scholarly journals Genome-wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet

2018 ◽  
Author(s):  
Matthew Johnson ◽  
Santosh Deshpande ◽  
Mani Vetriventhan ◽  
Hari D Upadhyaya ◽  
Jason G. Wallace
Keyword(s):  
Population Structure ◽  
Smallholder Farmers ◽  
Population Genetic Analysis ◽  
Proso Millet ◽  
Little Millet ◽  
Genome Wide ◽  
A Genome ◽  
Kodo Millet ◽  
Minor Millets ◽  
Wide Population

AbstractMillets are a diverse group of small-seeded grains that are rich in nutrients but have received relatively little advanced plant breeding research. Millets are important to smallholder farmers in Africa and Asia because of their short growing season, good stress tolerance, and high nutritional content. To advance the study and use of these species, we present a genome-wide marker datasets and population structure analyses for three minor millets: kodo millet (Paspalum scrobiculatum), little millet (Panicum sumatrense), and proso millet (Panicum miliaceum). We generated genome-wide marker data sets for 190 accessions of each species with genotyping-by-sequencing (GBS). After filtering, we retained between 161 and 165 accessions of each species, with 3461, 2245, and 1882 single-nucleotide polymorphisms (SNPs) for kodo, proso, and little millet, respectively. Population genetic analysis revealed 7 putative subpopulations of kodo millet and 8 each of proso millet and little millet. To confirm the accuracy of this genetic data, we used public phenotype data on a subset of these accessions to estimate the heritability of various agronomically relevant phenotypes. Heritability values largely agree with the prior expectation for each phenotype, indicating that these SNPs provide an accurate genome-wide sample of genetic variation. These data represent one of first genome-wide population genetics analyses, and the most extensive, in these species and the first genomic analyses of any sort for little millet and kodo millet. These data will be a valuable resource for researchers and breeders trying to improve these crops for smallholder farmers.

scholarly journals Genome‐Wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet

2019 ◽  
Vol 12 (3) ◽  
pp. 190021 ◽  
Author(s):  
Matthew Johnson ◽  
Santosh Deshpande ◽  
Mani Vetriventhan ◽  
Hari D. Upadhyaya ◽  
Jason G. Wallace
Keyword(s):  
Population Structure ◽  
Proso Millet ◽  
Little Millet ◽  
Genome Wide ◽  
Kodo Millet ◽  
Minor Millets ◽  
Wide Population

scholarly journals A Modification and development of threshing unit for minor millets

2018 ◽  
Vol 33 (00) ◽  
Author(s):  
Shalini Chaturvedi ◽  
Falguni Rathore ◽  
Shantanu Pandey
Keyword(s):  
Finger Millet ◽  
Cleaning Efficiency ◽  
Proso Millet ◽  
Seed Damage ◽  
Little Millet ◽  
The Family ◽  
Different Shapes ◽  
Kodo Millet ◽  
The Cost ◽  
Minor Millets

Minor millets are small sized cereal grains belonging to the family Poaceae (Gramineae) are grown mainly in America, Japan, China and India. In India minor millet grown are finger millet, proso millet, barnyard millet, kodo millet and little millet. Threshing is based on the principle that, some impact is given on crops, the grains are separated from panicles, cobs and pods. The performance of the threshing unit with development of five different shapes of pegs for threshing small millet. small millet thresher was tested at two different speed 712 rpm and 1068 rpm. The highest threshing efficiency with disc shape peg of 99.57 % cleaning efficiency 98.64 % output capacity 19.68 kg/ha was observed. In disc shape peg seed damage negalible. The cost of operation was also minimum. On the basis of above the disc type pe is recommended for minor millet.

scholarly journals Development and evaluation of multi millet thresher

2015 ◽  
Vol 7 (2) ◽  
pp. 939-948 ◽  
Author(s):  
K. P. Singh ◽  
Rahul R. Poddar ◽  
K. N. Agrawal ◽  
Smrutilipi Hota ◽  
Mukesh K. Singh
Keyword(s):  
Finger Millet ◽  
Foxtail Millet ◽  
Eleusine Coracana ◽  
Cleaning Efficiency ◽  
Proso Millet ◽  
Little Millet ◽  
Sieve Size ◽  
Kodo Millet ◽  
Tribal Areas ◽  
Minor Millets

In tribal areas of India, traditional methods of threshing of minor millets like little millet (Panicum sumatrense), M1, kodo millet (Paspalum scrobiculatum), M2, foxtail millet (Setaria italica), M3, proso millet (P. miliaceum), M4, barnyard millet (Echinochloa frumantacea), M5, finger millet (Eleusine coracana), M6 is done of beating by sticks or treading out the crop panicle under the feet of oxen. This operation is most time consuming, labour intensive, drudgery prone, uneconomical, lower output and obtain low quality products. A thresher for these millet crops was developed and optimization of the operating parameters with little millet was done by using Response surface methodology (RSM). The optimized parameters were 7.79% (d.b) moisture content, 105 kgh-1 feed rate, 625 rpm cylinder speed, 5 mm threshing sieve size which gave maximum threshing efficiency of 95.13% and cleaning efficiency of 94.12%. After optimization of parameters the thresher was tested for threshing of all the six minor millets with proper adjustments of sieve. Threshing capacity of M1, M2, M3, M4, M5 and M6 were obtained as 89, 137, 140, 91, 88 and 99 kg/h, respectively with more than 96% threshing efficiency and less than 2% broken grain.

scholarly journals From conservation genetics to conservation genomics: a genome-wide assessment of blue whales ( Balaenoptera musculus ) in Australian feeding aggregations

2018 ◽  
Vol 5 (1) ◽  
pp. 170925 ◽  
Author(s):  
Catherine R. M. Attard ◽  
Luciano B. Beheregaray ◽  
Jonathan Sandoval-Castillo ◽  
K. Curt S. Jenner ◽  
Peter C. Gill ◽  
...  
Keyword(s):  
Population Structure ◽  
Adaptive Divergence ◽  
Balaenoptera Musculus ◽  
Blue Whale ◽  
Conservation Genomics ◽  
Next Generation Sequencing Technology ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Blue Whales

Genetic datasets of tens of markers have been superseded through next-generation sequencing technology with genome-wide datasets of thousands of markers. Genomic datasets improve our power to detect low population structure and identify adaptive divergence. The increased population-level knowledge can inform the conservation management of endangered species, such as the blue whale ( Balaenoptera musculus ). In Australia, there are two known feeding aggregations of the pygmy blue whale ( B. m. brevicauda ) which have shown no evidence of genetic structure based on a small dataset of 10 microsatellites and mtDNA. Here, we develop and implement a high-resolution dataset of 8294 genome-wide filtered single nucleotide polymorphisms, the first of its kind for blue whales. We use these data to assess whether the Australian feeding aggregations constitute one population and to test for the first time whether there is adaptive divergence between the feeding aggregations. We found no evidence of neutral population structure and negligible evidence of adaptive divergence. We propose that individuals likely travel widely between feeding areas and to breeding areas, which would require them to be adapted to a wide range of environmental conditions. This has important implications for their conservation as this blue whale population is likely vulnerable to a range of anthropogenic threats both off Australia and elsewhere.

scholarly journals Revisiting demographic processes in cattle with genome-wide population genetic analysis

2015 ◽  
Vol 6 ◽  
Author(s):  
Pablo Orozco-terWengel ◽  
Mario Barbato ◽  
Ezequiel Nicolazzi ◽  
Filippo Biscarini ◽  
Marco Milanesi ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Population Genetic ◽  
Population Genetic Analysis ◽  
Genome Wide ◽  
Demographic Processes ◽  
Wide Population

scholarly journals Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

2019 ◽  
Vol 5 (9) ◽  
pp. eaaw3492 ◽  
Author(s):  
A. Raveane ◽  
S. Aneli ◽  
F. Montinaro ◽  
G. Athanasiadis ◽  
S. Barlera ◽  
...  
Keyword(s):  
Population Structure ◽  
Bronze Age ◽  
The Caucasus ◽  
Italian Peninsula ◽  
Nomadic Pastoralists ◽  
Genome Wide ◽  
A Genome ◽  
The World ◽  
European Populations

European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non–steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

scholarly journals Review: Population Structure in Genetic Studies: Confounding Factors and Mixed Models

2016 ◽  
Author(s):  
Lana S. Martin ◽  
Eleazar Eskin
Keyword(s):  
Population Structure ◽  
Mixed Models ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Laboratory Mouse ◽  
Mouse Strains ◽  
Genetic Studies ◽  
The Past ◽  
Genome Wide ◽  
A Genome

AbstractA genome-wide association study (GWAS) seeks to identify genetic variants that contribute to the development and progression of a specific disease. Over the past 10 years, new approaches using mixed models have emerged to mitigate the deleterious effects of population structure and relatedness in association studies. However, developing GWAS techniques to effectively test for association while correcting for population structure is a computational and statistical challenge. Using laboratory mouse strains as an example, our review characterizes the problem of population structure in association studies and describes how it can cause false positive associations. We then motivate mixed models in the context of unmodeled factors.

scholarly journals Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

2019 ◽  
Author(s):  
Tika B. Adhikari ◽  
Brian J. Knaus ◽  
Niklaus J. Grünwald ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Plant Pathogens ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Genome Wide ◽  
A Genome

ABSTRACTGenotyping by sequencing (GBS) is considered a powerful tool to discover single nucleotide polymorphisms (SNPs), which are useful to characterize closely related genomes of plant species and plant pathogens. We applied GBS to determine genome-wide variations in a panel of 187 isolates of three closely related Alternaria spp. that cause diseases on tomato and potato in North Carolina (NC) and Wisconsin (WI). To compare genetic variations, reads were mapped to both A. alternata and A. solani draft reference genomes and detected dramatic differences in SNPs among them. Comparison of A. linariae and A. solani populations by principal component analysis revealed the first (83.8% of variation) and second (8.0% of variation) components contained A. linariae from tomato in NC and A. solani from potato in WI, respectively, providing evidence of population structure. Genetic differentiation (Hedrick’s G’ST) in A. linariae populations from Haywood, Macon, and Madison counties in NC were little or no differentiated (G’ST 0.0 - 0.2). However, A. linariae population from Swain county appeared to be highly differentiated (G’ST > 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontin’s D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host.

scholarly journals Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Shijing Feng ◽  
Zhenshan Liu ◽  
Yang Hu ◽  
Jieyun Tian ◽  
Tuxi Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Gansu Province ◽  
Climatic Oscillations ◽  
Genome Wide ◽  
A Genome ◽  
Wild Accessions

Abstract Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

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