Crop genetic erosion: understanding and responding to loss of crop diversity

Khoury, Colin K.; Brush, Stephen B.; Costich, Denise E.; Curry, Helen Anne; Haan, Stef de; Engels, Johannes; Guarino, Luigi; Hoban, Sean; Mercer, Kristin L.; Miller, Allison J.; Nabhan, Gary Paul; Perales, Hugo; Richards, Christopher M.; Riggins, Chance W.; Thormann, I.

doi:10.1111/nph.17733

Cited by 215 publications

(199 citation statements)

References 385 publications

(384 reference statements)

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“…In the last century, the advances in plant breeding in search of the most productive and nutritional cultivars have allowed feeding millions of people ( Khush, 2001 ). However, food security is menaced by the decrease in the diversity of crop species and the genetically uniform crop cultivars resulting from the breeding for higher yields ( Esquinas-Alcázar, 2005 ; Khoury et al, 2014 , 2021 ). Climate change is affecting crop production and food security, with different impacts depending on the area of the world and the economic status of the country ( Rosenzweig and Parry, 1994 ; Challinor et al, 2009 , 2014 ; Wheeler and von Braun, 2013 ; Rosenzweig et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Searching for Abiotic Tolerant and Biotic Stress Resistant Wild Lentils for Introgression Breeding Through Predictive Characterization

et al. 2022

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Crop wild relatives are species related to cultivated plants, whose populations have evolved in natural conditions and confer them valuable adaptive genetic diversity, that can be used in introgression breeding programs. Targeting four wild lentil taxa in Europe, we applied the predictive characterization approach through the filtering method to identify populations potentially tolerant to drought, salinity, and waterlogging. In parallel, the calibration method was applied to select wild populations potentially resistant to lentil rust and broomrape, using, respectively, 351 and 204 accessions evaluated for these diseases. An ecogeographic land characterization map was used to incorporate potential genetic diversity of adaptive value. We identified 13, 1, 21, and 30 populations potentially tolerant to drought, soil salinity, waterlogging, or resistance to rust, respectively. The models targeting broomrape resistance did not adjust well and thus, we were not able to select any population regarding this trait. The systematic use of predictive characterization techniques may boost the efficiency of introgression breeding programs by increasing the chances of collecting the most appropriate populations for the desired traits. However, these populations must still be experimentally tested to confirm the predictions.

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Section: Introductionmentioning

confidence: 99%

Searching for Abiotic Tolerant and Biotic Stress Resistant Wild Lentils for Introgression Breeding Through Predictive Characterization

et al. 2022

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“…Whilst the cost and time implications of multiple reference genomes, resequencing and collecting global germplasm are not trivial, we believe that, given the climate crisis and the need to fast‐track the development of mainstream and novel crops, this is the most reliable way to ensure that underutilized crops are investigated to the depth at which reliable and meaningful data can be used. It is likely that some underutilized crops hold vital genetic variants to help the human population combat food insecurity in the next few decades; this genetic erosion is under‐investigated even in staple crops (Khoury et al ., 2022). Without fully investigating underutilized crop genomes, we do not know where these variants lie, and if we delay too long, we may lose alleles, varieties and crops entirely.…”

Section: The Way Forwardmentioning

confidence: 99%

Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

Chapman

Zhou

2022

New Phytologist

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Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress-and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.

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“…Whilst crop diversity has been shown to have increased at the national scale during the Anthropocene, particularly via the Colombian exchange and green revolution (Khoury et al ., 2016; Martin et al ., 2019), the success of a small number of crops has also catalysed the homogenisation of global agrisystems (Khoury et al ., 2014). This has led to concerns that the global expansion of these major crops could displace or replace indigenous crops (Shelef et al ., 2017; Borrell et al ., 2020; Khoury et al ., 2022), with associated loss of long term local adaptation, indigenous knowledge and autochthonous resilience strategies (Seburanga, 2013; Raeboline et al ., 2019).…”

Section: Introductionmentioning

confidence: 99%

Introduced crops supplement rather than replace indigenous crops in an African center of agrobiodiversity

Rampersad

Geto

Samuel

et al. 2022

Preprint

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Crop diversity plays a major role in underpinning food security. It is especially important to smallholder and subsistence farmers, who often rely on crop diversity for stable and resilient production. Despite this, global expansion of a small pool of major crops and the associated homogenisation of global agricultural systems may decrease on-farm crop diversity. We surveyed 1,369 subsistence farms stratified across climate gradients in the Ethiopian Highlands, to characterise the richness and cultivated area of the 83 edible crops they contained. We further categorise these crops by their period of introduction to Ethiopia. We apply non-metric multidimensional scaling and mixed effects modelling to characterise agrisystem composition and test the impact of crop introductions. We find a significant positive relationship between introduced and indigenous crop richness, suggesting that crop introductions have tended to supplement rather than replace or reduce indigenous crop diversity. Geographically matched farms with higher proportions of introduced crops, had significantly higher overall crop richness. Analysis of socio-economic drivers indicates that both poverty and low accessibility are associated with reduced cultivation of modern introductions. We conclude that global patterns of major crop expansion do not necessarily result in agrobiodiversity loss for subsistence farmers, in our Ethiopian case study. Importantly, socioeconomic factors may strongly influence the farmers propensity to adopt novel species, suggesting targets for agricultural extension policies. Given the rapid climatic, economic and demographic changes impacting global food systems and the threats to food security these entail, robust indigenous agricultural systems supplemented with diverse introduced crops may enhance resilience.

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Crop genetic erosion: understanding and responding to loss of crop diversity

Cited by 215 publications

References 385 publications

Searching for Abiotic Tolerant and Biotic Stress Resistant Wild Lentils for Introgression Breeding Through Predictive Characterization

Searching for Abiotic Tolerant and Biotic Stress Resistant Wild Lentils for Introgression Breeding Through Predictive Characterization

Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

Introduced crops supplement rather than replace indigenous crops in an African center of agrobiodiversity

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