Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems.
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ABSTRACT:
SUBMITTER: Westengen OT
PROVIDER: S-EPMC4191803 | biostudies-literature | 2014 Sep
REPOSITORIES: biostudies-literature
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Project description:Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia. Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here, we analyze newly generated genome-wide single-nucleotide polymorphism data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in Mainland Southeast Asia. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: There have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically diverse region, such as Vietnam.
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Project description:This article shows that higher ethnolinguistic diversity is associated with a greater risk of social tensions and conflict, which, in turn, is a dispersion force lowering urbanization and the incentives to move to big cities. We construct a worldwide dataset at a fine-grained level on urban settlement patterns and ethnolinguistic population composition. For 3,540 provinces of 170 countries, we find that increased ethnolinguistic fractionalization and polarization are associated with lower urbanization and an increased role for secondary cities relative to the primate city of a province. These striking associations are quantitatively important and robust to various changes in variables and specifications. We find that democratic institutions affect the impact of ethnolinguistic diversity on urbanization patterns.
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Project description:Sorghum is the important cereal crop around the world and hence understanding and utilizing the genetic variation in sorghum accessions are essential for improving the crop. A good understanding of genetic variability among the accessions will enable precision breeding. So profiling the genetic diversity of sorghum is imminent. In the present investigation, forty sorghum accessions consisting of sweet sorghum, grain sorghum, forage sorghum, mutant lines, maintainer lines, and restorer lines were screened for genetic diversity using quantitative traits. Observations were recorded on 14 quantitative traits, out of which 9 diverse traits contributing to maximum variability were selected for genetic diversity analysis. The principle component analysis revealed that the panicle width, stem girth, and leaf breadth contributed maximum towards divergence. By using hierarchical cluster analysis, the 40 accessions were grouped under 6 clusters. Cluster I contained maximum number of accessions and cluster VI contained the minimum. The maximum intercluster distance was observed between cluster VI and cluster IV. Cluster III had the highest mean value for hundred-seed weight and yield. Hence the selection of parents must be based on the wider intercluster distance and superior mean performance for yield and yield components. Thus in the present investigation quantitative data were able to reveal the existence of a wide genetic diversity among the sorghum accessions used providing scope for further genetic improvement.
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Project description:Uptake of improved sorghum varieties in the Sudan Savanna of West Africa has been limited, despite the economic importance of the crop and long-term investments in sorghum improvement. One reason why is that attaining substantial yield advantages has been difficult in this harsh, heterogeneous growing environment. Release in Mali of the first sorghum hybrids in Sub-Saharan Africa that have been developed primarily from local germplasm has the potential to change this situation. Utilizing plot data collected in Mali, we explain the adoption of improved seed with an ordered logit model and apply a multivalued treatment effects model to measure impacts on farm families, differentiating between improved varieties and hybrids. Since farm families both consume and sell their sorghum, we consider effects on consumption patterns as well as productivity. Status within the household, conferred by gender combined with marital status, generation, and education, is strongly related to the improvement status of sorghum seed planted in these extended family households. Effects of hybrid use on yields are large, widening the range of food items consumed, reducing the share of sorghum in food purchases, and contributing to a greater share of the sorghum harvest sold. Use of improved seed appears to be associated with a shift toward consumption of other cereals, and also to greater sales shares. Findings support on-farm research concerning yield advantages, also suggesting that the use of well-adapted sorghum hybrids could contribute to diet diversification and the crop's commercialization by smallholders.
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Project description:African populations have been drastically underrepresented in genomics research, and failure to capture the genetic diversity across the numerous ethnolinguistic groups (ELGs) found on the continent has hindered the equity of precision medicine initiatives globally. Here, we describe the whole-genome sequencing of 449 Nigerian individuals across 47 unique self-reported ELGs. Population structure analysis reveals genetic differentiation among our ELGs, consistent with previous findings. From the 36 million SNPs and insertions or deletions (indels) discovered in our dataset, we provide a high-level catalog of both novel and medically relevant variation present across the ELGs. These results emphasize the value of this resource for genomics research, with added granularity by representing multiple ELGs from Nigeria. Our results also underscore the potential of using these cohorts with larger sample sizes to improve our understanding of human ancestry and health in Africa.
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Project description:Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] and with unique ecogeographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing. We identified a total of 108,107 high-quality single-nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome-wide association studies. Although we found no evidence of genetic differentiation among administrative regions (FST = 0.02, P = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, P = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.
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Project description:Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.
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Project description:Early planted sorghum usually experiences cooler day/night temperatures, which may result in delayed growth, floral initiation, and infertile pollen, limiting productivity in high altitudes and temperate regions. Genetic variability for cold tolerance in sorghum has been evaluated by characterizing germination, emergence, vigor, and seedling growth under sub-optimal temperatures. However, the compounded effect of early season cold on plant growth and development and subsequent variability in potential grain yield losses has not been evaluated. Agro-morphological and physiological responses of sorghum grown under early-, mid-, and standard planting dates in West Texas were characterized from seed-to-seed. A set of diverse lines and hybrids with two major sources of tolerance, and previously selected for seedling cold tolerance were used. These were evaluated with a standard commercial hybrid known for its seedling cold tolerance and some cold susceptible breeding lines as checks. Variabilities in assessed parameters at seedling, early vegetative, and maturity stages were observed across planting dates for genotypes and sources of cold tolerance. Panicle initiation was delayed, and panicle size reduced, resulting in decreased grain yields under early and mid-planting dates. Coupled with final germination percent, panicle width and area were significant unique predictors of yield under early and mid-planting dates. Significant variability in performance was observed not only between cold tolerant and susceptible checks, but noticeably between sources of cold tolerance, with the Ethiopian highland sources having lesser yield penalties than their Chinese counterparts. Thus, screening for cold tolerance should not be limited to early seedling characterization but should also consider agronomic traits that may affect yield penalties depending on the sources of tolerance.
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Project description:BackgroundStudies of population genetic structures provide an indication of direction and magnitude of larval transport and hence are an important component in the assessment of the ability of reefs to recover from severe disturbance. This paper reports data on population genetic structures in the coral Pocillopora damicornis from 26 reefs in Kenya and Tanzania.ResultsGene flow among reefs was found to be variable, with a significant overall genetic subdivision (FST = 0.023 +/- 0.004 SE; p < 0.001), however, only 34% of all pairwise population comparisons showed significant differentiation. Panmixia could not be rejected between reefs separated by as much as 697 km, while other sites, separated by only a single kilometre, were found to be significantly differentiated. An analysis of molecular variance indicated that population genetic differentiation was significant only at the smaller spatial scale (< 10 km), whereas panmixia could not be rejected between groups of samples separated by over 100 km. Estimates of contemporary gene flow showed similar results, with numbers of first generation migrants within each population ranging from 0 to 4 (~5% of the total number of colonies sampled) and likely dispersal distances ranging between 5 and 500 km.ConclusionThis study showed that population differentiation in P. damicornis varied over spatial scales and that this variability occurred at both evolutionary and ecological time scales. This paradox is discussed in light of stochastic recruitment and small scale population structures found in other species of coral. The study also identifies potential source reefs, such as those within Mnemba Conservation area near Zanzibar and genetically isolated reefs such as those within Malindi Marine National Park and Reserve in northern Kenya.
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