Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa

The undomesticated rice relative Oryza longistaminata is a valuable genetic resource for the improvement of the domesticated Asian rice, Oryza sativa. To facilitate the conservation, management, and use of O. longistaminata germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between O. longistaminata and O. sativa. Though past plant breeding efforts to introgress genes from O. longistaminata have improved biotic stress resistance, ratooning ability, and yield in O. sativa, progress has been limited by substantial breeding barriers. Nevertheless, despite the strong breeding barriers observed by plant breeders who have attempted this interspecific cross, there have been multiple reports of spontaneous hybrids of O. sativa and O. longistaminata (aka "Obake") obtained from natural populations in Africa. However, the frequency and extent of such natural introgressions and their effect on the evolution of O. longistaminata had not been previously investigated. We studied 190 O. longistaminata accessions, primarily from the International Rice Research Institute genebank collection, along with 309 O. sativa, 25 Oryza barthii, and 83 Oryza glaberrima control outgroups, and 17 control interspecific O. sativa/O. longistaminata hybrids. We analyzed the materials using 178,651 single-nucleotide polymorphisms (SNPs) and seven plastid microsatellite markers. This study identified three genetic subpopulations of O. longistaminata, which correspond geographically to Northwestern Africa, Pan-Africa, and Southern Africa. We confirmed that O. longistaminata is, perhaps counterintuitively, more closely related to the Asian species, O. sativa, than the African species O. barthii and O. glaberrima. We identified 19 recent spontaneous interspecific hybrid individuals between O. sativa and O. longistaminata in the germplasm sampled. Notably, the recent introgression between O. sativa and O. longistaminata has been bidirectional. Moreover, low levels of O. sativa alleles admixed in many predominantly O. longistaminata accessions suggest that introgression also occurred in the distant past, but only in Southern Africa.

Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation

KEY MESSAGE

Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids. Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis.

New cycle, same old mistakes? Overlapping vs. discrete generations in long-term recurrent selection

Background

Recurrent selection is a foundational breeding method for quantitative trait improvement. It typically features rapid breeding cycles that can lead to high rates of genetic gain. Usually, generations are discrete in recurrent selection, which means that breeding candidates are evaluated and considered for selection for only one cycle. Alternately, generations can overlap, with breeding candidates considered for selection as parents for multiple cycles. With recurrent genomic selection but not phenotypic selection, candidates can be re-evaluated by using genomic estimated breeding values without additional phenotyping of the candidates themselves. Therefore, it may be that candidates with true high breeding values discarded in one cycle due to underestimation of breeding value could be identified and selected in subsequent cycles. The consequences of allowing generations to overlap in recurrent selection are unknown. We assessed whether maintaining overlapping and discrete generations led to differences in genetic gain for phenotypic, genomic truncation, and genomic optimum contribution recurrent selection by stochastic simulation.

Results

With phenotypic selection, overlapping generations led to decreased genetic gain compared to discrete generations due to increased selection error bias. Selected individuals, which were in the upper tail of the distribution of phenotypic values, tended to also have high absolute error relative to their true breeding value compared to the overall population. Without repeated phenotyping, these individuals erroneously believed to have high value were repeatedly selected across cycles, leading to decreased genetic gain. With genomic truncation selection, overlapping and discrete generations performed similarly as updating breeding values precluded repeatedly selecting individuals with inaccurately high estimates of breeding values in subsequent cycles. Overlapping generations did not outperform discrete generations in the presence of a positive genetic trend with genomic truncation selection, as individuals from previous breeding cycles typically had truly lower breeding values than candidates from the current generation. With genomic optimum contribution selection, overlapping and discrete generations performed similarly, but overlapping generations slightly outperformed discrete generations in the long term if the targeted inbreeding rate was extremely low.

Conclusion

Maintaining discrete generations in recurrent phenotypic selection leads to increased genetic gain, especially at low heritabilities, by preventing selection error bias. With genomic truncation selection and genomic optimum contribution selection, genetic gain does not differ between discrete and overlapping generations assuming non-genetic effects are not present. Overlapping generations may increase genetic gain in the long term with very low targeted rates of inbreeding in genomic optimum contribution selection.

Supplementary information

The online version contains supplementary material available at 10.1186/s12864-022-08929-3.

Genomic Prediction of Yield Traits in Single-Cross Hybrid Rice (Oryza sativa L.)

Hybrid rice varieties can outyield the best inbred varieties by 15 – 30% with appropriate management. However, hybrid rice requires more inputs and management than inbred rice to realize a yield advantage in high-yielding environments. The development of stress-tolerant hybrid rice with lowered input requirements could increase hybrid rice yield relative to production costs. We used genomic prediction to evaluate the combining abilities of 564 stress-tolerant lines used to develop Green Super Rice with 13 male sterile lines of the International Rice Research Institute for yield-related traits. We also evaluated the performance of their F₁ hybrids. We identified male sterile lines with good combining ability as well as F₁ hybrids with potential further use in product development. For yield per plant, accuracies of genomic predictions of hybrid genetic values ranged from 0.490 to 0.822 in cross-validation if neither parent or up to both parents were included in the training set, and both general and specific combining abilities were modeled. The accuracy of phenotypic selection for hybrid yield per plant was 0.682. The accuracy of genomic predictions of male GCA for yield per plant was 0.241, while the accuracy of phenotypic selection was 0.562. At the observed accuracies, genomic prediction of hybrid genetic value could allow improved identification of high-performing single crosses. In a reciprocal recurrent genomic selection program with an accelerated breeding cycle, observed male GCA genomic prediction accuracies would lead to similar rates of genetic gain as phenotypic selection. It is likely that prediction accuracies of male GCA could be improved further by targeted expansion of the training set. Additionally, we tested the correlation of parental genetic distance with mid-parent heterosis in the phenotyped hybrids. We found the average mid-parent heterosis for yield per plant to be consistent with existing literature values at 32.0%. In the overall population of study, parental genetic distance was significantly negatively correlated with mid-parent heterosis for yield per plant (r = −0.131) and potential yield (r = −0.092), but within female families the correlations were non-significant and near zero. As such, positive parental genetic distance was not reliably associated with positive mid-parent heterosis.

Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review

Although hybrid crop varieties are among the most popular agricultural innovations, the rationale for hybrid crop breeding is sometimes misunderstood. Hybrid breeding is slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection and exploitation of heterosis simultaneously. Inbred parental lines can identically reproduce both themselves and their F1 progeny indefinitely, whereas outbred lines cannot, so uniform outbred lines must be bred indirectly through their inbred parents to harness heterosis. Heterosis is an expected consequence of whole-genome non-additive effects at the population level over evolutionary time. Understanding heterosis from the perspective of molecular genetic mechanisms alone may be elusive, because heterosis is likely an emergent property of populations. Hybrid breeding is a process of recurrent population improvement to maximize hybrid performance. Hybrid breeding is not maximization of heterosis per se, nor testing random combinations of individuals to find an exceptional hybrid, nor using heterosis in place of population improvement. Though there are methods to harness heterosis other than hybrid breeding, such as use of open-pollinated varieties or clonal propagation, they are not currently suitable for all crops or production environments. The use of genomic selection can decrease cycle time and costs in hybrid breeding, particularly by rapidly establishing heterotic pools, reducing testcrossing, and limiting the loss of genetic variance. Open questions in optimal use of genomic selection in hybrid crop breeding programs remain, such as how to choose founders of heterotic pools, the importance of dominance effects in genomic prediction, the necessary frequency of updating the training set with phenotypic information, and how to maintain genetic variance and prevent fixation of deleterious alleles.