Elite Breeding Populations Research Articles

Development of a recurrent apple breeding programme in New Zealand: a synthesis of results, and a proposed revised breeding strategy

This paper describes an apple breeding population that has been developed in New Zealand since 1990 to broaden the genetic base for cultivar breeding. The population is now in its third generation, with recurrent selection for general combining ability being the underlying approach. During the 20 years of the programme, nearly 1,000 trees have been progeny tested. An early focus on selection within open-pollinated tests has been replaced by selection within control-pollinated tests. Genetic evaluation methods along with estimates of genetic parameters (e.g. heritability, genetic correlations, and genotype-by-environment interactions), genetic gain, and genetic diversity are summarised in this paper. The third-generation crossing programme involving nearly 350 parents is almost completed and seedlings from these crosses are in the nursery. In the revised breeding strategy, three hierarchal populations are envisioned to better integrate this broad-based population with the more commercially focused cultivar breeding programme: main breeding population (MBP), elite breeding populations (EBP) and cultivar development populations (CDP). A two-subline structure and a minimum of two crosses per parent will be implemented in the MBP. EBP will focus on developing parents for breeding goals of the CDP. Forward-selected (based on estimated breeding values) candidates from the main- and elite populations will be used as parents of the CDP. Cloning of seedlings in elite populations and also in the first-stage of cultivar development, will be investigated as a tool for enhancing predictability and shortening the cycle for delivering genetic gain.

Deterministic Simulation of Gains for Seedling and Cloned Main and Elite Breeding Populations of Pinus radiata and Implications for Strategy

Abstract Genetic gains in breast-height diameter were estimated using deterministic simulation. Simulations of gain from one generation of selection were undertaken in large Main and small Elite breeding populations for a range of heritabilities, with varying numbers of parents, families, seedlings/family, clones/family and ramets/ clone to aid revision of the New Zealand Pinus radiata breeding strategy. Cloned versus seedling populations of equal numbers of plants were simulated, derived from open pollination, polycrossing, and pair crossing. Balanced within-family selection was used for 200, 400 and 800-parent Main breeding populations and among- and within-family selection for 25-parent Elite populations of 25 up to 100 full-sib families. Predicted gains from within-family selection in the Main population were highest from cloned polycross families at all heritabilities and lowest for seedling fullsib families. Gains from cloned populations were higher than seedling equivalents at heritabilities ≤0.5, and their advantage in gain was greatest at lower heritabilities. Elite populations of 25 parents showed similar trends but intensive among- and within-family selection resulted in much higher gains than from the Main, highest from the cloned options. The increase in gain with increased number of families diminished with more than 2-3 times as many families as parents. A new strategy was proposed for P. radiata, based on the simulation results, involving an expanded Main breeding population of open-pollinated (OP) seedling families, together with pair-cross family seedlots already available, supported by parentage reconstruction using DNA markers. Forwards selection in small cloned Elite populations was proposed as the main source of seed orchard clones.

Molecular Markers in a Commercial Breeding Program

ABSTRACTIn the 1980s, DNA‐based molecular markers were identified as having the potential to enhance corn (Zea mays L.) breeding. Research has demonstrated the advantage of using molecular markers for selection of simply inherited traits, however only a few studies have evaluated the potential to enhance genetic gain for quantitative traits. In the late 1990s, Monsanto decided to implement marker assisted selection for quantitative traits in our global plant breeding programs. We built genotyping systems and information tools and developed marker assisted methodologies that increased the mean performance in elite breeding populations.

The Noble Foundation hardinggrass (Phalaris aquatica) breeding program

Hardinggrass has the potential to provide grazing during the fall to spring months in the south central USA. Here we describe a breeding program focused on developing improved hardinggrass cultivars for this region. More than 300 accessions were evaluated for persistence under heavy grazing in Oklahoma. The most promising of these accessions were evaluated for genetic diversity using AFLP markers. Accessions clustered closely in agreement with geographic origins with populations from Morocco representing a potentially novel source of germplasm. Two distinct breeding populations were constructed using this information. Additional populations, constructed using recurrent selection for survival under heavy grazing, have shown significantly greater persistence than currently available cultivars including 'Grasslands Maru'. Research is underway to develop high throughput methods to profile alkaloid composition and concentration in hardinggrass. These methods will be applied to determine genotype and genotype x environment effects on alkaloid composition of elite breeding populations and commercial cultivars. Results of these evaluations, along with animal safety trials, will be critical in determining which populations to release as improved hardinggrass cultivars for the south central USA.

Power of Microsatellite Markers for Fingerprinting and Parentage Analysis in Eucalyptus grandis Breeding Populations

We report the genetic analysis of 192 unrelated individuals of an elite breeding population of Eucalyptus grandis (Hill ex Maiden) with a selected set of six highly polymorphic microsatellite markers developed for species of the genus Eucalyptus. A full characterization of this set of six loci was carried out generating allele frequency distributions that were used to estimate parameters of genetic information content of these loci, including expected heterozygosity, polymorphism information content (PIC), power of exclusion, and probability of identity. The number of detected alleles per locus ranged from 6 to 33, with an average of 19.8 +/- 9.2. The average expected heterozygosity was 0.86 +/- 0.11 and the average PIC was 0.83 +/- 0.16. Using only three loci, it was possible to discriminate all 192 individuals. The overall probability of identity considering all six EMBRA microsatellite markers combined was lower than 1 in 2 billion. An analysis of the sample size necessary to estimate expected heterozygosity with minimum variance indicated that at least 64 individuals have to be genotyped to characterize this parameter with adequate accuracy for most microsatellites in Eucalyptus. The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide an extremely powerful system for the unique identification of Eucalyptus individuals for fingerprinting purposes and parentage testing.

Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags

Single nucleotide polymorphisms SNPs are useful for characterizing allelic variation, for genome-wide mapping, and as a tool for marker-assisted selection. Discovery of SNPs through de novo sequencing is inefficient within cultivated tomato Lycopersicon esculentum Mill. because the polymorphism rate is more than ten-fold lower than the sequencing error rate. The availability of expressed sequence tag EST data has made it feasible to discover putative SNPs “in silico” prior to experimental verification. By exploiting redundancy among EST data available for different varieties among 148,373 tomato ESTs, we have identified candidate SNPs for use within cultivated germplasm pools. 1,245 contigs having three EST sequences of Rio Grande and three EST sequences of TA496 were used for SNP discovery. We detected 1 SNP for every 8,500 bases analyzed, with 101 candidate SNPs in 44 genes identified. Sixty-six SNPs could be recognized by restriction enzymes, and subsequent experimental verification using restriction digestion or CEL I digestion confirmed 83% of the putative polymorphisms tested. SNPs between TA496 and Rio Grande have a high probability 53% of detecting polymorphisms between other L. esculentum varieties. Twenty-six SNPs in 18 unigenes were mapped to specific chromosomes. Two SNPs, LEOH23 and LEOH37, were shown to be linked to quantitative trait loci contributing to fruit color within elite breeding populations. These results suggest that the growing databases of DNA sequence will yield information that facilitates improvement within the germplasm pools that have contributed to productive modern varieties.

Exploiting Heterosis in Pearl Millet for Population Breeding in Arid Environments

In the desert region of Rajasthan, India, farmers mainly grow pearl millet [Pennisetum glaucum (L.) R. Br.] landraces. The adoption of modern cultivars is generally low because of their poor adaptation to extreme drought stress. The objective of this study was to evaluate the performance of six elite breeding populations and three landraces and to determine the heterotic pattern among the 36 diallel crosses of those populations. Field experiments were conducted in eight environments in India. Mean grain yields (GYs) in the three environments with favorable growing conditions were double to threefold those in the three arid environments. The elite populations generally showed higher GY than the landraces; stover yield (SY) was similar in both population types. The landraces flowered earlier, had a higher tillering potential, and smaller seeds. Mean level of midparent heterosis was generally low, ranging from 0.85% for time to flowering (TF) to 6.57% for SY. For GY, expression of heterosis for individual population crosses was between −14 and +30% under drought stress, and between −9 and +17% in the favorable environments. For SY, mean heterosis was always positive and higher than for GY. The elite × landrace population crosses with high mean GY and high levels of heterosis under drought stress could be beneficial to widen the germplasm base and to combine the high yield potential of elite materials with the good adaptation of the landraces.

Exploiting Heterosis in Pearl Millet for Population Breeding in Arid Environments

In the desert region of Rajasthan, India, farmers mainly grow pearl millet [Pennisetum glaucum (L.) R. Br.] landraces. The adoption of modern cultivars is generally low because of their poor adaptation to extreme drought stress. The objective of this study was to evaluate the performance of six elite breeding populations and three landraces and to determine the heterotic pattern among the 36 diallel crosses of those populations. Field experiments were conducted in eight environments in India. Mean grain yields (GYs) in the three environments with favorable growing conditions were double to threefold those in the three arid environments. The elite populations generally showed higher GY than the landraces; stover yield (SY) was similar in both population types. The landraces flowered earlier, had a higher tillering potential, and smaller seeds. Mean level of midparent heterosis was generally low, ranging from 0.85% for time to flowering (TF) to 6.57% for SY. For GY, expression of heterosis for individual population crosses was between −14 and +30% under drought stress, and between −9 and +17% in the favorable environments. For SY, mean heterosis was always positive and higher than for GY. The elite × landrace population crosses with high mean GY and high levels of heterosis under drought stress could be beneficial to widen the germplasm base and to combine the high yield potential of elite materials with the good adaptation of the landraces.

Changes in genetic diversity during seven cycles of recurrent selection for grainyield in oat, Avena sativa L.

AbstractVariability for desirable alleles within elite breeding populations is a requirement for long‐term genetic improvement. Changes in genetic diversity were evaluated in a recurrent selection programme for enhanced grain yield in oat, Avena sativa L., using coefficient of parentage (rp) and restriction fragment length polymorphism (RFLP) based genetic similarity (S) estimates. Both rp and s increased during seven cycles of recurrent selection, indicating a reduction in the level of genetic diversity within the population. The relationship between genetic diversity and agronomic performance was also examined. Genetic similarity measures were poor predictors of the near‐homozygous progeny performance and general and specific combining ability effects for three agronomic traits in the recurrent selection programme. In addition, there was no apparent trend for preferential selection of progeny from either more similar or more diverse parents within a given cycle of selection. The overall reduction in genetic diversity in this population has not affected selection response for grain yield. Variability remaining at important loci or de novo variation are possible explanations for the continued selection progress.

RANDOMLY AMPLIFIED POLYMORPHIC DNA (RAPDs) IN OCTOPLOID FRAGARIA

We have been screening Fragaria chiloensis, F. virginiana and elite breeding populations of F. × ananassa for polymorphisms using PCR and random 10 base sequences. Over 60% of the primers result in fragments that distinguish between the various genotypes. Many of them segregate as alleles at a single locus. This technology shows high promise as a means of distinguishing cultivars and developing a genetic map to aid in breeding.