Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping

Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.

Grain, sugar and biomass accumulation in tropical sorghums. I. Trade-offs and effects of phenological plasticity

Grain and sweet sorghum (Sorghum bicolor (L.) Moench) differ in their ability to produce either high grain yield or high sugar concentration in the stems. Some cultivars of sorghum may yield both grains and sugar. This paper investigates the trade-offs among biomass, grain and sugar production. Fourteen tropical sorghum genotypes with contrasted sweetness and PP sensitivity were evaluated in the field near Bamako (Mali) at three sowing dates under favourable rainfed conditions. Plant phenology, morphology, dry matter of different organs and stem sugar content were measured at anthesis and grain maturity. A panicle pruning treatment was implemented after anthesis. Late sowing (shorter days) led to a decrease in total leaf number, dry mass and sugar yield even in PP-insensitive genotypes because of an increased phyllochron. Dry matter production and soluble sugar accumulation were strongly correlated with leaf number. Sugar concentration varied little among sowing dates or between anthesis and maturity. This indicates that sugar accumulation happened mainly before anthesis, thus largely escaping from competition with grain filling. This was confirmed by the low impact of panicle pruning on sugar concentration. Changes in sugar concentration from anthesis to maturity were negatively correlated with harvest index but not with grain yield. Physiological trade-offs among sugar, biomass and grain production under favourable rainfall are small in late-maturing and PP-sensitive sweet sorghums cultivated under sudano-sahelian conditions. The results differ from earlier reports that focussed on early maturing, PP-insensitive germplasm. Further research is needed on the interactions of these traits with agricultural practices and drought.

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region

Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.