scholarly journals Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Janet Higgins ◽  
Bruno Santos ◽  
Tran Dang Khanh ◽  
Khuat Huu Trung ◽  
Tran Duy Duong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heading Date ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Asian Rice ◽  
Rice Landraces ◽  
Shared Ancestry ◽  
Production Areas ◽  
Rice Diversity ◽  
Trait Associations

Abstract Background Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. Results We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. Conclusions We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

scholarly journals Resequencing of 672 native rice accessions to explore genetic diversity and trait associations along Vietnam

2020 ◽  
Author(s):  
Janet Higgins ◽  
Bruno Santos ◽  
Tran Dang Khanh ◽  
Khuat Huu Trung ◽  
Tran Duy Duong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heading Date ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Shared Ancestry ◽  
Production Areas ◽  
Genomic Regions ◽  
New Generation ◽  
Trait Associations

Abstract BACKGROUND: Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. RESULTS: We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. CONCLUSIONS: Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

scholarly journals Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

2020 ◽  
Author(s):  
Janet Higgins ◽  
Bruno Santos ◽  
Tran Dang Khanh ◽  
Khuat Huu Trung ◽  
Tran Duy Duong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heading Date ◽  
Cultivated Rice ◽  
Region Of Origin ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Shared Ancestry ◽  
Production Areas ◽  
Genomic Regions ◽  
New Generation

AbstractVietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns.We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. We identified genomic regions selected in both Indica and Japonica subtypes during the breeding of these subpopulations within Vietnam and discuss in detail fifty-two selected regions in I5, which constitute an untapped resource of cultivated rice diversity.Our results highlight traits and their associated genomic regions, which were identified by fine phenotyping and data integration. These are a potential source of novel loci and alleles to breed a new generation of sustainable and resilient rice.

Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 782-792 ◽  
Author(s):  
J. C. Glaszmann
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Indian Subcontinent ◽  
Indica Rice ◽  
Japonica Rice ◽  
Geographic Pattern ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Himalayan Foothills

The geographic pattern of isozyme variation among rice varieties (Oryza sativa L.) in Asia is described based on an electrophoretic survey of 1688 accessions for 15 loci. The distribution patterns are strongly determined by the existence of several varietal groups that are characterized by contrasting multilocus types with dissimilar environmental and macrogeographic distributions. The two main groups correspond to the indica and japonica subspecies. Other types are frequently found in the Indian subcontinent, especially along the Himalayan foothills. These types are predominant in the Indus River basin. They are differentiated into four groups in the eastern part of the Himalayan foothills. There is variation within the groups. Non-random allele distributions are observed, such as regional clines and narrow localization of alleles. Diversity among indica rice is evenly distributed in whole tropical Asia. Variation among japonica rice shows the hilly part of continental Southeast Asia to be the region of highest genetic diversity and its probable area of origin. All this information provides a guide for further analysis aimed at elucidating the history of cultivated rice in Asia and, subsequently, in other continents.Key words: Asian rice, genetic diversity, isozymes, geographic distributions.

scholarly journals Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 995
Author(s):  
Wanchana Aesomnuk ◽  
Siriphat Ruengphayak ◽  
Vinitchan Ruanjaichon ◽  
Tanee Sreewongchai ◽  
Chanate Malumpong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Mantel Test ◽  
Snp Markers ◽  
High Yield ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Geographical Regions

Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to indica and japonica groups. The indica group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise FST showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding.

Population genetics analyses of North-East Indian indigenous rice landraces revealed divergent history and alternate origin of aroma in aus group

2019 ◽  
Vol 17 (5) ◽  
pp. 437-447
Author(s):  
Debarati Chakraborty ◽  
Avik Ray
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Indian Subcontinent ◽  
High Genetic Diversity ◽  
East Indian ◽  
North East ◽  
Rice Landraces ◽  
Shared Ancestry ◽  
History Of ◽  
The Rich

AbstractThe rice-based agriculture of the Indian subcontinent has been interwoven in the rich socio-cultural fabric of the country. Of which, bio-culturally diverse North-Eastern states nurture thousands of landraces with poorly tapped agronomic traits. In the present study, 27 standard microsatellite data from 171 rice landraces from six states were analysed to understand their genetic diversity and population structure. Further, combining with a global dataset, we determined subpopulation identity using both model-based and multivariate analyses to uncover their history. We found moderate to high genetic diversity and high differentiation [standardized G”ST = 0.57]. The AMOVA partitioned overall variance into within population (75%) and among population (25%). The landraces from six states remained at various degrees of differentiation (pairwise FST = 0.09–0.41). We have detected a preponderance of aus-type in a majority of aromatic landraces. Rests were japonica and admixed with a little representation of indica. The presence of aromatic aus probably implied assimilation into local culture from the primary aus growing region of Bangladesh and India. Likewise, the arrival of japonica may stem from the exchange of goods among neighbouring dynasties via Southern and Southwestern Silk routes. The shared ancestry may reflect a merger of two ancient cultures. Our analyses also uncovered the existence of aus-type short and medium grain aromatic rice predicting an origin of aroma in aus subpopulation. Collectively, it demonstrated the diversity and divergent history of the rice landraces have been shaped by various socio-cultural interactions operative over time and space.

scholarly journals Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice

2019 ◽  
Author(s):  
Yong Zhou ◽  
Dmytro Chebotarov ◽  
Dave Kudrna ◽  
Victor Llaca ◽  
Seunghee Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Variation ◽  
Full Range ◽  
Critical Role ◽  
Rice Genome ◽  
Environmental Footprint ◽  
Cultivated Rice ◽  
Asian Rice ◽  
Admixed Population ◽  
Reference Genomes

AbstractAs the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a pan-genome template to map resequencing data to detect virtually all standing natural variation that exists in the pan-cultivated rice genome.

Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR

Genome ◽  
2007 ◽  
Vol 50 (1) ◽  
pp. 72-83 ◽  
Author(s):  
Hongliang Zhang ◽  
Junli Sun ◽  
Meixing Wang ◽  
Dengqun Liao ◽  
Yawen Zeng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Oryza Sativa L ◽  
Cropping System ◽  
Analysis Model ◽  
Cultivated Rice ◽  
Model Based ◽  
Rice Landraces ◽  
Southwest Region

Yunnan Province is one of the largest centers of genetic diversity of Oryza sativa L. in China, and in the world. Using a genetically representative core collection of 692 rice landraces from Yunnan, the genetic structure, differentiation, and geographic diversity of this rice germplasm were analyzed. The accessions were classified into different populations, according to the model-based structure analysis. Model-based populations were characterized through the reconstruction of a neighbor-joining tree, principal coordinate analysis, and the estimation of morphologic and SSR variations. Finally, the distribution of genetic diversity and differentiation among districts were studied. Seven model-based populations were identified on the basis of the structure analysis. This classification was partly consistent with Ting’s 5-level taxonomic system. Differentiation between 2 rice subspecies is the most apparent, with a clearer differentiation between soil-watery ecotypes in japonica than in indica; however, differentiation among seasonal ecotypes in indica is clearer than in japonica. Cropping system and man-made restricted-growth environments could be considered to be the main forces driving the intraspecific differentiation of cultivated rice. It has been suggested that, because it possesses the highest genetic diversity and all the necessary conditions as a center of genetic diversity, the southwest region of Yunnan, encompassing Simao, Lincang, and Xishuangbanna districts, is the center of genetic diversity of Yunnan rice landraces.

scholarly journals Microsatellite diversity within Oryza sativa with emphasis on indica–japonica divergence

2005 ◽  
Vol 85 (1) ◽  
pp. 1-14 ◽  
Author(s):  
LI-ZHI GAO ◽  
CHI-HONG ZHANG ◽  
LI-PING CHANG ◽  
JI-ZENG JIA ◽  
ZONG-EN QIU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Gene Diversity ◽  
Rice Genome ◽  
Chromosome 1 ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Allele Number ◽  
Clustering Patterns ◽  
Microsatellite Diversity

The molecular evolution of cultivated rice Oryza sativa L. has long been a subject of rice evolutionists. To investigate genetic diversity within and differentiation between the indica and japonica subspecies, 22 accessions of indica and 35 of japonica rice were examined by five microsatellite loci from each chromosome totalling 60 loci. Mean gene diversity value in the indica rice (H=0·678) was 1·18 times larger than in the japonica rice (H=0·574). Taking the sampling effect into consideration, average allele number in the indica rice was 1·40 times higher than that in the japonica rice (14·6 vs 10·4 per variety). Chromosome-based comparisons revealed that nine chromosomes (1, 2, 3, 4, 5, 8, 9, 10 and 11) harboured higher levels of genetic diversity within the indica rice than the japonica rice. An overall estimate of FST was 0·084–0·158, indicating that the differentiation is moderate and 8·4–15·8% of the total genetic variation resided between the indica and japonica groups. Our chromosome-based comparisons further suggested that the extent of the indica–japonica differentiation varied substantially, ranging from 7·62% in chromosome 3 to 28·72% in chromosome 1. Cluster analyses found that most varieties formed merely two clusters for the indica and japonica varieties, in which two japonica varieties and five indica varieties were included in the counterpart clusters, respectively. The 12 chromosome-based trees further showed that 57 rice varieties cannot be clearly clustered together into either the indica or japonica groups, but displayed relatively different clustering patterns. The results suggest that the process of indica–japonica differentiation may have proceeded through an extensive contribution by the alleles of the majority in the rice genome.

scholarly journals Tailoring rice varieties to consumer preferences induced by cultural and colonial heritage: Lessons from New Rice for Africa (NERICA) in The Gambia

2021 ◽  
pp. 003072702110197
Author(s):  
Kofi Britwum ◽  
Matty Demont
Keyword(s):  
Consumer Preferences ◽  
Rice Variety ◽  
Import Substitution ◽  
The Gambia ◽  
Rice Varieties ◽  
Auction Market ◽  
Asian Rice ◽  
Market Competitiveness ◽  
New Varieties ◽  
Locally Grown

Rice breeding priorities in Africa often focus on agronomic gains. However, being a net importer of rice, the continent’s varietal replacement success also crucially hinges on new varieties’ market competitiveness vis-à-vis imports. Markets have been profoundly shaped by cultural and colonial heritage. Indigenous preferences for African rice can be traced back to ancient rice domestication and have been subsequently influenced by Asian rice import standards as a result of colonial import substitution policies. New Rice for Africa (NERICA) crosses between African and Asian rice species have the potential to reconcile these dual indigenous/import preferences, but little is known about their market competitiveness. We use auction market data to assess the intrinsic and extrinsic consumer value of NERICA in The Gambia relative to two market standards: branded, Asian rice imports and the most popular locally grown Asian rice variety. We categorize rice consumers into four market segments, based on their heritage as evidenced by their preferences and genealogical lineages. NERICA outperforms both Asian rice standards in terms of market competitiveness, and its value is further reinforced by colonial heritage and labeling, but somewhat weakened by cultural heritage. Consumers were found to pay price premiums for NERICA in the range of 5% to 22% relative to Asian rice imports, with the highest premiums offered by consumers with colonial heritage, representing 86% of the sample. Maintaining and expanding this market will require breeders to incorporate trait mixes that reconcile agronomic gains and consumer preferences induced by cultural and colonial heritage.

Sign in / Sign up

Export Citation Format

Share Document