Re-imagining crop domestication in the era of high throughput phenomics

Tassel, David L. Van; DeHaan, Lee R.; Diaz‐Garcia, Luis; Hershberger, Jenna; Rubin, Matthew J.; Schlautman, Brandon; Turner, Kathryn; Miller, Allison J.

doi:10.1016/j.pbi.2021.102150

Cited by 25 publications

(17 citation statements)

References 53 publications

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“…The Gossypium pan-genome shows the expansion of new genes in Gh -like species that can provide the basis for crop improvement. The domestication and crop improvement history of cotton has entailed sequential genetic bottlenecks and an accompanying loss of genetic diversity ( 68 – 70 ); some of this lost diversity might have potential to mitigate problems associated with adaptation to various abiotic and biotic stresses. Compared with domesticated cotton, wild relatives have greater resistance to different abiotic and biotic stresses, including disease, drought, and salinity ( 7 , 17 ).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Peng

Tian

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Allotetraploid cotton ( Gossypium ) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD) 6 , Ge ] and Gossypium stephensii [(AD) 7 , Gs ], and one early form of domesticated Gossypium hirsutum , race punctatum [(AD) 1 , Ghp ]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs , Ge , and domesticated G. hirsutum . We describe genomic structural variation that arose during Gossypium evolution and describe its correlates—including phenotypic differentiation, genetic isolation, and genetic convergence—that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.

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Section: Discussionmentioning

confidence: 99%

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Peng

Tian

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…While sequencing costs and/or the assembly of a reference genome remain a barrier in some cases (particularly for underutilized crops), the limiting factor for other crops is now the collection of phenotypic data. High-throughput phenotyping (“phenomics”) represents an important advance ( 66 – 70 ), utilizing sensors on autonomous ground or aerial vehicles to impute plant traits including height and yield in the field, or to complement (or perhaps replace) DNA “fingerprints” with multidimensional phenomic profiles to enable rapid, prediction-based breeding.…”

Section: How Can Domestication Increase Diversity To Enable Agricultu...mentioning

confidence: 99%

The next era of crop domestication starts now

Krug

Drummond

Tassel

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Current food systems are challenged by relying on a few input-intensive, staple crops. The prioritization of yield and the loss of diversity during the recent history of domestication has created contemporary crops and cropping systems that are ecologically unsustainable, vulnerable to climate change, nutrient poor, and socially inequitable. For decades, scientists have proposed diversity as a solution to address these challenges to global food security. Here, we outline the possibilities for a new era of crop domestication, focused on broadening the palette of crop diversity, that engages and benefits the three elements of domestication: crops, ecosystems, and humans. We explore how the suite of tools and technologies at hand can be applied to renew diversity in existing crops, improve underutilized crops, and domesticate new crops to bolster genetic, agroecosystem, and food system diversity. Implementing the new era of domestication requires that researchers, funders, and policymakers boldly invest in basic and translational research. Humans need more diverse food systems in the Anthropocene—the process of domestication can help build them.

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“…Marker-assisted selection for foreground and background selection makes gene introgression easier while retaining and maximizing the background genetic diversity. High-throughput precision phenotyping in association with genomic selection can help in rapid genetic improvement (Van Tassel et al, 2022). Domestication of crops and plant breeding led to the development of crops with a high yield, which is adjusted well to native growing circumstances.…”

Section: Strategy To Accelerate Crop Domesticationmentioning

confidence: 99%

Section: Strategy To Accelerate Crop Domesticationmentioning

confidence: 99%

Unraveling Origin, History, Genetics, and Strategies for Accelerated Domestication and Diversification of Food Legumes

et al. 2022

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Domestication is a dynamic and ongoing process of transforming wild species into cultivated species by selecting desirable agricultural plant features to meet human needs such as taste, yield, storage, and cultivation practices. Human plant domestication began in the Fertile Crescent around 12,000 years ago and spread throughout the world, including China, Mesoamerica, the Andes and Near Oceania, Sub-Saharan Africa, and eastern North America. Indus valley civilizations have played a great role in the domestication of grain legumes. Crops, such as pigeon pea, black gram, green gram, lablab bean, moth bean, and horse gram, originated in the Indian subcontinent, and Neolithic archaeological records indicate that these crops were first domesticated by early civilizations in the region. The domestication and evolution of wild ancestors into today’s elite cultivars are important contributors to global food supply and agricultural crop improvement. In addition, food legumes contribute to food security by protecting human health and minimize climate change impacts. During the domestication process, legume crop species have undergone a severe genetic diversity loss, and only a very narrow range of variability is retained in the cultivars. Further reduction in genetic diversity occurred during seed dispersal and movement across the continents. In general, only a few traits, such as shattering resistance, seed dormancy loss, stem growth behavior, flowering–maturity period, and yield traits, have prominence in the domestication process across the species. Thus, identification and knowledge of domestication responsive loci were often useful in accelerating new species’ domestication. The genes and metabolic pathways responsible for the significant alterations that occurred as an outcome of domestication might aid in the quick domestication of novel crops. Further, recent advances in “omics” sciences, gene-editing technologies, and functional analysis will accelerate the domestication and crop improvement of new crop species without losing much genetic diversity. In this review, we have discussed about the origin, center of diversity, and seed movement of major food legumes, which will be useful in the exploration and utilization of genetic diversity in crop improvement. Further, we have discussed about the major genes/QTLs associated with the domestication syndrome in pulse crops and the future strategies to improve the food legume crops.

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Re-imagining crop domestication in the era of high throughput phenomics

Cited by 25 publications

References 53 publications

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

The next era of crop domestication starts now

Unraveling Origin, History, Genetics, and Strategies for Accelerated Domestication and Diversification of Food Legumes

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