Biology subjects

Leakey, A. D. B.

Publications and source records attributed to Leakey, A. D. B..

4 recordsLinked to original sources

bioRxiv2018

Leveraging mutational burden for complex trait prediction in sorghum

Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. Though selection keeps deleterious mutations rare, their complete removal from the genome is impeded due to lack of recombination, drift, and their coupling with favorable loci. To study how deleterious mutations impact agronomic phenotypes, we identified putative deleterious mutations among ~5.5M segregating variants of 229 diverse sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that about 33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups; the caudatum shows higher mutation burden while the guinea has lower burden. Across racial groups, the mutation burden correlated negatively with biomass, plant height, Specific Leaf Area (SLA), and tissue starch content, suggesting deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (5.2%). There is no advantage in total heritable variance for SLA and starch. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, our results suggest that including putatively deleterious variants in models do not significantly improve breeding accuracy because of extensive linkage. However, knowledge of deleterious variants could be leveraged for sorghum breeding through genome editing.

genetics↗

bioRxiv2017

Elevated ozone reduces photosynthetic carbon gain by accelerating leaf senescence of inbred and hybrid maize in a genotype-specific manner

Exposure to elevated tropospheric ozone concentration ([O3]) accelerates leaf senescence in many C3 crops. However, the effects of elevated [O3] on C4 crops including maize (Zea mays L.) are poorly understood in terms of physiological mechanism and genetic variation in sensitivity. Using Free Air gas Concentration Enrichment (FACE), we investigated the photosynthetic response of 18 diverse maize inbred and hybrid lines to season-long exposure to elevated [O3] (~100 nL L-1) in the field. Gas exchange was measured on the leaf subtending the ear throughout the grain filling period. On average over the lifetime of the leaf, elevated [O3] led to reductions in photosynthetic CO2 assimilation of both inbred (-22%) and hybrid (-33%) genotypes. There was significant variation among both inbred and hybrid lines in the sensitivity of photosynthesis to elevated [O3], with some lines showing no change in photosynthesis at elevated [O3]. Based on analysis of inbred line B73, the reduced CO2 assimilation at elevated [O3] was associated with accelerated senescence decreasing photosynthetic capacity, and not altered stomatal limitation. These findings across diverse maize genotypes could advance the development of more ozone tolerant maize, and provide experimental data for parameterization and validation of studies modeling how O3 impacts crop performance.

plant biology↗

bioRxiv2017

High fidelity detection of crop biomass QTL from low-cost imaging in the field

Above-ground biomass production is a key target for studies of crop abiotic stress tolerance, disease resistance and yield improvement. However, biomass is slow and laborious to evaluate in the field using traditional destructive methods. High-throughput phenotyping (HTP) is widely promoted as a potential solution that can rapidly and non-destructively assess plant traits by exploiting advances in sensor and computing technology. A key potential application of HTP is for quantitative genetics studies that identify loci where allelic variation is associated with variation in crop production. And, the value of performing such studies in the field, where environmental conditions match that of production farming, is recognized. To date, HTP of biomass productivity in field trials has largely focused on expensive and complex methods, which - even if successful - will limit their use to a subset of wealthy research institutions and companies with extensive research infrastructure and highly-trained personnel. Even with investment in ground vehicles, aerial vehicles and gantry systems ranging from thousands to millions of dollars, there are very few examples where Quantitative trait loci (QTLs) detected by HTP of biomass production in a field-grown crop are shown to match QTLs detected by direct measures of biomass traits by destructive harvest techniques. Until such proof of concept for HTP proxies is generated it is unlikely to replace existing technology and be widely adopted. Therefore, there is a need for methods that can be used to assess crop performance by small teams with limited training and at field sites that are remote or have limited infrastructure. Here we use an inexpensive and simple, miniaturized system of hemispherical imaging and light attenuation modeling to identify the same set of key QTLs for biomass production as traditional destructive harvest methods applied to a field-grown Setaria mapping population. This provides a case study of a HTP technology that can deliver results for QTL mapping without high costs or complexity.

plant biology↗

bioRxiv2016

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria

Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed twelve controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The nondestructive nature of plant height measurements has enabled us to monitor vertical growth throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development.

plant biology↗