The influence of genetic architecture on responses to selection under drought in rice

Accurately predicting responses to selection is a major goal in biology and important for successful crop breeding in changing environments. However, evolutionary responses to selection can be constrained by such factors as genetic and cross-environment correlations, linkage, and pleiotropy, and our understanding of the extent and impact of such constraints is still developing. Here, we conducted a field experiment to investigate potential constraints to selection for drought resistance in rice (Oryza sativa) using phenotypic selection analysis and quantitative genetics. We found that traits related to drought response were heritable, and some were under selection, including selection for earlier flowering, which could allow drought escape. However, patterns of selection generally were not opposite under wet and dry conditions, and we did not find individual or closely linked genes that influenced multiple traits, indicating a lack of evidence that antagonistic pleiotropy, linkage, or cross-environment correlations would constrain selection for drought resistance. In most cases, genetic correlations had little influence on responses to selection, with direct and indirect selection largely congruent. The exception to this was seed mass under drought, which was predicted to evolve in the opposite direction of direct selection due to correlations. Because of this indirect effect on selection on seed mass, selection for drought resistance was not accompanied by a decrease in seed mass, and yield increased with fecundity. Furthermore, breeding lines with high fitness and yield under drought also had high fitness and yield under wet conditions, indicating that there was no evidence for a yield penalty on drought resistance. We found multiple genes in which expression influenced both water use efficiency (WUE) and days to first flowering, supporting a genetic basis for the trade-off between drought escape and avoidance strategies. Together, these results can provide helpful guidance for understanding and managing evolutionary constraints and breeding stress-resistant crops

Domestication history and geographical adaptation inferred from a SNP map of African rice

African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa-3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began-13,000-15,000 years ago with effective population size reaching its minimum value-3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within-300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species

Haplotype Network

Phased vcf file for the genes sh1, sh4, and PROG1 region. Data used to estimate the haplotype network

O. rufipogon genome aligned to O. barthii or O. glaberrima

O. rufipogon reference genome sequence was aligned to O. barthii or O. glaberrima reference genome. For every O. barthii or O. glaberrima coordinate was converted into O. rufipogon sequence resulting in a O. barthii-ized or O. glaberrima-ized O. rufipogon genome sequence. Not alignable regions were indicated as 'N'

Genotypes surrounding domestication gene

File used to visualize the SNPs (genotypes) surroinding domestication gene of interest

Filtered VCF file used in study (chr7) - barthii as reference genome

O. barthii reference genome based SNP calls. Filtering process described in paper

Phylogenomic and phylogenetic tree plotted with iTol

Newick format trees for genome-wide and the 3 domestication genes. Tree can be visualized on iTol (http://itol.embl.de) and colored using the supplied itol file

Filtered VCF file used in study (chr10) - glaberrima as reference genome

O. glaberrima reference genome based SNP calls. Filtering process described in paper

Filtered VCF file used in study (chr2) - barthii as reference genome

O. barthii reference genome based SNP calls. Filtering process described in paper

ngsAdmix ancestry proportion

ngsAdmix results estimating ancestry proportions from K=2 to K=9 for all 282 samples