Adaptation to novel environments during crop diversification

Cortinovis, Gaia; Vittori, Valerio Di; Bellucci, Elisa; Bitocchi, Elena; Papa, Roberto

doi:10.1016/j.pbi.2019.12.011

Cited by 28 publications

(28 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, an excellent example of the potential population genomics approach was offered by Exposito-Alonso et al [88] for the A. thaliana model system. As well as improving our knowledge of the genomic basis of past selection and adaptation to specific agro-ecosystems, Exposito-Alonso et al [88] were able to build genome-wide environmental selection models to predict how evolutionary pressures on species will work in inaccessible environments or even under future hypothetical climates [9]. Figure 1 shows the critical role of marker mutations in describing the diversity of plant populations; the higher the mutation rate, the lower the loss of diversity detectable.…”

Section: Discussionmentioning

confidence: 99%

“…Its applications can address questions that have long been studied using previous tools (e.g., effective population size, population structure, phylogeography and demography) [5]. The use of novel tools and statistical tests now allows previously inaccessible issues to be addressed, such as physical mapping of adaptive variations and of molecular variants that underlie genotype fitness and relevant phenotypic variations throughout the genome [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Current State and Perspectives in Population Genomics of the Common Bean

Cortinovis

Frascarelli

Vittori

et al. 2020

Plants

Self Cite

View full text Add to dashboard Cite

Population genomics integrates advances in sequencing technologies, bioinformatics tools, statistical methods and software into research on evolutionary and population genetics. Its application has provided novel approaches that have significantly advanced our understanding of new and long-standing questions in evolutionary processes. This has allowed the disentangling of locus-specific effects from genome-wide effects and has shed light on the genomic basis of fitness, local adaptation and phenotypes. “-Omics” tools have provided a comprehensive genome-wide view of the action of evolution. The specific features of the Phaseolus genus have made it a unique example for the study of crop evolution. The well-documented history of multiple domestications in Phaseolus vulgaris L. (common bean) and its further adaptation to different environments have provided the opportunity to investigate evolutionary issues, such as convergent evolution in the same species across different domestication events. Moreover, the availability of the P. vulgaris reference genome now allows adaptive variations to be easily mapped across the entire genome. Here, we provide an overview of the most significant outcomes obtained in common bean through the use of different computational tools for analysis of population genomics data.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Current State and Perspectives in Population Genomics of the Common Bean

Cortinovis

Frascarelli

Vittori

et al. 2020

Plants

Self Cite

View full text Add to dashboard Cite

show abstract

“…The conservation and valorization of plant genetic resources (PGR) is crucial for the future of agriculture [29]. Indeed, the genetic diversity of PGR and particularly of food legumes represents a strategic tool for agriculture today, to guarantee food security and food quality, to cope with climate change and to protect the environment [9,30]. To conserve such precious resources is not enough; it is crucial to also characterize them and to be able to fully exploit the genetic diversity they hold for plant breeding.…”

Section: Discussionmentioning

confidence: 99%

The Development of a European and Mediterranean Chickpea Association Panel (EMCAP)

et al. 2020

Self Cite

View full text Add to dashboard Cite

Association panels represent a useful tool for quantitative trait loci (QTL) mapping and pre-breeding. In this study, we report on the development of a European and Mediterranean chickpea association panel as a useful tool for gene discovery and breeding. Chickpea (Cicer arietinum L.) is one of the most important food legumes worldwide and a key crop in the Mediterranean environments. The selection of genotypes followed criteria aimed to build a set of materials representative of the genetic diversity of chickpea germplasm focusing on the European and Mediterranean environments, which have largely been ignored to date. This tool can help breeders to develop novel varieties adapted to European and Mediterranean agro-ecosystems. Initially, 1931 chickpea accessions were phenotypically evaluated in a field trial in central Italy. From these, an association panel composed by 480 genotypes derived from single-seed descent was identified and phenotypically evaluated. Current and future phenotypic data combined with the genotypic characterization of the association panel will allow to dissect the genetic architecture of important adaptive and quality traits and accelerate breeding. This information can be used to predict phenotypes of unexploited chickpea genetic resources available in genebanks for breeding.

show abstract

“…Extending these ultimate analytical approaches will help to resolve major basic questions in the field [205] such as to which scale diversifying selection promotes [206] and gene flow precludes [207,208] local adaptation, and whether large haplotype blocks are pervasive in adaptation signatures due to structural variants [209] such as chromosomal inversions [210,211]. Targeting these issues will allow trans-disciplinary research teams to move into more applied matters like (1) how GP and ML can be intermingled to turbocharge genebanks [212] while disentangling the correlated trade-off complexity in proxy traits as part of speed breeding strategies [125,126], and (2) what is the optimum pathway for pan-genomes [213] and epigenetics [214] to unlock the properties of plants for sustainable development [215].…”

Section: Geavs Geavsmentioning

confidence: 99%

Harnessing Crop Wild Diversity for Climate Change Adaptation

Cortés

López-Hernández

2021

Genes

View full text Add to dashboard Cite

Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent ‘big data’ developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these ‘big data’ approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.

show abstract

Adaptation to novel environments during crop diversification

Cited by 28 publications

References 82 publications

Current State and Perspectives in Population Genomics of the Common Bean

Current State and Perspectives in Population Genomics of the Common Bean

The Development of a European and Mediterranean Chickpea Association Panel (EMCAP)

Harnessing Crop Wild Diversity for Climate Change Adaptation

Contact Info

Product

Resources

About