scholarly journals Gene disruption by structural mutations drives selection in US rice breeding over the last century

PLoS Genetics ◽  
2021 ◽  
Vol 17 (3) ◽  
pp. e1009389
Author(s):  
Justin N. Vaughn ◽  
Walid Korani ◽  
Joshua C. Stein ◽  
Jeremy D. Edwards ◽  
Daniel G. Peterson ◽  
...  
Keyword(s):  
Size Variation ◽  
Poor Performance ◽  
Structural Data ◽  
Common Source ◽  
Oryza Glaberrima ◽  
Ancestral State ◽  
Major Interest ◽  
Long Read ◽  
Structural Mutations ◽  
Rice Improvement

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection.

scholarly journals Gene disruption by structural mutations drives selection in US rice breeding over the last century

2020 ◽  
Author(s):  
Justin N. Vaughn ◽  
Walid Korani ◽  
Joshua C. Stein ◽  
Jeremy D. Edwards ◽  
Daniel G. Peterson ◽  
...  
Keyword(s):  
Superior Performance ◽  
Common Source ◽  
Oryza Glaberrima ◽  
Ancestral State ◽  
Rice Breeding ◽  
Rice Varieties ◽  
Mutational Spectrum ◽  
Major Interest ◽  
Long Read ◽  
Structural Mutations

AbstractThe genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion is the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection.Significance StatementSome crop varieties have superior performance across years and environments. In hybrids, harmful mutations in one parent are masked by the ancestral alleles in the other parent, resulting in increased vigor. Unfortunately, these mutations are very difficult to identify precisely because, individually, they only have a small effect. In this study, we use long-read sequencing to characterize the entire mutational spectrum between two rice varieties. We then track these mutations through the last century of rice breeding. We show that large structural mutations in exons are selected against at a greater rate than any other mutational class. These findings illuminate the nature of deleterious alleles and will guide attempts to predict variety vigor based solely on genomic information.

scholarly journals Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
PingHsun Hsieh ◽  
Vy Dang ◽  
Mitchell R. Vollger ◽  
Yafei Mao ◽  
Tzu-Hsueh Huang ◽  
...  
Keyword(s):  
Copy Number ◽  
Homo Sapiens ◽  
Segmental Duplications ◽  
Sensor Protein ◽  
Long Read ◽  
Number Variation ◽  
Selective Forces ◽  
Structural Mutations ◽  
Cold Sensor ◽  
Human Specific

AbstractTRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. Here, our results of TCAF copy number expansion, selection signals in hominins, and differential TCAF2 expression between haplogroups and high TCAF2 and TRPM8 expression in liver and prostate in modern-day humans imply TCAF diversification among hominins potentially in response to cold or dietary adaptations.

scholarly journals De novo diploid genome assembly for genome-wide structural variant detection

2019 ◽  
Author(s):  
Lu Zhang ◽  
Xin Zhou ◽  
Ziming Weng ◽  
Arend Sidow
Keyword(s):  
De Novo ◽  
Pairwise Alignment ◽  
Cost Effective ◽  
Personal Genome ◽  
Ancestral State ◽  
Short Fragment ◽  
Fundamental Limitations ◽  
Long Read ◽  
Alternative Means ◽  
Variant Detection

AbstractStructural variants (SVs) in a personal genome are important but, for all practical purposes, impossible to detect comprehensively by standard short-fragment sequencing. De novo assembly, traditionally used to generate reference genomes, offers an alternative means for variant detection and phasing but has not been applied broadly to human genomes because of fundamental limitations of short-fragment approaches and high cost of long-read technologies. We here show that 10x linked-read sequencing, which has been applied to assemble human diploid genomes into high quality contigs, supports accurate SV detection. We examined variants in six de novo 10x assemblies with diverse experimental parameters from two commonly used human cell lines, NA12878 and NA24385. The assemblies are effective in detecting mid-size SVs, which were discovered by simple pairwise alignment of the assemblies’ contigs to the reference (hg38). Our study also shows that the accuracy of SV breakpoint at base-pair level is high, with a majority (80% for deletion and 70% for insertion) of SVs having precisely correct sizes and breakpoints (<2bp difference). Finally, setting the ancestral state of SV loci by comparing to ape orthologs allows inference of the actual molecular mechanism (insertion or deletion) causing the mutation, which in about half of cases is opposite to that of the reference-based call. Interestingly, we uncover 214 SVs that may have been maintained as polymorphisms in the human lineage since before our divergence from chimp. Overall, we show that de novo assembly of 10x linked-read data can achieve cost-effective SV detection for personal genomes.

scholarly journals Large genomic variants reveal unexplored intraspecific diversity in Brassica rapa genomes

2020 ◽  
Author(s):  
Julien Boutte ◽  
Loeiz Maillet ◽  
Thomas Chaussepied ◽  
Sébastien Letort ◽  
Jean-Marc Aury ◽  
...  
Keyword(s):  
Genome Size ◽  
Brassica Rapa ◽  
Core Collection ◽  
Size Variation ◽  
Intraspecific Diversity ◽  
Phenotypic Traits ◽  
Genome Size Variation ◽  
F1 Hybrid ◽  
Genomic Variants ◽  
Long Read

ABSTRACTTraditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Using two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection.We explored the structural consequences of the presence of large repeated sequences in B. rapa ‘Z1’ genome versus the B. rapa ‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09 and A10 are due to large insertions and inversions when comparing B. rapa ‘Z1’ and B. rapa ‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimated in silico to be 55Mb and 29Mb, respectively. To validate these observations, we compared using fluorescent in-situ hybridization (FISH) the two A06 chromosomes present in a F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu’. Alternatively, using a Copy Number Variation approach, we were able to quantify the presence of a higher number of rDNA and Gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions.This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.

scholarly journals Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 376
Author(s):  
Peterson W. Wambugu ◽  
Marie-Noelle Ndjiondjop ◽  
Robert Henry
Keyword(s):  
Oryza Glaberrima ◽  
Trait Variation ◽  
African Rice ◽  
Sequencing Technologies ◽  
Climate Resilience ◽  
Sequencing Studies ◽  
Important Trait ◽  
Genetics And Genomics ◽  
Rice Improvement ◽  
Rice Genetic

African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.

scholarly journals Impact of some local organic by-products on Acheta domesticus growth and meal production

2021 ◽  
pp. 1-10
Author(s):  
C. Jucker ◽  
S. Belluco ◽  
S. Bellezza Oddon ◽  
A. Ricci ◽  
L. Bonizzi ◽  
...  
Keyword(s):  
Fruits And Vegetables ◽  
Growth Parameters ◽  
Control Diet ◽  
Nutritional Composition ◽  
Acheta Domesticus ◽  
Common Source ◽  
Alternative Protein ◽  
Major Interest ◽  
Maize Grain ◽  
By Products

The house cricket Acheta domesticus is one of the species of major interest as alternative protein source for humans in the recent research of sustainable and nutritious sources of food. However, grain feeds, feed for poultry and soybean still represent common source of feeds for the insect industry. The aim of this study was to evaluate the influence of some agro-food by-products on the growth parameters of the crickets and the nutritional composition of the final cricket meal. Our study included five by-products (maize grain distiller, fruits and vegetables, grape marc, and two brewery’s wastes), while hen feed was used as a control diet. Substrates were analysed for their microbiological contamination prior to be provided to crickets. No Listeria and Salmonella were detected, but high microbial counts were observed. Crickets grown on the given by-products showed significant differences on the insect’s weight starting from the third week. High mortality was observed on all substrates, except on maize distiller and the control diet. The final cricket meal showed a similar protein content (66-68% as is), while the lipid content was higher in the meal from cricket reared on maize distiller (22% as is). Finally, microbiological and chemical analyses on the cricket meals did not show safety concerns for the consumers. The by-products studied, except maize grain distiller, did not support an optimal cricket rearing, but more studies are necessary to identify a mix-formulation meeting the cricket nutritional requirements.

scholarly journals De novo diploid genome assembly for genome-wide structural variant detection

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Lu Zhang ◽  
Xin Zhou ◽  
Ziming Weng ◽  
Arend Sidow
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Pairwise Alignment ◽  
Cost Effective ◽  
Difficult Problem ◽  
Ancestral State ◽  
Fundamental Limitations ◽  
Human Genomes ◽  
Genome Wide ◽  
Long Read

Abstract Detection of structural variants (SVs) on the basis of read alignment to a reference genome remains a difficult problem. De novo assembly, traditionally used to generate reference genomes, offers an alternative for SV detection. However, it has not been applied broadly to human genomes because of fundamental limitations of short-fragment approaches and high cost of long-read technologies. We here show that 10× linked-read sequencing supports accurate SV detection. We examined variants in six de novo 10× assemblies with diverse experimental parameters from two commonly used human cell lines: NA12878 and NA24385. The assemblies are effective for detecting mid-size SVs, which were discovered by simple pairwise alignment of the assemblies’ contigs to the reference (hg38). Our study also shows that the base-pair level SV breakpoint accuracy is high, with a majority of SVs having precisely correct sizes and breakpoints. Setting the ancestral state of SV loci by comparing to ape orthologs allows inference of the actual molecular mechanism (insertion or deletion) causing the mutation. In about half of cases, the mechanism is the opposite of the reference-based call. We uncover 214 SVs that may have been maintained as polymorphisms in the human lineage since before our divergence from chimp. Overall, we show that de novo assembly of 10× linked-read data can achieve cost-effective SV detection for personal genomes.

scholarly journals Development and Field Test of New Environmentally Friendly Water-Rich Sand Grout Material

2019 ◽  
Vol 2019 ◽  
pp. 1-8
Author(s):  
Wang Hongbo ◽  
Liu Rentai ◽  
Zhang Qingsong
Keyword(s):  
Fly Ash ◽  
Stone Formation ◽  
Poor Performance ◽  
Environmental Water ◽  
High Ratio ◽  
Common Source ◽  
Underground Engineering ◽  
Grouting Material ◽  
New Type ◽  
Grouting Materials

The water-rich sand layer is a common source for underground engineering disasters. Considering the poor performance, high cost, and serious environmental pollution of conventional grouting materials, based on the requirements of environmental grouting treatment, a new type of environmental water-rich sand grouting material was proposed, which was mainly based on fly ash and cement and supplemented by water glass. The performance of the slurry was studied. The parameters such as the initial set time, the ratio of stone, and the compressive strength of the material under different water contents and fly ash contents were determined by experiments. The new grouting material was obtained with rapid setting, early strength, high ratio of stone formation, and strength, which were less affected by water content. The successful application of the new environmental grouting material in the Qingdao Metro not only ensures the safety of the project but also meets the requirements of environmental protection. It also verifies the scientificity of the material and will be useful for the innovation of the water-rich sand grouting material.

scholarly journals Opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

2020 ◽  
Author(s):  
PingHsun Hsieh ◽  
Vy Dang ◽  
Mitchell Vollger ◽  
Yafei Mao ◽  
Tzu-Hsueh Huang ◽  
...  
Keyword(s):  
Copy Number ◽  
Homo Sapiens ◽  
Segmental Duplications ◽  
Long Read ◽  
Number Variation ◽  
Selective Forces ◽  
Structural Mutations ◽  
Positive Effect ◽  
Cold Sensor ◽  
Human Specific

Abstract TRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in human and nonhuman primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations that altered TCAF copy number and regulation. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. The significant, positive effect of H4 on TCAF2 expression in modern-day humans with candidate associations for hypothyroidism, nerve compression, and diabetes suggests TCAF diversification among hominins potentially in response to cold or dietary adaptations.

scholarly journals Hidden Rice Diversity in the Guianas

2019 ◽  
Author(s):  
Tinde van Andel ◽  
Margret Veltman ◽  
Alice Bertin ◽  
Harro Maat ◽  
Thomas Polime ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Glaberrima ◽  
Crop Varieties ◽  
Geographic Structure ◽  
External Pressures ◽  
History Of ◽  
Rice Improvement ◽  
Modern Breeding ◽  
The Guianas ◽  
Rice Diversity

AbstractTraditional crop varieties are an important source of genetic diversity for crop adaptation and modern breeding. Landraces of Asian (Oryza sativa) and African (Oryza glaberrima) rice have been well studied on the continents where they were domesticated. However, their history of cultivation in northern South America is poorly understood. Here we reveal the rice diversity that is maintained by Maroons, descendants of enslaved Africans who fled to the interior forests of the Guianas ca. 300 years ago. We interviewed subsistence farmers who practice shifting cultivation along the Maroni and Lawa rivers that form the natural border between French Guiana and Suriname, and used ethnobotanical and morphological methods to identify around 50 varieties, of which 15 were previously undocumented. The genetic origin of these varieties was explored using the Angiosperms-353 universal probe set. Despite the large distances between sites and relative inaccessibility of the area, phenotypic and genetic diversity did not display any geographic structure, which is consistent with knowledge of seed exchange among members of the same ethnolinguistic group. Although improved US cultivars were introduced in Maroon villages in the 1940s, these have not displaced the traditional landraces, which are cherished for their taste and nutritious qualities and for their importance in Maroon spiritual life. The unique agricultural and ritual practices of Maroons confirm their role as custodians of rice diversity, a role that is currently under threat from external pressures and encroaching globalization. We expect that the rice diversity uncovered in this study represents only a fraction of the total diversity in the Guianas and may constitute a large untapped resource that holds promise for future rice improvement. Further efforts to inventory and preserve these landraces will help to protect a precious cultural heritage and local food security.

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