Evolutionary Relationships Among the Oryza Species

Wambugu, Peterson W.; Nyamongo, D. O.; Ndjiondjop, Marie-Noëlle; Henry, Robert J.

doi:10.1007/978-3-319-71997-9_3

Cited by 8 publications

(10 citation statements)

References 76 publications

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“…Rice breeders have selected for the characteristics of rice grains that make them more appealing as a food source, including grain size, shape, color, and fragrance (Kovach et al, 2007). Despite being widely studied, the domestication of these two cultivated species remains controversial (Wambugu et al, 2018). Modern genetic and genomic studies of cultivated and wild rice will provide useful information and vital insights into the evolution and domestication of rice (Kovach et al, 2007).…”

Section: The Complex Oryza Genus and The Evolution And Domestication mentioning

confidence: 99%

Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice

et al. 2020

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Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na + exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na + in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K + retention in both root and leaf mesophyll cells; and (4) incorporating Na + sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice.

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Section: The Complex Oryza Genus and The Evolution And Domestication mentioning

confidence: 99%

Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice

et al. 2020

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“…O. longistaminata in Africa and O. glumaepatula in South America have similar chloroplast genomes [4] despite their more distant nuclear genome sequences. O. glumaepatula is a part of the A genome clade of close relatives of domesticated rice but has a divergent chloroplast genome being the most divergent A genome species.…”

Section: Discussionmentioning

confidence: 99%

“…Analysis of wild rices (Oryza species) in the group related to domesticated rice, the A genome species has revealed that the wild rices from South America and Africa (Oryza longistaminata and O. glumaepatula) have the most divergent chloroplast genome [4][5][6] while the Australian populations [7] (O. meridionalis [8]and related taxa) have the most divergent nuclear genomes [9]. The chloroplast genomes of wild Oryza have been widely studied and related to those of domesticated rice [4][5][6]. We recently reported a study of the whole chloroplast genomes of 58 mainly wild Oryza, identifying groups major groups based on geographic regions with some overlap in Asian accessions due to the absence of natural borders and human movement [5].…”

Section: Introductionmentioning

confidence: 99%

“…Recently DNA sequence data for more than 3018 domesticated rice genotypes was reported [10]. Reliable analysis of the whole genome sequence of the chloroplast was demonstrated for rice using sequence data from total plant DNA in rice [4]. Because of the high copy number of the chloroplast in the cell, reads from total plant DNA can be used to determine the whole chloroplast sequence with high accuracy.…”

Section: Introductionmentioning

confidence: 99%

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Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production

2020

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Background The whole chloroplast genomes of 3018 rice genotypes were assembled from available sequence data by alignment with a reference rice chloroplast genome sequence, providing high quality chloroplast genomes for analysis of diversity on a much larger scale than in any previous plant study. Results Updated annotation of the chloroplast genome identified 13 more tRNA genes and 30 more introns and defined the function of more of the genes. Domesticated rice had chloroplast genomes that were distinct from those in wild relatives. Analysis confirms an Australian chloroplast clade as a sister to the domesticated clade. All domesticated rice genotypes could be assigned to one of two main clades suggesting the domestication of two distinct maternal genome clades that diverged long before domestication. These clades were very distinct having 4 polymorphisms between all 1486 accession in clade A and all 1532 accessions in clade B. These would result in expression of 3 proteins with altered amino acid sequences and a tRNA with an altered sequence and may be associated with adaptive evolution of the two chloroplast types. Diversity within these pools may have been captured during domestication with subclades enriched in specific groups such as basmati, tropical japonica and temperate japonica. However the phylogenies of the chloroplast and nuclear genomes differed possibly due to modern rice breeding and reticulate evolution prior to domestication. Indica and aus genotypes were common in both chloroplast clades while japonica genotypes were more likely to be found in the same clade (cladeB). Conclusions The different evolutionary paths of the cytoplasmic and nuclear genomes of rice have resulted in the presence of apparently functional chloroplast genome diversity and the implications for rice crop performance require further investigation.

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“…Advances in DNA sequencing technology have made it possible to analyze the genomes of large numbers of individuals. This has had significant impact on human genetics but also on rice biology revealing much about the diversity of the populations, the relationships between different populations, and the evolutionary events leading up to domestication by humans (Wambugu et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Australian Wild Rice Populations: A Key Resource for Global Food Security

Henry

2019

Front. Plant Sci.

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Rice is one of the most important food crops contributing to the diet of large numbers of people especially in Asia. Rice (Oryza sativa) was domesticated in Asia many thousands of years ago and more recently independently in Africa. Wild rice populations are found around the tropical world. The extensive production of rice in many areas has displaced the wild populations that were the basis of the original domestications by humans. Recent research, reviewed here, has identified wild rice species in northern Australia that have been isolated from the impact of domestication in Asia. Wild rice populations contain novel alleles that are a source of desirable traits such as erect habit, disease resistance, large grain size, and unique starch properties. These populations include the most divergent genotypes within the primary gene pool of rice and more distant wild relatives. Genome sequencing also suggests the presence of populations that are close relatives of domesticated rice. Hybrid populations that demonstrate mechanisms of ongoing evolution of wild Oryza have been identified in the wild. These populations provide options for both new domestications and utilization of novel alleles to improve or adapt domesticated rice using conventional or preferably new breeding technologies. Climate change and growing food demands associated with population and economic growth are major challenges for agriculture including rice production. The availability of diverse genetic resources to support crop adaptation and new crop domestication is critical to continued production, and increased efforts to support in situ and ex situ conservation of wild Oryza and related species are warranted.

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Evolutionary Relationships Among the Oryza Species

Cited by 8 publications

References 76 publications

Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice

Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice

Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production

Australian Wild Rice Populations: A Key Resource for Global Food Security

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