QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea

AbstractTo identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.

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Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

10.21203/rs.2.13122/v3 ◽

2019 ◽

Author(s):

Jaime Osorio ◽

Gina Garzón ◽

Paola Delgadillo ◽

Silvio Bastidas ◽

Leidy Moreno ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Oil Palm ◽

Plant Architecture ◽

Elaeis Guineensis ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Elaeis Oleifera ◽

Genome Wide ◽

Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis , Elaeis oleifera , genotyping-by-sequencing, plant architecture, yield.

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Defining the functional significance of intergenic transcribed regions

10.1101/127282 ◽

2017 ◽

Cited By ~ 1

Author(s):

John P. Lloyd ◽

Zing Tsung-Yeh Tsai ◽

Rosalie P. Sowers ◽

Nicholas L. Panchy ◽

Shin-Han Shiu

Keyword(s):

Flowering Plant ◽

Sequence Structure ◽

Transcriptional Noise ◽

Novel Genes ◽

Protein Coding ◽

Genome Wide ◽

Intergenic Regions ◽

Flowering Plant Species ◽

Genomic Regions ◽

Rna Genes

ABSTRACTWith advances in transcript profiling, the presence of transcriptional activities in intergenic regions has been well established. However, whether intergenic expression reflects transcriptional noise or activity of novel genes remains unclear. We identified intergenic transcribed regions (ITRs) in 15 diverse flowering plant species and found that the amount of intergenic expression correlates with genome size, a pattern that could be expected if intergenic expression is largely nonfunctional. To further assess the functionality of ITRs, we first built machine learning classifiers using Arabidopsis thaliana as a model that accurately distinguish functional sequences (phenotype genes) and likely nonfunctional ones (pseudogenes and unexpressed intergenic regions) by integrating 93 biochemical, evolutionary, and sequence-structure features. Next, by applying the models genome-wide, we found that 4,427 ITRs (38%) and 796 annotated ncRNAs (44%) had features significantly similar to benchmark protein-coding or RNA genes and thus were likely parts of functional genes. Approximately 60% of ITRs and ncRNAs were more similar to nonfunctional sequences and were likely transcriptional noise. The predictive framework established here provides not only a comprehensive look at how functional, genic sequences are distinct from likely nonfunctional ones, but also a new way to differentiate novel genes from genomic regions with noisy transcriptional activities.

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Identification of Loci Controlling the Dwarfism Trait in the White Sailfin Molly (Poecilia latipinna) Using Genome-Wide Association Studies Based on Genotyping-By-Sequencing

Genes ◽

10.3390/genes10060418 ◽

2019 ◽

Vol 10 (6) ◽

pp. 418

Author(s):

Fan Shao ◽

Jing Liu ◽

Mengyuan Ren ◽

Junying Li ◽

Haigang Bao ◽

...

Keyword(s):

Candidate Genes ◽

Association Studies ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Expression Level ◽

Genome Wide Association Studies ◽

Sailfin Molly ◽

Genome Wide ◽

Genomic Regions ◽

Sailfin Mollies

Dwarfism is a condition defined by low harvest weight in fish, but also results in strange body figures which may have potential for the selective breeding of new ornamental fish strains. The objectives of this study are to reveal the physiological causes of dwarfism and identify the genetic loci controlling this trait in the white sailfin molly. Skeletons of dwarf and normal sailfin mollies were observed by X-ray radioscopy and skeletal staining. Genome-wide association studies based on genotyping-by-sequencing (n = 184) were used to map candidate genomic regions associated with the dwarfism trait. Quantitative real-time PCR was performed to determine the expression level of candidate genes in normal (n = 8) and dwarf (n = 8) sailfin mollies. We found that the dwarf sailfin molly has a short and dysplastic spine in comparison to the normal fish. Two regions, located at NW_015112742.1 and NW_015113621.1, were significantly associated with the dwarfism trait. The expression level of three candidate genes, ADAMTS like 1, Larp7 and PPP3CA, were significantly different between the dwarf and normal sailfin mollies in the hepatopancreas, with PPP3CA also showing significant differences in the vertebrae and Larp7 showing significant differences in the muscle. This study identified genomic regions and candidate genes associated with the dwarfism trait in the white sailfin molly and would provide a reference to determine dwarf-causing variations.

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A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis

PLoS Genetics ◽

10.1371/journal.pgen.1009705 ◽

2021 ◽

Vol 17 (8) ◽

pp. e1009705

Author(s):

Masatoshi Nakamoto ◽

Tsubasa Uchino ◽

Eriko Koshimizu ◽

Yudai Kuchiishi ◽

Ryota Sekiguchi ◽

...

Keyword(s):

Genotyping By Sequencing ◽

Genome Wide Association ◽

Whole Genome ◽

Type Ii ◽

Genome Resequencing ◽

Plecoglossus Altivelis ◽

Genome Wide ◽

Males And Females ◽

Whole Genome Resequencing ◽

Male Specific

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-Müllerian hormone type-II receptor gene (amhr2bY) was found within these male-specific regions, distinct from the autosomal copy of amhr2. Expression of the Y-linked amhr2 gene was male-specific in sox9b-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal amhr2 transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for amhr2bY induced male to female sex reversal. Taken together with the known role of Amh and Amhr2 in sex differentiation, these results indicate that the paralog of amhr2 on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.

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Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas

Genome Biology and Evolution ◽

10.1093/gbe/evaa160 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1943-1952

Author(s):

Kai Song

Keyword(s):

Crassostrea Gigas ◽

Large Scale ◽

Expression Patterns ◽

Mutational Bias ◽

Expression Levels ◽

Selective Pressures ◽

Genome Wide ◽

Scale Levels ◽

Whole Genome Resequencing ◽

Genomic Regions

Abstract Mutation is a driving force of evolution that has been shaped by natural selection and is universally biased. Previous studies determined genome-wide mutational patterns for several species and investigated the heterogeneity of mutational patterns at fine-scale levels. However, little evidence of the heterogeneity of mutation rates over large genomic regions was shown. Hence, the mutational patterns of different large-scale genomic regions and their association with selective pressures still need to be explored. As the second most species-rich animal phylum, little is known about the mutational patterns in Mollusca, especially oysters. In this study, the mutational bias patterns are characterized by using whole-genome resequencing data in the Crassostrea gigas genome. I studied the genome-wide relative rates of the pair mutations and found that the predominant mutation is GC -> AT, irrespective of the genomic regions. This analysis reveals that mutational biases were associated with gene expression levels across the C. gigas genome. Genes with higher expression levels and breadth expression patterns, longer coding length, and more exon numbers had relatively higher GC -> AT rates. I also found that genes with larger dN/dS values had relatively higher GC -> AT rates. This work represents the first comprehensive research on the mutational biases in Mollusca species. Here, I comprehensively investigated the relationships between mutational biases with some intrinsic genetic factors and evolutionary indicators and proposed that selective pressures are important forces shaping the mutational biases across the C. gigas genome.

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Genome wide association study (GWAS) for morphological and yield-related traits in oil palm hybrids (Elaeis oleifera x Elaeis guineensis)

10.21203/rs.2.13122/v2 ◽

2019 ◽

Author(s):

Jaime Osorio ◽

Gina Garzón ◽

Paola Delgadillo ◽

Silvio Bastidas ◽

Leidy Moreno ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Oil Palm ◽

Plant Architecture ◽

Elaeis Guineensis ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Elaeis Oleifera ◽

Genome Wide ◽

Genomic Regions

Abstract Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. The work presented herein provides, to our knowledge, the first association mapping study in an interspecific OxG hybrid population of oil palm which presents tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3,776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrids for 10 agronomic traits. Twelve genomic regions were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on candidate genes that mapped on genomic regions involved in plant architecture and yield; however, these potential candidate genes need to be confirmed for future targeted functional analysis. The associated markers may be valuable resources for the development of marker-assisted selection in oil palm breeding. Keywords: Association mapping, Elaeis guineensis, Elaeis oleifera, genotyping-by-sequencing, plant architecture, yield.

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Genome-wide association study and Genomic Prediction of spot blotch disease in wheat (Triticum aestivum L.) using genotyping by sequencing

10.21203/rs.2.22818/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Vipin Tomar ◽

Ravi P Singh ◽

Jesse Poland ◽

Daljit Singh ◽

Arun K Joshi ◽

...

Keyword(s):

Disease Resistance ◽

Genomic Prediction ◽

Prediction Accuracy ◽

Genome Wide Association Study ◽

Genotyping By Sequencing ◽

Spot Blotch ◽

Genomic Region ◽

Genome Wide Association ◽

Genome Wide ◽

Genomic Regions

Abstract Background Spot blotch caused by Bipolaris sorokiniana is a major constraint in wheat production in tropics and subtropics. There is limited information available on GWAS and study on genomic prediction is completely lacking. To reveal the genetic markers associated with disease resistance, we performed a genome-wide association study (GWAS) for spot blotch disease in 141 spring wheat lines. Results Based on the testing under natural infection in three years at hot spots location in Pusa, India and Jamalpur, Bangladesh, the genotypes showed significant genetic variation for disease severity. Using Genotyping-by-Sequencing (GBS) based 18637 polymorphic SNP markers and phenotyping from diverse environments, we identified 23 genomic regions across the genome ( p < 0.001) on 14 chromosomes associated with disease scores. Consistent with the previous reports, a most stable genomic region on chromosome 2B, 5B and 7D were detected across the environments. The new genomic region on chromosome 3D was also identified. We performed functional annotation with wheat genome assembly annotation (IWGSC Ref Seq v1.0) and identified NBS-LRR and 35 other plant defense-related protein families across multiple chromosome regions. Using a five-fold cross-validation scheme, we observed moderate prediction accuracy for 3 of 4 environments indicated that our model was able to successfully capture the quantitative variation underlying the SB variation in our population. Conclusions The GWAS based on the phenotypic data from PUSA India and BARI Bangladesh resulted in a total of 23 genomic regions on 14 chromosomes. The new genomic region appeared on chromosome 3D associated with Zinc finger protein that play important role in plant disease resistance. The genomic prediction model for spot blotch disease resistance in wheat was tested and obtained moderate prediction accuracy.

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Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

PLoS ONE ◽

10.1371/journal.pone.0242500 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242500

Author(s):

Saher Islam ◽

Umesh K. Reddy ◽

Purushothaman Natarajan ◽

Venkata Lakshmi Abburi ◽

Amna Arshad Bajwa ◽

...

Keyword(s):

Body Weight ◽

Population Structure ◽

Association Study ◽

Milk Yield ◽

Genome Wide Association Study ◽

Water Buffalo ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Genome Wide ◽

Genomic Regions

The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.

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Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

10.21203/rs.2.13122/v4 ◽

2019 ◽

Author(s):

Jaime Osorio ◽

Gina Garzón ◽

Paola Delgadillo ◽

Silvio Bastidas ◽

Leidy Moreno ◽

...

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Oil Palm ◽

Plant Architecture ◽

Elaeis Guineensis ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Elaeis Oleifera ◽

Genome Wide ◽

Genomic Regions

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Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

Science Advances ◽

10.1126/sciadv.abd1239 ◽

2021 ◽

Vol 7 (11) ◽

pp. eabd1239

Author(s):

Mark Simcoe ◽

Ana Valdes ◽

Fan Liu ◽

Nicholas A. Furlotte ◽

David M. Evans ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Color Variation ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Melanin Pigmentation ◽

Eye Color ◽

Human Eye ◽

Genome Wide ◽

Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

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