138. GENOME-WIDE LINKAGE SCAN FOR FAMILIAL DIZYGOTIC TWINNING

The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning we have conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism (SNP) marker panels. Non-parametric linkage analyses including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL) produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential (exp)LOD score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (p = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family-specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5’ untranslated region of FSHR that segregated with the DZ twinning phenotype in the UT family. Work is continuing screening candidate genes. Our data provide further evidence for complex inheritance of familial DZ twinning.

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An Integrative Analysis of Transcriptome and GWAS Data to Identify Potential Candidate Genes Influencing Meat Quality Traits in Pigs

Frontiers in Genetics ◽

10.3389/fgene.2021.748070 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xianxian Liu ◽

Junjie Zhang ◽

Xinwei Xiong ◽

Congying Chen ◽

Yuyun Xing ◽

...

Keyword(s):

Gene Expression ◽

Candidate Genes ◽

Meat Quality ◽

Integrative Analysis ◽

Potential Candidate ◽

Quality Traits ◽

Eqtl Mapping ◽

Meat Quality Traits ◽

Genome Wide ◽

A Genome

Understanding the genetic factors behind meat quality traits is of great significance to animal breeding and production. We previously conducted a genome-wide association study (GWAS) for meat quality traits in a White Duroc × Erhualian F2 pig population using Illumina porcine 60K SNP data. Here, we further investigate the functional candidate genes and their network modules associated with meat quality traits by integrating transcriptomics and GWAS information. Quantitative trait transcript (QTT) analysis, gene expression QTL (eQTL) mapping, and weighted gene co-expression network analysis (WGCNA) were performed using the digital gene expression (DGE) data from 493 F2 pig’s muscle and liver samples. Among the quantified 20,108 liver and 23,728 muscle transcripts, 535 liver and 1,014 muscle QTTs corresponding to 416 and 721 genes, respectively, were found to be significantly (p < 5 × 10−4) correlated with 22 meat quality traits measured on longissiums dorsi muscle (LM) or semimembranosus muscle (SM). Transcripts associated with muscle glycolytic potential (GP) and pH values were enriched for genes involved in metabolic process. There were 42 QTTs (for 32 genes) shared by liver and muscle tissues, of which 10 QTTs represent GP- and/or pH-related genes, such as JUNB, ATF3, and PPP1R3B. Furthermore, a genome-wide eQTL mapping revealed a total of 3,054 eQTLs for all annotated transcripts in muscle (p < 2.08 × 10−5), including 1,283 cis-eQTLs and 1771 trans-eQTLs. In addition, WGCNA identified five modules relevant to glycogen metabolism pathway and highlighted the connections between variations in meat quality traits and genes involved in energy process. Integrative analysis of GWAS loci, eQTL, and QTT demonstrated GALNT15/GALNTL2 and HTATIP2 as strong candidate genes for drip loss and pH drop from postmortem 45 min to 24 h, respectively. Our findings provide valuable insights into the genetic basis of meat quality traits and greatly expand the number of candidate genes that may be valuable for future functional analysis and genetic improvement of meat quality.

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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

BMC Plant Biology ◽

10.1186/s12870-019-2153-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Jaime A. Osorio-Guarín ◽

Gina A. Garzón-Martínez ◽

Paola Delgadillo-Duran ◽

Silvio Bastidas ◽

Leidy P. Moreno ◽

...

Keyword(s):

Candidate Genes ◽

Oil Palm ◽

Elaeis Guineensis ◽

Genome Wide Association ◽

Hybrid Population ◽

Potential Candidate ◽

Elaeis Oleifera ◽

Genome Wide ◽

A Genome ◽

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 3776 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.

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GWAS Analysis of Wheat Pre-breeding Germplasm for Terminal Drought Stress Using Next Generation Sequencing Technology

10.20944/preprints202002.0272.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Sajid Shokat ◽

Deepmala Sehgal ◽

Fulai Liu ◽

Sukhwinder Singh

Keyword(s):

Drought Stress ◽

Candidate Genes ◽

Vegetation Index ◽

Genome Wide Association Study ◽

Potential Candidate ◽

Terminal Drought ◽

Genome Wide ◽

Population Structure Analysis ◽

A Genome ◽

Terminal Drought Stress

Bread wheat (Triticum aestivum L.) is one of the most important cereal crops for food security. Of all the stresses that curtail wheat productivity, drought has the most detrimental effects. Especially terminal drought stress i.e. at the time of flowering imposes a big challenge to sustain grain production. In the current study, 339 pre-breeding lines derived from three-way crosses of exotics x elite lines were evaluated in the irrigated and drought stress environments at Obregon, Mexico for the year 2016 and 2018. Drought significantly reduced yield (Y), spike length (SL), number of grains per spikes (NGS) and thousand kernel weight (TKW) by 46.4, 19.2, 23.5 and 25.9%, respectively in comparison to irrigated conditions. Kernel abortion (KA), highly correlated with Y, increased significantly (11.6%) under drought stress environment. Population structure analysis in this panel revealed three sub-populations and a genome wide linkage disequilibrium (LD) decay was at 2.5 cM. Single marker and haplotypes-based genome wide association study (GWAS) revealed significant associations on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12) with Y, SL and TKW, respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were identified for NGS and on 3A (HB7.12) for KA. Five traits i.e. normalized difference vegetation index (NDVI), canopy temperature depression (CTD) days to heading (DTH), NGS, KA were associated at chromosome 3A both under irrigated and drought conditions however, different haplotypes were estimated. Twenty-six SNPs were part of 10 haplotype blocks associated with Y, SL, TKW, NGS and KA. In silico analysis of the associated SNPs/haplotypes showed hits with candidate genes known to confer abiotic stress resistance in model species and crops. Potential candidate genes include those coding for sulfite exporter TauE/SafE family in Arabidopsis thaliana, TBC domain containing protein in Oryza sativa subsp. Japonica and heat shock proteins in Aegilops tauschii subsp. tauschii were revealed. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.

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Genetic Dissection of Drought Resistance of Common Bean at the Seedling Stage by Genome-wide Association Study

10.21203/rs.3.rs-752443/v1 ◽

2021 ◽

Author(s):

Lei Wu ◽

Yujie Chang ◽

Lanfen Wang ◽

Shumin Wang ◽

Jing Wu

Keyword(s):

Common Bean ◽

Candidate Genes ◽

Drought Resistance ◽

Survival Rates ◽

Seedling Stage ◽

Genome Wide Association ◽

Potential Candidate ◽

Chromosome 11 ◽

Genome Wide ◽

A Genome

Abstract A variety of adverse conditions, including drought stress, severely affect common bean production. Molecular breeding for drought resistance has been proposed as an effective and practical way to improve the drought resistance of common bean. A genome-wide association analysis was conducted to identify drought-related loci based on survival rates at the seedling stage using a natural population consisting of 400 common bean accessions and 3832340 SNPs. The coefficient of variation ranged from 40.90% to 56.22% for survival rates in three independent experiments. A total of 12 associated loci containing 89 significant SNPs were identified for survival rates at the seedling stage. Four loci overlapped in the region of the QTLs reported to be associated with drought resistance. According to the expression profiles, gene annotations and references of the functions of homologous genes in Arabidopsis, 39 genes were considered potential candidate genes selected from 199 genes annotated within all associated loci. A stable locus (Locus_10) was identified on chromosome 11, which contained LEA, aquaporin, and proline-rich protein genes. We further confirmed the drought-related function of an aquaporin (PvXIP1;2) located at Locus_10 by expression pattern analysis, phenotypic analysis of PvXIP1;2-overexpressing Arabidopsis and Agrobacterium rhizogenes-mediated hairy root transformation systems, indicating that the association results can facilitate the efficient identification of genes related to drought resistance. These loci and their candidate genes provide a foundation for crop improvement via breeding for drought resistance in common bean.

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Genetic characterization of Addison’s disease in Bearded Collies

BMC Genomics ◽

10.1186/s12864-020-07243-0 ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 1

Author(s):

Liza C. Gershony ◽

Janelle M. Belanger ◽

Marjo K. Hytönen ◽

Hannes Lohi ◽

Thomas R. Famula ◽

...

Keyword(s):

Candidate Genes ◽

Addison’S Disease ◽

Genome Wide Association ◽

Complex Nature ◽

Addison's Disease ◽

Regulatory Sequences ◽

Potential Candidate ◽

Genome Wide ◽

A Genome ◽

Increased Risk

Abstract Background Primary hypoadrenocorticism (or Addison’s disease, AD) is an autoimmune disease that results in destruction of the adrenal cortex and consequent adrenal insufficiency. The disease has been described in purebred and mixed breed dogs, although some breeds, including the Bearded Collie, are at increased risk for AD. Candidate gene approaches have yielded few associations that appear to be breed-specific. A single other genome-wide association study reported no significant regions of association for AD in Standard Poodles. The present study aimed to identify genomic regions of association for canine AD in Bearded Collies. Results Our study consists of the first genome-wide association analysis to identify a genome-wide significant region of association with canine AD (CFA18). Peaks of suggestive association were also noted on chromosomes 11, 16 and 29. Logistic regression analysis supported an additive effect of risk genotypes at these smaller effect loci on the probability of disease associated with carrying a risk genotype on CFA18. Potential candidate genes involved in adrenal steroidogenesis, regulation of immune responses and/or inflammation were identified within the associated regions of chromosomes 11 and 16. The gene-poor regions of chromosomes 18 and 29 may, however, harbor regulatory sequences that can modulate gene expression and contribute to disease susceptibility. Conclusion Our findings support the polygenic and complex nature of canine AD and identified a strongly associated locus on CFA18 that, when combined with three other smaller effect loci, was predictive of disease. The results offer progress in the identification of susceptibility loci for canine AD in the Bearded Collie. Further studies are needed to confirm association with the suggested candidate genes and identify actual causative mutations involved with AD susceptibility in this breed.

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Genome-Wide Association Analysis Identifies Resistance Loci for Bacterial Leaf Streak Resistance in Rice (Oryza sativa L.)

Plants ◽

10.3390/plants9121673 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1673

Author(s):

Wannapa Sattayachiti ◽

Samart Wanchana ◽

Siwaret Arikit ◽

Phakchana Nubankoh ◽

Sujin Patarapuwadol ◽

...

Keyword(s):

Candidate Genes ◽

Broad Spectrum ◽

Genome Wide Association Study ◽

Oryza Sativa L ◽

Genome Wide Association ◽

Potential Candidate ◽

Bacterial Leaf Streak ◽

Genome Wide ◽

Broad Spectrum Resistance ◽

A Genome

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating diseases in rice production areas, especially in humid tropical and subtropical zones throughout Asia and worldwide. A genome-wide association study (GWAS) analysis conducted on a collection of 236 diverse rice accessions, mainly indica varieties, identified 12 quantitative trait loci (QTLs) on chromosomes 1, 2, 3, 4, 5, 8, 9 and 11, conferring resistance to five representative isolates of Thai Xoc. Of these, five QTLs conferred resistance to more than one Xoc isolates. Two QTLs, qBLS5.1 and qBLS2.3, were considered promising QTLs for broad-spectrum resistance to BLS. The xa5 gene was proposed as a potential candidate gene for qBLS5.1 and three genes, encoding pectinesterase inhibitor (OsPEI), eukaryotic zinc-binding protein (OsRAR1), and NDP epimerase function, were proposed as candidate genes for qBLS2.3. Results from this study provide an insight into the potential QTLs and candidate genes for BLS resistance in rice. The recessive xa5 gene is suggested as a potential candidate for strong influence on broad-spectrum resistance and as a focal target in rice breeding programs for BLS resistance.

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The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.042390 ◽

2017 ◽

Vol 7 (7) ◽

pp. 2391-2403 ◽

Cited By ~ 11

Author(s):

Amanda S Lobell ◽

Rachel R Kaspari ◽

Yazmin L Serrano Negron ◽

Susan T Harbison

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Natural Populations ◽

Direct Role ◽

Genome Wide ◽

A Genome ◽

Fitness Trait ◽

Sleep Parameters ◽

Activity Behavior ◽

Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

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Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽

10.3390/ani11010192 ◽

2021 ◽

Vol 11 (1) ◽

pp. 192

Author(s):

Xinghai Duan ◽

Bingxing An ◽

Lili Du ◽

Tianpeng Chang ◽

Mang Liang ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Growth Curve ◽

Growth And Development ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Coefficient Of Determination ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽

10.3390/agriculture11040318 ◽

2021 ◽

Vol 11 (4) ◽

pp. 318

Author(s):

Tae-Ho Ham ◽

Yebin Kwon ◽

Yoonjung Lee ◽

Jisu Choi ◽

Joohyun Lee

Keyword(s):

Association Study ◽

Candidate Genes ◽

Cold Tolerance ◽

Genome Wide Association Study ◽

Seedling Stage ◽

Genome Wide Association ◽

Matrix Analysis ◽

Rice Seedlings ◽

Genome Wide ◽

A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

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Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice

Scientific Reports ◽

10.1038/s41598-021-85921-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raju Bheemanahalli ◽

Montana Knight ◽

Cherryl Quinones ◽

Colleen J. Doherty ◽

S. V. Krishna Jagadish

Keyword(s):

Grain Size ◽

Candidate Genes ◽

Gene Network ◽

Genome Wide Association ◽

Potential Candidate ◽

Genetic Loci ◽

Stay Green ◽

Yield And Quality ◽

Genome Wide ◽

Wide Range

AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

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