Genomic Selection In Perennial Ryegrass

Genomic selection (GS) for crop improvement makes use of genome-wide molecular marker information available in more and more species. The aim is to enable accurate prediction of breeding values for target traits of a quantitative nature by determining the effect on phenotype of all the markers simultaneously. GS has proven its usefulness in animal breeding programmes, but its impact in plant breeding is only just emerging. GS can potentially increase the speed of the breeding cycle, reduce the cost and effort of phenotyping, and achieve faster selection of candidates for crossing programmes and production of synthetic varieties. Phenotypic predictions are based on models developed in a training population for which both phenotypic and genotypic data are available. The size of the training population and the density of molecular marker coverage are key constraints for prediction accuracy. The perennial ryegrass recurrent selection breeding programme at IBERS is based on a relatively small founder population, theoretically decreasing the number of molecular markers needed to achieve a certain level of prediction accuracy. Evidence will be presented for estimation of the extent of LD in this population. This will be followed by a description of how we aim to integrate GS into the existing breeding programme. Some initial cross-validation results will be presented using existing phenotypic data and molecular marker data of approximately 3000 markers, largely based on a ridge-regression best linear unbiased prediction model.publishersversionPeer reviewe

Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplasm

Background: Sainfoin is a perennial forage legume with beneficial properties for animal husbandry due to the presence of secondary metabolites. However, worldwide cultivation of sainfoin is marginal due to the lack of varieties with good agronomic performance, adapted to a broad range of environmental conditions. Little is known about the genetics of sainfoin and only few genetic markers are available to assist breeding and genetic investigations. The objective of this study was to develop a set of SSR markers useful for genetic studies in sainfoin and their characterization in diverse germplasm.Results: A set of 400 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 32 sainfoin individuals, representing distinct varieties or landraces. Alleles were scored for presence or absence and polymorphism information content of each SSR locus was calculated with an adapted formula taking into account the tetraploid character of sainfoin. Relationships among individuals were visualized using cluster and principle components analysis. Of the 400 primer combinations tested, 101 reliably detected polymorphisms among the 32 sainfoin individuals. Among the 1154 alleles amplified 250 private alleles were observed. The number of alleles per locus ranged from 2 to 24 with an average of 11.4 alleles. The average polymorphism information content reached values of 0.14 to 0.36. The clustering of the 32 individuals suggested a separation into two groups depending on the origin of the accessions.Conclusions: The SSR markers characterized and tested in this study provide a valuable tool to detect polymorphisms in sainfoin for future genetic studies and breeding programs. As a proof of concept, we showed that these markers can be used to separate sainfoin individuals based on their origin

Germplasm dynamics:The role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne

Perennial ryegrass (Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass

Phenotypic and Genotypic Characterization and Correlation Analysis of Pea ( Pisum sativum L.) Diversity Panel

Phenotypic and genotypic characterization were performed to assess heritability, variability, and seed yield stability of pea genotypes used in breeding to increase the pea production area. A European pea diversity panel, including genotypes from North America, Asia, and Australia consisting of varieties, breeding lines, pea, and landraces was examined in 2019 and 2020 in Serbia and Belgium using augmented block design. The highest heritability was for thousand seed weight; the highest coefficient of variation was for seed yield. The highest positive correlation was between number of seeds per plant and number of pods per plant; the highest negative correlation was between seed yield and protein content. Hierarchical clustering separated pea germplasm based on use and type. Different Principal component analysis grouping of landraces, breeding lines, and varieties, as well as forage types and garden and dry peas, confirms that there was an apparent decrease in similarity between the genotypes, which can be explained by their different purposes. Pea breeding should be focused on traits with consistent heritability and a positive effect on seed yield when selecting high-yielding genotypes, and on allowing for more widespread use of pea in various agricultural production systems

A novel multivariate approach to phenotyping and association mapping of multi-locus gametophytic self-incompatibility reveals S, Z and other loci in a perennial ryegrass (Poaceae) population

Self-incompatibility (SI) is a mechanism that many flowering plants employ to preventfertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour.Although a number of single locus mechanisms have been characterised in detail, nomulti-locus systems have been fully elucidated. Historically, examples of the geneticanalysis of multi-locus SI, to make analysis tractable, are either made on the progenyof bi-parental crosses, where the number of alleles at each locus is restricted, or oncrosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass(Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophyticincompatibility system. A more universal, realistic proof of principle study was conductedin a perennial ryegrass population in which allelic and non-allelic diversity was notartificially restricted. A complex pattern of pollinations from a diallel cross was revealedwhich could not possibly be interpreted easily per se, even with an already establishedgenetic model. Instead, pollination scores were distilled into principal component scoresdescribed as Compatibility Components (CC1-CC3). These were then subjected toa conventional genome-wide association analysis. CC1 associated with markers onlinkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic regionon LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodiumphysical map revealed highly significantly associated markers with peak associationswith genes adjacent and four genes away from the chromosomal locations of candidateSI genes, S- and Z-DUF247, respectively. Further significant associations were found in aBrachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genomebetween B. distachyon and L. perenne. Significant associations with gene sequencesaligning with marker sequences on Lolium LGs 3 and 6 were also identified. We thereforedemonstrate the power of a novel association genetics approach to identify the genescontrolling multi-locus gametophytic SI systems and to identify novel loci potentiallyinvolved in already established SI systems.publishersversionPeer reviewe

Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits

A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance

Implementation of genomic prediction in Lolium perenne (L.) breeding populations

Perennial ryegrass (Lolium perenne L.) is one of the most widely grown forage grasses in temperate agriculture. In order to maintain and increase its usage as forage in livestock agriculture, there is a continued need for improvement in biomass yield, quality, disease resistance and seed yield. Genetic gain for traits such as biomass yield has been relatively modest. This has been attributed to its long breeding cycle, and the necessity to use population based breeding methods. Thanks to recent advances in genotyping techniques there is increasing interest in genomic selection from which genomically estimated breeding values (GEBV) are derived. In this paper we compare the classical RRBLUP model with state-of-the-art machine learning (ML) techniques that should yield themselves easily to use in GS and demonstrate their application to predicting quantitative traits in a breeding population of L. perenne. Prediction accuracies varied from 0 to 0.59 depending on trait, prediction model and composition of the training population. The BLUP model produced the highest prediction accuracies for most traits and training populations. Forage quality traits had the highest accuracies compared to yield related traits. There appeared to be no clear pattern to the effect of the training population composition on the prediction accuracies. The heritability of the forage quality traits was generally higher than for the yield related traits, and could partly explain the difference in accuracy. Some population structure was evident in the breeding populations, and probably contributed to the varying effects of training population on the predictions. The average linkage disequilibrium (LD) between adjacent markers ranged from 0.121 to 0.215. Higher marker density and larger training population closely related with the test population are likely to improve the prediction accuracy

A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses

Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as forage in the tropics because of their resilience and low demand for nutrients, show greater tolerance to high concentrations of aluminium cations (Al3+) than most other grass crops. In this work, we explored the natural variation in tolerance to Al3+ between high and low tolerant Brachiaria species and characterized their transcriptional differences during stress. We identified three QTLs (quantitative trait loci) associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we identified 30 genes putatively responsible for Al3+ tolerance in Brachiaria. We observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition, and vesicle location homologous to aluminiuminduced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which suggests that exudation of organic acids and other external tolerance mechanisms, common in other grasses, might not be relevant in Brachiaria. The contrasting regulation of RNA translation and response signalling suggests that response timing is critical in high Al3+-tolerant Brachiaria