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 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 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 Effect of age at first calving and heat stress at parturition on reproductive efficiency and postpartum disorders in Holstein heifers

2019 ◽  
Vol 17 (2) ◽  
pp. e0405
Author(s):  
Miguel Mellado ◽  
Vanessa Alba ◽  
Leticia Gaytán ◽  
José E. García ◽  
Jesús Mellado
Keyword(s):  
Heat Stress ◽  
Age Groups ◽  
Dairy Farm ◽  
Climatic Conditions ◽  
Conception Rate ◽  
Age At First Calving ◽  
Hot Climate ◽  
Postpartum Disorders ◽  
Humidity Index ◽  
The Impact

The objective of this study was to evaluate the impact of age at first calving (AFC) and climatic conditions at calving on peripartum disorders and reproductive performance in Holstein heifers in a hot environment. A total of 3000 reproductive records from a large highly technified dairy farm were used; the variables evaluated were temperature humidity index (THI; <77, 77-83, >83) at calving and AFC (<2.0, 2.0-2.2 and >2.2 years). Across age groups, the cases of dystocic parturition increased (p<0.05) when the deliveries occurred with severe heat stress (4.3% vs. 3.3% for THI >83 and <83 units, respectively). Across THI, conception rate at the first postpartum artificial insemination (AI) was lower (p=0.02) for heifers calving for the first time >2.2 years compared to heifers calving between 2.0 and 2.2 and <2.0 years (9.8, 15.3 and 13.7%, respectively). Conception rate at first AI postcalving was higher (p<0.01) in heifers calving with THI less than 83 units than in heifers calving with a THI >83 units (16.8 vs. 5.4%). The conception rate considering all services was affected (p<0.05) by AFC (42.7, 50.4 and 40.9% for AFC <2.0, 2.0-2.2 and >2.2 years, respectively). The interaction AFC × THI at calving was significant (p<0.05). The occurrence of metritis was higher (p<0.05) in heifers <2.0 years of age at calving than those calving after 2 years of age. The presence of ovarian cysts was less common (p<0.05) in heifers with greater AFC. In conclusion, increasing the AFC in Holstein heifers had no benefits in reproduction and health, compared with heifers calving at <2.0 years. These data in a hot climate suggest that heifers should be selected to begin their first lactation before 2 years of age.

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 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.

scholarly journals Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

2020 ◽  
Author(s):  
Qasim Raza ◽  
Awais Riaz ◽  
Khurram Bashir ◽  
Muhammad Sabar
Keyword(s):  
Heat Stress ◽  
Abiotic Stress ◽  
Heat Shock ◽  
Candidate Genes ◽  
Heat Tolerance ◽  
Fast Track ◽  
Reproductive Tissue ◽  
Rice Cultivars ◽  
Tissue Specific ◽  
Heat Tolerant

AbstractRice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigsating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.Key MessageBy integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.

Insights into the heat-responsive transcriptional network of tomato contrasting genotypes

2021 ◽  
Vol 19 (1) ◽  
pp. 44-57
Author(s):  
Sirine Werghi ◽  
Charfeddine Gharsallah ◽  
Nishi Kant Bhardwaj ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Candidate Genes ◽  
Expression Patterns ◽  
Response Strategies ◽  
Transcriptional Reprogramming ◽  
Genes Encoding ◽  
Breeding Programmes ◽  
Gene Transcripts ◽  
Resource Data

AbstractDuring recent decades, global warming has intensified, altering crop growth, development and survival. To overcome changes in their environment, plants undergo transcriptional reprogramming to activate stress response strategies/pathways. To evaluate the genetic bases of the response to heat stress, Conserved DNA-derived Polymorphism (CDDP) markers were applied across tomato genome of eight cultivars. Despite scattered genotypes, cluster analysis allowed two neighbouring panels to be discriminate. Tomato CDDP-genotypic and visual phenotypic assortment permitted the selection of two contrasting heat-tolerant and heat-sensitive cultivars. Further analysis explored differential expression in transcript levels of genes, encoding heat shock transcription factors (HSFs, HsfA1, HsfA2, HsfB1), members of the heat shock protein (HSP) family (HSP101, HSP17, HSP90) and ascorbate peroxidase (APX) enzymes (APX1, APX2). Based on discriminating CDDP-markers, a protein functional network was built allowing prediction of candidate genes and their regulating miRNA. Expression patterns analysis revealed that miR156d and miR397 were heat-responsive showing a typical inverse relation with the abundance of their target gene transcripts. Heat stress is inducing a set of candidate genes, whose expression seems to be modulated through a complex regulatory network. Integrating genetic resource data is required for identifying valuable tomato genotypes that can be considered in marker-assisted breeding programmes to improve tomato heat tolerance.

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