scholarly journals Genetic Divergence and Population Structure in Weedy and Cultivated Broomcorn Millets (Panicum miliaceum L.) Revealed by Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

2021 ◽  
Vol 12 ◽  
Author(s):  
Chunxiang Li ◽  
Minxuan Liu ◽  
Fengjie Sun ◽  
Xinyu Zhao ◽  
Mingyue He ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Divergence ◽  
High Throughput Sequencing ◽  
Eating Habits ◽  
Genetic Introgression ◽  
Nucleotide Polymorphisms ◽  
Panicum Miliaceum ◽  
Broomcorn Millet ◽  
Specific Locus ◽  
Western Eurasia

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops in the world. Weedy broomcorn millet [Panicum ruderale (Kitag.) Chang or Panicum miliaceum subsp. ruderale (Kitag.) Tzvel] is thought to be the descendant of the wild ancestor or the feral type of this cereal. The genealogical relationships and genetic divergence among these taxa have not been clarified. In this study, the genetic diversity and population structure of weedy and cultivated broomcorn millets were investigated by using the high-throughput sequencing technology, i.e., the specific-locus amplified fragment sequencing (SLAF-seq). Our analyses consistently revealed both the wild and the feral genotypes in the weedy broomcorn millets. The single nucleotide polymorphisms (SNPs) at the genomic level provided useful evidence to distinguish the wild and the endoferal/exoferal types of weedy broomcorn millets. The genetic divergence revealed between the cultivated broomcorn millet from eastern Eurasia and those from central-western Eurasia was probably derived from either the genetic introgression from weedy broomcorn millets along the spread routes or the founder effect, while the limited gene flow of broomcorn millets from eastern and central-western Eurasia was probably due to the different uses of broomcorn millets and eating habits of the local people.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

scholarly journals Domestication and Spread of Broomcorn Millet (Panicum miliaceum L.) Revealed by Phylogeography of Cultivated and Weedy Populations

Agronomy ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 835
Author(s):  
Yue Xu ◽  
Minxuan Liu ◽  
Chunxiang Li ◽  
Fengjie Sun ◽  
Ping Lu ◽  
...  
Keyword(s):  
Population Structure ◽  
Northeast China ◽  
Genetic Relationships ◽  
Staple Food ◽  
Panicum Miliaceum ◽  
The Loess Plateau ◽  
Structure Pattern ◽  
Broomcorn Millet ◽  
In The Wild ◽  
Simple Sequence

Cultivated broomcorn millet (Panicum miliaceum L.), one of the most ancient crops, has long been an important staple food in the semiarid regions of Eurasia. Weedy broomcorn millet (Panicum ruderale (Kitag.) Chang comb. Nov.), the companion weed of cultivated broomcorn millet, is also widely distributed throughout Eurasia and can produce fertile offspring by crossing with cultivated broomcorn millet. The evolutionary and genetic relationships between weedy and cultivated broomcorn millets, and the explicit domestication areas and detailed spread routes of this cereal are still unclear. The genetic diversity and population structure of 200 accessions of weedy and cultivated broomcorn millets were explored to elucidate the genetic relationship between weedy and cultivated broomcorn millets, and to trace the explicit domestication areas and detailed spread routes of broomcorn millets by using 23 simple sequence repeats (SSR) markers. Our results show that the weedy populations in China may harbor the ancestral variations that gave rise to the domesticated broomcorn millet. The population structure pattern observed in the wild and domesticated broomcorn millets is consistent with the hypothesis that there may be at least two independent domestication areas in China for the cultivated broomcorn millet, the Loess Plateau and the Northeast China, with both following the westward spread routes. These two westward spread routes of cultivated broomcorn millet coincide exactly with the prehistoric Oasis Route and Steppe Route, respectively.

scholarly journals Revealing a 5,000-y-old beer recipe in China

2016 ◽  
Vol 113 (23) ◽  
pp. 6444-6448 ◽  
Author(s):  
Jiajing Wang ◽  
Li Liu ◽  
Terry Ball ◽  
Linjie Yu ◽  
Yuanqing Li ◽  
...  
Keyword(s):  
Hordeum Vulgare ◽  
Direct Evidence ◽  
Panicum Miliaceum ◽  
Fermentation Conditions ◽  
Beer Brewing ◽  
Broomcorn Millet ◽  
Chemical Residues ◽  
Job’S Tears ◽  
Western Eurasia

The pottery vessels from the Mijiaya site reveal, to our knowledge, the first direct evidence of in situ beer making in China, based on the analyses of starch, phytolith, and chemical residues. Our data reveal a surprising beer recipe in which broomcorn millet (Panicum miliaceum), barley (Hordeum vulgare), Job’s tears (Coix lacryma-jobi), and tubers were fermented together. The results indicate that people in China established advanced beer-brewing technology by using specialized tools and creating favorable fermentation conditions around 5,000 y ago. Our findings imply that early beer making may have motivated the initial translocation of barley from the Western Eurasia into the Central Plain of China before the crop became a part of agricultural subsistence in the region 3,000 y later.

scholarly journals Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Zhiyong Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. Results We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264–364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. Conclusions As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.

scholarly journals Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10186
Author(s):  
Derek W. Kraft ◽  
Emily E. Conklin ◽  
Evan W. Barba ◽  
Melanie Hutchinson ◽  
Robert J. Toonen ◽  
...  
Keyword(s):  
Population Structure ◽  
Mitochondrial Genome ◽  
Control Region ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Population Level ◽  
Mitochondrial Control Region ◽  
Nucleotide Polymorphisms ◽  
Silky Shark ◽  
Carcharhinus Falciformis

Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Hydrogen isotopic fractionations during syntheses of lipid biomarkers in the seeds of broomcorn millet (Panicum miliaceum L.) under controlled environmental conditions

2021 ◽  
Vol 154 ◽  
pp. 104221
Author(s):  
Jérémy Jacob ◽  
Nicolas Bossard ◽  
Thierry Bariac ◽  
Valery Terwilliger ◽  
Philippe Biron ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Lipid Biomarkers ◽  
Panicum Miliaceum ◽  
Broomcorn Millet
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