Dataset Information

Linkage analysis between dominant and co-dominant makers in full-sib families of out-breeding species.

ABSTRACT: As high-throughput genomic tools, such as the DNA microarray platform, have lead to the development of novel genotyping procedures, such as Diversity Arrays Technology (DArT) and Single Nucleotide Polymorphisms (SNPs), it is likely that, in the future, high density linkage maps will be constructed from both dominant and co-dominant markers. Recently, a strictly genetic approach was described for estimating recombination frequency (r) between co-dominant markers in full-sib families. The complete set of maximum likelihood estimators for r in full-sib families was almost obtained, but unfortunately, one particular configuration involving dominant markers, segregating in a 3:1 ratio and co-dominant markers, was not considered. Here we add nine further estimators to the previously published set, thereby making it possible to cover all combinations of molecular markers with two to four alleles (without epistasis) in a full-sib family. This includes segregation in one or both parents, dominance and all linkage phase configurations.

SUBMITTER: Alves AA

PROVIDER: S-EPMC3036129 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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Linkage analysis between dominant and co-dominant makers in full-sib families of out-breeding species.

Alves Alexandre Alonso AA Bhering Leonardo Lopes LL Cruz Cosme Damião CD Alfenas Acelino Couto AC

Genetics and molecular biology 20100701 3

As high-throughput genomic tools, such as the DNA microarray platform, have lead to the development of novel genotyping procedures, such as Diversity Arrays Technology (DArT) and Single Nucleotide Polymorphisms (SNPs), it is likely that, in the future, high density linkage maps will be constructed from both dominant and co-dominant markers. Recently, a strictly genetic approach was described for estimating recombination frequency (r) between co-dominant markers in full-sib families. The complete ...[more]

PMID: 21637424

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Project description:Key messageGenomic prediction of GCA effects based on model training with full-sib rather than half-sib families yields higher short- and long-term selection gain in reciprocal recurrent genomic selection for hybrid breeding, if SCA effects are important. Reciprocal recurrent genomic selection (RRGS) is a powerful tool for ensuring sustainable selection progress in hybrid breeding. For training the statistical model, one can use half-sib (HS) or full-sib (FS) families produced by inter-population crosses of candidates from the two parent populations. Our objective was to compare HS-RRGS and FS-RRGS for the cumulative selection gain ([Formula: see text]), the genetic, GCA and SCA variances ([Formula: see text],[Formula: see text], [Formula: see text]) of the hybrid population, and prediction accuracy ([Formula: see text]) for GCA effects across cycles. Using SNP data from maize and wheat, we simulated RRGS programs over 10 cycles, each consisting of four sub-cycles with genomic selection of [Formula: see text] out of 950 candidates in each parent population. Scenarios differed for heritability [Formula: see text] and the proportion [Formula: see text] of traits, training set (TS) size ([Formula: see text]), and maize vs. wheat. Curves of [Formula: see text] over selection cycles showed no crossing of both methods. If [Formula: see text] was high, [Formula: see text] was generally higher for FS-RRGS than HS-RRGS due to higher [Formula: see text]. In contrast, HS-RRGS was superior or on par with FS-RRGS, if [Formula: see text] or [Formula: see text] and [Formula: see text] were low. [Formula: see text] showed a steeper increase and higher selection limit for scenarios with low [Formula: see text], high [Formula: see text] and large [Formula: see text]. [Formula: see text] and even more so [Formula: see text] decreased rapidly over cycles for both methods due to the high selection intensity and the role of the Bulmer effect for reducing [Formula: see text]. Since the TS for FS-RRGS can additionally be used for hybrid prediction, we recommend this method for achieving simultaneously the two major goals in hybrid breeding: population improvement and cultivar development.

Project description:We combined heritability analysis of larval development rate with a global expression analysis of this phenotype to investigate genotype by environment interactions across three ecologically relevant temperatures in the Glanville fritillary butterfly (Melitaea cinxia). We focused upon the development of final instar caterpillars which is greatly affected by temperature, and during this stage the caterpillars build up most of the resources for adult life. Second generation, lab reared larvae, initially collected from the Åland metapopulation, were reared in standard lab condition until 6th larval instar. At the beginning of the final (7th) instar stage the larvae were separated into of three temperature conditions: Cold treatment (temperature profile: 8°C 18:00-9:59, 14°C 10:00-11:59, 20°C 12:00-15:59 and 14°C 16:00-17:59) Standard treatment (temperature profile: 15°C 17:00-6:59, 18°C 7:00-8:59, 22°C 9:00-10:59 and 26°C 11:00-16:59) Hot treatment (temperature profile: 8°C 20:00-7:59, 15°C 8:00-9:59, 35°C 10:00-17:59 and 15°C 18:00-19:59) The temperature profiles mimic the diurnal thermal variation of the natural habitat (Åland islands) of samples. Cold treatment mimics a cool and cloudy summer, Standard represents an average temperature profile in the Åland islands and Hot treatment mimics an exceptionally hot and sunny summer, with cold night-time temperatures. The experiment contained several larval families (full-sib) of which three were selected for gene expression analysis. Samples were snap-frozen in liquid nitrogen during mid-development (after 6, 5 and 4 days, for Cold, Standard and Hot respectively). Additional larvae from the same treatments were assayed for survival and growth. Gene expression was analyzed using a mixed model approach to identify genes with potential heritable expression variation (variation among families), genes with plastic expression responses (treatment induced changes) and genes with treatment dependent expression that varies among families (family by treatment interactions).

Project description:We combined heritability analysis of larval development rate with a global expression analysis of this phenotype to investigate genotype by environment interactions across three ecologically relevant temperatures in the Glanville fritillary butterfly (Melitaea cinxia). We focused upon the development of final instar caterpillars which is greatly affected by temperature, and during this stage the caterpillars build up most of the resources for adult life. Second generation, lab reared larvae, initially collected from the M-CM-^Eland metapopulation, were reared in standard lab condition until 6th larval instar. At the beginning of the final (7th) instar stage the larvae were separated into of three temperature conditions: Cold treatment (temperature profile: 8M-BM-0C 18:00-9:59, 14M-BM-0C 10:00-11:59, 20M-BM-0C 12:00-15:59 and 14M-BM-0C 16:00-17:59) Standard treatment (temperature profile: 15M-BM-0C 17:00-6:59, 18M-BM-0C 7:00-8:59, 22M-BM-0C 9:00-10:59 and 26M-BM-0C 11:00-16:59) Hot treatment (temperature profile: 8M-BM-0C 20:00-7:59, 15M-BM-0C 8:00-9:59, 35M-BM-0C 10:00-17:59 and 15M-BM-0C 18:00-19:59) The temperature profiles mimic the diurnal thermal variation of the natural habitat (M-CM-^Eland islands) of samples. Cold treatment mimics a cool and cloudy summer, Standard represents an average temperature profile in the M-CM-^Eland islands and Hot treatment mimics an exceptionally hot and sunny summer, with cold night-time temperatures. The experiment contained several larval families (full-sib) of which three were selected for gene expression analysis. Samples were snap-frozen in liquid nitrogen during mid-development (after 6, 5 and 4 days, for Cold, Standard and Hot respectively). Additional larvae from the same treatments were assayed for survival and growth. Gene expression was analyzed using a mixed model approach to identify genes with potential heritable expression variation (variation among families), genes with plastic expression responses (treatment induced changes) and genes with treatment dependent expression that varies among families (family by treatment interactions). Full-sib larvae from three families (N170, N74 and O171) were exposed to three temperature treatments (Cold, Standard and Hot) during final (7th) instar stage. A total of 35 samples were used to analyze family, treatment and family by treatment interactions in gene expression, using a mixed model approach. This included 3 biological replicates in Cold and Hot treatments from each family and 5-6 biological replicates in Standard (5 in O171) per family. Techinal replicates from each family and additional techical replicates in family O171 (including dye swap replicates) were used to assess robustness of the findings.

Dataset Information

Linkage analysis between dominant and co-dominant makers in full-sib families of out-breeding species.

Publications

Linkage analysis between dominant and co-dominant makers in full-sib families of out-breeding species.

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