Consistency of linkage disequilibrium between Chinese and Nordic Holsteins and genomic prediction for Chinese Holsteins using a joint reference population

Zhou, Lei; Ding, Xiangdong; Zhang, Qin; Wang, Yachun; Lund, Mogens Sandø; Su, Guosheng

doi:10.1186/1297-9686-45-7

Cited by 45 publications

(56 citation statements)

References 19 publications

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“…So far, studies of the extent of LD have been reported mostly for dairy and beef cattle breeds under selection, but there is little information about the degree of genome-wide LD in local cattle breeds and populations. Considering the LD levels between adjacent markers, the average r 2 in the MOD breed was comparable to those reported for] indigenous Swiss Eringer (r 2 = 0.24; Flury et al, 2010), Blonde d'Aquitaine (r 2 = 0.20; Beghain et al, 2013), and Chinese and Nordic Holsteins (r 2 = 0.20 and 0.21, respectively; Zhou et al, 2013), whereas the CIN breed had lower values. The results may be explained by considering the influence of selection on LD; in fact, the CIN breed is not subject to breeding programs, whereas the MOD breed is characterized by low selection pressure.…”

Section: Linkage Disequilibriumsupporting

confidence: 76%

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Mastrangelo

Saura

Tolone

et al. 2014

Journal of Animal Science

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ABSTRACT:Genomic technologies, such as highthroughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (N e ), and the patterns of linkage disequilibrium (LD) in 2 economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus taurus from Eurasia and formed nonoverlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to the CIN breed showed a lower value of assignment, the presence of substructure, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of N e were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r 2 in the MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these 2 local cattle breeds.

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Section: Linkage Disequilibriumsupporting

confidence: 76%

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Mastrangelo

Saura

Tolone

et al. 2014

Journal of Animal Science

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“…When combining Holstein Friesian (HF) populations large improvements were realized in North American studies (Schenkel et al, 2009;Vanraden et al, 2012) and in the EuroGenomics collaboration . As an example of a small HF population, genomic predictions for Chinese HF using a joint reference with Nordic HF increases accuracies substantially (Zhou et al, 2013). This could be regarded as more surprising since environmental and management factors are very different between Chinese and Nordic Holstein populations.…”

Section: Reliability Of Gebvs In Relation To Genomic Relationshipmentioning

confidence: 99%

Review: How to improve genomic predictions in small dairy cattle populations

Lund

Berg

et al. 2016

Animal

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This paper reviews strategies and methods to improve accuracies of genomic predictions from the perspective of a numerically small population. Improvements are realized by influencing one or both of the main factors: (1) improve or increase genomic connections to phenotypic records in training data. (2) Models and strategies to focus genomic predictions on markers closer to the causative variants. Combining populations into a joint reference population results in high improvements when combining populations of the same breed and diminishes as the genetic distance between populations increases. For distantly related breeds sophisticated Bayesian variable selection models in combination with denser markers sets or functional subsets of markers is needed. This is expected to be further improved by the efficient use of sequence information. In addition predictions can be improved by the use of phenotypes of genotyped and non-genotyped cows directly. For a small population the optimal approach will combine the above components.

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“…In terms of genomic prediction accuracy, the results of these studies vary widely. The reported increase in accuracy has reached up to 32% (Zhou et al, 2013), but also losses in reliability have been observed when using joint reference populations (e.g. Erbe et al, 2012).…”

Section: Combining Populations From Different Countries or Different mentioning

confidence: 99%

“…Sharing genotypes has been shown to be especially profitable if one population has a very small size. Zhou et al (2013) increased nearly four times the Chinese Holstein Friesian reference population by adding Nordic reference animals. They gained an increase in reliability between 25% and 32% for milk performance traits.…”

Section: Combining Populations From Different Countries or Different mentioning

confidence: 99%

“…Thus, it accounts for interactions between marker and breed as well as for interactions between marker and environment interaction . Multi-trait GBLUP model have been applied in several studies on multi-breed reference populations in dairy cattle (Karoui et al, 2012;Zhou et al, 2013;Haile-Mariam et al, 2015). For production traits analyzed in three different US-American dairy cattle populations, the gain in accuracy was very small (0% to 3%), predictions resulting from multi-trait compared with those from single trait model .…”

Section: Combining Populations From Different Countries or Different mentioning

confidence: 99%

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Review: Opportunities and challenges for small populations of dairy cattle in the era of genomics

Schöpke¹,

Swalve

2016

Animal

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In modern dairy cattle breeding, genomic breeding programs have the potential to increase efficiency and genetic gain. At the same time, the requirements and the availability of genotypes and phenotypes present a challenge. The set-up of a large enough reference population for genomic prediction is problematic for numerically small breeds but also for hard to measure traits. The first part of this study is a review of the current literature on strategies to overcome the lack of reference data. One solution is the use of combined reference populations from different breeds, different countries, or different research populations. Results reveal that the level of relationship between the merged populations is the most important factor. Compiling closely related populations facilitates the accurate estimation of marker effects and thus results in high accuracies of genomic prediction. Consequently, mixed reference populations of the same breed, but from different countries are more promising than combining different breeds, especially if those are more distantly related. The use of female reference information has the potential to enlarge the reference population size. Including females is advisable for small populations and difficult traits, and maybe combined with genotyping females and imputing those that are un-genotyped.The efficient use of imputation for un-genotyped individuals requires a set of genotyped related animals and well-considered selection strategies which animals to choose for genotyping and phenotyping. Small populations have to find ways to derive additional advantages from the cost-intensive establishment of genomic breeding schemes. Possible solutions may be the use of genomic information for inbreeding control, parentage verification, within-herd selection, adjusted mating plans or conservation strategies.The second part of the paper deals with the issue of high-quality phenotypes against the background of new, difficult and hard to measure traits. The use of contracted herds for phenotyping is recommended, as additional traits, when compared to standard traits used in dairy cattle breeding can be measured at set moments in time. This can be undertaken even for the recording of health traits, thus resulting in complete contemporary groups for health traits. Future traits to be recorded and used in genomic breeding programs, at least partly will be traits for which traditional selection based on widespread phenotyping is not possible. Enabling phenotyping of sufficient numbers to enable genomic selection will rely on cooperation between scientists from different disciplines and may require multidisciplinary approaches.

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Consistency of linkage disequilibrium between Chinese and Nordic Holsteins and genomic prediction for Chinese Holsteins using a joint reference population

Cited by 45 publications

References 19 publications

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Review: How to improve genomic predictions in small dairy cattle populations

Review: Opportunities and challenges for small populations of dairy cattle in the era of genomics

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