed that specific combinations are better suited across geographical regions. Overall, the findings suggest that breeding for LT would increase sorghum yield in the drought-prone areas of the US without tradeoffs.

genetics↗

bioRxiv2022

Automated analysis of PD1 and PDL1 in lymph nodes and the microenvironment of transmissible tumors in Tasmanian devils

The wild Tasmanian devil (Sarchophilus harrisii) population has suffered a devastating decline due to two clonal transmissible cancers. Devil facial tumor 1 (DFT1) was first observed in 1996, followed by a second genetically distinct transmissible tumor, devil facial tumor 2 (DFT2), in 2014. DFT1/2 frequently metastasize, with lymph nodes being common metastatic sites. Downregulation of MHC-I by DFT1 cells is a primary means of evading allograft immunity aimed at polymorphic MHC-I proteins. DFT2 cells constitutively express MHC-I, and MHC-I is upregulated on DFT1/2 cells by interferon gamma, suggesting other immune evasion mechanisms may contribute to overcoming allograft and anti-tumor immunity. Human clinical trials have demonstrated PD1/PDL1 blockade effectively treats patients showing increased expression of PD1 in tumor draining lymph nodes, and PDL1 on peritumoral immune cells and tumor cells. The effects of DFT1/2 on systemic immunity remain largely uncharacterized. This study applied the open-access software QuPath to develop a semiautomated pipeline for whole slide analysis of stained tissue sections to quantify PD1/PDL1 expression in devil lymph nodes. The QuPath protocol provided strong correlations to manual counting. PD-1 expression was approximately 10-fold higher than PD-L1 expression in lymph nodes and was primarily expressed in germinal centers, whereas PD-L1 expression was more widely distributed throughout the lymph nodes. The density of PD1 positive cells was increased in lymph nodes containing DFT2 metastases, compared to DFT1. This suggests PD1/PDL1 exploitation may contribute to the poorly immunogenic nature of transmissible tumors in some devils and could be targeted in therapeutic or prophylactic treatments.

immunology↗

bioRxiv2022

Genomics and Phenomics Enabled Prebreeding Improved Early-Season Chilling Tolerance in Sorghum

In temperate climates, earlier planting of tropical-origin crops can provide longer growing seasons, reduce water loss, suppress weeds, and escape post-flowering drought stress. However, chilling sensitivity of sorghum, a tropical-origin cereal crop, limits early planting and over 50 years of conventional breeding has been stymied by coinheritance of chilling tolerance (CT) loci with undesirable tannin and dwarfing alleles. In this study, phenomics and genomics-enabled approaches were used for prebreeding of sorghum early-season CT. Uncrewed aircraft systems (UAS) high-throughput phenotyping platform tested for improving scalability showed moderate correlation between manual and UAS phenotyping. UAS normalized difference vegetation index (NDVI) values from the chilling nested association mapping population detected CT QTL that colocialized with manual phenotyping CT QTL. Two of the four first-generation KASP molecular markers, generated using the peak QTL SNPs, failed to function in an independent breeding program as the CT allele was common in diverse breeding lines. Population genomic FST analysis identified SNP CT alleles that were globally rare but common to the CT donors. Second-generation markers, generated using population genomics, were successful in tracking the donor CT allele in diverse breeding lines from two independent sorghum breeding programs. Marker-assisted breeding, effective in introgressing CT allele from Chinese sorghums into chilling-sensitive US elite sorghums, improved early-planted seedling performance ratings in lines with CT alleles by up to 13-24% compared to the negative control under natural chilling stress. These findings directly demonstrate the effectiveness of high-throughput phenotyping and population genomics in molecular breeding of complex adaptive traits.

genetics↗

bioRxiv2022

Microglia associations with brain pericytes and the vasculature are reduced in Alzheimer's disease

Cerebral blood flow is important for the maintenance of brain function and its dysregulation has been implicated in Alzheimers disease (AD). Subpopulations of microglia have well-characterised associations with the vasculature in the central nervous system but the precise relationship between microglia and cells which exist on the vasculature is not yet clear. In this study we explored the relationship between microglia and pericytes, a vessel-resident cell type that has a major role in the regulation of cerebral blood flow and maintenance of the blood brain barrier. Using fixed tissue sections and in vivo live imaging, we discovered a subset of microglia that closely associated with pericytes, termed PEricyte-associated Microglia (PEM). PEM are present throughout all regions of the brain and spinal cord in NG2DsRed x CX3CR1+/GFP mice, and in the human frontal cortex. They reside adjacent to pericytes at all levels of the capillary tree and can maintain their position for at least 28 days. PEM associate with pericytes lacking astroglial endfeet coverage but are segregated from pericytes by capillary basement membranes and capillary vessel width is similarly increased beneath pericytes with or without an associated PEM. Deletion of the microglia fractalkine receptor (CX3CR1) did not disrupt the association between pericytes and PEM, suggesting the association is not reliant on fractalkine signalling. Finally, we found that the proportion of microglia that are capillary-associated and PEM declines in the superior frontal gyrus (SFG) in AD, which is exacerbated by the APOE {varepsilon}3/{varepsilon}4 genotype. In summary, we identify and characterise a subpopulation of microglia that specifically associate with pericytes and find this population is reduced in the SFG in AD. This reduction may be a novel mechanism contributing to vascular dysfunction in diseases such as AD.

neuroscience↗

bioRxiv2021

Ecophysiological genomics identifies a pleiotropic locus mediating drought tolerance in sorghum

Drought is a key constraint on plant productivity and threat to food security. Sorghum (Sorghum bicolor L. Moench), a global staple food and forage crop, is among the most drought-adapted cereal crops, but its adaptation is not yet well understood. This study aims to better understand the genetic basis of preflowering drought in sorghum and identify loci underlying variation in water use and yield components under drought. A panel of 219 diverse sorghum from West Africa was phenotyped for yield components and water use in an outdoor large-tube lysimeter system under well-watered (WW) versus a preflowering drought water-stressed (WS) treatment. The experimental system was validated based on characteristic drought response in international drought tolerance check genotypes and genome-wide association studies (GWAS) that mapped the major height locus at QHT7.1 and Dw3. GWAS further identified marker trait associations (MTAs) for drought-related traits (plant height, flowering time, forage biomass, grain weight, water use) that each explained 7-70% of phenotypic variance. Most MTAs for drought-related traits correspond to loci not previously reported, but some MTA for forage biomass and grain weight under WS co-localized with staygreen post-flowering drought tolerance loci (Stg3a and Stg4). A globally common allele at S7_50055849 is associated with several yield components under drought, suggesting that it tags a major pleiotropic variant controlling assimilate partitioning to grain versus vegetative biomass. The GWAS findings revealed oligogenic variants for drought tolerance in sorghum landraces which could be used as trait predictive markers for improved drought adaptation.

plant biology↗

bioRxiv2021

Autoimmune Alleles at the Major Histocompatibility Locus Modify Melanoma Susceptibility

Autoimmunity and cancer represent two different aspects of immune dysfunction. Autoimmunity is characterized by breakdowns in immune self-tolerance, while impaired immune surveillance can allow for tumorigenesis. The class I major histocompatibility complex (MHC-I), which displays derivatives of the cellular peptidome for immune surveillance by CD8+ T cells, serves as a common genetic link between these conditions. As melanoma-specific CD8+ T-cells have been shown to target melanocyte-specific peptide antigens more often than melanoma-specific antigens, we investigated whether vitiligo and psoriasis predisposing MHC-I alleles conferred a melanoma protective effect. In individuals with cutaneous melanoma from both The Cancer Genome Atlas (N = 451) and an independent validation cohort (N = 586), MHC-I autoimmune allele carrier status was significantly associated with a later age of melanoma diagnosis. Furthermore, MHC-I autoimmune allele carriers were significantly associated with decreased risk of developing melanoma in the Million Veterans Program cohort (OR = 0.962, p = 0.024). Existing melanoma polygenic risk scores (PRS) did not predict autoimmune allele carrier status, suggesting these alleles provide new risk-relevant information. Mechanisms of autoimmune protection were neither associated with improved melanoma-driver mutation association nor improved gene-level conserved antigen presentation relative to common alleles (population frequency > 1%). However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte conserved antigens suggesting a potential relationship between antigen processing, binding, and cell-surface presentation. Overall, this study presents evidence that MHC-I autoimmune risk alleles modulate melanoma risk unaccounted for by current PRS.

cancer biology↗

bioRxiv2021

Quantitative and population genomics suggest a broad role of staygreen loci in the drought adaptation of sorghum

O_LIDrought is a major constraint on plant productivity globally. Sorghum (Sorghum bicolor) landraces have evolved in drought-prone regions, but the genetics of their adaptation is not yet understood. Loci underlying stay-green post-flowering drought tolerance (Stg), have been identified in a temperate breeding line, but their role in drought adaptation of tropical sorghum is to be elucidated. C_LIO_LIWe phenotyped 590 diverse sorghum accessions from West Africa under field-based managed drought stress, pre-flowering (WS1) and post-flowering (WS2) over several years and conducted genome-wide association studies (GWAS). C_LIO_LIBroad-sense heritability for grain and biomass yield components was high (33-92%) across environments. There was a significant correlation between stress tolerance index (STI) for grain weight across WS1 and WS2. GWAS revealed that SbZfl1 and SbCN12, orthologs of maize flowering genes, likely underlie flowering time variation under these conditions. GWAS further identified associations (n = 134) for STI and drought effects on yield components, including 16 putative pleiotropic associations. Thirty of the associations colocalized with Stg1-4 loci and had large effects. Seven lead associations, including some within Stg1, overlapped with positive selection outliers. C_LIO_LIOur findings reveal natural genetic variation for drought tolerance-related traits, and suggest a broad role of Stg loci in drought adaptation of sorghum. C_LI

plant biology↗

bioRxiv2021

RNA silencing by CRISPR in plants does not require Cas13

RNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation and expanded function including anti-viral immunity. Here, we report the use of CRISPR-Cas13 in plants to reduce both viral and endogenous RNA. Unexpectedly, we discovered that crRNA designed to guide Cas13 could, in the absence of the Cas13 protein, cause substantial reduction in RNA levels as well. We demonstrate Cas13-independent guide-induced gene silencing (GIGS) in three plant species, including stable transgenic Arabidopsis. We determined that GIGS utilizes endogenous RNAi machinery despite the fact that crRNA are unlike canonical triggers of RNAi such as miRNA, hairpins or long double-stranded RNA. These results suggest that GIGS offers a novel and flexible approach to RNA reduction with potential benefits over existing technologies for crop improvement. Our results demonstrate that GIGS is active across a range of plant species, evidence similar to recent findings in an insect system, which suggests that GIGS is potentially active across many eukaryotes.

plant biology↗

bioRxiv2021

The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange

Rapid environmental change can lead to extinction of populations or evolutionary rescue via genetic adaptation. In the past several years, smallholder and commercial cultivation of sorghum (Sorghum bicolor), a global cereal and forage crop, has been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). Here we characterized genomic signatures of adaptation in a Haitian sorghum breeding population, which had been recently founded from admixed global germplasm, extensively intercrossed, and subjected to intense selection under SCA infestation. We conducted evolutionary population genomics analyses of 296 post-selection Haitian lines compared to 767 global accessions at 159,683 single nucleotide polymorphisms. Despite intense selection, the Haitian population retains high nucleotide diversity through much of the genome due to diverse founders and an intercrossing strategy. A genome-wide fixation (FST) scan and geographic analyses suggests that adaptation to SCA in Haiti is conferred by a globally-rare East African allele of RMES1, which has also spread to other breeding programs in Africa, Asia, and the Americas. De novo genome sequencing data for SCA resistant and susceptible lines revealed putative causative variants at RMES1. Convenient low-cost markers were developed from the RMES1 selective sweep and successfully predicted resistance in independent U.S. x African breeding lines and eight U.S. commercial and public breeding programs, demonstrating the global relevance of the findings. Together, the findings highlight the potential of evolutionary genomics to develop adaptive trait breeding technology and the value of global germplasm exchange to facilitate evolutionary rescue.

evolutionary biology↗

bioRxiv2021

An automated approach to improve the speed and accuracy of pericyte and microglia quantification in whole mouse brain sections

Whole slide scanning technology has enabled the generation of high-resolution images of complete tissue sections. However, commonly used analysis software is often unable to handle the large data files produced. Here we present a method using the open-source software QuPath to detect, classify and quantify fluorescently-labelled cells (microglia and pericytes) in whole coronal brain tissue sections. Whole brain sections from both male and female NG2DsRed x CX3CR1+/GFP mice were analysed. Small regions of interest were selected and manual counts were compared to counts generated from an automated approach, across a range of detection parameters. The optimal parameters for detecting cells and classifying them as microglia or pericytes in each brain region were determined and applied to annotations corresponding to the entire cortex, hippocampus, thalamus and hypothalamus in each section. 3.71% of all detected cells were classified as pericytes, however this proportion was significantly higher in the thalamus (6.39%) than in other regions. In contrast, microglia (4.45% of total cells) were more abundant in the cortex (5.54%). No differences were detected between male and female mice. In conclusion, QuPath offers a user-friendly, rapid and accurate solution to whole-slide image analysis which could lead to important new discoveries in both health and disease. Significance StatementRapid and accurate quantification of cell numbers and distributions from whole tissue sections represents a difficult challenge in biomedical research. Slide scanning microscopes generate high-resolution images of complete tissue sections but most common image analysis software packages struggle to cope with the large data files they produce. We provide a method for rapidly and accurately quantifying pericyte and microglia cell numbers in whole brain tissue sections using QuPath, a new open-source software designed specifically to overcome this challenging roadblock.

neuroscience↗

bioRxiv2021

Crop modeling defines opportunities and challenges for drought escape, water capture, and yield increase using chilling-tolerant sorghum

Many crop species, particularly those of tropical origin, are chilling sensitive so improved chilling tolerance can enhance production of these crops in temperate regions. For the cereal crop sorghum (Sorghum bicolor L.) early planting and chilling tolerance have been investigated for >50 years, but the potential value or tradeoffs of this genotype x management change has not been formally evaluated with modeling. To assess the potential of early-planted chilling-tolerant grain sorghum in the central US sorghum belt, we conducted CERES-Sorghum simulations and characterized scenarios under which this change would be expected to enhance (or diminish) drought escape, water capture, and yield. We conducted crop growth modeling for full- and short-season hybrids under rainfed systems that were simulated to be planted in very early (April), early (May 15), and normal (June 15) planting dates over 1986-2015 in four locations in Kansas representative of the central US sorghum belt. Simulations indicated that very early planting will generally lead to lower initial soil moisture, longer growing periods, and higher evapotranspiration. Very early planting is expected to extend the growing period by 20% for short- or full-season hybrids, reduce evaporation during fallow periods, and increase plant transpiration in the two-thirds of years with the highest precipitation (mean > 428 mm), leading to 11% and 7% increase grain yield for short- and full-season hybrids, respectively. Thus, in this major sorghum growing region very early and early planting could reduce risks of terminal droughts, extend seasons, and increase rotation options, suggesting that further development of chilling tolerant hybrids is warranted.

plant biology↗

bioRxiv2020

A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to generate 159,101 high-quality biallelic SNPs, with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP ({pi} = 0.00045), only slightly less than in a global diversity panel ({pi} = 0.00055). Linkage disequilibrium decayed to background level (r2 < 0.1) by ~50 kb in the WASAP. Genome-wide diversity was structured both by botanical type, and by populations within botanical type, with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies of days to flowering and plant height revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height loci Dw3 and SbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in US germplasm (Ma6 and SbCN8) suggests that photoperiodic flowering in WA sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in West Africa.

genomics↗

bioRxiv2020

Genome-wide mapping and prediction of plant architecture in a sorghum nested association mapping population

Modifying plant architecture is often necessary for yield improvement and climate adaptation, but we lack understanding of the genotype-phenotype map for plant morphology in sorghum. Here, we use a nested association mapping (NAM) population that captures global allelic diversity of sorghum to characterize the genetics of leaf erectness, leaf width (at two stages), and stem diameter. Recombinant inbred lines (n = 2200) were phenotyped in multiple environments (35,200 observations) and joint linkage mapping was performed with [~]93,000 markers. Fifty-four QTL of small to large effect were identified for trait BLUPs (9-16 per trait) each explaining 0.4-4% of variation across the NAM population. While some of these QTL colocalize with sorghum homologs of grass genes [e.g. involved in hormone synthesis (maize spi1), floral transition (SbCN8), and transcriptional regulation of development (rice Ideal plant architecture1)], most QTL did not colocalize with an a priori candidate gene (82%). Genomic prediction accuracy was generally high in five-fold cross-validation (0.65-0.83), and varied from low to high in leave-one-family-out cross-validation (0.04-0.61). The findings provide a foundation to identify the molecular basis of architecture variation in sorghum and establish genomic-enabled breeding for improved plant architecture. Core ideasO_LIUnderstanding the genetics of plant architecture could facilitate the development of crop ideotypes for yield and adaptation C_LIO_LIThe genetics of plant architecture traits was characterized in sorghum using multi-environment phenotyping in a global nested association mapping population C_LIO_LIFifty-five quantitative trait loci were identified; some colocalize with homologs of known developmental regulators but most do not C_LIO_LIGenomic prediction accuracy was consistently high in five-fold cross-validation, but accuracy varied considerably in leave-one-family-out predictions C_LI

genetics↗

bioRxiv2019

A sorghum Practical Haplotype Graph facilitates genome-wide imputation and cost-effective genomic prediction

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, we developed a sorghum Practical Haplotype Graph (PHG) pangenome database that stores all identified haplotypes and variant information for a given set of individuals. We developed two PHGs in sorghum, one with 24 individuals and another with 398 individuals, that reflect the diversity across genic regions of the sorghum genome. 24 founders of the Chibas sorghum breeding program were sequenced at low coverage (0.01x) and processed through the PHG to identify genome-wide variants. The PHG called SNPs with only 5.9% error at 0.01x coverage - only 3% lower than its accuracy when calling SNPs from 8x coverage sequence. Additionally, 207 progeny from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes in the progeny were imputed from the parental haplotypes available in the PHG and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from 0.57-0.73 for different traits, and are similar to prediction accuracies obtained with genotyping-by-sequencing (GBS) or markers from sequencing targeted amplicons (rhAmpSeq). This study provides a proof of concept for using a sorghum PHG to call and impute SNPs from low-coverage sequence data and also shows that the PHG can unify genotype calls from different sequencing platforms. By reducing the amount of input sequence needed, the PHG has the potential to decrease the cost of genotyping for genomic selection, making GS more feasible and facilitating larger breeding populations that can capture maximum recombination. Our results demonstrate that the PHG is a useful research and breeding tool that can maintain variant information from a diverse group of taxa, store sequence data in a condensed but readily accessible format, unify genotypes from different genotyping methods, and provide a cost-effective option for genomic selection for any species.

genomics↗

bioRxiv2019

Dissecting adaptive traits with nested association mapping: Genetic architecture of inflorescence morphology in sorghum

In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. Here we characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under largely independent genetic control, while lower branch length and rachis diameter are pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1-22 QTL per trait, each explaining 0.1%-5.0% of variation across the entire NAM population. Overall, there is a significant enrichment (2.4-fold) of QTL colocalizing with homologs of grass inflorescence genes, notably with orthologs of maize (Ramosa2) and rice (Aberrant Panicle Organization1, TAWAWA1) inflorescence regulators. In global georeferenced germplasm, allelic variation at the major inflorescence morphology QTL is significantly associated with precipitation gradients, consistent with a role for these QTL in adaptation to agroclimatic zones. The findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. This genotype-phenotype trait dissection in global germplasm provides a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.

genetics↗

bioRxiv2019

Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population

Dissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (<15{degrees}) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 data points from [~]16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30-45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5-10 chilling tolerance loci explaining 20-41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and Dw3) that were under strong directional selection in the US during the 20th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.\n\nArticle SummaryChilling sensitivity limits productivity of tropical-origin crops in temperate climates, and remains poorly understood at a genetic level. We developed a nested association mapping resource in sorghum, a tropical-origin cereal, to understand the genetic architecture of chilling tolerance. Linkage mapping of growth traits from early-planted field trials revealed several major chilling tolerance loci, including some colocalized with genes that were selected in the origin of US grain sorghum. These findings suggest chilling sensitivity was inadvertently selected during 20th century breeding, but can be bypassed using a better understanding of the underlying genetic architecture.\n\nDisclaimerMention of a trademark, warranty, proprietary product, or vendor does not constitute a guarantee by the USDA and does not imply approval or recommendation of the product to the exclusion of others that may be suitable. USDA is an equal opportunity provider and employer.

genetics↗