Genetic Erosion Under Modern Plant Breeding: Case Studies in Canadian Crop Gene Pools

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

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Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

10.21203/rs.2.11849/v2 ◽

2019 ◽

Author(s):

Papius Dias Tibihika ◽

Manuel Curto ◽

Esayas Alemayehu ◽

Herwig Waidbacher ◽

Charles Masembe ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

East Africa ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Anthropogenic Activities ◽

Genetic Erosion ◽

Gene Pools ◽

East African ◽

Nile Tilapia Oreochromis Niloticus

Abstract Background The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. Results All three African regions were characterized by independent gene-pools, however, the Ethiopian population from lake Tana showed to be more divergent than expected suggesting that it might be a different species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities. O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction of genetic diversity, which can be a consequence of bottleneck caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stoking activities. Conclusions The anthropogenic activities particularly in the East African O. niloticus translocations, promoted admixture and contact with the native congenerics which may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.

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Generating novel plant genetic variation via genome editing to escape the breeding lottery

In Vitro Cellular & Developmental Biology - Plant ◽

10.1007/s11627-021-10213-0 ◽

2021 ◽

Author(s):

Nathaniel Schleif ◽

Shawn M. Kaeppler ◽

Heidi F. Kaeppler

Keyword(s):

Genetic Variation ◽

Plant Breeding ◽

Genome Editing ◽

Breeding Success ◽

Crop Improvement ◽

Random Mutagenesis ◽

Plant Genome ◽

Gene Pools ◽

Plant Genotype ◽

Wild Accessions

AbstractPlant breeding relies on the presence of genetic variation, which is generated by a random process of mutagenesis that acts on existing gene pools. This variation is then recombined into new forms at frequencies impacted by the local euchromatin and heterochromatin environment. The result is a genetic lottery where plant breeders face increasingly low odds of generating a “winning” plant genotype. Genome editing tools enable targeted manipulation of the genome, providing a means to increase genetic variation and enhancing the chances for plant breeding success. Editing can be applied in a targeted way, where known genetic variation that improves performance can be directly brought into lines of interest through either deletion or insertion. This empowers approaches that are traditionally difficult such as novel domestication and introgression of wild accessions into a germplasm pool. Furthermore, broader editing-mediated approaches such as recombination enhancement and targeted random mutagenesis bring novel ways of variation creation to the plant breeding toolbox. Continued development and application of plant genome editing tools will be needed to aid in meeting critical global crop improvement needs.

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Accessing Ancestral Origin and Diversity Evolution by Net Divergence of an Ongoing Domestication Mediterranean Olive Tree Variety

Frontiers in Plant Science ◽

10.3389/fpls.2021.688214 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hélia Sales ◽

Zlatko Šatović ◽

Mara Lisa Alves ◽

Pedro Fevereiro ◽

João Nunes ◽

...

Keyword(s):

Minimum Spanning Tree ◽

Genetic Relationships ◽

Morphological Variability ◽

Age Groups ◽

Genetic Erosion ◽

Olive Tree ◽

Gene Pools ◽

Central Mediterranean ◽

Ancestral Origin ◽

Olive Variety

Olea europaea ‘Galega vulgar’ variety is a blend of West and Central Mediterranean germplasm with cultivated-wild admixture characteristics. ‘Galega vulgar’ is known for its high rusticity and superior-quality olive oil, being the main Portuguese variety with high impact for bioeconomy. Nevertheless, it has been replaced by higher-yielding and more adapted to intensive production foreign varieties. To clarify the potential ancestral origin, genetic diversity evolution, and existing genetic relationships within the national heritage of ‘Galega vulgar’, 595 trees, belonging to ancient and centenary age groups and prospected among ten traditional production regions, were characterized using 14 SSR markers after variety validation by endocarp measurements. Ninety-five distinguishable genets were identified, revealing the presence of a reasonable amount of intra-genetic and morphological variability. A minimum spanning tree, depicting the complete genealogy of all identified genets, represented the ‘Galega vulgar’ intra-varietal diversity, with 94% of the trees showing only a two-allele difference from the most frequent genet (C001). Strong correlations between the number of differentiating alleles from C001, the clonal size, and their net divergence suggested an ancestral monoclonal origin of the ‘Galega vulgar’, with the most frequent genet identified as the most likely origin of all the genets and phenotypic diversification occurring through somatic mutations. Genetic erosion was detected through the loss of some allele combinations across time. This work highlights the need to recover the lost diversity in this traditional olive variety by including ancient private genets (associated with potential adaptation traits) in future breeding programs and investing in the protection of these valuable resources in situ by safeguarding the defined region of origin and dispersion of ‘Galega vulgar’. Furthermore, this approach proved useful on a highly diverse olive variety and thus applicable to other diverse varieties due either to their intermediate nature between different gene pools or to the presence of a mixture of cultivated and wild traits (as is the case of ‘Galega vulgar’).

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Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations

10.21203/rs.2.11849/v3 ◽

2019 ◽

Author(s):

Papius Dias Tibihika ◽

Manuel Curto ◽

Esayas Alemayehu ◽

Herwig Waidbacher ◽

Charles Masembe ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

East Africa ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Anthropogenic Activities ◽

Genetic Erosion ◽

Gene Pools ◽

East African ◽

Nile Tilapia Oreochromis Niloticus

Abstract Background The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. Results All three African regions were characterized by independent gene-pools, however, the Ethiopian population from lake Tana showed to be more divergent than expected suggesting that it might be a different species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities. O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction of genetic diversity, which can be a consequence of bottleneck caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stoking activities. Conclusions The anthropogenic activities particularly in the East African O. niloticus translocations, promoted admixture and contact with the native congenerics which may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.

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Genome projects and gene pools: New germplasm for plant breeding?

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.95.5.2001 ◽

1998 ◽

Vol 95 (5) ◽

pp. 2001-2004 ◽

Cited By ~ 39

Author(s):

M. Lee

Keyword(s):

Plant Breeding ◽

Gene Pools ◽

New Germplasm ◽

Genome Projects

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The management of rice genetic resources

Genome ◽

10.1139/g89-145 ◽

1989 ◽

Vol 31 (2) ◽

pp. 825-831 ◽

Cited By ~ 7

Author(s):

T. T. Chang

Keyword(s):

Genetic Resources ◽

Management System ◽

Germ Plasm ◽

In Situ Conservation ◽

Public Information ◽

Genetic Erosion ◽

Gene Bank ◽

Database Management System ◽

Gene Pools ◽

Bank Management

Rice growers and researchers are endowed with an enormously rich germ plasm of pantropical distribution, mostly conserved before serious genetic erosion sets in. Efficient management of the conserved resources and effective use of the diverse gene pools justify arduous and costly investments in conservation. A sound conservation system requires adequate field space for seed increase and rejuvenation, cost-efficient and secure storage facilities, a database management system, availability of conserved materials and related information to users, and vigilant monitoring of seed viability. Linkage with evaluators, breeders, and biotechnologists is essential for full use of the conserved materials. Periodic consultation with specialists will extend a collection's usefulness, through further collection or re-collection of germ plasm and in situ conservation, compatibility of documentation systems, and enhanced interinstitutional and international collaboration. Training of germ-plasm workers should be part of the management system. The continuity in human resources will provide security, their dedication will ensure service, interdisciplinary communication will promote use. Improving the capability of national genebanks augments the security of collections preserved at duplicate sites. Gene-bank management must be sustained by adequate administrative and financial support. An effective public information program will further ensure support and security.Key words: rice, Oryza sativa, genetic resources, genetic conservation, gene-bank management.

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