A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

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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Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle

Animals ◽

10.3390/ani10071185 ◽

2020 ◽

Vol 10 (7) ◽

pp. 1185

Author(s):

Laís Grigoletto ◽

Miguel Henrique Almeida Santana ◽

Fabiana Fernandes Bressan ◽

Joanir Pereira Eler ◽

Marcelo Fábio Gouveia Nogueira ◽

...

Keyword(s):

Candidate Genes ◽

Genetic Parameters ◽

Association Studies ◽

Antral Follicle ◽

Genome Wide Association Studies ◽

Hormone Levels ◽

Estrous Synchronization ◽

Nellore Cattle ◽

Genomic Regions ◽

Indicator Traits

Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (rG = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9–65.0 Mb and 109.1–109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors.

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Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle

Meat Science ◽

10.1016/j.meatsci.2020.108288 ◽

2021 ◽

Vol 171 ◽

pp. 108288

Author(s):

N.A. Marín-Garzón ◽

A.F.B. Magalhães ◽

L.F.M Mota ◽

L.F.S. Fonseca ◽

L.A.L. Chardulo ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Meat Color ◽

Genome Wide ◽

Color Traits ◽

Nellore Cattle ◽

Genomic Regions

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Genetic and Association Mapping Study of Wheat Agronomic Traits Under Contrasting Water Regimes

International Journal of Molecular Sciences ◽

10.3390/ijms13056167 ◽

2012 ◽

Vol 13 (5) ◽

pp. 6167-6188 ◽

Cited By ~ 26

Author(s):

Dejan Dodig ◽

Miroslav Zoric ◽

Borislav Kobiljski ◽

Jasna Savic ◽

Vesna Kandic ◽

...

Keyword(s):

Association Mapping ◽

Agronomic Traits ◽

Mapping Study ◽

Water Regimes ◽

Association Mapping Study

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Tolerance to mild salinity stress in japonica rice: A genome-wide association mapping study highlights calcium signaling and metabolism genes

PLoS ONE ◽

10.1371/journal.pone.0190964 ◽

2018 ◽

Vol 13 (1) ◽

pp. e0190964 ◽

Cited By ~ 13

Author(s):

Julien Frouin ◽

Antoine Languillaume ◽

Justine Mas ◽

Delphine Mieulet ◽

Arnaud Boisnard ◽

...

Keyword(s):

Association Mapping ◽

Calcium Signaling ◽

Salinity Stress ◽

Genome Wide Association ◽

Japonica Rice ◽

Mapping Study ◽

Genome Wide ◽

A Genome ◽

Association Mapping Study

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Genomic Regions and Candidate Genes Linked to Capped Hock in Pig

Life ◽

10.3390/life11060510 ◽

2021 ◽

Vol 11 (6) ◽

pp. 510

Author(s):

Lyubov Getmantseva ◽

Maria Kolosova ◽

Faridun Bakoev ◽

Anna Zimina ◽

Siroj Bakoev

Keyword(s):

Candidate Genes ◽

Genetic Markers ◽

Genetic Variants ◽

San Diego ◽

Negative Impact ◽

Carcass Traits ◽

Blood Parameters ◽

Pilot Studies ◽

Research Results ◽

Genomic Regions

Capped hock affects the exterior of pedigree pigs, making them unsalable and resulting in a negative impact on the efficiency of pig-breeding centers. The purpose of this paper was to carry out pilot studies aimed at finding genomic regions and genes linked to the capped hock in pigs. The studies were carried out on Landrace pigs (n = 75) and Duroc pigs (n = 70). To identify genomic regions linked to capped hock in pigs, we used smoothing FST statistics. Genotyping was performed with GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc, San Diego, CA, USA). The research results showed 70 SNPs linked to capped hock in Landrace (38 SNPs) and Duroc (32 SNPs). The identified regions overlapped with QTLs related with health traits (blood parameters) and meat and carcass traits (fatness). In total, 31 genes were identified (i.e., 17 genes in Landrace, 14 genes in Durocs). Three genes appeared in both the Landrace and Duroc groups, including A2ML1 (SSC5), ROBO2 (SSC13), and MSI1 (SSC14). We identified genomic regions directly or indirectly linked to capped hock, which thus might contribute to identifying genetic variants and using them as genetic markers in pig breeding.

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Genome-wide scan reveals genomic regions and candidate genes underlying direct and maternal effects of preweaning calf mortality in Nellore cattle

Genomics ◽

10.1016/j.ygeno.2021.02.021 ◽

2021 ◽

Author(s):

N.A. Marín-Garzón ◽

A.F.B. Magalhães ◽

P.I. Schmidt ◽

M. Serna ◽

L.F.S. Fonseca ◽

...

Keyword(s):

Candidate Genes ◽

Maternal Effects ◽

Genome Wide ◽

Nellore Cattle ◽

Calf Mortality ◽

Genomic Regions ◽

Genome Wide Scan

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Genetic and Association Mapping Study of English Grain Aphid Resistance and Tolerance in Bread Wheat Germplasm

Journal of Integrative Agriculture ◽

10.1016/s2095-3119(13)60356-1 ◽

2014 ◽

Vol 13 (1) ◽

pp. 40-53 ◽

Cited By ~ 3

Author(s):

Feng-qiz LI ◽

Jun-hua PENG

Keyword(s):

Association Mapping ◽

Bread Wheat ◽

Aphid Resistance ◽

Mapping Study ◽

Wheat Germplasm ◽

Grain Aphid ◽

Association Mapping Study

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Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii

10.1101/2021.01.31.428788 ◽

2021 ◽

Author(s):

Kumar Gaurav ◽

Sanu Arora ◽

Paula Silva ◽

Javier Sánchez-Martín ◽

Richard Horsnell ◽

...

Keyword(s):

Genetic Diversity ◽

Association Mapping ◽

Candidate Genes ◽

Bread Wheat ◽

Aegilops Tauschii ◽

Pest Resistance ◽

Wild Progenitor ◽

Genomic Regions ◽

Synthetic Hexaploids ◽

Diploid Ancestor

AbstractAegilops tauschii, the diploid wild progenitor of the D-subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D-subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D-subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer-based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverse Ae. tauschii genomes. This pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation in a hexaploid background amenable to breeding.

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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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