Dataset Information

Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus.

ABSTRACT:

Background

Miscanthus has potential as a biomass crop but the development of varieties that are consistently superior to the natural hybrid M. × giganteus has been challenging, presumably because of strong G × E interactions and poor knowledge of the complex genetic architectures of traits underlying biomass productivity and climatic adaptation. While linkage and association mapping studies are starting to generate long lists of candidate regions and even individual genes, it seems unlikely that this information can be translated into effective marker-assisted selection for the needs of breeding programmes. Genomic selection has emerged as a viable alternative, and prediction accuracies are moderate across a range of phenological and morphometric traits in Miscanthus, though relatively low for biomass yield per se.

Methods

We have previously proposed a combination of index selection and genomic prediction as a way of overcoming the limitations imposed by the inherent complexity of biomass yield. Here we extend this approach and illustrate its potential to achieve multiple breeding targets simultaneously, in the absence of a priori knowledge about their relative economic importance, while also monitoring correlated selection responses for non-target traits. We evaluate two hypothetical scenarios of increasing biomass yield by 20 % within a single round of selection. In the first scenario, this is achieved in combination with delaying flowering by 44 d (roughly 20 %), whereas, in the second, increased yield is targeted jointly with reduced lignin (-5 %) and increased cellulose (+5 %) content, relative to current average levels in the breeding population.

Key results

In both scenarios, the objectives were achieved efficiently (selection intensities corresponding to keeping the best 20 and 4 % of genotypes, respectively). However, the outcomes were strikingly different in terms of correlated responses, and the relative economic values (i.e. value per unit of change in each trait compared with that for biomass yield) of secondary traits included in selection indices varied considerably.

Conclusions

Although these calculations rely on multiple assumptions, they highlight the need to evaluate breeding objectives and explicitly consider correlated responses in silico, prior to committing extensive resources. The proposed approach is broadly applicable for this purpose and can readily incorporate high-throughput phenotyping data as part of integrated breeding platforms.

SUBMITTER: Slavov GT

PROVIDER: S-EPMC6821339 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus.

Slavov Gancho T GT Davey Christopher L CL Bosch Maurice M Robson Paul R H PRH Donnison Iain S IS Mackay Ian J IJ

Annals of botany 20191001 4

<h4>Background</h4>Miscanthus has potential as a biomass crop but the development of varieties that are consistently superior to the natural hybrid M. × giganteus has been challenging, presumably because of strong G × E interactions and poor knowledge of the complex genetic architectures of traits underlying biomass productivity and climatic adaptation. While linkage and association mapping studies are starting to generate long lists of candidate regions and even individual genes, it seems unlik ...[more]

PMID: 30351424

Similar Datasets

Project description:BACKGROUND: Miscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, attractive as a biofuel feedstock. The base chromosome number of Miscanthus (x = 19) is different from that of other Saccharinae and approximately twice that of the related Sorghum bicolor (x = 10), suggesting large-scale duplications may have occurred in recent ancestors of Miscanthus. Owing to the complexity of the Miscanthus genome and the complications of self-incompatibility, a complete genetic map with a high density of markers has not yet been developed. RESULTS: We used deep transcriptome sequencing (RNAseq) from two M. sinensis accessions to define 1536 single nucleotide variants (SNVs) for a GoldenGate™ genotyping array, and found that simple sequence repeat (SSR) markers defined in sugarcane are often informative in M. sinensis. A total of 658 SNP and 210 SSR markers were validated via segregation in a full sibling F1 mapping population. Using 221 progeny from this mapping population, we constructed a genetic map for M. sinensis that resolves into 19 linkage groups, the haploid chromosome number expected from cytological evidence. Comparative genomic analysis documents a genome-wide duplication in Miscanthus relative to Sorghum bicolor, with subsequent insertional fusion of a pair of chromosomes. The utility of the map is confirmed by the identification of two paralogous C4-pyruvate, phosphate dikinase (C4-PPDK) loci in Miscanthus, at positions syntenic to the single orthologous gene in Sorghum. CONCLUSIONS: The genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade. The recent timing of this tetraploidy complicates discovery and mapping of genetic markers for Miscanthus species, since alleles and fixed differences between paralogs are comparable. These difficulties can be overcome by careful analysis of segregation patterns in a mapping population and genotyping of doubled haploids. The genetic map for Miscanthus will be useful in biological discovery and breeding efforts to improve this emerging biofuel crop, and also provide a valuable resource for understanding genomic responses to tetraploidy and chromosome fusion.

Project description:BackgroundWhen complex health services interventions are implemented in real-world settings, adaptations are inevitable. Adaptations are changes made to an intervention, implementation strategy, or context prior to, during, and after implementation to improve uptake and fit. There is a growing interest in systematically documenting and understanding adaptations including what is changed, why, when, by whom, and with what impact. The rural Transitions Nurse Program (TNP) is a program in the Veterans Health Administration (VHA), designed to safely transition a rural veteran from a tertiary hospital back home. TNP has been implemented in multiple cohorts across 11 sites nationwide over 4 years. In this paper, we describe adaptations in five TNP sites from the first cohort of sites and implications for the scale-up of TNP and discuss lessons learned for the systematic documentation and analysis of adaptations.MethodsWe used the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) expanded version of the original Stirman framework to guide the rapid qualitative matrix analysis of adaptations. Adaptations were documented using multiple approaches: real-time database, semi-structured midpoint and exit interviews with implementors, and member checking with the implementation team. Interviews were recorded and transcribed. To combine multiple sources of adaptations, we used key domains from our framework and organized adaptations by time when the adaptation occurred (pre-, early, mid-, late implementation; sustainment) and categorized them as proactive or reactive.ResultsForty-one unique adaptations were reported during the study period. The most common type of adaptation was changes in target populations (patient enrollment criteria) followed by personnel changes (staff turnover). Most adaptations occurred during the mid-implementation time period and varied in number and type of adaptation. The reasons for this are discussed, and suggestions for future adaptation protocols are included.ConclusionsThis study demonstrates the feasibility of systematically documenting adaptations using multiple methods across time points. Implementors were able to track adaptations in real time across the course of an intervention, which provided timely and actionable feedback to the implementation team overseeing the national roll-out of the program. Longitudinal semi-structured interviews can complement the real-time database and elicit reflective adaptations.

Project description:We executed two live animal ranking experiments, own-flock and group-animal ranking, to identify the breeding objectives of Arab and Oromo goat keepers in northwestern Ethiopia as a preliminary step towards designing sustainable breeding programs for two goat populations. In the own-flock ranking experiment, a total of 147 households, out of which 46 were Arab and 101 were Oromo goat keepers that live in semi-arid and sub-humid agroecologies respectively, were visited at their homesteads and were asked to choose their first best, second best, third best and the most inferior does from their own flock. The reasons of ranking and life history of the does (age, previous production and reproduction information) were inquired and recorded; live body weight and some linear body measurements were taken. In the group-animal ranking experiment, 12 breeding does and 12 breeding bucks from Arab goats and the same number of animals from Oromo goats were randomly selected. Life history of selected does and bucks (age, birth type, libido and temperament) were inquired from the owners. The selected animals were randomly grouped into four in Arab goats (three animals per group) and the same was applied in Oromo goats. Twelve farmers for Arab goats and the same number of farmers for Oromo goats who have not known the experimental animals were invited to do the ranking. Each person ranked the three animals in each group as 1st, 2nd and 3rd, giving reasons of ranking. After a first round of ranking, s/he was then provided with the history of each individual animal and asked whether s/he would consider re-ranking them. This procedure was continued eight times until a person covered all groups of does and bucks. It was found out that in own-flock ranking experiment, keepers focus on productive, reproductive and behavioral traits (such as body size, mothering ability, twinning rate, kidding interval and temperament) while in group-animal ranking experiment, there was a general tendency to focus on observable physical traits like coat color, body size and body conformation. Simultaneous use of both own-flock and group-animal ranking experiments is advisable to identify breeding objective traits in production systems where record keeping is absent.

Dataset Information

Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus.

Background

Methods

Key results

Conclusions

Publications

Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets