Development and Genetic Characterization of Peanut Advanced Backcross Lines That Incorporate Root-Knot Nematode Resistance From Arachis stenosperma

Crop wild species are increasingly important for crop improvement. Peanut (Arachis hypogaea L.) wild relatives comprise a diverse genetic pool that is being used to broaden its narrow genetic base. Peanut is an allotetraploid species extremely susceptible to peanut root-knot nematode (PRKN) Meloidogyne arenaria. Current resistant cultivars rely on a single introgression for PRKN resistance incorporated from the wild relative Arachis cardenasii, which could be overcome as a result of the emergence of virulent nematode populations. Therefore, new sources of resistance may be needed. Near-immunity has been found in the peanut wild relative Arachis stenosperma. The two loci controlling the resistance, present on chromosomes A02 and A09, have been validated in tetraploid lines and have been shown to reduce nematode reproduction by up to 98%. To incorporate these new resistance QTL into cultivated peanut, we used a marker-assisted backcrossing approach, using PRKN A. stenosperma-derived resistant lines as donor parents. Four cycles of backcrossing were completed, and SNP assays linked to the QTL were used for foreground selection. In each backcross generation seed weight, length, and width were measured, and based on a statistical analysis we observed that only one generation of backcrossing was required to recover the elite peanut’s seed size. A populating of 271 BC3F1 lines was genome-wide genotyped to characterize the introgressions across the genome. Phenotypic information for leaf spot incidence and domestication traits (seed size, fertility, plant architecture, and flower color) were recorded. Correlations between the wild introgressions in different chromosomes and the phenotypic data allowed us to identify candidate regions controlling these domestication traits. Finally, PRKN resistance was validated in BC3F3 lines. We observed that the QTL in A02 and/or large introgression in A09 are needed for resistance. This present work represents an important step toward the development of new high-yielding and nematode-resistant peanut cultivars.

Polyploidy but Not Range Size Is Associated With Seed and Seedling Traits That Affect Performance of Pomaderris Species

Ploidy and species range size or threat status have been linked to variation in phenotypic and phenological seed and seedling traits, including seed size, germination rate (speed) and seedling stature. There is surprisingly little known about the ecological outcomes of relationships between ploidy, key plant traits and the drivers of range size. Here we determined whether ploidy and range size in Pomaderris, a genus of shrubs that includes many threatened species, are associated with variation in seed and seedling traits that might limit the regeneration performance of obligate seeders in fire-prone systems. We experimentally quantified seed dormancy and germination processes using fire-related heat treatments and evaluated seedling performance under drought stress. We also examined the association of seed size with other seed and seedling traits. Polyploids had bigger seeds, a faster germination rate and larger and taller seedlings than diploids. There was a lack of any clear relationship between range size and seed or seedling traits. The ploidy effects observed for many traits are likely to be indirect and associated with the underlying seed size differences. These findings indicate that there is a higher potential competitive advantage in polyploid than diploid Pomaderris during regeneration, a critical stage in the post-fire environment. This insight to the regeneration phase may need to be considered when planning and prioritising management of threatened species.

Genetic and QTL Analysis for Hilum-Eye Types in Cowpea (Vigna Unguiculata L. Walp)

Cowpea is an important food legume widely grown in the semi-arid tropics and serves as a main source of dietary protein, minerals, and vitamins. However, varieties differ from region to region based on the consumer’s preference for seed types determined by seed size, seed coat texture, seed color, and hilum-eye types. The genetics of seed size, seed color, and seed coat texture have been well documented, but the hilum-eye types have not been studied well because they represent seven different types with complex interactions. We studied the genetic segregation for hilum-eye types and determined the number of genes involved in a recombinant inbred line (RIL) population derived from a cross between a small eye parent ‘GEC’ and a Watson eye parent ‘IT98K-476-8’. The results demonstrated a three-gene model, W (Watson), S (small), and R (large), for cowpea seed hilum-eye type pattern and the interaction of these three genes, W, S, and R, resulted in five phenotypes, viz. self, Watson, small, large, and ring hilum-eye types. Moreover, we also mapped the RILs for hilum-eye types, identified three quantitative trait loci (QTLs), and aligned to the cowpea reference genome as QTL qHilum7.1, qHilum9.1, and qHilum10.1, corresponding to these three genes, Ring type (R), Watson type (W), and Small type (S) hilum-eye type patterns, respectively. Therefore, there was a complete agreement between the genetic analysis and QTL mapping for the number of genes controlling the hilum types in cowpea.

Genetic Parameters for Determining Useful Parents in Mungbean (Vigna radiata (L.) Wilczek) Breeding for Early Maturity, Small Seed Size, and High Seed Yield

Early maturity, small seed size, and high seed yield are important characters of mungbean in Indonesia. The objective of the study was to determine the useful parents in mungbean crosses for early maturity, small seed size, and high seed yield varieties by estimating the genetic parameters and their inheritance. The study was conducted at the ILETRI, Malang, East Java, Indonesia, during the dry season of 2014. 20 F1 and 5 parents were evaluated using a randomized block design, repeated three times. Results of the study showed that all observed traits showed the importance of both additive and dominance gene effects. The relative value of general combining ability (GCA) was greater than specific combining ability (SCA) for number of pod clusters per plant, number of branches per plant, plant height, days to maturity, and 100-seed weight which indicated the importance of additive gene effect. The dominance gene effect occurred on number of pods and seed yield per plant. Among five parents, G3 was the best combiner for all the observed characters except pod length; therefore, G3 could be exploited for late maturity, small seed size, high number of branches and pod cluster, and high seed yield. G5 has a high GCA for 100-seed weight. G1 and G2 have good GCA for early maturity. G3 and G5 genotypes are useful as parents in mungbean breeding for small and large seed size varieties, respectively. The best combination for seed yield was G2 × G3 and G3 × G1 crosses and could be proceeded with selection for early maturity, small seed size, and high seed yield varieties.

The ecology and quantitative genetics of seed and seedling traits in upland and lowland ecotypes of a perennial grass

Plants have evolved diverse reproductive allocation strategies and seed traits to aid in dispersal, persistence in the seed bank, and establishment. In particular, seed size, dormancy, and early seedling vigor are thought to be key functional traits with important recruitment and fitness consequences across abiotic stress gradients. Selection for favored seed-trait combinations, or against maladaptive combinations, is likely an important driver shaping recruitment strategies. Here, we test for seed-trait plasticity and local adaptation in contrasting upland and lowland ecotypes of Panicum hallii with field experiments in native versus foreign habitats. Furthermore, we test whether seed traits have been under directional selection in P. hallii using the v-test (Fraser 2020) based on trait variance in a genetic cross. Finally, we evaluate the genetic architecture of ecotypic divergence for these traits with Quantitative Trait Locus (QTL) mapping. Field experiments reveal little plasticity but support a hypothesis of local adaptation among ecotypes based on recruitment. Patterns of segregation within recombinant hybrids provides strong support for directional selection driving ecotypic divergence in seeds traits. Genetic mapping revealed a polygenic architecture with evidence of genetic correlation between seed mass, dormancy, and seedling vigor. Our results suggest that the evolution of these traits may involve constraints that affect the direction of adaptive divergence. For example, seed size and germination percentage shared two colocalized QTL with antagonistic additive effects. This supports the hypothesis of a functional genetic relationship between these traits, resulting in either large seed/strong dormancy or small seed/weak dormancy trait combinations. Overall, our study provides insights into the factors facilitating and potentially constraining ecotypic differentiation in seed traits.

Selection for seed size has uneven effects on specialized metabolite abundance in oat (Avena sativa L)

Plant breeding strategies to optimize metabolite profiles are necessary to develop health-promoting food crops. In oats (Avena sativa L.), seed metabolites are of interest for their antioxidant properties, yet have not been a direct target of selection in breeding. In a diverse oat germplasm panel spanning a century of breeding, we investigated the degree of variation of these specialized metabolites and how it has been molded by selection for other traits, like yield components. We also ask if these patterns of variation persist in modern breeding pools. Integrating genomic, transcriptomic, metabolomic and phenotypic analyses for three types of seed specialized metabolites – avenanthramides, avenacins, and avenacosides – we found reduced heritable genetic variation in modern germplasm compared to diverse germplasm, in part due to increased seed size associated with more intensive breeding. Specifically, we found that abundance of avenanthramides increases with seed size, but additional variation is attributable to expression of biosynthetic enzymes. In contrast, avenacoside abundance decreases with seed size and plant breeding intensity. In addition, these different specialized metabolites do not share large-effect loci. Overall, we show that increased seed size associated with intensive plant breeding has uneven effects on the oat seed metabolome, but variation also exists independently of seed size to use in plant breeding. This work broadly contributes to our understanding of how plant breeding has influenced plant traits and tradeoffs between traits (like growth and defense) and the genetic bases of these shifts.

Community Ecology of Epiphytes and other Arboreal Plants in the New Zealand Eco-region

<p><b>Epiphytes and other structurally-dependent plants have a spatial ecology and community structure intrinsically linked to that of the host trees in the forest, unlike fully terrestrial plants. Understanding of the ecological implications of this from a theoretical perspective is in its infancy. New Zealand’s south temperate rainforest, whilst not as species rich as tropical forests, hosts one of the richest temperate epiphyte floras. Our understanding of the ecological processes structuring the epiphyte communities of New Zealand forests is however lacking. Here, I present four key studies seeking to add to our knowledge of epiphyte community structure, host specificity and spatial ecology in the New Zealand eco-region.</b></p> <p>First, I tested if seed size determined the likelihood of woody plant species occurring epiphytically on tree ferns (their arboreality) – Chapter 2. Arboreality was negatively related to seed size, with only smaller-seeded species commonly occurring on tree ferns. However, the effect of seed size reduced in later life history stages, as expected. These small-seeded species, most notably Weinmannia racemosa, appear to be utilising an alternative recruitment strategy by establishing epiphytically on the tree fern trunks.</p> <p>Second, on Cyathea dealbata host tree ferns, I tested patterns of species accumulation, metacommunity network structure, and differences in vertical stratification (Chapter 3). Epiphytes and climbers followed a species accumulation model of succession between tree ferns of different sizes and between older and younger portions of the tree fern. The metacommunity network showed patterns of species co-occurrence and nestedness consistent with null expectations. Epiphytes of different habits and different dispersal syndromes show different vertical profiles of occurrence, with bird-dispersed species occurring more often near the top of the tree fern than other taxa.</p> <p>To understand an unusual pattern in epiphyte between-host structuring, I quantified the relationship between epiphytic plant and sooty mould assemblages in New Zealand montane beech forest (Chapter 4). Due to the presence of host specific scale insects, the sooty mould was limited to two of three co-dominant canopy tree species. On these two host species, epiphyte richness was significantly reduced. The host size-richness relationship in these two species was also removed, with species composition significantly altered compared to the mould free host species. My results are consistent with the sooty mould amensally excluding the epiphytes and it can be considered as a part of a keystone species complex (with the host beeches and scale insects). This produces a strong pattern of parallel host specificity otherwise not seen in epiphyte assemblages.</p> <p>Lastly, I compared the differences in spatial niche and host species diversity between three arboreal plants, with divergent ecophysiology, on Lord Howe Island (Chapter 5). These focal species were a dwarf mistletoe, an epiphytic orchid and an epiphytic fern. The mistletoe was restricted to thinner branches, and had a significantly different niche to both epiphyte taxa. The host diversity of the mistletoe and orchid both differed significantly from null model expectations. However, the epiphytic fern (Platycerium bifurcatum) had a host diversity consistent with null expectations.</p> <p>Taken together, these studies increase our understanding of epiphyte community assembly in New Zealand and provide a platform to encourage further work in this field. They also provide results that expand understanding of spatial patterns between host and up vertical clines.</p>

Community Ecology of Epiphytes and other Arboreal Plants in the New Zealand Eco-region

<p><b>Epiphytes and other structurally-dependent plants have a spatial ecology and community structure intrinsically linked to that of the host trees in the forest, unlike fully terrestrial plants. Understanding of the ecological implications of this from a theoretical perspective is in its infancy. New Zealand’s south temperate rainforest, whilst not as species rich as tropical forests, hosts one of the richest temperate epiphyte floras. Our understanding of the ecological processes structuring the epiphyte communities of New Zealand forests is however lacking. Here, I present four key studies seeking to add to our knowledge of epiphyte community structure, host specificity and spatial ecology in the New Zealand eco-region.</b></p> <p>First, I tested if seed size determined the likelihood of woody plant species occurring epiphytically on tree ferns (their arboreality) – Chapter 2. Arboreality was negatively related to seed size, with only smaller-seeded species commonly occurring on tree ferns. However, the effect of seed size reduced in later life history stages, as expected. These small-seeded species, most notably Weinmannia racemosa, appear to be utilising an alternative recruitment strategy by establishing epiphytically on the tree fern trunks.</p> <p>Second, on Cyathea dealbata host tree ferns, I tested patterns of species accumulation, metacommunity network structure, and differences in vertical stratification (Chapter 3). Epiphytes and climbers followed a species accumulation model of succession between tree ferns of different sizes and between older and younger portions of the tree fern. The metacommunity network showed patterns of species co-occurrence and nestedness consistent with null expectations. Epiphytes of different habits and different dispersal syndromes show different vertical profiles of occurrence, with bird-dispersed species occurring more often near the top of the tree fern than other taxa.</p> <p>To understand an unusual pattern in epiphyte between-host structuring, I quantified the relationship between epiphytic plant and sooty mould assemblages in New Zealand montane beech forest (Chapter 4). Due to the presence of host specific scale insects, the sooty mould was limited to two of three co-dominant canopy tree species. On these two host species, epiphyte richness was significantly reduced. The host size-richness relationship in these two species was also removed, with species composition significantly altered compared to the mould free host species. My results are consistent with the sooty mould amensally excluding the epiphytes and it can be considered as a part of a keystone species complex (with the host beeches and scale insects). This produces a strong pattern of parallel host specificity otherwise not seen in epiphyte assemblages.</p> <p>Lastly, I compared the differences in spatial niche and host species diversity between three arboreal plants, with divergent ecophysiology, on Lord Howe Island (Chapter 5). These focal species were a dwarf mistletoe, an epiphytic orchid and an epiphytic fern. The mistletoe was restricted to thinner branches, and had a significantly different niche to both epiphyte taxa. The host diversity of the mistletoe and orchid both differed significantly from null model expectations. However, the epiphytic fern (Platycerium bifurcatum) had a host diversity consistent with null expectations.</p> <p>Taken together, these studies increase our understanding of epiphyte community assembly in New Zealand and provide a platform to encourage further work in this field. They also provide results that expand understanding of spatial patterns between host and up vertical clines.</p>