Genomic Variation Among and Within SixJuglansSpecies

Abstract

Genomic analysis in Juglans (walnuts) is expected to transform the breeding and agricultural production of both nuts and lumber. To that end, we report here the determination of reference sequences for six additional relatives of Juglans regia: Juglans sigillata (also from section Dioscaryon), Juglans nigra, Juglans microcarpa, Juglans hindsii (from section Rhysocaryon), Juglans cathayensis (from section Cardiocaryon), and the closely related Pterocarya stenoptera. While these are ‘draft’ genomes, ranging in size between 640Mbp and 990Mbp, their contiguities and accuracies can support powerful annotations of genomic variation that are often the foundation of new avenues of research and breeding. We annotated nucleotide divergence and synteny by creating complete pairwise alignments of each reference genome to the remaining six. In addition, we have re-sequenced a sample of accessions from four Juglans species (including regia). The variation discovered in these surveys comprises a critical resource for experimentation and breeding, as well as a solid complementary annotation. To demonstrate the potential of these resources the structural and sequence variation in and around the polyphenol oxidase loci, PPO1 and PPO2 were investigated. As reported for other seed crops variation in this gene is implicated in the domestication of walnuts. The apparently Juglandaceae specific PPO1 duplicate shows accelerated divergence and an excess of amino acid replacement on the lineage leading to accessions of the domesticated nut crop species, Juglans regia and sigillata.

A new genomic tool for walnut (Juglans regia L.): development and validation of the high‐density Axiom™ J. regia 700K SNP genotyping array

“…The initial step in the transition from conventional breeding to genomics-assisted breeding is the discovery of DNA sequence variation. Stevens et al (2018) re-sequenced 27 walnut accessions selected as either representing the UC Davis WIP founders or showing interesting phenotypes for traits of interest in walnut (e.g., kernel colour; Mart ınez-Garc ıa et al, 2017). The discovery panel is mostly comprised of US accessions, but also includes wild germplasm and cultivars introduced to the UC Davis WIP from other leading countries in global walnut production, namely China, France, Afghanistan, Japan and Bulgaria (Table S1).…”

“…Based on the mapped reads, 17 800 528 SNPs distributed over 9042 scaffolds were identified (available at https://www.ha rdwoodgenomics.org/Genome-assembly/2209433). The number of SNPs was then reduced by almost 50% (9 582 656 variants) after applying quality filters (Figure 1; Stevens et al, 2018). Following Affymetrix (now part of Thermo Fisher Scientific, Waltham, MA) recommendations (see Figure 1), we selected 2 412 872 SNPs potentially suitable for incorporation on the SNP array, by discarding polymorphisms with complex genotypic patterns (i.e.…”

“…Recently, Stevens et al . () reported the whole‐genome resequencing of samples from four Juglans species to capture and compare nucleotide diversity at the inter‐species level. In Persian walnut, they re‐sequenced 27 accessions and discovered over 9.6 m SNPs.…”

“…The release of the first reference genome sequence in walnut offers the opportunity to align sequences from different walnut genotypes and identify variation in their genome sequences (Mart ınez-Garc ıa et al, 2016). Recently, Stevens et al (2018) reported the whole-genome resequencing of samples from four Juglans species to capture and compare nucleotide diversity at the inter-species level. In Persian walnut, they re-sequenced 27 accessions and discovered over 9.6 M SNPs.…”

Functional analysis of walnut polyphenol oxidase gene (JrPPO1) in transgenic tobacco plants and PPO induction in response to walnut bacterial blight

“…regia genome sequencing, a second homologue of PPO ( JrPPO2 ) was discovered (Martínez‐García et al , ) and this was subsequently identified in several additional Juglans species using comparative genomics resources (Stevens et al , ). In both studies, the JrPPO1 and JrPPO2 transcripts were differentially expressed, with JrPPO1 expressed in a wide range of green tissues and JrPPO2 expressed in callus, catkins, vegetative buds, pistillate flower, immature hull, and hull cortex but not in hull tissue, immature fruit, and leaves (Martínez‐García et al , ; Stevens et al , ). Therefore, differences in tissue‐based expression of PPO genes might be an explanation for the detection of only one melanin band in immature walnut hulls.…”