Comparison of genomic predictions for carcass and reproduction traits in Berkshire, Duroc and Yorkshire populations in Korea

The usefulness of genomic selection was assessed for female reproduction in tropically adapted breeds in northern Australia. Records from experimental populations of Brahman (996) and Tropical Composite (1097) cattle that had had six calving opportunities were used to derive genomic predictions for several measures of female fertility. These measures included age at first corpus luteum (AGECL), at first calving and subsequent postpartum anoestrous interval and measures of early and lifetime numbers of calves born or weaned. In a second population, data on pregnancy and following status (anoestrous or pregnancy) were collected from 27 commercial herds from northern Australia to validate genomic predictions. Cows were genotyped with a variety of single nucleotide polymorphism (SNP) panels and, where necessary, genotypes imputed to the highest density (729 068 SNPs). Genetic parameters of subsets of the complete data were estimated. These subsets were used to validate genomic predictions using genomic best linear unbiased prediction using both univariate cross-validation and bivariate analyses. Estimated heritability ranged from 0.56 for AGECL to 0.03 for lifetime average calving rate in the experimental cows, and from 0.09 to 0.25 for early life reproduction traits in the commercial cows. Accuracies of predictions were generally low, reflecting the limited number of data in the experimental populations. For AGECL and postpartum anoestrous interval, the highest accuracy was 0.35 for experimental Brahman cows using five-fold univariate cross-validation. Greater genetic complexity in the Tropical Composite cows resulted in the corresponding accuracy of 0.23 for AGECL. Similar level of accuracies (from univariate and bivariate analyses) were found for some of the early measures of female reproduction in commercial cows, indicating that there is potential for genomic selection but it is limited by the number of animals with phenotypes.

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Cloning and expression analysis of HoxA10, a candidate gene influencing reproduction traits in pigs

JOURNAL OF HUNAN AGRICULTURAL UNIVERSITY ◽

10.3724/sp.j.1238.2011.00060 ◽

2011 ◽

Vol 37 (1) ◽

pp. 60-64

Author(s):

Xiao-ning ZHOU ◽

Mei-xia FANG ◽

Xiao-mei HE ◽

Qing-hua NIE ◽

Xi-quan ZHANG

Keyword(s):

Candidate Gene ◽

Expression Analysis ◽

Cloning And Expression ◽

Reproduction Traits

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Structural variations in papaya genomes

BMC Genomics ◽

10.1186/s12864-021-07665-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhenyang Liao ◽

Xunxiao Zhang ◽

Shengcheng Zhang ◽

Zhicong Lin ◽

Xingtan Zhang ◽

...

Keyword(s):

Agronomic Traits ◽

Enrichment Analysis ◽

Copy Number Variant ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Structural Variations ◽

Reproduction Traits ◽

Depth Study ◽

Environmental Adaptability ◽

The Impact

Abstract Background Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers. Results We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress. Conclusions SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.

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Recent genetic advances on boar taint reduction as an alternative to castration: a review

Journal of Applied Genetics ◽

10.1007/s13353-020-00598-w ◽

2021 ◽

Author(s):

Darlene Ana Souza Duarte ◽

Martine Schroyen ◽

Rodrigo Reis Mota ◽

Sylvie Vanderick ◽

Nicolas Gengler

Keyword(s):

Genetic Selection ◽

Boar Taint ◽

Production Traits ◽

Fat Tissue ◽

Reproduction Traits ◽

Unpleasant Odor ◽

High Heritability ◽

Pig Meat ◽

Or Genes ◽

Synthesis And Degradation

AbstractBoar taint is an unpleasant odor in male pig meat, mainly caused by androstenone, skatole, and indole, which are deposited in the fat tissue. Piglet castration is the most common practice to prevent boar taint. However, castration is likely to be banished in a few years due to animal welfare concerns. Alternatives to castration, such as genetic selection, have been assessed. Androstenone and skatole have moderate to high heritability, which makes it feasible to select against these compounds. This review presents the latest results obtained on genetic selection against boar taint, on correlation with other traits, on differences in breeds, and on candidate genes related to boar taint. QTLs for androstenone and skatole have been reported mainly on chromosomes 6, 7, and 14. These chromosomes were reported to contain genes responsible for synthesis and degradation of androstenone and skatole. A myriad of work has been done to find markers or genes that can be used to select animals with lower boar taint. The selection against boar taint could decrease performance of some reproduction traits. However, a favorable response on production traits has been observed by selecting against boar taint. Selection results have shown that it is possible to reduce boar taint in few generations. In addition, modifications in diet and environment conditions could be associated with genetic selection to reduce boar taint. Nevertheless, costs to measure and select against boar taint should be rewarded with incentives from the market; otherwise, it would be difficult to implement genetic selection.

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Genetic importance of fat and eye muscle depth in Merino breeding programs

Animal Production Science ◽

10.1071/an14645 ◽

2016 ◽

Vol 56 (4) ◽

pp. 690 ◽

Cited By ~ 15

Author(s):

D. J. Brown ◽

A. A. Swan

Keyword(s):

Carcass Traits ◽

Genetic Correlations ◽

Fibre Diameter ◽

Economic Index ◽

Parasite Resistance ◽

Eye Muscle ◽

Breeding Programs ◽

Dual Purpose ◽

Internal Parasite ◽

Reproduction Traits

Australian Merino breeders have traditionally selected animals for breeding predominately on the basis of wool characteristics. Over recent decades, an increasing proportion of Merino breeders are interested in producing a ewe that can be used for prime-lamb production, but that also performs well for wool characteristics. Correlations between ultrasound carcass traits and other traits such as wool, internal parasite resistance and reproduction traits, are not very well known. The aims of this study were three-fold: (1) to estimate the genetic relationships between ultrasound carcass traits and wool, internal parasite resistance and reproduction traits, (2) to determine the value of recording ultrasound carcass traits in Merino breeding programs, and (3) to evaluate the impact of improving ewe genetic merit for fatness on their reproduction performance. Ultrasound fat and eye muscle depth had small to moderate genetic correlations with most traits, with positive correlations observed for bodyweight, fibre diameter, fibre curvature and reproduction, and negative correlations observed for fleece weight, fibre diameter coefficient of variation, worm egg count and breech wrinkle. As expected on the basis of these genetic correlations, estimated breeding values for fat depth of ewes had a positive association with their observed reproduction performance, but the effect explained only minimal variation in reproductive performance, and was extremely variable among flocks and years. A range of measurement scenarios was investigated for three standard MERINOSELECT indexes. Measuring fat and eye muscle depth resulted in 3%, 4% and 21% additional economic index gain for the fine, medium and dual purpose indexes, respectively, whereas measuring reproduction traits directly resulted in 17%, 27% and 45% additional gain in the economic index. Dual purpose index gains benefited more from measuring ultrasound carcass traits as it is the only index with a direct economic value placed on carcass traits. Measuring fat and eye muscle depth also resulted in a greater reduction in worm egg count. The results indicated that desirable genetic progress can be made in wool, ultrasound carcass, internal parasite resistance and number of lambs born and weaned simultaneously using multiple trait selection to account for the mix of favourable and unfavourable correlations between these traits. These results also demonstrated that the best method to maximise economic gain is to measure as many traits (or closely correlated traits) in the breeding objective as possible.

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Crossbreeding of Hair goats with Alpine and Saanen bucks: Production and reproduction traits of Native Hair goats in supplementary feeding in different physiological stage in natural pasture-based system

Small Ruminant Research ◽

10.1016/j.smallrumres.2021.106494 ◽

2021 ◽

pp. 106494

Author(s):

H. Erduran

Keyword(s):

Supplementary Feeding ◽

Natural Pasture ◽

Physiological Stage ◽

Reproduction Traits

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Effect of prepubertal and postpubertal growth and age at first calving on production and reproduction traits during the first 3 lactations in Holstein dairy cattle

Journal of Dairy Science ◽

10.3168/jds.2013-7419 ◽

2014 ◽

Vol 97 (5) ◽

pp. 3017-3027 ◽

Cited By ~ 19

Author(s):

L. Krpálková ◽

V.E. Cabrera ◽

M. Vacek ◽

M. Štípková ◽

L. Stádník ◽

...

Keyword(s):

Dairy Cattle ◽

Age At First Calving ◽

Reproduction Traits

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Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions

Genetics Selection Evolution ◽

10.1186/s12711-014-0074-4 ◽

2015 ◽

Vol 47 (1) ◽

Cited By ~ 69

Author(s):

Kathryn E Kemper ◽

Coralie M Reich ◽

Philip J Bowman ◽

Christy J vander Jagt ◽

Amanda J Chamberlain ◽

...

Keyword(s):

Qtl Mapping ◽

Bayesian Method ◽

Genomic Predictions

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Reliability of Genomic Predictions Across Multiple Populations

Genetics ◽

10.1534/genetics.109.104935 ◽

2009 ◽

Vol 183 (4) ◽

pp. 1545-1553 ◽

Cited By ~ 204

Author(s):

A. P. W. de Roos ◽

B. J. Hayes ◽

M. E. Goddard

Keyword(s):

Multiple Populations ◽

Genomic Predictions

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36 Effect of Blending and Tuning Relationship Matrices in Single-step Genomic BLUP

Journal of Animal Science ◽

10.1093/jas/skab235.032 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 19-20

Author(s):

Taylor M McWhorter ◽

Andre Garcia ◽

Matias Bermann ◽

Andres Legarra ◽

Ignacio Aguilar ◽

...

Keyword(s):

Single Step ◽

Fixation Index ◽

Genomic Information ◽

Software Suite ◽

Genetic Base ◽

Actual Difference ◽

The Impact ◽

Genomic Predictions

Abstract Single-step GBLUP (ssGBLUP) relies on the combination of genomic (G) and pedigree relationships for all (A) and genotyped animals (A22). The procedure implemented in the BLUPF90 software suite first involves combining a small percentage of A22 into G (blending) to avoid singularity problems, then an adjustment to account for the fact the genetic base in G and A22 is different (tuning). However, blending before tuning may not reflect the actual difference between pedigree and genomic base because the blended matrix already contains a portion of A22. The objective of this study was to evaluate the impact of tuning before blending on predictivity, bias, and inflation of GEBV, indirect predictions (IP), and SNP effects from ssGBLUP using American Angus and US Holstein data. We used four different scenarios to obtain genomic predictions: BlendFirst_TunedG2, TuneFirst_TunedG2, BlendFirst_TunedG4, and TuneFirst_TunedG4. TunedG2 adjusts mean diagonals and off-diagonals of G to be similar to the ones in A22, whereas TunedG4 adjusts based on the fixation index. Over 6 million growth records were available for Angus and 5.9 million udder depth records for Holsteins. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Predictivity and reliability were obtained for 19,056 and 1,711 validation Angus and Holsteins, respectively. We observed the same predictivity and reliability for GEBV or IP in all four scenarios, ranging from 0.47 to 0.60 for Angus and was 0.67 for Holsteins. Slightly less bias was observed when tuning was done before blending. Correlation of SNP effects between scenarios was > 0.99. Refined tuning before blending had no impact on GEBV and marginally reduced the bias. This option will be implemented in the BLUPF90 software suite.

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