Selection plans in plant and animal breeding are driven by genetic evaluation. Recent developments suggest using massive genetic marker information, known as “genomic selection.” There is little evidence of its performance, though. We empirically compared three strategies for selection: (1) use of pedigree and phenotypic information, (2) use of genomewide markers and phenotypic information, and (3) the combination of both. We analyzed four traits from a heterogeneous mouse population (http://gscan.well.ox.ac.uk/), including 1884 individuals and 10,946 SNP markers. We used linear mixed models, using extensions of association analysis. Cross-validation techniques were used, providing assumption-free estimates of predictive ability. Sampling of validation and training data sets was carried out across and within families, which allows comparing across- and within-family information. Use of genomewide genetic markers increased predictive ability up to 0.22 across families and up to 0.03 within families. The latter is not statistically significant. These values are roughly comparable to increases of up to 0.57 (across family) and 0.14 (within family) in accuracy of prediction of genetic value. In this data set, within-family information was more accurate than across-family information, and populational linkage disequilibrium was not a completely accurate source of information for genetic evaluation. This fact questions some applications of genomic selection.

background

https://www.genetics.org/content/genetics/180/1/611.full.pdf

Importance and implementation of molecular markers in selective breeding programs for aquaculture species.

Performance of Genomic Selection in Mice

background or methods

Marker-assisted selection in fish and shellfish breeding schemes.

ABSTRACT Haliotis midae, is the only commercially important species of the six abalone species found in South African coastal waters and has become a lucrative commercial commodity. Wild stocks of H. midae are, however, no longer commercially sustainable due to a combination of environmental factors and poaching. The solution to the crisis is artificial production systems in the form of abalone farms. An abalone enhancement programme was initiated in South Africa in 2006, funded by industry and government. This programme focuses on the elucidation of the abalone genome and genetic factors contributing to increased productivity, thereby aiding the commercial production of abalone.Haliotis midae, is the only commercially important species of the six abalone species found in South African coastal waters and has become a lucrative commercial commodity. Wild stocks of H. midae are, however, no longer commercially sustainable due to a combination of environmental factors and poaching. The solution to the crisis is artificial production systems in the form of abalone farms. An abalone enhancement programme was initiated in South Africa in 2006, funded by industry and government. This programme focuses on the elucidation of the abalone genome and genetic factors contributing to increased productivity, thereby aiding the commercial production of abalone. The aims of this study, the first of its kind concerning H. midae, were to develop AFLPbased markers (specifically fluorescent AFLP analysis); to monitor the segregation of these markers in a single full-sib family and to use the markers and additional microsatellite markers to generate the first preliminary linkage map for H. midae. Genomic DNA of sufficient quality and purity for fluorescent AFLP analysis was obtained from 3.5-month-old H. midae juveniles. Preliminary linkage maps were constructed using AFLP and microsatellite markers segregating in an F1 family following a pseudo-testcross mapping strategy. Twelve AFLP primer combinations, producing 573 segregating peaks, and 10 microsatellite markers were genotyped in the parents and 108 progeny of the mapping family. Of the 573 segregating AFLP peaks genotyped, 241 segregated in a 1:1 ratio and 332 in a 3:1 ratio. Of these AFLP markers, 90 segregated according to the expected 1:1 Mendelian ratio and 164 segregated according to the expected 3:1 Mendelian ratio at the P = 0.05 level and were used for linkage analysis. Of the 10 microsatellite markers genotyped, nine were informative for linkage mapping analysis. Preliminary male and female genetic linkage maps were developed using markers segregating in the female or male parent. A total of 12 and 10 linkage groups were detected for the female and male maps respectively. The female map covered 1473.5cM and consisted of 56 markers, and the male map covered 738.9cM consisting of 30 markers. Markers with segregation distortion were observed as previously reported in other abalone species and potential homology between one of the linkage groups of the Stellenbosch University http://scholar.sun.ac.za

Importance and implementation of molecular markers in selective breeding programs for aquaculture species.

Citations

Performance of Genomic Selection in Mice

Marker-assisted selection in fish and shellfish breeding schemes.

Development of AFLP markers for Haliotis midae for linkage mapping

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