Genome wide QTL mapping to identify candidate genes for carcass traits in Hanwoo (Korean Cattle)

2012 ◽  
Vol 34 (1) ◽  
pp. 43-49 ◽  
Author(s):  
Seung Hwan Lee ◽  
Julius van der Werf ◽  
Sang Hong Lee ◽  
Da Jeong Lim ◽  
Eung Woo Park ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Carcass Traits ◽  
Korean Cattle ◽  
Genome Wide

scholarly journals Haplotype-Based Genome-Wide Association Study and Identification of Candidate Genes Associated with Carcass Traits in Hanwoo Cattle

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 551
Author(s):  
Swati Srivastava ◽  
Krishnamoorthy Srikanth ◽  
Sohyoung Won ◽  
Ju-Hwan Son ◽  
Jong-Eun Park ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Haplotype Block ◽  
Genome Wide Association Study ◽  
Carcass Traits ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Hanwoo Cattle

Hanwoo, is the most popular native beef cattle in South Korea. Due to its extensive popularity, research is ongoing to enhance its carcass quality and marbling traits. In this study we conducted a haplotype-based genome-wide association study (GWAS) by constructing haplotype blocks by three methods: number of single nucleotide polymorphisms (SNPs) in a haplotype block (nsnp), length of genomic region in kb (Len) and linkage disequilibrium (LD). Significant haplotype blocks and genes associated with them were identified for carcass traits such as BFT (back fat thickness), EMA (eye Muscle area), CWT (carcass weight) and MS (marbling score). Gene-set enrichment analysis and functional annotation of genes in the significantly-associated loci revealed candidate genes, including PLCB1 and PLCB4 present on BTA13, coding for phospholipases, which might be important candidates for increasing fat deposition due to their role in lipid metabolism and adipogenesis. CEL (carboxyl ester lipase), a bile-salt activated lipase, responsible for lipid catabolic process was also identified within the significantly-associated haplotype block on BTA11. The results were validated in a different Hanwoo population. The genes and pathways identified in this study may serve as good candidates for improving carcass traits in Hanwoo cattle.

scholarly journals A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Sèyi Fridaïus Ulrich Vanvanhossou ◽  
Carsten Scheper ◽  
Luc Hippolyte Dossa ◽  
Tong Yin ◽  
Kerstin Brügemann ◽  
...  
Keyword(s):  
Immune Response ◽  
Candidate Genes ◽  
Feed Efficiency ◽  
Morphological Traits ◽  
Carcass Traits ◽  
Potential Candidate ◽  
Adaptive Traits ◽  
Morphometric Traits ◽  
Indigenous Cattle ◽  
Genome Wide

Abstract Background Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. Results SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). Conclusions Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

Detection of candidate genes for growth and carcass traits using genome-wide association strategy in Chinese Simmental beef cattle

2018 ◽  
Vol 58 (2) ◽  
pp. 224 ◽  
Author(s):  
Wengang Zhang ◽  
Lingyang Xu ◽  
Huijiang Gao ◽  
Yang Wu ◽  
Xue Gao ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Carcass Traits ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Economic Traits ◽  
Cattle Industry ◽  
Genome Wide

In Chinese beef cattle industry, there are more than 60 million livestock, nearly half of which are Chinese Simmental beef cattle or Simmental crossbreds. Over the past decades, numerous quantitative trait loci for economic traits in cattle have been identified, while few studies for growth and carcass traits have been reported in Simmental beef cattle. In the present study, we conducted genome-wide association study based on BovineHD BeadChip and identified 41, 15, 3, 22 and 16 single-nucleotide polymorphisms significantly associated with average daily gain, liveweight before slaughter, carcass weight, dressing percentage and pure meat percentage respectively. In total, 18 candidate genes were found for growth and carcass traits, and four haplotype blocks for growth and carcass traits were discovered. These findings will facilitate detection of major genes and genetic variants involved in growth and carcass traits of beef cattle in further studies.

scholarly journals Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205576 ◽  
Author(s):  
Iulia Blaj ◽  
Jens Tetens ◽  
Siegfried Preuß ◽  
Jörn Bennewitz ◽  
Georg Thaller
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Meta Analysis ◽  
Carcass Traits ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals An Integrated Approach of QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame (Sesamum indicum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Sovetgul Asekova ◽  
Eunyoung Oh ◽  
Krishnanand P. Kulkarni ◽  
Muhammad Irfan Siddique ◽  
Myoung Hee Lee ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Sesamum Indicum ◽  
Genome Wide Association ◽  
Phytophthora Blight ◽  
Chromosome 10 ◽  
Resistant Parent ◽  
Exon 2 ◽  
Genome Wide

Phytophthora blight (PB) caused by Phytophthora nicotianae is a highly destructive disease in sesame (Sesamum indicum L.). In this study, we used linkage mapping and genome-wide association study (GWAS) to identify quantitative trait loci (QTL) and candidate genes associated with PB resistance. The QTL mapping in 90 RILs of the Goenbaek × Osan cross using genotyping-by-sequencing detected significant QTLs for PB resistance on chromosome 10, explaining 12.79%–13.34% of phenotypic variation. Association of this locus to PB resistance was also revealed through bulked segregant analysis in second RIL population (Goenbaek × Milsung cross) comprising 188 RILs. The GWAS of 87 sesame accessions evaluated against three P. nicotianae isolates identified 29 SNPs on chromosome 10 significantly associated with PB resistance. These SNPs were located within a 0.79 Mb region, which co-located with the QTL intervals identified in RIL populations, and hence scanned for identifying candidate genes. This region contained several defense-related candidate R genes, five of which were selected for quantitative expression analysis. One of these genes, SIN_1019016 was found to show significantly higher expression in the resistant parent compared to that in the susceptible parents and selected RILs. Paired-end sequencing of the gene SIN_1019016 in parental cultivars revealed two synonymous SNPs between Goenbaek and Osan in exon 2 of coding DNA sequence. These results suggested SIN_1019016 as one of the candidate gene conferring PB resistance in sesame. The findings from this study will be useful in the marker-assisted selection as well as the functional analysis of PB resistance candidate gene(s) in sesame.

scholarly journals A Combinatorial Approach of Biparental QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame

2020 ◽  
Author(s):  
Asekova Sovetgul ◽  
Eunyoung Oh ◽  
Krishnanand P. Kulkarni ◽  
Myoung Hee Lee ◽  
Jung In Kim ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genome Wide Association ◽  
Blight Resistance ◽  
Combinatorial Approach ◽  
Phytophthora Blight ◽  
Resistant Parent ◽  
Significant Qtls ◽  
Gwas Analysis ◽  
Genome Wide

SummaryPhytophthora blight, caused by pathogen Phytophthora nicotianae, is responsible for a huge reduction in sesame (Sesamum indicum L.) crop yields. In this study, we utilized a combinatorial approach involving biparental QTL mapping and genome-wide association (GWAS) analysis to identify genes associated with Phytophthora blight resistance in sesame. Evaluation of resistant of the parental varieties (Goenbaek, Osan and Milsung) and the RILs of both the populations in greenhouse conditions suggested the qualitative nature of the trait.. The genetic map comprised thirteen LGs covering a total map length of 887.49 cM with an average inter-marker distance of 4.69 cM. Significant QTLs explaining phenotypic variation in the range of 2.25% to 69.24% were identified on chromosomes 10 and 13 (Chr10 and Chr13). A resistance locus detected on Chr10 was found to be highly significant. The association of this locus to PBR was also identified through BSA and single marker analysis in Goenbaek × Milsung cross and through genome-wide association mapping of 87 sesame accessions. The GWAS analysis identified 44 SNP loci significantly associated with Phytophthora disease-resistant traits on Chr10. Further, the haplotype block analysis conducted in order to find whether the SNPs associated with resistance in this study showed that the SNPs are in high LD with the resistance QTL. We obtained a total of 68 candidate genes, which included a number of defense-related R genes. One of the genes, SIN_1019016 (At1g58390) showed high expression in the resistant parent. The results from this study would be highly useful in identifying genetic and molecular factors associated with Phytophthora blight resistance in sesame.

scholarly journals Quantitative Trait Loci for Floral Morphology in Arabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1379-1392 ◽  
Author(s):  
Thomas Juenger ◽  
Michael Purugganan ◽  
Trudy F C Mackay
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Qtl Mapping ◽  
Candidate Genes ◽  
Inbred Line ◽  
Recombinant Inbred Line Population ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Genetic Basis ◽  
Genome Wide

Abstract A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these same traits in the Landsberg erecta × Columbia recombinant inbred line population. There was significant genetic variation for all traits in both the sample of naturally occurring ecotypes and in the Ler × Col recombinant inbred line population. In addition, broad-sense genetic correlations among the traits were positive and high. A composite interval mapping (CIM) analysis detected 18 significant QTL affecting at least one floral character. Eleven QTL were associated with several floral traits, supporting either pleiotropy or tight linkage as major determinants of flower morphological integration. We propose several candidate genes that may underlie these QTL on the basis of positional information and functional arguments. Genome-wide QTL mapping is a promising tool for the discovery of candidate genes controlling morphological development, the detection of novel phenotypic effects for known genes, and in generating a more complete understanding of the genetic basis of floral development.

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