The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Abstract

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought 1 . Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives 2,3 , including numerous extremophile species 4 . Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences 5 and required single-molecule realtime sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade 6 and a sunflowerspecific whole-genome duplication around 29 million years ago 7 . An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs 8,9 .As the only major crop domesticated in North America, with its sunlike inflorescence that inspired artists, the sunflower is both a social icon and a major research focus for scientists. In evolutionary biology, the Helianthus genus is a long-time model for hybrid speciation and adaptive introgression 10 . In plant science, the sunflower is a model for understanding solar tracking 11 and inflorescence development 12 .Despite this large interest, assembling its genome has been extremely difficult as it mainly consists of long and highly similar repeats. This complexity has challenged leading-edge assembly protocols for close to a decade 13 .To finally overcome this challenge, we generated a 102× sequencing coverage of the genome of the inbred line XRQ using 407 singlemolecule real-time (SMRT) cells on the PacBio RS II platform. Production of 32 million very long reads allowed us to generate a genome assembly that captures 3 gigabases (Gb) (80% of the estimated genome size) in 13,957 sequence contigs. Four high-density genetic maps were combined with a sequence-based physical map to build the sequences of the 17 pseudo-chromosomes that anchor 97% of the gene content (Fig.

Genomic sequence and copy number evolution during hybrid crop development in sunflowers

“…The percent absent genes for HA 412 HO inside and outside of probable introgressed regions. Introgressed regions were identified using Structure linkage model (Badouin et al., )…”

“…Thus, we propose that introgression is removing genes during the breeding process. To confirm this, we examined cultivar line HA412HO, which has had introgressed regions in its genome previously mapped (Badouin et al., ). As predicted, we find that absent genes are much more common in the introgressed regions (Figure ).…”

Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement

“…The recommended parameters for paleogenomic datasets were utilized, including removing adapter sequences with AdapterRemoval 2 (Schubert, Lindgreen, & Orlando, ), mapping of reads with BWA aln with the seed disabled (Li & Durbin, ), removal of duplicate reads with Picard Tools (http://broadinstitute.github.io/picard), realignment around indels with GATK 3.7 (McKenna et al., ), and rescaling of base qualities due to aDNA damage with mapDamage2.0 (Jónsson, Ginolhac, Schubert, Johnson, & Orlando, ). Reads were mapped against the entire sunflower XRQ draft genome (Badouin et al., ), including unplaced contigs, the plastid genome, and the mitochondrial genome. We report endogenous DNA content based on all mapped reads, regardless of mapping quality, because high content of long terminal repeat retrotransposons in the sunflower genome (74.7% of the genome, Badouin et al., ) cause many endogenous reads to map to multiple loci.…”

Genetic Characterization of Maximilian Sunflower for the Development of a Locally Adapted Perennial Grain Oilseed

“…Plants were phenotyped in 2013 and 2014 for the Julian date of first anthesis, Julian date of fifth anthesis, Julian date of first new resources for the characterization of crop wild relatives in the genus Helianthus, facilitating the acceleration of breeding efforts (Badouin et al, 2017) and application of novel tools such as landscape genomics. Plants were organized in a randomized complete block design, and each site contained four blocks with two individuals representing each collection site in each block.…”

“…The rapid linkage decay we observed is in line with previous estimates from wild Helianthus species (Liu and Burke, 2006;Mandel et al, 2011) and is largely a function of the obligate outcrossing nature of the genus. Recent efforts using association mapping and genome-wide association approaches in sunflower have employed marker densities ranging from ?5300 to ?450,000 SNPs (Mandel et al, 2013;Nambeesan et al, 2015;Badouin et al, 2017) with linkage decays within ?1100 bp (Liu and Burke, 2006). The rate of linkage decay based on marker order in the cultivated H. annuus reference genome (?93 bp) and the large genome size of diploid Helianthus species (?3.6 Gb) suggests that similar to other wild Helianthus species, marker density for genome wide association studies or genomic selection in Maximilian sunflower would need to be high to capture historic recombination events in wild collected germplasm.…”