Characterizing Genetic Mechanisms Involved in Measuring Day-length in Drosophila melanogaster

Catalytic Domain ◽

Day Length ◽

Photoperiod Response ◽

Circadian Period ◽

A Genome ◽

Genetic Mechanisms ◽

Length Changes

AbstractMany organisms are known to regulate seasonal behaviors and physiological processes in response to day length changes through photoperiodism. Extreme changes in photoperiods have detrimental effects on human health, which can impair development and serve as the origin of adult diseases. Since the seminal work by Bünning in 1936, there are studies supporting the view that organisms can measure the day length through an endogenous 24-hour cellular circadian clock. However, the mechanisms involved in measuring seasonal or day-length changes are not understood. In the current study, we performed a genome-wide association study (GWAS) on photoperiodism using the Drosophila Genetic Reference Panel. The GWAS identified 32 candidate genes responsible for photoperiodic regulations. The knockout mutants of the top four candidate genes (Protein Kinase C delta (Pkcdelta), Glucuronyltransferase-P (GlcAT-P), Brain-specific homeobox (Bsh), and Diuretic hormone 31 Receptor (Dh31-R1)) were analyzed for their photoperiod and circadian period phenotypes. PKCdelta and GlcAT-P mutants show a significantly different photoperiod response compared to that of the wild type strain, and also had an altered circadian period phenotype. Further molecular characterization revealed that the mutant two independent mutant alleles of PKCdelta with a defective catalytic domain had distinct photoperiod responses. Taken these data together, we concluded that there is overlap between the circadian clock and photoperiodic regulations in Drosophila, and PKCdelta is a component that is involved in both circadian and photoperiodic regulations. By identifying novel molecular components of photoperiod, the current study provides new insights into the genetic mechanisms of determining the seasonal changes.

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 ◽

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.

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 ◽

Coefficient Of Determination ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

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.

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 ◽

Seedling Stage ◽

Genome Wide Association ◽

Matrix Analysis ◽

Rice Seedlings ◽

Genome Wide ◽

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.

Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens

Scientific Reports ◽

10.1038/s41598-021-86176-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Juniper A. Lake ◽

Jack C. M. Dekkers ◽

Behnam Abasht

Keyword(s):

Candidate Genes ◽

Broiler Chickens ◽

Genetic Basis ◽

Specific Protein ◽

Chromosome 11 ◽

A Genome ◽

White Striping ◽

Commercial Broiler ◽

Wooden Breast

AbstractWooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes include potassium voltage-gated channel subfamily Q member 1 (KCNQ1), involved in insulin secretion and cardiac electrical activity, lymphocyte-specific protein 1 (LSP1), involved in inflammation and immune response.

Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans

Journal of Allergy and Clinical Immunology ◽

10.1016/j.jaci.2009.09.007 ◽

2010 ◽

Vol 125 (2) ◽

pp. 321-327.e13 ◽

Cited By ~ 60

Author(s):

Hao Wu ◽

Isabelle Romieu ◽

Min Shi ◽

Dana B. Hancock ◽

Huiling Li ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Childhood Asthma ◽

Genome Wide Association ◽

Genome Wide ◽

Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon

Plant Disease ◽

10.1094/pdis-08-21-1611-re ◽

2021 ◽

Author(s):

Dennis Katuuramu ◽

Sandra Branham ◽

Amnon Levi ◽

Patrick Wechter

Keyword(s):

Candidate Genes ◽

Citrullus Lanatus ◽

Phenotypic Variability ◽

Germplasm Collection ◽

Snp Markers ◽

Genome Wide Association ◽

Pseudoperonospora Cubensis ◽

Genome Wide ◽

Cultivated sweet watermelon (Citrullus lanatus) is an important vegetable crop for millions of people around the world. There are limited sources of resistance to economically important diseases within C. lanatus, whereas Citrullus amarus has a reservoir of traits that can be exploited to improve C. lanatus for resistance to biotic and abiotic stresses. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is an emerging threat to watermelon production. We screened 122 C. amarus accessions for resistance to CDM over two tests (environments). The accessions were genotyped by whole-genome resequencing to generate 2,126,759 single nucleotide polymorphic (SNP) markers. A genome-wide association study was deployed to uncover marker-trait associations and identify candidate genes underlying resistance to CDM. Our results indicate the presence of wide phenotypic variability (1.1 - 57.8%) for leaf area infection, representing a 50.7-fold variation for CDM resistance across the C. amarus germplasm collection. Broad-sense heritability estimate was 0.55, implying the presence of moderate genetic effects for resistance to CDM. The peak SNP markers associated with resistance to P. cubensis were located on chromosomes Ca03, Ca05, Ca07, and Ca11. The significant SNP markers accounted for up to 30% of the phenotypic variation and were associated with promising candidate genes encoding disease resistance proteins, leucine-rich repeat receptor-like protein kinase, and WRKY transcription factor. This information will be useful in understanding the genetic architecture of the P. cubensis-Citrullus spp. patho-system as well as development of resources for genomics-assisted breeding for resistance to CDM in watermelon.

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

International Journal of Molecular Sciences ◽

10.3390/ijms19103145 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3145 ◽

Cited By ~ 8

Author(s):

Jie Yu ◽

Weiguo Zhao ◽

Wei Tong ◽

Qiang He ◽

Min-Young Yoon ◽

...

Keyword(s):

Salt Tolerance ◽

Association Study ◽

Candidate Genes ◽

Rice Genome ◽

Genome Wide Association ◽

Phenotypic Correlation ◽

Genome Wide ◽

A Genome ◽

Germination Stage

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

Genomic Regions Associated with the Control of Flowering Time in Durum Wheat

10.20944/preprints202010.0112.v1 ◽

2020 ◽

Author(s):

Priyanka Gupta ◽

Hafssa Kabbaj ◽

Khaoula El Hassouni ◽

Marco Maccaferri ◽

Miguel Sabchez-Garcia ◽

...

Keyword(s):

Durum Wheat ◽

Flowering Time ◽

Strong Association ◽

Triticum Aestivum L ◽

Day Length ◽

Significant Qtls ◽

A Genome ◽

Days To Heading ◽

Genomic Regions

Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperatures, day length and other climatic variables. Genotyping with 35K Axiom array generated 7,652 polymorphic SNPs in addition to 3 KASP markers associated to known flowering genes. In total, 34 significant QTLs were identified in both landraces and modern lines. Some QTLs had strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B and vernalization genes Vrn-A1, and Vrn3. However, these loci explained only 5 to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-17 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-11 and Q.ICD.Ppd-12 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.)

Genome-Wide Association Mapping for Heat and Drought Adaptive Traits in Pea

Genes ◽

10.3390/genes12121897 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1897

Author(s):

Endale G. Tafesse ◽

Krishna K. Gali ◽

V. B. Reddy Lachagari ◽

Rosalind Bueckert ◽

Thomas D. Warkentin

Keyword(s):

Association Mapping ◽

Candidate Genes ◽

Vegetation Index ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Adaptive Traits ◽

Flowering Duration ◽

Genome Wide ◽

Heat and drought, individually or in combination, limit pea productivity. Fortunately, substantial genetic diversity exists in pea germplasm for traits related to abiotic stress resistance. Understanding the genetic basis of resistance could accelerate the development of stress-adaptive cultivars. We conducted a genome-wide association study (GWAS) in pea on six stress-adaptive traits with the aim to detect the genetic regions controlling these traits. One hundred and thirty-five genetically diverse pea accessions were phenotyped in field studies across three or five environments under stress and control conditions. To determine marker trait associations (MTAs), a total of 16,877 valuable single nucleotide polymorphisms (SNPs) were used in association analysis. Association mapping detected 15 MTAs that were significantly (p ≤ 0.0005) associated with the six stress-adaptive traits averaged across all environments and consistent in multiple individual environments. The identified MTAs were four for lamina wax, three for petiole wax, three for stem thickness, two for the flowering duration, one for the normalized difference vegetation index (NDVI), and two for the normalized pigment and chlorophyll index (NPCI). Sixteen candidate genes were identified within a 15 kb distance from either side of the markers. The detected MTAs and candidate genes have prospective use towards selecting stress-hardy pea cultivars in marker-assisted selection.

Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation

10.1101/460360 ◽

2018 ◽

Cited By ~ 1

Author(s):

Nadia Bouain ◽

Arthur Korte ◽

Santosh B. Satbhai ◽

Seung Y. Rhee ◽

Wolfgang Busch ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Root Growth ◽

Candidate Genes ◽

Functional Module ◽

Molecular Genetic ◽

Chromatin Modification ◽

Nutrient Deficiency ◽

Mineral Nutrient ◽

AbstractThe molecular genetic mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using a panel of Arabidopsis thaliana natural accessions, we provide a comprehensive combinatorial analysis of RGR variation under macro- and micronutrient deficiency, namely phosphorus (P), iron (Fe), and zinc (Zn), which affect root growth in opposite directions. We found that while -P stimulates early RGR of most accessions, -Fe or -Zn reduces it. The combination of either -P-Fe or -P-Zn leads to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, Arabidopsis reference accession Columbia (Col-0) is not representative of the species under -P and -Zn. Using a genome wide association study, we identify candidate genes that control RGR under the assayed nutrient deficiency conditions. By using a network biology driven search using these candidate genes, we further identify a functional module enriched in regulation of cell cycle, DNA replication and chromatin modification that possibly underlies the suppression of root growth reduction in -P-Fe conditions. Collectively, our findings provide a framework for understanding the regulation of RGR under nutrient deficiency, and open new routes for the identification of both large effect genes and favorable allelic variations to improve root growth.