High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

2021 ◽  
Author(s):  
Congcong Li ◽  
Genping Wang ◽  
Haiquan Li ◽  
Guoliang Wang ◽  
Jian Ma ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Foxtail Millet ◽  
Heading Date ◽  
Genomic Variation ◽  
Homologous Gene ◽  
Natural Environments ◽  
Transposon Insertion ◽  
Genome Wide ◽  
Genome Level ◽  
High Depth

Abstract Key message Based on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Abstract Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1–Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.

scholarly journals Correction to: High‑depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

2021 ◽  
Author(s):  
Congcong Li ◽  
Genping Wang ◽  
Haiquan Li ◽  
Guoliang Wang ◽  
Jian Ma ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Foxtail Millet ◽  
High Depth

scholarly journals Local adaptation and sexual selection drive intra-island diversification in a songbird lineage: differential divergence in autosomes and sex chromosomes

2018 ◽  
Author(s):  
Yann XC Bourgeois ◽  
Joris AM Bertrand ◽  
Boris Delahaie ◽  
Hélène Holota ◽  
Christophe Thébaud ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Reproductive Isolation ◽  
Local Adaptation ◽  
Sex Chromosomes ◽  
Genomic Variation ◽  
Color Variation ◽  
Mating Signals ◽  
Genome Wide

AbstractRecently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to test the relative importance of two major evolutionary mechanisms, adaptation to local ecological conditions by natural selection, or mechanisms of reproductive isolation such as assortative mating mediated by sexually selected mating signals or post-zygotic incompatibilities. Whereas local adaptation is expected to affect many loci throughout the genome, traits acting as mating signals are expected to be located on sex chromosomes and have a simple genetic basis. We used genome-wide markers to test these predictions in Reunion Island’s gray-white eye (Zosterops borbonicus), which has recently diversified into five distinct plumage forms. Two of them correspond to a polymorphic highland population that is separated by a steep ecological gradient from three distinct lowland forms that show narrow contact zones in plumage color traits, yet no association with environmental variables. An analysis of population structure using genome-wide SNP loci revealed two major clades corresponding to highland and lowland forms, respectively, with the latter separated further into three independent lineages corresponding to plumage forms. Coalescent tests of alternative demographic scenarios provided support for divergence of highland and lowland lineages with an intensification of gene flow in the last 60,000 years. Landscapes of genomic variation revealed that signatures of selection associated with elevation are found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. A gene ontology analysis identified TYRP1, a Z-linked color gene, as a likely candidate locus underlying color variation among lowland forms. Our results are consistent with the role of natural selection in driving the divergence of locally adapted highland populations, and the role of sexual selection in differentiating lowland forms through reproductive isolation mechanisms, showing that both modes of lineage divergence can take place at very small geographic scales in birds.

scholarly journals Genome-wide association mapping for agronomic and quality traits in foxtail millet

2019 ◽  
Author(s):  
Yanhong Lou ◽  
Yun Chen ◽  
Zhihao Liu ◽  
Mingjie Sun ◽  
Fei Han ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Foxtail Millet ◽  
Significant Snps ◽  
Genomic Variation ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genome Wide ◽  
A Genome

Abstract Background: Foxtail millet [Setaria italica (L.) P. Beauv.] is a particularly important cereal and fodder crop in arid and semi-arid regions. The genomic variation and alleles underpinning agronomic and quality traits are important for foxtail millet improvement. To better understand the diversity of foxtail millet and facilitate the genetic dissection of its agronomic and quality traits, we used high-quality single nucleotide polymorphisms (SNPs) to perform a genome-wide association study (GWAS). Results: Using genotyping-by-sequencing, 107 foxtail millet accessions were sequenced, and further analysis revealed 72,181 high-quality SNPs, of which 53 were significantly associated with 15 agronomic and quality traits. These SNPs were distributed across the nine chromosomes of foxtail millet; 44 were located in intergenic regions, whereas one and eight SNPs were located in exon and intron regions, respectively. The GWAS revealed that 28 SNPs were associated with a single trait. Conclusions: For some of the significant SNPs, favourable genotypes showed pyramiding effects for several traits. The 53 loci identified in this study will therefore be useful for breeding programs aimed at foxtail millet improvement.

scholarly journals Genomic analyses provide insights into peach local adaptation and responses to climate change

2020 ◽  
Author(s):  
Yong Li ◽  
Ke Cao ◽  
Nan Li ◽  
Gengrui Zhu ◽  
Weichao Fang ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Cold Hardiness ◽  
Association Studies ◽  
Sugar Content ◽  
Evolutionary Genetics ◽  
Genomic Variation ◽  
Genome Wide ◽  
Environmental Association ◽  
Molecular Bases ◽  
Bloom Date

The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map by re-sequencing genomes of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach local adaptation to diverse climates comprehensively. A total of 2,092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using GWEAS, a total of 3,496 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UV-B, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 years of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds valuable genome resources and candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and future breeding.

Genome-wide Identification of Molecular Markers Based on Genomic Re-sequencing of Foxtail Millet Elite Cultivar Jingu 21

2018 ◽  
Vol 44 (5) ◽  
pp. 686 ◽  
Author(s):  
Qing-Ying ZHAO ◽  
Rui-Juan ZHANG ◽  
Rui-Liang WANG ◽  
Jian-Hua GAO ◽  
Yuan-Huai HAN ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Foxtail Millet ◽  
Genome Wide ◽  
Elite Cultivar

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals Genome diversity in Ukraine

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Taras K Oleksyk ◽  
Walter W Wolfsberger ◽  
Alexandra M Weber ◽  
Khrystyna Shchubelka ◽  
Olga T Oleksyk ◽  
...  
Keyword(s):  
Sequence Data ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
High Coverage ◽  
Genome Data ◽  
New Information ◽  
Genome Wide ◽  
Public Data ◽  
Genome Wide Data ◽  
Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

scholarly journals Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cooper J. Park ◽  
Nicole A. Caimi ◽  
Debbie C. Buecher ◽  
Ernest W. Valdez ◽  
Diana E. Northup ◽  
...  
Keyword(s):  
New Mexico ◽  
Genetic Manipulation ◽  
Distinct Species ◽  
Biosynthetic Gene Cluster ◽  
Genomic Variation ◽  
Species Variation ◽  
Nucleotide Polymorphisms ◽  
Peptide Synthetases ◽  
Genome Wide ◽  
Diversity Estimates

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

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