A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Abstract

Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (~12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

Wheat Landrace Genome Diversity

“… c haffin et al (2016) reported on a consensus map for hexaploid oat from 12 biparental populations, from a total of 19 different parental lines. They detected a number of chromosomal rearrangements and speculated that allo-hexaploid plants have mechanisms for “a very high amount of genetic buffering” and can, thus, accommodate wild introgression, duplications, and deficiencies arising from reciprocal and nonreciprocal chromosomal rearrangements.…”

Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection

“…-logP-values from the association analyses were visualized as Manhattan plots using the map positions reported in Chaffin et al (2016). A significance threshold adjusted for multiple testing was calculated by the method described in Li and Ji (2005), separately for AVEQ08 (-logP = 3.365) and AVEQ09 (-logP = 3.246), with a = 0.05.…”

“…The numbers at the top of the plot indicate the consensus chromosomes as named in Chaffin et al (2016) validity of continuous scoring. Three out of 19 markers were discarded by the Illumina quality filters as discrete scores could not be assigned, indicating that continuous scoring is able to use information from more markers.…”

“…The recent development of new genomic tools, notably the 6K Infinium SNP array (Tinker et al 2014) and the dense hexaploid oat consensus map (12,000 markers) based on 12 bi-parental populations (Chaffin et al 2016;Yan et al 2016), have made it possible to map oat traits at a high resolution (Esvelt Klos et al 2016). Winkler et al (2016) used the array for a genome-wide association study (GWAS) in a diverse panel of oat accessions from the USDA National Small Grains Collection, assembled to represent a gene pool relatively unaffected by 20th century breeding activities, but failed to find significant associations for lodging tolerance.…”

Genetic mapping in polyploids

“…Examples of allopolyploid SNP arrays include cotton (Hulse-Kemp et al, 2015), oat (Tinker et al, 2014), oilseed rape (Dalton- Morgan et al, 2014;Clarke et al, 2016), peanut (Pandey et al, 2017), strawberry (Bassil et al, 2015) and wheat (Akhunov et al, 2009;Cavanagh et al, 2013;Wang et al, 2014b;Winfield et al, 2016). Untargeted approaches such as genotyping-by-sequencing have also been applied, for example in autopolyploids such as alfalfa Yu et al, 2017), blueberry (McCallum et al, 2016), bluestem prairie grass (Andropogon gerardii) (McAllister and Miller, 2016), cocksfoot (Dactylis glomerata) (Bushman et al, 2016), potato (Uitdewilligen et al, 2013;Sverrisdóttir et al, 2017), sugarcane (Balsalobre et al, 2017;Yang et al, 2017b) and sweet potato (Shirasawa et al, 2017), and in allopolyploids such as coffee (Moncada et al, 2016), cotton (Islam et al, 2015;Reddy et al, 2017), intermediate wheatgrass (Thinopyrum intermedium) (Kantarski et al, 2017), oat (Chaffin et al, 2016), prairie cordgrass (Spartina pectinata) (Crawford et al, 2016), shepherd's purse (Capsella bursa-pastoris) (Cornille et al, 2016), wheat (Poland et al, 2012;Edae et al, 2015) and zoysiagrass (Zoysia japonica) (McCamy et al, 2018) (noting that the precise classification of some of these species as auto-or allopolyploids has yet to be conclusively determined). Whatever the technology used, it is clear that we are currently witnessing an explosion of interest in polyploid genomics.…”