Sean Mayes

The potential for underutilized crops to improve security of food production

Staple crops face major challenges in the near future and a diversification away from over-reliance on staples will be important as part of the progress towards the goal of achieving security of food production. Underutilized or neglected crops species are often indigenous ancient crop species which are still used at some level within the local, national or even international communities, but have the potential to contribute further to the mix of food sources than they currently do. The most cost-effective and easily disseminated changes that can be made to a crop are changes to the genetics, as these are contained within the seed itself and, for many species, the seed is a pure breeding, self-replicating, resource. This article focuses on the potential of underutilized crops to contribute to food security and, in particular, whether genetics and breeding can overcome some of the constraints to the enhanced uptake of these species in the future. The focus here is on overview rather than detail and subsequent articles will examine the current evidence base.

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects

Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

Quantitative trait loci for yield components in oil palm (Elaeis guineensis Jacq.)

Abstract The development of an oil palm RFLP marker map has enabled marker-based QTL mapping studies to be undertaken. Information from 153 RFLP markers was used in combination with phenotypic data from an F2 population to estimate the position and effects of quantitative trait loci (QTLs) for traits including yield of fruit and its components and measures of vegetative growth. The mapping population consisted of 84 palms segregating for the major gene influencing shell thickness. Marker data were analysed to produce a linkage map consisting of 22 linkage groups. The QTL mapping analysis was carried out by interval mapping and single-marker analysis for the unlinked markers; significance thresholds were generated by permutation. Using both single-marker and interval-mapping analysis significant marker associated QTL effects were found for 11 of the 13 traits analysed. The results of interval-mapping analysis of fruit weight, petiole cross section and rachis length, and ratios of shell:fruit, mesocarp:fruit and kernel:fruit indicated significant (P<0.05) QTLs at the genome-wide threshold. The putative QTLs were associated with between 8.2% and 44.0% of the phenotypic variation, with an average of 27% for the single-marker analysis and 19% for the interval-mapping analysis. The higher percentage of phenotypic variation explained in the single-marker analysis, when compared to the interval-mapping analysis, is likely to be due to the lower stringency associated with the single-marker analysis. Large dominance deviations were associated with a sizeable proportion of the putative QTLs. The ultimate objective of mapping QTLs in commercial populations is to utilise novel breeding strategies such as marker-assisted selection (MAS). The potential impact of MAS in oil palm breeding programmes is discussed.

Using principle component analysis to compare genetic diversity across polyploidy levels within plant complexes: an example from British Restharrows (Ononis spinosa and Ononis repens).

The investigation of genetic diversity between related plant populations which differ in ploidy levels is problematic, with common statistical methods developed for diploids being inappropriate for polyploid species. Studies into gene flow in such complexes are critical and can shed light on the mechanisms that generate and maintain populations of different polyploidy levels. We have investigated the use of principle component (PCO) analysis as one approach to elucidate population structure within British Restharrows (Leguminsoae, Ononis spp). Restharrows were common agricultural weed species until the advent of mechanical ploughing and both diploid (2n=2x=30; O. spinosa and O. intermedia) and tetraploid (2n=4x=60; O. repens and O. maritima) taxa exist. Patterns of genetic diversity were investigated among British Restharrows using 10 microsatellite loci with 21 Restharrow populations analysed (411 individual plants) from Central and Eastern Britain. PCO analysis revealed clear genetic differentiation of the sampled plants into two groups, corresponding to O. spinosa/O. intermedia (diploid) and O. repens/O. maritima (tetraploid) plants. Evidence of genetic differentiation by distance was also revealed for O. repens/O. maritima, but not for O. spinosa/O. intermedia. The data suggest the presence of strong reproductive barriers between diploid and tetraploid Restharrows in Britain, but not within ploidy levels. This genetic isolation between ploidy levels is confirmed by a detailed analysis of a sympatric site (Harton Down Hill). These results demonstrate that PCA analysis is a suitable general tool for comparing related species of different ploidy levels.

Global agricultural intensification during climate change: a role for genomics

Summary Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic‐assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.

Regulatory Hotspots Are Associated with Plant Gene Expression under Varying Soil Phosphorus Supply in Brassica rapa

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.

Female multiple mating in wild and laboratory populations of the two-spot ladybird, Adalia bipunctata

Female mating rate is an important variable for understanding the role of females in the evolution of mating systems. Polyandry influences patterns of sexual selection and has implications for sexual conflict over mating, as well as for wider issues such as patterns of gene flow and levels of genetic diversity. Despite this, remarkably few studies of insects have provided detailed estimates of polyandry in the wild. Here we combine behavioural and molecular genetic data to assess female mating frequency in wild populations of the two‐spot ladybird, Adalia bipunctata (Coleoptera: Coccinellidae). We also explore patterns of sperm use in a controlled laboratory environment to examine how sperm from multiple males is used over time by females, to link mating with fertilization. We confirm that females are highly polyandrous in the wild, both in terms of population mating rates (~20% of the population found in copula at any given time) and the number of males siring offspring in a single clutch (three to four males, on average). These patterns are consistent across two study populations. Patterns of sperm use in the laboratory show that the number of mates does not exceed the number of fathers, suggesting that females have little postcopulatory influence on paternity. Instead, longer copulations result in higher paternity for males, probably due to the transfer of larger numbers of sperm in multiple spermatophores. Our results emphasize the importance of combining field and laboratory data to explore mating rates in the wild.

The use of molecular markers to investigate the genetic structure of an oil palm breeding programme

RFLP markers (40 probes covering 60% of the oil palm genome) have been used to assess genetic diversity within 54 palms of a specific oil palm breeding programme. A further 10 palms encompassing a broader range of origins were also included to provide a wider framework for comparative analysis. These palms represent a majority of the parents in a crossing programme which aims to combine the best features of African tenera germplasm with South-east Asian Deli dura material. Progeny from these crosses are planted in up to six sites on three continents, where the palms are being assessed in detail for yield components. A total of 157 RFLP bands were scored and the data analysed by calculating genetic distances according to Nei & Li, and by correspondence and cluster analysis. The relationships that emerge through this molecular analysis correspond well with known pedigree and provenance. For example, south-east Asian Deli dura material forms a cluster clearly distinct from AVROS pisifera gene pools, and a selection of African breeding material forms a further and broader grouping. The potential ability of markers to assist in oil palm breeding through examination of the genetic structure of crossing programmes is discussed, as is their value in parental selection to maintain residual diversity within specific breeding pools and use in evaluating the fidelity of breeding lineages.

Assessment of nuclear, mitochondrial and chloroplast RFLP markers in oil palm (Elaeis guineensis Jacq.).

A variety of DNA probes was used to screen a diverse set of oil palm accessions in order to identify markers with a utility in genotype discrimination. This survey included samples of the commercial oil palm native to Africa (Elaeis guineensis Jacq.), the closely-related South American species [E.oleifera (HBK) Cortes] and inter-specific hybrids of the two. Of 106 major chloroplast bands none showed differences between E. guineensis and E. Oleifera. Mitochondrial and ribosomal probes were more informative inter-specifically (the former allowing identification of the maternal inheritance of mitochondria) and may be useful in hybrid breeding programmes; however, they were unable to identify polymorphism within E. guineensis. In contrast, low-copy nuclear genomic clones were able to identify intra-specific variation, though in most cases they revealed a relatively small number of allelic variants. One DNA probe showed a much larger number of band variants, revealing ten patterns amongst 13 E. guineensis accessions, and should prove useful in genetic fingerprinting and evaluation of oil-palm germplasm collections.

Genetic relationships and genotype tracing in date palms ( Phoenix dactylifera L.) in Oman, based on microsatellite markers

Microsatellite markers (SSRs) were used to screen and analyse the genetic diversity among clonal genotypes of date palm ( Phoenix dactylifera L.) derived by somatic embryogenesis in Oman. Twenty-one palms, representing 14 Omani, five Bahraini, one Iraqi and one Moroccan genotype, were screened with ten microsatellite markers. All primer pairs produced an amplification product in the expected size range and detected high levels of polymorphism among the analysed samples. Correspondence analysis revealed that the genotypes from Bahrain and Iraq showed a close relationship with accessions already grown in Oman. The genotype from Morocco (Medjool) appeared distinct from the rest of the material. Three independent clonal lines derived from a single Khalas Aldahra genotype were found to give identical genetic fingerprints. The value of this work for date palm production and conservation in Oman is discussed.