- Optimal cross selection is particularly adapted to jointly identify bridging, introduction and elite crosses to ensure an overall consistency of the genetic base broadening strategy.. - We also evaluated the effect of the training set composition on the success of. - fraction of the available crop diversity [15, 50]. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - Full list of author information is available at the end of the article. - However, in cases where the performance gap be- tween the donors released from pre-breeding and elites is too large, one may consider a buffer population be- tween donors and elites before introduction in the elite breeding population, further referred to as bridging. - GS efficiency de- pends on the relationship between individuals in the TS and the target population of individuals to predict [28, 49]. - In the context of genetic base broadening, GS is also interesting to fasten and reduce the costs for the evalu- ation and identification of genetic resources in gene banks [18, 77]. - proposed to use the optimal contribution selection to improve diversity sources while maintaining a certain level of diversity in the pre-breeding population. - Optimal contribution selection aims at identifying the optimal parental contributions to the next generation in order to maximize the expected genetic value in the pro- geny under a certain constraint on diversity. - [21] observed that allow- ing for the introductions of old individuals in the breeding population increased long-term response to selection. - UCPC based OCS differs from standard OCS in that it uses within-family variance to predict the expected mean performance and the ex- pected genetic diversity in the selected fraction of the progeny while standard OCS predicts the expected mean performance and genetic diversity in the unselected pro- geny. - Using OCS, the donor by elite crosses are selected complemen- tarily to the elite by elite crosses in order to ensure an overall consistency of the genetic base broadening strat- egy. - We considered either donors corresponding to the generation of the founders of breeding pools or im- proved varieties released 20 years ago and 5 years ago.. - Our objectives were to evaluate (i) the advantage of re- current introductions of diversity in the breeding popu- lation compared to a benchmark scenario with no introduction, (ii) the interest to conduct or not bridging and (iii) the impact of the training set composition on within family genomewide prediction accuracies.. - The advantage of recurrent introductions in the com- mercial breeding program after or without bridging depended on the type of donor considered. - Donors is- sued from a panel assembling founders of the breeding pool, referred to as panel donors, showed a large per- formance gap with the elites they were crossed to. - When consid- ering the mean performance of the 10 best progeny (μ 10. - The introduction of panel donors after bridging (Bridging_Panel) did not sig- nificantly penalize the short-term mean performance of the breeding population (at 5 years, μ = 8.688. - Direct introductions of 20-year old donors without bridging (Nobridging_20y) yielded a penalty in the mid-. - 2a, Table S1) and this advantage in- creased until the end of the 60 years evaluated period (μ. - Introductions after bridging significantly outperformed the direct in- troductions until the end of the 60 years evaluated period (μ = 69.154. - We observed that the recurrent introductions of do- nors impacted the genetic diversity of the commercial germplasm. - The faster the commercial program had ac- cess to recent germplasm of the external program, the more the varieties released by the commercial program. - 2 Evolution of the breeding population over generations. - b mean performance of the 10 best progeny ( μ 10 ) and c frequency of the favorable alleles that were rare at the end of burn-in (i.e. - In the scenario where only panel donors were accessible for introductions, the internal program diversity did not converge toward the external program (Fig. - The evolution of the mean frequency of initially rare favorable alleles (i.e. - favorable allele that had a frequency at the end of burn-in ≤0.05 in the elite breeding popula- tion) also highlighted differences between strategies. - 3 Principal component analysis of the modified Roger ’ s genetic distance matrix [76] of the 338 founders (gray: points for the 57 Iodent lines and triangles for the 281 remaining lines), the commercial 10 best performing E progeny per generation (colored circle sign) and the 20 donors per generation released by the external program (colored plus sign). - At constant TS size of 3600 DH, the increase in propor- tion of DE progeny from 0 to 1/3 in the TS increased the prediction accuracy within introduction DExE families ( corðu. - The increase in proportion of DE progeny from 0 to 1/3 in the TS increased the prediction accuracy within intro- duction DExE families ( corðσ. - Despite the recognition of the importance to broaden the elite genetic base in most crops, commercial breeders are reluctant to penalize the result of several generations of intensive selection by crossing elite ma- terial to unimproved diversity sources. - 4 Evolution of the breeding population over generations. - identification of the useful genetic diversity to broaden the elite pool is difficult and might dishearten breeders.. - The identification of diversity sources for polygenic en- richment of the elite pool should account for the com- plementarity between diversity sources and elites as reviewed in Allier et al. - diversity sources and elite recipients based on the ex- pected performance and diversity in the most perform- ing fraction of the progeny. - gen- etic resource and elite recipient, we expect a higher cross variance that should be accounted for to properly evalu- ate the usefulness of the cross . - Additionally, we expect the best performing fraction of the progeny to be genetically closer to the best parent. - This deviation from the average parental value should be considered to evaluate properly the genetic diversity in the next gener- ation [4, 5]. - u Þ ) considering genotypes simulated at generations in the scenario Bridging_20y. - σÞ ) considering genotypes simulated at generations in the scenario Bridging_20y. - In this study, the external breeding program was de- signed to release every generation several improved lines, later considered as donors for genetic base broad- ening of the commercial breeding program. - This was done to mimic in a sim- ple way the outcome of the activity of several companies conducting separate programs and therefore maintaining a global diversity. - The selection intensity was lower in the external breeding than in the commercial breeding programs (10% vs 5% of progeny selected, respectively). - Our results highlighted a clear beneficial effect of introducing external diversity in the elite program. - This benefit increased with increasing performance level of the introduced material from unimproved genetic re- sources collections (panel donors) to recently improved diversity sources (5-year old donors). - pre-breeding, may be beneficial before introduction in the elite germplasm. - Advantages of bridging relative to direct introductions in the elite pool. - The high inter-family additive variance in this scenario (Figure S1 A) reflected the structuration of the breeding population into badly performing intro- duction families and performing elite families with only limited gene flow between them. - Intro- ductions penalized slightly the mean breeding popula- tion performance in the first generations (Fig. - Next generations of recombination and selection partially broke the linkage between favorable and un- favorable alleles in introduced regions, resulting in a higher genetic gain than in the benchmark (Fig. - 2a-b) and an increase of the frequency of novel favorable al- leles (Fig. - The more performing the donor, the less unfavorable alleles linked to favorable alleles and the more rapidly novel favorable alleles were introduced and spread in the breeding population (Fig. - In absence of bridging, the introduction progeny (DxE) carried on expectation one half of the donor genome. - The pre- diction of elite (ExE) and introduction (DExE) crosses usefulness and the prediction within crosses were based on a model trained on the breeding progeny of the three corresponding previous generations. - This higher selection accuracy favored the spreading of the introduced favorable alleles in the breeding popula- tion and resulted in an increased mid- and long-term performance (Fig. - At constant TS size, increas- ing the proportion of bridging progeny (DE) up to one third in the TS significantly increased the family variance prediction accuracy (corðσ. - Conversely, these higher proportions of bridging pro- geny (DE) in the TS significantly decreased corðσ. - For instance, considering later genera- tions, a large proportion of DE in the TS penalized less the within elite prediction accuracy (Figure S3 C).. - The optimal balance between bridging and breeding progeny in the training set might be defined using an optimization criterion such as the CDmean [52] ex- tended to account for linkage disequilibrium as sug- gested by Mangin et al. - This in- volves practical changes in the breeding organization that remain to be studied. - We considered a single trait selected in both the exter- nal and the commercial breeding programs in the same population of environments for a total of 8 years. - Each QTL was assigned an additive effect sampled from a Gaussian distribution with a mean of zero and a variance of 0.05 and the favorable allele was attributed at random to one of the two SNP alleles. - Every year T, progeny of the three last generations T− 3, T− 4 and T− 5 were considered as potential parents of the next. - Every year, progeny phenotypes and genotypes of the three last available generations were used to fit a G- BLUP model (Additional file 1). - The genetic material in the external breeding is re- ferred to as improved donors (D). - After 20 years of burn-in, we considered GS trained on the D progeny of the three last generations (i.e. - D progeny with the largest GEBVs as potential parents of the next generation, i.e. - material in the internal breeding is referred to as elite progeny (E). - During 17 years, we considered as potential parents of the next generation the 50 E progeny with the largest phenotypic mean from the three last generations, i.e. - In absence of introductions (benchmark), the E pro- geny were selected based on the elite GS model trained on E progeny of the three last generations (i.e. - 4 DH) in the three last breeding generations were considered as potential par- ents. - To mimic a situation close to that of the US maize ex-PVPA system [44], we considered donors released 20 to 24 years before the current year (i.e. - 7c), the E candi- date parents were selected every year among the 5% E progeny showing the largest GEBVs per family in the three last breeding generations resulting in N E = 4 DH × 20 families × 3 years = 240 potential E parents. - The E progeny were selected based on the elite GS model trained on E progeny of the three last generations (i.e.. - The E progeny were selected based on the elite GS model trained on all E progeny of the three last generations (i.e. - The DE candidate parents for introduction in the breeding popula- tion were similarly selected among the three last bridging generations, resulting in N DE = 4 DH/family × 5 families × 3 years = 60 potential DE parents. - The DE progeny were se- lected based on the bridging GS model trained on all DE progeny of the three last generations (i.e. - The optimal cross selection selects the set of crosses (nc) that maximizes the expected genetic value in the progeny (V) under a constraint on the genomewide genetic diver- sity in the progeny (D . - total of 1600 DH/year) with recur- rent introductions (i) either direct or with a bridging step and (ii) considering three types of potential donors, resulting in the six genetic base broadening scenarios:. - We ran 10 inde- pendent simulation replicates of the external program that generated donors, the commercial benchmark pro- gram without introductions, and the six genetic base broadening scenarios. - We followed several indicators in the breeding families (i.e. - mean(TBV(T)) and of the 10 most per- forming E progeny μ 10 ðT Þ ¼ meanð max. - 10 ðTBV ðT ÞÞÞ as a proxy of the performance that could be achieved at the commercial level by releasing these lines as varieties. - We also measured the frequency of the favorable allele in the E progeny p j (T) at each QTL j among the 1000 QTLs. - We further investigated the effect of the proportion of DE and E progeny in the TS at constant size on within. - We considered the 1200 DE and 3600 E progeny genotypes and pheno- types simulated at generations in the first rep- licate of scenario Bridging_20y. - (Evolution of the breeding population over generations for two different weightings α. - This research beneficiated from a support and helpful discussions with the members of the “ Gdiv-Selgen ” and “ R2D2 ” projects within the framework of the INRA “ Selgen ” meta-program.. - AA performed the simulations, analysis and wrote the early version of the manuscript. - Table 2 Description of the compared training sets. - 1/12 – DE DE DE The full training sets considering all available progeny of the last three generations and training sets at constant size (1200 progeny or 3600 progeny) with variable proportion of DE progeny. - The funding body ANRT CIFRE played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.. - The funding body RAGT2 played a role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript in the persons of AA, CL and ST.. - Dutfield G., 2011 The role of the international Union for the Protection of new varieties of plants (UPOV). - The history and success of the public-private project on germplasm enhancement of maize (GEM). - A critical evaluation of the HOPE breeding system as a means for broadening the deployed germplasm base in maize. - 259 – 272 in The Impact of Plant Molecular Genetics, edited by. - The state of the use of maize genetic diversity in the USA and sub-Saharan Africa, pp
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