scholarly journals Genotype-by-environment interaction in Holstein heifer fertility traits using single-step genomic reaction norm models

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rui Shi ◽  
Luiz Fernando Brito ◽  
Aoxing Liu ◽  
Hanpeng Luo ◽  
Ziwei Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Heat Tolerance ◽  
Reaction Norm ◽  
Single Step ◽  
Conception Rate ◽  
Critical Periods ◽  
Genotype By Environment ◽  
Fertility Traits

Abstract Background The effect of heat stress on livestock production is a worldwide issue. Animal performance is influenced by exposure to harsh environmental conditions potentially causing genotype-by-environment interactions (G × E), especially in highproducing animals. In this context, the main objectives of this study were to (1) detect the time periods in which heifer fertility traits are more sensitive to the exposure to high environmental temperature and/or humidity, (2) investigate G × E due to heat stress in heifer fertility traits, and, (3) identify genomic regions associated with heifer fertility and heat tolerance in Holstein cattle. Results Phenotypic records for three heifer fertility traits (i.e., age at first calving, interval from first to last service, and conception rate at the first service) were collected, from 2005 to 2018, for 56,998 Holstein heifers raised in 15 herds in the Beijing area (China). By integrating environmental data, including hourly air temperature and relative humidity, the critical periods in which the heifers are more sensitive to heat stress were located in more than 30 days before the first service for age at first calving and interval from first to last service, or 10 days before and less than 60 days after the first service for conception rate. Using reaction norm models, significant G × E was detected for all three traits regarding both environmental gradients, proportion of days exceeding heat threshold, and minimum temperature-humidity index. Through single-step genome-wide association studies, PLAG1, AMHR2, SP1, KRT8, KRT18, MLH1, and EOMES were suggested as candidate genes for heifer fertility. The genes HCRTR1, AGRP, PC, and GUCY1B1 are strong candidates for association with heat tolerance. Conclusions The critical periods in which the reproductive performance of heifers is more sensitive to heat stress are trait-dependent. Thus, detailed analysis should be conducted to determine this particular period for other fertility traits. The considerable magnitude of G × E and sire re-ranking indicates the necessity to consider G × E in dairy cattle breeding schemes. This will enable selection of more heat-tolerant animals with high reproductive efficiency under harsh climatic conditions. Lastly, the candidate genes identified to be linked with response to heat stress provide a better understanding of the underlying biological mechanisms of heat tolerance in dairy cattle.

scholarly journals Genotype-by-environment Interaction in Holstein Heifer Fertility Traits using Single-step Genomic Reaction Norm Models

2020 ◽  
Author(s):  
Rui Shi ◽  
Luiz Brito ◽  
Aoxing Liu ◽  
Hanpeng Luo ◽  
Ziwei Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Candidate Genes ◽  
Heat Tolerance ◽  
Reaction Norm ◽  
Single Step ◽  
Conception Rate ◽  
Critical Periods ◽  
Age At First Calving ◽  
Genotype By Environment ◽  
Fertility Traits

Abstract Background: The effect of heat stress on livestock production is a worldwide issue, where animal performance is influenced by exposure to high environmental temperatures, indicating the existence of possible genotype-by-environment interactions (G´E). The main objectives of this study were to (1) detect the time periods in which heifer fertility traits are more sensitive to the exposure to high environmental temperature and/or humidity, (2) investigate G´E due to heat stress in heifer fertility traits, and (3) identify genomic regions associated with heifer fertility and heat stress in Holstein cattle. Results: Phenotypic records for three heifer fertility traits (i.e., age at first calving, interval from first to last service, and conception rate at the first service) were collected, from 2005 to 2018, for 56,998 Holstein heifers raised in 15 herds in the Beijing area (China). By integrating environmental data including hourly air temperature and relative humidity, the critical periods in which the heifers are more sensitive to heat stress were defined as <=30 days before the first service for age at first calving and interval from first to last service, or 10 days before and <= 60 days after the first service for conception rate. Using reaction norm models, significant G´E was detected for all three traits regarding both environmental gradients, proportion of days exceeding heat threshold and minimum temperature humidity index. Through single-step genome-wide association study, PLAG1, AMHR2, SP1, KRT8, KRT18, MLH1, and EOMES were suggested as candidate genes for heifer fertility while HCRTR1, AGRP, PC, and GUCY1B1 were for heat tolerance. Conclusions: The critical periods in which reproductive perfromances of heifers are more sensitive to heat stress are trait-dependent. Thus, detailed analysis should be conducted to determine this particular period for other fertility traits. The considerable magnitude of G´E and sire re-ranking indicates the necessity to consider G´E in breeding schemes. This will enable selection of more heat-tolerant animals with high reproductive efficiency under harsh climatic conditions. The candidate genes identified to be linked with response to heat stress provide a better understanding of the underlying biological mechanisms of heat tolerance in dairy cattle.

scholarly journals Genotype-by-environment interaction of fertility traits in Danish Holstein cattle using a single-step genomic reaction norm model

Heredity ◽  
2019 ◽  
Vol 123 (2) ◽  
pp. 202-214 ◽  
Author(s):  
Zhe Zhang ◽  
Morten Kargo ◽  
Aoxing Liu ◽  
Jørn Rind Thomasen ◽  
Yuchun Pan ◽  
...  
Keyword(s):  
Reaction Norm ◽  
Genotype By Environment Interaction ◽  
Single Step ◽  
Holstein Cattle ◽  
Environment Interaction ◽  
Genotype By Environment ◽  
Norm Model ◽  
Fertility Traits

scholarly journals Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Shi-Yi Chen ◽  
Pedro H. F. Freitas ◽  
Hinayah R. Oliveira ◽  
Sirlene F. Lázaro ◽  
Yi Jian Huang ◽  
...  
Keyword(s):  
Body Composition ◽  
Candidate Genes ◽  
X Chromosome ◽  
Reaction Norm ◽  
Single Step ◽  
Residual Variance ◽  
Large White ◽  
Maternal Line ◽  
Genotype By Environment ◽  
Genomic Regions

Abstract Background There is an increasing need to account for genotype-by-environment (G × E) interactions in livestock breeding programs to improve productivity and animal welfare across environmental and management conditions. This is even more relevant for pigs because selection occurs in high-health nucleus farms, while commercial pigs are raised in more challenging environments. In this study, we used single-step homoscedastic and heteroscedastic genomic reaction norm models (RNM) to evaluate G × E interactions in Large White pigs, including 8686 genotyped animals, for reproduction (total number of piglets born, TNB; total number of piglets born alive, NBA; total number of piglets weaned, NW), growth (weaning weight, WW; off-test weight, OW), and body composition (ultrasound muscle depth, MD; ultrasound backfat thickness, BF) traits. Genetic parameter estimation and single-step genome-wide association studies (ssGWAS) were performed for each trait. Results The average performance of contemporary groups (CG) was estimated and used as environmental gradient in the reaction norm analyses. We found that the need to consider heterogeneous residual variance in RNM models was trait dependent. Based on estimates of variance components of the RNM slope and of genetic correlations across environmental gradients, G × E interactions clearly existed for TNB and NBA, existed for WW but were of smaller magnitude, and were not detected for NW, OW, MD, and BF. Based on estimates of the genetic variance explained by the markers in sliding genomic windows in ssGWAS, several genomic regions were associated with the RNM slope for TNB, NBA, and WW, indicating specific biological mechanisms underlying environmental sensitivity, and dozens of novel candidate genes were identified. Our results also provided strong evidence that the X chromosome contributed to the intercept and slope of RNM for litter size traits in pigs. Conclusions We provide a comprehensive description of G × E interactions in Large White pigs for economically-relevant traits and identified important genomic regions and candidate genes associated with GxE interactions on several autosomes and the X chromosome. Implementation of these findings will contribute to more accurate genomic estimates of breeding values by considering G × E interactions, in order to genetically improve the environmental robustness of maternal-line pigs.

scholarly journals Definition of Environmental Variables and Critical Periods to Evaluate Heat Tolerance in Large White Pigs Based on Single-Step Genomic Reaction Norms

2021 ◽  
Vol 12 ◽  
Author(s):  
P. H. F. Freitas ◽  
J. S. Johnson ◽  
S. Chen ◽  
H. R. Oliveira ◽  
F. Tiezzi ◽  
...  
Keyword(s):  
Heat Tolerance ◽  
Environmental Variables ◽  
Critical Period ◽  
Single Step ◽  
Climatic Variables ◽  
Maximum Temperature ◽  
Critical Periods ◽  
Genetic Progress ◽  
Large White ◽  
Definition Of

Properly quantifying environmental heat stress (HS) is still a major challenge in livestock breeding programs, especially as adverse climatic events become more common. The definition of critical periods and climatic variables to be used as the environmental gradient is a key step for genetically evaluating heat tolerance (HTol). Therefore, the main objectives of this study were to define the best critical periods and environmental variables (ENV) to evaluate HT and estimate variance components for HT in Large White pigs. The traits included in this study were ultrasound backfat thickness (BFT), ultrasound muscle depth (MDP), piglet weaning weight (WW), off-test weight (OTW), interval between farrowing (IBF), total number of piglets born (TNB), number of piglets born alive (NBA), number of piglets born dead (NBD), number of piglets weaned (WN), and weaning to estrus interval (IWE). Seven climatic variables based on public weather station data were compared based on three criteria, including the following: (1) strongest G×E estimate as measured by the slope term, (2) ENV yielding the highest theoretical accuracy of the genomic estimated breeding values (GEBV), and (3) variable yielding the highest distribution of GEBV per ENV. Relative humidity (for BFT, MDP, NBD, WN, and WW) and maximum temperature (for OTW, TNB, NBA, IBF, and IWE) are the recommended ENV based on the analyzed criteria. The acute HS (average of 30 days before the measurement date) is the critical period recommended for OTW, BFT, and MDP in the studied population. For WN, WW, IBF, and IWE, a period ranging from 34 days prior to farrowing up to weaning is recommended. For TNB, NBA, and NBD, the critical period from 20 days prior to breeding up to 30 days into gestation is recommended. The genetic correlation values indicate that the traits were largely (WN, WW, IBF, and IWE), moderately (OTW, TNB, and NBA), or weakly (MDP, BFT, and NBD) affected by G×E interactions. This study provides relevant recommendations of critical periods and climatic gradients for several traits in order to evaluate HS in Large White pigs. These observations demonstrate that HT in Large White pigs is heritable, and genetic progress can be achieved through genetic and genomic selection.

scholarly journals Genomic Selection Improves Heat Tolerance in Dairy Cattle

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
J. B. Garner ◽  
M. L. Douglas ◽  
S. R. O Williams ◽  
W. J. Wales ◽  
L. C. Marett ◽  
...  
Keyword(s):  
Heat Stress ◽  
Dairy Cattle ◽  
Genomic Selection ◽  
Milk Production ◽  
Heat Tolerance ◽  
Dairy Products ◽  
Dairy Herds ◽  
Physiological Indicators ◽  
Genome Wide ◽  
Heat Tolerant

Abstract Dairy products are a key source of valuable proteins and fats for many millions of people worldwide. Dairy cattle are highly susceptible to heat-stress induced decline in milk production, and as the frequency and duration of heat-stress events increases, the long term security of nutrition from dairy products is threatened. Identification of dairy cattle more tolerant of heat stress conditions would be an important progression towards breeding better adapted dairy herds to future climates. Breeding for heat tolerance could be accelerated with genomic selection, using genome wide DNA markers that predict tolerance to heat stress. Here we demonstrate the value of genomic predictions for heat tolerance in cohorts of Holstein cows predicted to be heat tolerant and heat susceptible using controlled-climate chambers simulating a moderate heatwave event. Not only was the heat challenge stimulated decline in milk production less in cows genomically predicted to be heat-tolerant, physiological indicators such as rectal and intra-vaginal temperatures had reduced increases over the 4 day heat challenge. This demonstrates that genomic selection for heat tolerance in dairy cattle is a step towards securing a valuable source of nutrition and improving animal welfare facing a future with predicted increases in heat stress events.

scholarly journals QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

2021 ◽  
Vol 11 ◽  
Author(s):  
Lei Chen ◽  
Qiang Wang ◽  
Maoyan Tang ◽  
Xiaoli Zhang ◽  
Yinghua Pan ◽  
...  
Keyword(s):  
Heat Stress ◽  
Abiotic Stress ◽  
High Temperature ◽  
Candidate Genes ◽  
Heat Tolerance ◽  
Bulked Segregant Analysis ◽  
Abiotic Stress Tolerance ◽  
Chromosome 8 ◽  
Flowering Stage ◽  
Heat Tolerant

High-temperature stress can cause serious abiotic damage that limits the yield and quality of rice. Heat tolerance (HT) during the flowering stage of rice is a key trait that can guarantee a high and stable yield under heat stress. HT is a complex trait that is regulated by multiple quantitative trait loci (QTLs); however, few underlying genes have been fine mapped and cloned. In this study, the F2:3 population derived from a cross between Huanghuazhan (HHZ), a heat-tolerant cultivar, and 9311, a heat-sensitive variety, was used to map HT QTLs during the flowering stage in rice. A new major QTL, qHTT8, controlling HT was identified on chromosome 8 using the bulked-segregant analysis (BSA)-seq method. The QTL qHTT8 was mapped into the 3,555,000–4,520,000 bp, which had a size of 0.965 Mb. The candidate region of qHTT8 on chromosome 8 contained 65 predicted genes, and 10 putative predicted genes were found to be associated with abiotic stress tolerance. Furthermore, qRT-PCR was performed to analyze the differential expression of these 10 genes between HHZ and 9311 under high temperature conditions. LOC_Os08g07010 and LOC_Os08g07440 were highly induced in HHZ compared with 9311 under heat stress. Orthologous genes of LOC_Os08g07010 and LOC_Os08g07440 in plants played a role in abiotic stress, suggesting that they may be the candidate genes of qHTT8. Generally, the results of this study will prove useful for future efforts to clone qHTT8 and breed heat-tolerant varieties of rice using marker-assisted selection.

256 GENOMIC EVALUATION OF FERTILITY TRAITS AND DISCOVERY OF HAPLOTYPES THAT AFFECT FERTILITY OF US DAIRY CATTLE

2016 ◽  
Vol 28 (2) ◽  
pp. 260
Author(s):  
G. R. Wiggans ◽  
D. J. Null ◽  
J. B. Cole ◽  
H. D. Norman
Keyword(s):  
Dairy Cattle ◽  
Sequence Data ◽  
Reference Population ◽  
Bioinformatic Analysis ◽  
The United States ◽  
Conception Rate ◽  
National Database ◽  
Nucleotide Polymorphisms ◽  
Fertility Traits ◽  
Sire Conception Rate

Genomic evaluations of dairy cattle became official in the United States in January 2009 for Holsteins and Jerseys, and later for Brown Swiss, Ayrshires, and Guernseys. Up to 33 yield, fitness, calving, and conformation traits are evaluated, and the fertility traits included daughter pregnancy rate and heifer and cow conception rates. Additional fertility traits, such as age at first calving and days from calving to first insemination, also are being studied. Male fertility (sire conception rate) is evaluated phenotypically rather than through genomics. Over 1 million animals have genotypes in the national database, which reflects collaboration with Canada and Europe. Most of the genotypes are from females and are from genotyping chips with <30 000 single nucleotide polymorphisms (SNP). To combine data across chips, genotypes are imputed to a set of >77 000 SNP. The imputation process involves dividing the chromosome into segments of approximately equal length and determining the paternal or maternal origin of the alleles. Because some segments were never homozygous, they were assumed to contain an abnormality that resulted in early embryonic death. If a decrease in sire conception rate could be associated with a bull that was a carrier of such a chromosomal segment, the haplotype was designated as affecting fertility. Once the region was identified, bioinformatic analysis was used to discover the causative variant for many of those haplotypes. Accuracy of genomic evaluations is determined by size of the reference population and heritability of the trait. The reference population for Holsteins includes >180 000 bulls and cows. Because fertility traits have low heritabilities, genomic information is particularly useful in improving evaluation accuracy. Accuracy of fertility evaluations is expected to increase further by discovering causative variants for various aspects of conception and gestation through investigation of sequence data.

scholarly journals PSIII-12 Genetic analysis of heat tolerance in Holsteins using test-day production records and satellite-based meteorological data

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 229-230
Author(s):  
Paige L Rockett ◽  
Flavio Schenkel ◽  
Christine F Baes ◽  
Filippo Miglior ◽  
Dan Tulpan
Keyword(s):  
Heat Stress ◽  
Dairy Cattle ◽  
Heat Tolerance ◽  
Meteorological Data ◽  
Genetic Selection ◽  
Weather Station ◽  
Station Data ◽  
Weather Station Data ◽  
Weather Stations ◽  
Selection For

Abstract Heat stress in dairy cattle is an existing issue in temperate regions that can cause reduced milk production, impaired fertility, and mortality. Genetic selection for heat tolerance using test-day production records and weather station data is a potential mitigation strategy. However, weather stations can have temporal data gaps and a low spatial resolution, which reduces the number of herds that can be incorporated into an analysis. The objectives for this study include: (1) compare satellite-based meteorological data from the NASA POWER database to weather station records in Ontario and Quebec, (2) evaluate the effects of heat stress on Canadian Holsteins, and (3) assess breeding value estimates for heat tolerance in the same population. Daily estimates of ambient temperature, dewpoint temperature, relative humidity, and wind speed from 481 weather stations in Ontario and Quebec were compared to the parameters estimated by the NASA POWER project using an ordinary least squares regression. The coordinates of herds in Ontario and Quebec were estimated using their addresses and Google Maps Geocoding. The best weather data for each herd location will be incorporated into two random regression animal models to analyze three test-day production traits: milk, fat, and protein yield. The first model will be used to estimate general and specific additive genetic merits over the thermal gradient. The second model will estimate the traditional additive genetic merit. In conclusion, this study explores the use of satellite estimated meteorological parameters in addition to or alternatively to weather station data in heat tolerance studies, quantifies the sensitivity of Canadian dairy cattle to heat stress, and evaluates if genetic selection for increased heat tolerance in Canadian dairy herds is possible.

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