Ferguson, J. N. | bioRxiv Science

bioRxiv2018

Non-functional and weak alleles of FRIGIDA and FLOWERING LOCUS C reduce lifetime water-use independent of leaf-level water-use-efficiency traits in Arabidopsis thaliana

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (TE). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water-use but also drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water use strategies, namely C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci (QTL) mapping and validation through near-isogenic lines identified two causal QTLs, which showed that a combination of weak and non-functional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water-use without penalising reproductive performance. Drought tolerance traits, stomatal conductance, intrinsic water use efficiency ({delta}13C) and rosette water-use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining life-time plant water use, but not leaf-level traits.

plant biology↗

bioRxiv2018

Leveraging mutational burden for complex trait prediction in sorghum

Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. Though selection keeps deleterious mutations rare, their complete removal from the genome is impeded due to lack of recombination, drift, and their coupling with favorable loci. To study how deleterious mutations impact agronomic phenotypes, we identified putative deleterious mutations among ~5.5M segregating variants of 229 diverse sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that about 33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups; the caudatum shows higher mutation burden while the guinea has lower burden. Across racial groups, the mutation burden correlated negatively with biomass, plant height, Specific Leaf Area (SLA), and tissue starch content, suggesting deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (5.2%). There is no advantage in total heritable variance for SLA and starch. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, our results suggest that including putatively deleterious variants in models do not significantly improve breeding accuracy because of extensive linkage. However, knowledge of deleterious variants could be leveraged for sorghum breeding through genome editing.

genetics↗