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

Abstract

Hybrid crops, an important part of modern agriculture, rely on the development of male and female heterotic gene pools. In sunflowers, heterotic gene pools were developed through the use of crop‐wild relatives to produce cytoplasmic male sterile female and branching, fertility restoring male lines. Here, we use genomic data from a diversity panel of male, female, and open‐pollinated lines to explore the genetic changes brought during modern improvement. We find the male lines have diverged most from their open‐pollinated progenitors and that genetic differentiation is concentrated in chromosomes, 8, 10 and 13, due to introgressions from wild relatives. Ancestral variation from open‐pollinated varieties almost universally evolved in parallel for both male and female lines suggesting little or no selection for heterotic overdominance. Furthermore, we show that gene content differs between the male and female lines and that differentiation in gene content is concentrated in high F ST regions. This means that the introgressions that brought branching and fertility restoration to the male lines, brought with them different gene content from the ancestral haplotypes, including the removal of some genes. Although we find no evidence that gene complementation genomewide is responsible for heterosis between male and female lines, several of the genes that are largely absent in either the male or female lines are associated with pathogen defense, suggesting complementation may be functionally relevant for crop breeders.

Massive haplotypes underlie ecotypic differentiation in sunflowers

“…The call set included the 1518 samples described above, the Sunflower Association Mapping (SAM) population (a set of cultivated H. annuus lines 54 ), and wild Helianthus samples previously sequenced for other projects [54][55][56] , for a total of 2392 samples (Supplementary Table 1). The additional samples were included to improve SNP calling, and to identify haploblock genotypes.…”

Characterization for Drought Tolerance and Physiological Efficiency in Novel Cytoplasmic Male Sterile Sources of Sunflower (Helianthus annuus L.)

“…The hybrid system based on a CMS commonly comprises of a three-line system: the male sterile genotype (A line), which is maintained by maintainer (B line) usually with a fertile cytoplasm, and a restorer (R line) for restoring the male fertility in hybrids via dominant fertility restorer genes [8,13]. Earlier efforts of sunflower breeders using this system have resulted in the significant increase of the production and quality [14,15]. Drought is among the biggest crop production challenges of the 21st century and sunflower is not an exception to drought stress [16].…”

The genomics of domestication special issue editorial

“…The third section concerns introgression between wild and domestic populations (Owens, Baute, Hubner, & Rieseberg, ; Schreiber, Himmelbach, Börner, & Mascher, ; Taitano et al., ; Vigueira et al., ). The first of these studies authored by Vigueira et al.…”

“…In sunflower, Owens et al. () analyze a late phase in domestication, hybrid crop development, which involved widespread introgression from wild relatives as populations were partitioned into male and female lines. Further, they showed that there was minimal selection for overdominance, but that selection was centered around branching and fertility/sterility mechanisms.…”

“…The third section concerns introgression between wild and domestic populations (Owens, Baute, Hubner, & Rieseberg, 2018;Schreiber, Himmelbach, Börner, & Mascher, 2018;Taitano et al, 2018;Vigueira et al, 2017). The first of these studies authored by Vigueira et al (2017) explores weedy rice inside and outside the rice native range, to understand diverse mechanisms for de-domestication.…”