Dissecting Adaptive Traits with Nested Association Mapping: Genetic Architecture of Inflorescence Morphology in Sorghum

Abstract

In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under somewhat independent control, while lower branch length and rachis diameter are highly pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1–22 QTL per trait, each explaining 0.1–5.0% of variation across the entire NAM population. There is a significant enrichment (2.twofold) of QTL colocalizing with grass inflorescence gene homologs, notably with orthologs of maize Ramosa2 and rice Aberrant Panicle Organization1 and TAWAWA1. Still, many QTL do not colocalize with inflorescence gene homologs. In global georeferenced germplasm, allelic variation at the major inflorescence QTL is geographically patterned but only weakly associated with the gradient of annual precipitation. Comparison of NAM with diversity panel association suggests that naive association models may capture some true associations not identified by mixed linear models. Overall, the findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. The findings also provide a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.

Genome‐wide mapping and prediction of plant architecture in a sorghum nested association mapping population

“…Flowering time was scored as the number of days from planting to the day in which 50% of the individuals in a plot are in anthesis. Inflorescence architecture phenotypes were previously described (Olatoye et al., 2020).…”

Correlation Among Morphological Characters of Local Sweet Potato (Ipomea batatas L.) Accessions in Kerinci Regency

“…Consequently, new genotype with specific adaptability was created for such environment. In line with that, Frison et al, (2010) [15] stated that ecogeographical environment stress during adaptation process in long period might cause micro evolution so that genetic diversity increased.…”

Registration of the sorghum nested association mapping (NAM) population in RTx430 background

“…A total of 2,214 NAM RILs from F 6 were used to characterize the inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter) from four multi-environment trials in Kansas (Hays: summer 2014 dryland, summer 2015 dryland, and irrigated; Manhattan: summer 2015 dryland). The findings from this study suggested that the genetic architecture of these traits is oligogenic, epistatic, and pleiotropic in ancestral regulatory networks and provides a clear basis for genomic-enabled breeding to improve the inflorescence traits in sorghum (Olatoye et al, 2020). A total of 210 RILs from RTx430/SC35 (F 7 ), one of the biparental NAM families (KS-RTx430NAM 5), was used to identify the genomic regions for key physiological traits related to source (effective quantum yield of photosystem II [PSII] and chlorophyll index), sink (grain yield), and panicle neck diameter.…”