Estimating heritability using family-pooled phenotypic and genotypic data: a simulation study applied to aquaculture.

Estimating heritability based on individual phenotypic and genotypic measurements can be expensive and labour-intensive in commercial aquaculture breeding. Here, the feasibility of estimating heritability using within-family means of phenotypes and allelic frequencies was investigated. Different numbers of full-sib families and family sizes across ten generations with phenotypic and genotypic information on 10 K SNPs were analysed in ten replicates. Three scenarios, representing differing numbers of pools per family (one, two and five) were considered. The results showed that using one pool per family did not reliably estimate the heritability of family means. Using simulation parameters appropriate for aquaculture, at least 200 families of 60 progeny per family divided equally in two pools per family was required to estimate the heritability of family means effectively. Although application of five pools generated more within- and between- family relationships, it reduced the number of individuals per pool and increased within-family residual variation, hence, decreased the heritability of family means. Moreover, increasing the size of pools resulted in increasing the heritability of family means towards one. In addition, heritability of family mean estimates were higher than family heritabilities obtained from Falconer's formula due to lower intraclass correlation estimate compared to the coefficient of relationship.

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep.

BACKGROUND: Discerning the traits evolving under neutral conditions from those traits evolving rapidly because of various selection pressures is a great challenge. We propose a new method, composite selection signals (CSS), which unifies the multiple pieces of selection evidence from the rank distribution of its diverse constituent tests. The extreme CSS scores capture highly differentiated loci and underlying common variants hauling excess haplotype homozygosity in the samples of a target population. RESULTS: The data on high-density genotypes were analyzed for evidence of an association with either polledness or double muscling in various cohorts of cattle and sheep. In cattle, extreme CSS scores were found in the candidate regions on autosome BTA-1 and BTA-2, flanking the POLL locus and MSTN gene, for polledness and double muscling, respectively. In sheep, the regions with extreme scores were localized on autosome OAR-2 harbouring the MSTN gene for double muscling and on OAR-10 harbouring the RXFP2 gene for polledness. In comparison to the constituent tests, there was a partial agreement between the signals at the four candidate loci; however, they consistently identified additional genomic regions harbouring no known genes. Persuasively, our list of all the additional significant CSS regions contains genes that have been successfully implicated to secondary phenotypic diversity among several subpopulations in our data. For example, the method identified a strong selection signature for stature in cattle capturing selective sweeps harbouring UQCC-GDF5 and PLAG1-CHCHD7 gene regions on BTA-13 and BTA-14, respectively. Both gene pairs have been previously associated with height in humans, while PLAG1-CHCHD7 has also been reported for stature in cattle. In the additional analysis, CSS identified significant regions harbouring multiple genes for various traits under selection in European cattle including polledness, adaptation, metabolism, growth rate, stature, immunity, reproduction traits and some other candidate genes for dairy and beef production. CONCLUSIONS: CSS successfully localized the candidate regions in validation datasets as well as identified previously known and novel regions for various traits experiencing selection pressure. Together, the results demonstrate the utility of CSS by its improved power, reduced false positives and high-resolution of selection signals as compared to individual constituent tests.

Detection of carrier Booroola (FecB) allele in BMPR1B gene of MEGA (Merino × Garut) sheep and its association with growth traits.

BACKGROUND: Bone morphogenetic protein receptor 1B (BMPR1B) gene is one of candidate genes for reproductive and growth traits in sheep. The present study was aimed to detect the Booroola (FecB) allele in BMPR1B gene and its association with growth traits in MEGA (Merino × Garut) sheep. A total of 82DNA samples collected from individual lamb (mixed-sex) blood were genotyped for allelic polymorphism using a PCR-RFLP method. RESULTS: The PCR analysis in BMPR1B gene resulted the amplicons with size of140 bp. The RFLP analysis with AvaII restriction enzymeresultedtwo allelic types of wildtype (A/Fec+) and mutant or Booroola (G/FecB) with frequency of 0.89 and 0.11, respectively. However, the genetic diversity in BMPR1B/AvaII gene of animal studies was categorized tolow category (PIC = 0.18)and under in a genetic equilibrium (χ2 = 1.25). CONCLUSIONS: Itshowed us that carrying FecB allele in the heterozygous sheep were not associated with growth traits in MEGA sheep.