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      Breeding Beyond Monoculture: Putting the “Intercrop” Into Crops

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          Abstract

          Intercropping is both a well-established and yet novel agricultural practice, depending on one’s perspective. Such perspectives are principally governed by geographic location and whether monocultural practices predominate. Given the negative environmental effects of monoculture agriculture (loss of biodiversity, reliance on non-renewable inputs, soil degradation, etc.), there has been a renewed interest in cropping systems that can reduce the impact of modern agriculture while maintaining (or even increasing) yields. Intercropping is one of the most promising practices in this regard, yet faces a multitude of challenges if it is to compete with and ultimately replace the prevailing monocultural norm. These challenges include the necessity for more complex agricultural designs in space and time, bespoke machinery, and adapted crop cultivars. Plant breeding for monocultures has focused on maximizing yield in single-species stands, leading to highly productive yet specialized genotypes. However, indications suggest that these genotypes are not the best adapted to intercropping systems. Re-designing breeding programs to accommodate inter-specific interactions and compatibilities, with potentially multiple different intercropping partners, is certainly challenging, but recent technological advances offer novel solutions. We identify a number of such technology-driven directions, either ideotype-driven (i.e., “trait-based” breeding) or quantitative genetics-driven (i.e., “product-based” breeding). For ideotype breeding, plant growth modeling can help predict plant traits that affect both inter- and intraspecific interactions and their influence on crop performance. Quantitative breeding approaches, on the other hand, estimate breeding values of component crops without necessarily understanding the underlying mechanisms. We argue that a combined approach, for example, integrating plant growth modeling with genomic-assisted selection and indirect genetic effects, may offer the best chance to bridge the gap between current monoculture breeding programs and the more integrated and diverse breeding programs of the future.

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          Most cited references145

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          Planetary boundaries: Guiding human development on a changing planet

          The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system into a new state should they be substantially and persistently transgressed.
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            Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps

            Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of ∼50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size (Ne = 100), the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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              Agricultural sustainability and intensive production practices.

              A doubling in global food demand projected for the next 50 years poses huge challenges for the sustainability both of food production and of terrestrial and aquatic ecosystems and the services they provide to society. Agriculturalists are the principal managers of global usable lands and will shape, perhaps irreversibly, the surface of the Earth in the coming decades. New incentives and policies for ensuring the sustainability of agriculture and ecosystem services will be crucial if we are to meet the demands of improving yields without compromising environmental integrity or public health.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                18 November 2021
                2021
                : 12
                : 734167
                Affiliations
                [1] 1Plant Breeding, Wageningen University & Research , Wageningen, Netherlands
                [2] 2Centre for Crops Systems Analysis, Wageningen University & Research , Wageningen, Netherlands
                [3] 3Animal Breeding and Genomics, Wageningen University & Research , Wageningen, Netherlands
                [4] 4Farming Systems Ecology Group, Wageningen University & Research , Wageningen, Netherlands
                [5] 5Field Crops, Wageningen University & Research , Lelystad, Netherlands
                [6] 6Soil Biology, Wageningen University & Research , Wageningen, Netherlands
                [7] 7Plant Ecology and Nature Conservation, Wageningen University & Research , Wageningen, Netherlands
                Author notes

                Edited by: Jérôme Enjalbert, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), France

                Reviewed by: Nobuhito Sekiya, Mie University, Japan; Radu E. Sestras, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania; Jean-Paul Sampoux, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), France

                *Correspondence: Guusje Bonnema, guusje.bonnema@ 123456wur.nl

                This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2021.734167
                8636715
                34868116
                3f0a308a-8f49-4617-989b-b93976b99c7f
                Copyright © 2021 Bourke, Evers, Bijma, van Apeldoorn, Smulders, Kuyper, Mommer and Bonnema.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 30 June 2021
                : 22 October 2021
                Page count
                Figures: 4, Tables: 0, Equations: 9, References: 147, Pages: 17, Words: 15378
                Funding
                Funded by: Wageningen University & Research
                Award ID: KB-40-005-004
                Award ID: KB-34-007-019
                Funded by: Top Sectors programme Agri & Food
                Categories
                Plant Science
                Review

                Plant science & Botany
                intercropping,plant breeding,functional–structural plant modeling,indirect genetic effects,plant–plant interactions,mycorrhiza,plasticity

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