Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Abstract Background: Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5,000 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.

Download Full-text

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽

10.1186/s12284-020-00445-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Ai-ling Hour ◽

Wei-hsun Hsieh ◽

Su-huang Chang ◽

Yong-pei Wu ◽

Han-shiuan Chin ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Indigenous Peoples ◽

Oryza Sativa L ◽

Crop Improvement ◽

Genetic Erosion ◽

Germplasm Conservation ◽

Gene Pools ◽

Improved Varieties ◽

Breeding Goals

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.

Download Full-text

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

10.21203/rs.3.rs-44140/v2 ◽

2020 ◽

Author(s):

Ai-ling Hour ◽

Wei-hsun Hsieh ◽

Su-huang Chang ◽

Yong-pei Wu ◽

Han-shiuan Chin ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Indigenous Peoples ◽

Oryza Sativa L ◽

Crop Improvement ◽

Genetic Erosion ◽

Germplasm Conservation ◽

Gene Pools ◽

Improved Varieties ◽

Breeding Goals

Abstract Background: Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5,000 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.

Download Full-text

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

10.21203/rs.3.rs-44140/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ai-ling Hour ◽

Wei-hsun Hsieh ◽

Su-huang Chang ◽

Yong-pei Wu ◽

Han-shiuan Chin ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Indigenous Peoples ◽

Oryza Sativa L ◽

Crop Improvement ◽

Genetic Erosion ◽

Germplasm Conservation ◽

Gene Pools ◽

Improved Varieties ◽

Breeding Goals

Download Full-text

Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

PLoS ONE ◽

10.1371/journal.pone.0243238 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243238

Author(s):

Wilson Nkhata ◽

Hussein Shimelis ◽

Rob Melis ◽

Rowland Chirwa ◽

Tenyson Mzengeza ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Common Bean ◽

Southern Africa ◽

Crop Improvement ◽

Phenotypic Expression ◽

Snp Markers ◽

High Yield ◽

Gene Pools

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

Download Full-text

Genetic Diversity and Population Structure of Serbian Barley (Hordeum vulgare L.) Collection during a 40-Year Long Breeding Period

Agronomy ◽

10.3390/agronomy11010118 ◽

2021 ◽

Vol 11 (1) ◽

pp. 118

Author(s):

Ljiljana Brbaklić ◽

Dragana Trkulja ◽

Sanja Mikić ◽

Milan Mirosavljević ◽

Vojislava Momčilović ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Hordeum Vulgare ◽

Crop Improvement ◽

Genetic Erosion ◽

Breeding Period ◽

Phenotypic Variance ◽

Hordeum Vulgare L ◽

Phenotypic Data ◽

Breeding Material

Determination of genetic diversity and population structure of breeding material is an important prerequisite for discovering novel and valuable alleles aimed at crop improvement. This study’s main objective was to characterize genetic diversity and population structure of a collection representing a 40-year long historical period of barley (Hordeum vulgare L.) breeding, using microsatellites, pedigree, and phenotypic data. The set of 90 barley genotypes was phenotyped during three growing seasons and genotyped with 338 polymorphic alleles. The indicators of genetic diversity showed differentiation changes throughout the breeding periods. The population structure discriminated the breeding material into three distinctive groups. The principal coordinate analysis grouped the genotypes according to their growth habit and row type. An analysis of phenotypic variance (ANOVA) showed that almost all investigated traits varied significantly between row types, seasons, and breeding periods. A positive effect on yield progress during the 40-year long breeding period could be partly attributed to breeding for shorter plants, which reduced lodging and thus provided higher yield stability. The breeding material revealed a considerable diversity level based on microsatellite and phenotypic data without a tendency of genetic erosion throughout the breeding history and implied dynamic changes in genetic backgrounds, providing a great gene pool suitable for further barley improvement.

Download Full-text

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.

Download Full-text

Genetic diversity of high-molecular-weight glutenin subunit compositions in bread wheat landraces originated from Turkey

Plant Genetic Resources ◽

10.1017/s1479262116000356 ◽

2016 ◽

Vol 16 (1) ◽

pp. 28-38 ◽

Cited By ~ 1

Author(s):

Ridvan Temizgul ◽

Mikail Akbulut ◽

Domenico Lafiandra

Keyword(s):

Genetic Diversity ◽

Molecular Weight ◽

Genetic Variation ◽

High Molecular Weight ◽

Bread Wheat ◽

Gene Diversity ◽

Polyacrylamide Gel Electrophoresis ◽

Genetic Erosion ◽

Allele Polymorphism ◽

Wheat Landraces

AbstractFocusing on 116 bread wheat landraces, this study investigated high molecular weight glutenin allele polymorphism, gene diversity, genetic variation and linkage disequilibrium (LD) inGlu-1loci. To identify gluten alleles, sodium dodesyl sulphate-polyacrylamide, gel electrophoresis was used and for statistical analyses POPGENE software was employed. The results indicated that average genetic variation (h) was the highest inGlu-B1(0.6421) and the lowest inGlu-A1locus (0.4548); genetic similarity ratio (I) was the highest inGlu-B1(1.4170); the highest average genetic diversity (Ht) was observed inGlu-B1(0.6575) and the lowest diversity was observed inGlu-A1(0.4558). It was also observed that genetic diversity inGlu-1locus was largely due to intra-population variations. Inter-population gene flow was also calculated as 4.0051. Marmara and Southeastern Anatolia regions, the results further indicated, had the highest (2.8691) and lowest (0.1694) heterozygosity. Genetic erosion risk for Turkish bread wheat landraces was also seen to be high. Considering the mutual analyses of subunits of nationwide wheat landraces, it is possible to speculate about a limited migration between the landraces. LD of the landraces was largely because of this limited migration and/or epistatic natural selection. Since Turkey is known as the gene centre for major cereals including wheat, barley, rye and oat, where they diversified and spread throughout the world, studying the gluten allele diversity of Turkish bread wheat landraces is important. In addition, this study has revealed the applicability of LD, and neutrality tests to gluten protein diversity for the first time.

Download Full-text

The Impact of Genetic Changes during Crop Domestication

Agronomy ◽

10.3390/agronomy8070119 ◽

2018 ◽

Vol 8 (7) ◽

pp. 119 ◽

Cited By ~ 38

Author(s):

Petr Smýkal ◽

Matthew Nelson ◽

Jens Berger ◽

Eric Von Wettberg

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gene Pools ◽

Human Society ◽

Selective Sweeps ◽

Crop Domestication ◽

Effective Population ◽

Evolutionary Trajectory ◽

Nutrient Levels ◽

The Impact

Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.

Download Full-text

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.

Download Full-text

Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

10.21203/rs.2.18928/v1 ◽

2019 ◽

Author(s):

Alemneh Mideksa Egu ◽

Kifle Dagne ◽

Kassahun Tesfaye ◽

Xuebo Hu

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Major Gene ◽

In Situ Conservation ◽

Germplasm Conservation ◽

Pharmaceutical Products ◽

Gene Pools ◽

Vernonia Galamensis ◽

Diversity Assessment

Abstract BackgroundVernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidised oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. This study is initiated for the systematic and intensive genetic diversity assessment of V. galamensis accessions by SSR molecular markers to minimize the existing research gaps, provide a clue for germplasm conservation and further research. ResultsTwenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified across the entire loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations despite low differentiation among populations which accounted for only 11% of the total variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the 150 accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. These analyses showed accessions collected from the same region of origin did not often grouped entirely together within a given major groups. ConclusionsThe result suggested that the markers applied to ten populations, in which East Showa and East Harerghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

Download Full-text