scholarly journals Genome-wide association and prediction reveals the genetic architecture of cassava mosaic disease resistance and prospects for rapid genetic improvement

2015 ◽  
Author(s):  
Marnin Wolfe ◽  
Ismail Y Rabbi ◽  
Chiedozie Egesi ◽  
Martha Hamblin ◽  
Robert Kawuki ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Major Gene ◽  
Mosaic Disease ◽  
Chromosome 8 ◽  
Genome Wide Association ◽  
Cassava Mosaic Disease ◽  
Breeding Lines ◽  
Genome Wide ◽  
Single Region ◽  
Association Mapping Study

Cassava (Manihot esculenta) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Bi-parental mapping studies suggest primarily a single major gene mediates resistance. To be certain and to potentially identify new loci we conducted the first genome-wide association mapping study in cassava with 6128 African breeding lines. We also assessed the accuracy of genomic selection to improve CMD resistance. We found a single region on chromosome 8 accounts for most resistance but also identified 13 small effect regions. We found evidence that two epistatic loci and/or alternatively multiple resistance alleles exist at major QTL. We identified two peroxidases and one thioredoxin as candidate genes. Genomic prediction of additive and total genetic merit was accurate for CMD and will be effective both for selecting parents and identifying highly resistant clones as varieties.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Genetic architecture of common bunt resistance in winter wheat using genome-wide association study

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Amira M. I. Mourad ◽  
Ahmed Sallam ◽  
Vikas Belamkar ◽  
Ezzat Mahdy ◽  
Bahy Bakheit ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Association Study ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Common Bunt ◽  
Genome Wide ◽  
Bunt Resistance

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis

2022 ◽  
Author(s):  
Rongrong Ding ◽  
Zhanwei Zhuang ◽  
Yibin Qiu ◽  
Donglin Ruan ◽  
Jie Wu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Analysis ◽  
Large Scale ◽  
Major Gene ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Backfat Thickness ◽  
Lean Meat ◽  
Genome Wide Association Analysis ◽  
Genome Wide

Abstract Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1 and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1 and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggests that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits, and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

scholarly journals A New Polygenic Model for Nonfamilial Colorectal Cancer Inheritance Based on the Genetic Architecture of the Azoxymethane-Induced Mouse Model

Genetics ◽  
2019 ◽  
Vol 214 (3) ◽  
pp. 691-702
Author(s):  
Anika C. Bissahoyo ◽  
Yuying Xie ◽  
Lynda Yang ◽  
R. Scott Pearsall ◽  
Daekee Lee ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Mouse Model ◽  
Genetic Architecture ◽  
Inbred Strains ◽  
Genome Wide Association ◽  
Polygenic Resistance ◽  
Genetic Studies ◽  
Polygenic Model ◽  
Genome Wide ◽  
Dominant Characteristic

The azoxymethane model of colorectal cancer (CRC) was used to gain insights into the genetic heterogeneity of nonfamilial CRC. We observed significant differences in susceptibility parameters across 40 mouse inbred strains, with 6 new and 18 of 24 previously identified mouse CRC modifier alleles detected using genome-wide association analysis. Tumor incidence varied in F1 as well as intercrosses and backcrosses between resistant and susceptible strains. Analysis of inheritance patterns indicates that resistance to CRC development is inherited as a dominant characteristic genome-wide, and that susceptibility appears to occur in individuals lacking a large-effect, or sufficient numbers of small-effect, polygenic resistance alleles. Our results suggest a new polygenic model for inheritance of nonfamilial CRC, and that genetic studies in humans aimed at identifying individuals with elevated susceptibility should be pursued through the lens of absence of dominant resistance alleles rather than for the presence of susceptibility alleles.

scholarly journals Generalised Anxiety Disorder – A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0134865 ◽  
Author(s):  
Matthew N. Davies ◽  
Serena Verdi ◽  
Andrea Burri ◽  
Maciej Trzaskowski ◽  
Minyoung Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Anxiety Disorder ◽  
Differential Gene Expression ◽  
Twin Study ◽  
Genetic Architecture ◽  
Genome Wide Association ◽  
Generalised Anxiety Disorder ◽  
Genome Wide ◽  
Differential Gene
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