Dataset Information

Simulation-based optimization of genomic selection scheme for accelerating genetic gain while preventing inbreeding depression in onion breeding.

ABSTRACT: Genomic selection (GS) is being increasingly employed in plant breeding programs to accelerate genetic gain of economically important traits. However, its efficiency differs greatly across species, due to differences in reproduction and breeding strategies. Onion (Allium cepa L.) is an out-crossing crop but can be easily self-pollinated. High inbreeding depression occurs, and contamination of self-pollinated seeds is unavoidable in onion breeding. Taking this into consideration, 10-year breeding programs with and without GS were simulated. In addition to general GS, we proposed GS schemes to prevent inbreeding depression by avoiding co-selection of close relatives and combining the shortening of generation time and updating of the prediction model. The results showed that general GS with shortening of generation time yielded the highest genetic gain among the selection schemes in early years. However, inbreeding increased rapidly, reaching very high levels in later years. The proposed GS combining shortening of generation time with updating of the prediction model was superior to the others in later years, as it yielded relatively high genetic gain while maintaining significantly low levels of inbreeding. These results suggested that GS can be beneficial in onion breeding, and an optimal scheme should be selected depending on the selection period.

SUBMITTER: Sekine D

PROVIDER: S-EPMC7878936 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Simulation-based optimization of genomic selection scheme for accelerating genetic gain while preventing inbreeding depression in onion breeding.

Sekine Daisuke D Yabe Shiori S

Breeding science 20201117 5

Genomic selection (GS) is being increasingly employed in plant breeding programs to accelerate genetic gain of economically important traits. However, its efficiency differs greatly across species, due to differences in reproduction and breeding strategies. Onion (<i>Allium cepa</i> L.) is an out-crossing crop but can be easily self-pollinated. High inbreeding depression occurs, and contamination of self-pollinated seeds is unavoidable in onion breeding. Taking this into consideration, 10-year b ...[more]

PMID: 33603556

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Project description:Faba bean is a cool-season grain legume crop, which is grown worldwide for food and feed. Despite a decrease in area under faba bean in the past, the interest in growing faba bean is increasing globally due to its high seed protein content and its excellent ecological service. The crop is, however, exposed to diverse biotic and abiotic stresses causing unstable, low grain yield. Although, sources of resistance to main diseases, such as ascochyta blight (Ascochyta fabae Speg.), rust (Uromyces viciae-fabae (Pers.) Schroet.), chocolate spot (Botrytis fabae Sard.) and gall disease (Physioderma viciae), have been identified, their resistance is only partial and cannot prevent grain yield losses without agronomical practices. Tightly associated DNA markers for host plant resistance genes are needed to enhance the level of resistance. Less progress has been made for abiotic stresses. Different breeding methods are proposed, but until now line breeding, based on the pedigree method, is the dominant practice in breeding programs. Nonetheless, the low seed multiplication coefficient and the requirement for growing under insect-proof enclosures to avoid outcrossing hampers breeding, along with the lack of tools such as double haploid system and cytoplasmic male sterility. This reduces breeding population size and speed of breeding hence the chances of capturing rare combinations of favorable alleles. Availability and use of the DNA markers such as vicine-convicine (vc -) and herbicide tolerance in breeding programs have encouraged breeders and given confidence in marker assisted selection. Closely linked QTL for several biotic and abiotic stress tolerance are available and their verification and conversion in breeder friendly platform will enhance the selection process. Recently, genomic selection and speed breeding techniques together with genomics have come within reach to accelerate the genetic gains in faba bean. Advancements in genomic resources with other breeding tools, methods and platforms will enable to accelerate the breeding process for enhancing genetic gain in this species.

Project description:BackgroundEfficient breeding programs are difficult to implement in honeybees due to their biological specificities (polyandry and haplo-diploidy) and complexity of the traits of interest, with performances being measured at the colony scale and resulting from the joint effects of tens of thousands of workers (called direct effects) and of the queen (called maternal effects). We implemented a Monte Carlo simulation program of a breeding plan designed specifically for Apis mellifera's populations to assess the impact of polyandry versus monoandry on colony performance, inbreeding level and genetic gain depending on the individual selection strategy considered, i.e. complete mass selection or within-family (maternal lines) selection. We simulated several scenarios with different parameter setups by varying initial genetic variances and correlations between direct and maternal effects, the selection strategy and the polyandry level. Selection was performed on colony phenotypes.ResultsAll scenarios showed strong increases in direct breeding values of queens after 20 years of selection. Monoandry led to significantly higher direct than maternal genetic gains, especially when a negative correlation between direct and maternal effects was simulated. However, the relative increase in these genetic gains depended also on their initial genetic variability and on the selection strategy. When polyandry was simulated, the results were very similar with either 8 or 16 drones mated to each queen. Across scenarios, polyandrous mating resulted in equivalent or higher gains in performance than monoandrous mating, but with considerably lower inbreeding rates. Mass selection conferred a ~ 20% increase in performance compared to within-family selection, but was also accompanied by a strong increase in inbreeding levels (25 to 50% higher).ConclusionsOur study is the first to compare the long-term effects of polyandrous versus monoandrous mating in honeybee breeding. The latter is an emergent strategy to improve specific traits, such as resistance to varroa, which can be difficult or expensive to phenotype. However, if used during several generations in a closed population, monoandrous mating increases the inbreeding level of queens much more than polyandrous mating, which is a strong limitation of this strategy.

Dataset Information

Simulation-based optimization of genomic selection scheme for accelerating genetic gain while preventing inbreeding depression in onion breeding.

Publications

Simulation-based optimization of genomic selection scheme for accelerating genetic gain while preventing inbreeding depression in onion breeding.

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