Mating design

Abstract: Domestication and the Application of Genetic Improvement in Aquaculture.- The Success of Selective Breeding in Aquaculture.- The Theoretical Basis for Breeding and Selection.- Initiating Breeding Programs.- Breeding Strategies.- Selection Methods.- Mating Design.- Estimation of Breeding Values.- Genotype-Environment Interaction.- Measuring Response to Selection.- Structure of Breeding Programs.- Undesirable Side Effects in Breeding Programs.- Biotechnology in Breeding Programs.- Reproduction Techniques.- Economic Benefits of Breeding Programs.

Abstract: Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3–4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.

Abstract: Preface. 1. Genetic Foundations: The Historical Setting. Part One: Quantitative Variation: Its Detection, Estimation and Utilization. 2. Genetic Models and their Predictive Value. 3. Experimental Mating Designs: An Assessment of their Use and Efficiency in Breeding Programs. 4. The Diallel Cross: The Ultimate Mating Design? 5. Selection with and without Competition. Part Two: Genotype and Environment: Their Interrelationships. 6. Genotype-Environment Interactions: Analysis and Problems. 7. Stability, Adaptability and Adaptation. 8. Breeding for Biotic and Abiotic Stress. 9. Genetic Resources, Genetic Diversity and Ecogeographic Breeding. Index.

Abstract: The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial cultivars at a very early stage. Thus GS has the potential to accelerate breeding efficiency significantly because of decreased generation interval or increased selection intensity. We evaluated the accuracy of GS in a population of 1120 seedlings generated from a factorial mating design of four females and two male parents. All seedlings were genotyped using an Illumina Infinium chip comprising 8,000 single nucleotide polymorphisms (SNPs), and were phenotyped for various fruit quality traits. Random-regression best liner unbiased prediction (RR-BLUP) and the Bayesian LASSO method were used to obtain GEBV, and compared using a cross-validation approach for their accuracy to predict unobserved BLUP-BV. Accuracies were very similar for both methods, varying from 0.70 to 0.90 for various fruit quality traits. The selection response per unit time using GS compared with the traditional BLUP-based selection were very high (>100%) especially for low-heritability traits. Genome-wide average estimated linkage disequilibrium (LD) between adjacent SNPs was 0.32, with a relatively slow decay of LD in the long range (r2 = 0.33 and 0.19 at 100 kb and 1,000 kb respectively), contributing to the higher accuracy of GS. Distribution of estimated SNP effects revealed involvement of large effect genes with likely pleiotropic effects. These results demonstrated that genomic selection is a credible alternative to conventional selection for fruit quality traits.